title: NKM-1, SF153 2.2

city: Memphis

first: Chao-Yie

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

description: Library name: 94_NKM-1_SF-1-153_2_B_331_246_S117

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.  Base calls are transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis.
Primary analysis - sample de-multiplexing and alignment to the human genome - is performed using Illumina's CASAVA 1.8.2 software suite and subsequently using STAR aligner with two-pass mode basic enabled, GRCh38 primary assembly as the reference and Gencode v43 annotation. Subsequent to the alignment, read quantification is done using Salmon
Differential expression analysis is done using tximport/edgeR framework and splicing patterns were investigated via rMATS software.
The data are kept if the sample error rate is less than 2% and the distribution of reads per sample in a lane is within reasonable tolerance.
Assembly: GRCh38 primary assembly as the reference and Gencode v43 annotation
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: csv files containing TPM values for each sample

growth_protocol: NKM-1 cells were cultured in RPMI (Gibco, 11875119) supplemented with 10% Bovine serum albumin (R&D systems, S11550) and 1% Penicillin/Streptomycin (Corning, 30-009-CI)

extract_protocol:
Total RNA was extracted using the Kapa RNA HyperPrep Kit with RiboErase (KR1351).
Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351), rRNA is depleted starting from 25-1000ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA.  Samples are then fragmented using heat and magnesium.  1st strand synthesis is performed using random priming.  2nd strand synthesis incorporates dUTPs into the 2nd strand cDNA.  Adapters are then ligated, and the library is amplified.  Strands marked with dUTPs are not amplified allowing for strand-specific sequencing.  Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: Cells were treated with DMSO or SF153 (30 uM) for 48 hours

value: Myeloid

value: wildtype


title: enriched nuclei_MD_4874_8047

status: Public on Sep 24 2025

type: SRA

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

library_source: transcriptomic

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for initial quality control. Adapter trimming was performed with Cutadapt v1.12 (Dobin et al., 2013). Reads were aligned to the hg38 human genome build (NCBI primary analysis set) using STAR aligner v2.5.2b (Wang et al., 2012) with splice junction files generated from Gencode release 27 and RefSeq GRCh38.p10. Post-alignment quality control was performed by examination of the STAR alignment metrics, Picard tools v2.8.2 (CollectRNASeqMetrics) (https://broadinstitute.github.io/picard/) and RSeQC v2.6.4 (tin.py) (Anders et al., 2015). Expression quantitation was performed with htseq-count v0.6.1p1 (Anders et al., 2015) using a custom annotation file based on RefSeq where both exonic and intronic reads are counted for each gene.  The read counts table from each sample was imported into RStudio (version 1.1.423; R version 3.4.3) running under CentOS Linux 7. Using edgeR (version 3.20.9), the read counts were normalized into Counts Per Million (TPM), log transformed, and batch corrected. For each individual cell type, we removed technical variance associated with batch effect using sva R package. Hierarchal clustering analysis was performed using the pheatmap R package (Kolde R et al., 2018). Principal component analysis was performed using pcaMethods R package. Metabolic flux analysis was computed using scFEA R package (https://github.com/changwn/scFEA, Alghamdi N et al., 2021). Cell type specific genes were identified using the specificity index algorithm previous described in (Xu et al., 2018) and (Dougherty et al., 2010). log2(TPM) values were used as gene expression input and ranks were averaged across 1,000 iterations.
Assembly: Gencode release 27 and RefSeq GRCh38.p10
Supplementary files format and content: fastq file containing raw data
Supplementary files format and content: txt files with raw counts

molecule: nuclear RNA

organism: Homo sapiens

source_name: Cerebellum

extract_protocol:
RNA extractions from sorted nuclei were carried out with FFPE RNA Purification kits (Norgen: Product # 25300) using the manufacturer’s protocol from Step 2 (Lysate Preparation) with the following modifications: The On-column DNA removal Protocol was omitted. RNA binding and Column Wash centrifuge steps were carried out at 1,789×g for 2 min, followed by 1,789×g for 5 min to dry the resin. Elution was carried out in two steps, with 25 µL Elution Solution A added to each column followed by a 1 min room temperature incubation and centrifugation at 200×g for 2 min, then a further 15 µL Elution Solution A was added to each column with centrifugation at 1,789×g for 5 min. For samples containing >2,000 nuclei, the final 30 µL elution was split into two 15 µL aliquots. Purified RNA was vacuum dried in a CentriVap Benchtop Vacuum Concentrator (Labconco) for 40 min (or until no liquid was visible) at 4˚C and either used directly for library preparation or stored at -20˚C.
Sequencing library generation was carried out using the Trio RNA-Seq, Human rRNA Library Preparation Kit (Tecan: Product # 0506-A01) using the manufacturer’s protocol with the following modifications: Lyophilized RNA was resuspended in 12.5 µL DNAse mix and incubated at 37˚C for 30 min followed by 60˚C for 5 min and 4˚C Hold. Library Amplification I was carried out as 72˚C 2 min/95˚C 2 min/2×(95˚C 30 s/ 60˚C 60 s)/6×(95˚C 30 s/ 65˚C 60 s)/65˚C 5 min/4˚C Hold Library Amplification II was carried out as 95˚C 2 min/2×(95˚C 30 s/ 60˚C 60 s)/6×(95˚C 30 s/ 65˚C 60 s)/65˚C 5 min/4˚C Hold Final Libraries eluted in 30 µL DNA Resuspension Buffer (DR1) were checked on Agilent Bioanalyzer DNA 1000 chips, then measured on a Nanodrop 8000 and 32 sample pools (normalized to 500 ng/sample then diluted to 5 ng/µL) were sent for sequencing on an Illumina NextSeq High Output platform.

tag: tissue

value: Cerebellum

tag: cell type


title: enriched nuclei_MD_5391_6638

value: Microglia


title: enriched nuclei_MD_5512_6718

value: Astrocyte


title: UTD T cells, ABE8e mRNA, mock, 48hrs post EP, donor ND637

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

country: USA

institute: University of Pennsylvania

description: Library name: ND637 UTD ABE Mock

data_processing:
Sequence reads were trimmed using Trimmomatic v0.36
Reads were aligned to the Homo sapiens GRCh38 reference genome with the STAR aligner v2.5.2b
Unique gene hit counts were obtained using featureCounts from the Subread package v1.5.2, counting only unique reads within exon regions
Assembly: GRCh38
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

molecule: polyA RNA

source_name: primary human T cells

growth_protocol: Primary human T cells were maintained in CTS Optimizer media in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cultured T cells were preserved in RNAprotect Cell Reagent with storage at -80C until processing. Total RNA was extracted using the Qiagen RNeasy Plus Universal Mini Kit.
Strand-specific RNA sequencing libraries were prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: Primary human T cells were activated with Dynabeads CD3/CD28 CTS (Gibco) at a 3:1 bead-to-cell ratio for 48 hrs. Forty-eight hours after stimulation, beads were removed, and T cells were centrifuged at 300g, washed once with PBS, and resuspended at 5 × 10⁶ cells/100 μl in P3 Solution with Supplement (Lonza). 100 µl of cell suspension was combined with 25 µg of Cas9 WT or ABE8e mRNA (8.33 µl of 3 µg/µl solution) and 11.11µl gRNA mix (5 µg per gRNA, up to 100 µg). Electroporation was performed using the Lonza 4D-Nucleofector Core/X Unit and the P3 Primary Cell 4-D Kit (Lonza) using the program EO-115.

value: primary human T cells

tag: cell line

tag: treatment

value: 48 hrs after electroporation of editing components


title: Neural stem cells_ control_cells (2)

city: Oxford

first: Farah

last: Alammari

address: Sherrington road

institute: Oxford University

description: Library name: Control_2

data_processing:
Original image data file from high-throughput sequencing (like Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality
Perform alignments with HISAT2 to the reference. HISAT2 uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons(Kim D et al., 2015).
Assembly: Stringtie has specific parameters for different libraries, allows accurate assembling of transcripts and quantifies transcripts (Ghosh S et al., 2016) . So we used the Stringtie software to assemble reads into transcripts and quantify them based on comparisons to genomes (Pertea M et al., 2015).
Supplementary files format and content: Excel file includes transcript id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj

molecule: total RNA

organism: Mus musculus

source_name: Brain-SVZ

growth_protocol: Under laminar flow hood, the SVZ tissues were dissected and dissociated with Accutase (Sigma) at 37 °C. Cells were then cultured in Neurobasal medium (Gibco) containing B27 (Gibco), L-glutamine (Invitrogen), Pen Strep (Invitrogen), EGF (20 ng/mL, Sigma), and FGF-2 (20 ng/mL, R&D).

extract_protocol:
Total RNA was isolated using the Qiagen Mini RNeasy kit (Qiagene 74104). DNA was removed using RNase-Free DNase Set (Qiagen 79254).
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using RNA Library Prep Kit for Illumina following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) library quality was assessed on the Agilent 5400 system Agilent USA and quantified by QPCR (1.5 nM). The Qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy, according to effective library concentration and data amount required.

treatment_protocol: shhRNA Neural stem cell nucleofection was performed following the protocol of LONZA (VPG-1004).

value: Brain-SVZ

value: Neural Stem Cells


title: enriched nuclei_MD_4874_6772


title: NKM-1, SF153 2.1

last: Yang

description: Library name: 94_NKM-1_SF-1-153_2_A_332_245_S109

source_name: cell line

tag: genotype

tag: batch


title: enriched nuclei_MD_4874_6753


title: Neural stem cells_ control_cells (1)

description: Library name: Control_1


title: NKM-1, SF153 1.2

description: Library name: 98_NKM-1_SF-1-153_B_378_199_S121


title: enriched nuclei_MD_4874_6752


title: Neural stem cells_ shKAP1 cells (4)

description: Library name: KAP1_4

data_processing:
Quality controls were applied for cleaning data for adapters and trimming of low quality sequence ends using trim_galore version 0.4.4
We used kallisto to create a reference index and estimate transcript abundances. Mouse reference transcriptome from Ensembl (release 101) including cdna and ncrna sequences.                                                                       We removed sequences in scaffolds and kept only chromosomes 1, 2, …, 19, MT, X and Y. We also included ERCCs into the reference (in case they were added). Gene annotations parsed from fasta headers “Annotation_Mus_musculus.GRCm38.cdna.ncrna.rmCHR.101.txt”. We removed features with zero expression across all samples. Gene-level TPM (transcripts per million) using tximport. We kept: 1. 2. All gene biotypes only overview. Protein coding genes (plus mitochondrial and ribosomal genes) for downstream analysis.
Statistical analysis was performed with the Bioconductor package DESeq2
Assembly: Gencode m38
Supplementary files format and content: Excel file includes transcript id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj

extract_protocol:
Total RNA was isolated using the Qiagen Mini RNeasy kit (Qiagene 74104). DNA was removed using RNase-Free DNase Set (Qiagen 79254).
polyA RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for strand specific library.


title: enriched nuclei_MD_1722_8060

value: Oligo


title: NKM-1, SF153 1.1

description: Library name: 98_NKM-1_SF-1-153_A_379_198_S113


title: enriched nuclei_MD_1722_8035


title: Neural stem cells_ shKAP1 cells (3)

description: Library name: KAP1_3


title: enriched nuclei_MD_1722_6758


title: NKM-1, control 2.2

description: Library name: 97_NKM-1_C2_B_295_282_S120

value: DMSO


title: enriched nuclei_MD_4874_8048


title: enriched nuclei_MD_1722_6731


title: Neural stem cells_ shKAP1 cells (2)

description: Library name: KAP1_2


title: Neural stem cells_ shKAP1 cells (1)

description: Library name: KAP1_1


title: enriched nuclei_MD_1485_6676


title: NKM-1, control 1.2

description: Library name: 99_NKM-1_C1_B_366_211_S122


title: enriched nuclei_MD_1485_6656


title: Neural stem cells_control cells (3)

description: Library name: Control_4


title: NKM-1, control 1.1

description: Library name: 99_NKM-1_C1_A_367_210_S114


title: enriched nuclei_MD_1485_6654


title: enriched nuclei_MD_1485_6585

value: Purkinje


title: Neural stem cells_ control cells (2)

description: Library name: Control_2


title: enriched nuclei_MD_1485_6559


title: enriched nuclei_MD_1485_6558


title: T67_T_24HR

first: Jeries

last: Abu-Hanna

address: Oxford Haemophilia and Thrombosis Centre, Windmill Road

institute: University of Oxford

description: Library name: Sample 24

data_processing:
Raw reads were trimmed with fastp v0.20.1 (adapter removal and quality filtering).
Clean reads were aligned to GRCh38 using STAR v2.7.9a with --quantMode GeneCounts.
Strand-specific counts were extracted from column 4 (reverse-stranded) of ReadsPerGene.out.tab.
QC metrics compiled via MultiQC.
Assembly: GRCh38
Supplementary files format and content: txt files include counts and FPKM for each sample

source_name: ECFCs

growth_protocol: ECFCs were cultured in Endothelial Cell Growth Medium 2 (Lonza) with 10% FBS in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
Library preparation was performed by Novogene Co., Ltd.

treatment_protocol: ECFCs were treated with 0.1 ng/ml TNFα, 0.1 ng/ml IL-6, 500 ng/ml HMGB1, 1 nM epineprhine, 10 μm H2O2 and hypoxia (1% O2) for 2 or 24 hr.

value: ECFCs

value: Treated for 24 hr


title: Neural stem cells_ control cells (1)

description: Library name: Control_1


title: enriched nuclei_MD_1485_6557

value: OPC


title: enriched nuclei_MD_1722_8028


title: T67_T_2HR

description: Library name: Sample 23

value: Treated for 2 hr


title: enriched nuclei_MD_1459_8347


title: enriched nuclei_MD_1722_6743


title: NKM-1, control 2.1

description: Library name: 97_NKM-1_C2_A_296_281_S112


title: T67_U_24HR

description: Library name: Sample 22

value: Untreated for 24 hr


title: enriched nuclei_MD_1459_8345


title: enriched nuclei_MD_1459_8346


title: enriched nuclei_MD_1215_6679


title: enriched nuclei_MD_1485_6673


title: Normoxic mice

city: San Antonio

first: Nathaniel

middle: A

last: Jeske

state: TX

address: 7703 Floyd Curl Dr

department: OMS

institute: UTHSA

description: Library name: Sample 1

data_processing:
Using an Illumina NovaSeq instrument samples were sequenced using a 2x150bp Paired-End (PE) configuration, targeting 30 M reads/sample. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification. Reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: NEBNext Ultra II RNA Library Prep Kit for Illumina
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Dorsal Root Ganglion

extract_protocol:
RNA was extracted from cells using a Trizol-Chlorofom based method. 1mL of Trizol was added to the cell samples and mixed by inversion then incubated on ice for 5 minutes. 0.2mL of chloroform was added, mixed vigorously and vortexed before incubating at room temp for 3 minutes. Samples were then centrifuged at 11600 x g for 15 mins at 4oC. After which the aqueous phase was transferred to a microcentrifuge tube containing 0.5mL of isopropanol. The sample was pipetted up and down gently 20 times to precipitate the RNA. Samples were incubated at room temp for 10 minutes before being centrifuged at 11600 x g for 10 mins at 4oC. Supernatant was discarded and RNA pellet was washed using 1mL 75% ice-cold ethanol, mixed by inversion and centrifuged at 10000 x g for 5 mins at 4oC. Supernatant was discarded and the RNA pellet was air dried at room temp for 30 minutes. RNA pellet was resuspended in 50uL of nuclease-free water and incubated in a water bath at 60oC for 10 minutes.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer's instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Mice in their home cages were placed inside commercially supplied hypoxia chambers (Biospherix, Ltd., Parish, New York) 5 to 7 days prior to beginning a previously described CIH protocol (Jia et al., 2022).  Briefly, percent oxygen in each chamber was continuously monitored and software-controlled valves supplied either 100% nitrogen to reduce ambient O2 from ~21% (normoxia) to 8% (hypoxia) or pressurized room air to raise O2 back to the normoxic level.  The duration of each normoxic-hypoxic cycle was 6 minutes (10 hypoxia cycles/h).  Mice were exposed to CIH for 8 hours/day from 08:00 to16:00 h for 14 consecutive days.  Normoxic control mice underwent sham treatment, which was identical except that both flow regulating valves supplied room air (~21% oxygen) so that mice remained normoxic throughout the protocol.  Experiments were performed ~18 hours after completion of the last CIH/sham-CIH exposure.

value: Dorsal Root Ganglion

value: Macrophage

value: Normoxia


title: T67_U_2HR

description: Library name: Sample 21

value: Untreated for 2 hr


title: Hippocampus nuclears, KI, rep2

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

country: South Korea

institute: Korea University College of Medicine

description:
Library name: KI_2
10x Genomics

library_source: transcriptomic single cell

data_processing:
cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate feature-barcode matrices, determine clusters, and perform gene expression analysis. The count pipeline can take input from multiple sequencing runs on the same GEM well. cellranger count also processes Feature Barcoding data alongside Gene Expression reads.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

growth_protocol: The mice were fed and had access to water ad libitum and were group housed (4–6 mice per cage) under a 12-h light-dark cycle (light on from am 8:00 to pm 8:00, brain samples were collected pm 2:00–4:00) at 18–25°C.

extract_protocol:
Mice were deeply anesthetized with isoflurane and decapitated. The hippocampus from both hemispheres was dissected and rapidly frozen in liquid nitrogen. The tissue was stored at -80°C until further processing for single-nucleus isolation for snRNA-seq.
The Chromium Single Cell 3' Protocol enables to profile 3' digital gene expression of 500 - 10,000 individual cells per sample. Single cells, reagents and a single Gel Bead containing barcoded oligonucleotides are encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology.Next GEM Technology samples a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein. It does so by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. The Single Cell 3' v3 Gel Beads include two additional primer sequences, that facilitate capture and priming of targets containing interested feature.

treatment_protocol: Cyfip2+/R87C (KI)

value: Hippocampus

value: Mouse glial and neurons

value: KI


title: enriched nuclei_MD_1459_8344

value: Cerebellum


title: CIH mice

description: Library name: Sample 2

value: Chronic Intermittent Hypoxia


title: enriched nuclei_MD_1215_7250


title: T48_T_24HR

description: Library name: Sample 20


title: enriched nuclei_MD_1215_6678

value: Oligo


title: enriched nuclei_KO_712


title: T48_T_2HR

description: Library name: Sample 19


title: Hippocampus nuclears, KI, rep1

description:
Library name: KI_1
10x Genomics


title: Hippocampus nuclears, WT, rep2

description:
Library name: WT_2
10x Genomics

value: WT


title: enriched nuclei_KO_3969

value: Microglia


title: T48_U_24HR

description: Library name: Sample 18

value: ECFCs


title: enriched nuclei_KO_3960


title: Hippocampus nuclears, WT, rep1

description:
Library name: WT_1
10x Genomics


title: enriched nuclei_KO_3958


title: T48_U_2HR

description: Library name: Sample 17


title: enriched nuclei_KO_3956


title: enriched nuclei_HC_640


title: T16_T_24HR

description: Library name: Sample 16

value: Treated for 24 hr


title: 18_ATAC_seq_shSMRT_rp3

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

description: Library name: Sample 18

library_source: genomic

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
RNA-seq raw files (fastq, PE150) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.

molecule: genomic DNA

source_name: monocyte

growth_protocol:
WT RAW264.7 cells, lentivirus-medicated knockdown cells were maintained normal 10% FBS DMEM medium.
RAW264.7 cells  with lentivirus-medicated knockdown cells were maintained normal 10% FBS DMEM medium.
RAW264.7  cells were maintained normal 10% FBS DMEM medium.
shGFP, shNCOR and shSMRT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
Fresh cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) for 30 minutes, followed by 1% formaldehyde for 10 minutes at room temperature. Nuclei were isolated, sonicated, and incubated with magnetic bead-antibody complexes.  Antibodies to NCOR (bethyl, A301-145A), SMRT (bethyl, A301-147A), and GPS2 (homemade) were used.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×105 cells one day before the experiments. Cells were washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
2×105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
No treatment
No treatment
No treatment
RAW264.7 cells were treated with or without LPS (100ng/ml), IL4 (20ng/ml), GW3965 (5uM) for 3 hours. H3K27ac (Abcam, ab4729) was used for the Cut&Tag experiment.

value: monocyte

value: Macrophages

value: BALB/c

value: ATAC-seq


title: 17_ATAC_seq_shSMRT_rp2

description: Library name: Sample 17


title: enriched nuclei_HC_1489

value: OPC


title: T16_T_2HR

description: Library name: Sample 15

value: Treated for 2 hr


title: enriched nuclei_HC_2429


title: 16_ATAC_seq_shSMRT_rp1

description: Library name: Sample 16


title: T16_U_24HR

description: Library name: Sample 14

value: Untreated for 24 hr


title: enriched nuclei_FX_1607


title: 15_ATAC_seq_shNCOR_rp3

description: Library name: Sample 15


title: enriched nuclei_KO_710


title: 14_ATAC_seq_shNCOR_rp2

description: Library name: Sample 14


title: enriched nuclei_FX_3886

value: Purkinje


title: enriched nuclei_HC_1488


title: T16_U_2HR

description: Library name: Sample 13

value: Untreated for 2 hr


title: enriched nuclei_FX_1605


title: 13_ATAC_seq_shNCOR_rp1

description: Library name: Sample 13


title: enriched nuclei_FX_1606


title: JC_T_24HR

description: Library name: Sample 12


title: JC_T_2HR

description: Library name: Sample 11


title: enriched nuclei_FX_10453


title: enriched nuclei_FX_1604


title: enriched nuclei_FM_709


title: JC_U_24HR

description: Library name: Sample 10


title: enriched nuclei_FM_702


title: 11_ATAC_seq_shGFP_rp2

description: Library name: Sample 11


title: enriched nuclei_HC_2410


title: enriched nuclei_FM_701


title: enriched nuclei_FM_700


title: 10_ATAC_seq_shGFP_rp1

description: Library name: Sample 10


title: enriched nuclei_FJ_687


title: JC_U_2HR

description: Library name: Sample 9


title: enriched nuclei_FJ_686


title: enriched nuclei_FX_3713


title: 9_shSMRT_RNAseq_3

description: Library name: Sample 9

value: RNA-seq


title: CF_T_2HR

description: Library name: Sample 7


title: enriched nuclei_FJ_685

value: Cerebellum


title: 8_shSMRT_RNAseq_2

description: Library name: Sample 8


title: enriched nuclei_EJ2_629


title: enriched nuclei_EJ2_1466


title: CF_U_2HR

description: Library name: Sample 5


title: enriched nuclei_DZ_697


title: enriched nuclei_EJ2_630


title: 12_ATAC_seq_shGFP_rp3

description: Library name: Sample 12


title: enriched nuclei_DZ_696


title: FM_T_24HR

description: Library name: Sample 4


title: enriched nuclei_DZ_3858


title: enriched nuclei_DZ_695


title: 6_shNCOR_RNAseq_3

description: Library name: Sample 6


title: enriched nuclei_DZ_3820


title: FM_T_2HR

description: Library name: Sample 3


title: CF_T_24HR

description: Library name: Sample 8


title: 4_shNCOR_RNAseq_1

description: Library name: Sample 4


title: enriched nuclei_DZ_3819


title: enriched nuclei_DRLU102018A_3500


title: FM_U_24HR

description: Library name: Sample 2


title: enriched nuclei_DRLU102018A_3499


title: enriched nuclei_DRLU102018A_3095


title: FM_U_2HR

description: Library name: Sample 1


title: enriched nuclei_DRLU102018A_3094

value: Astrocyte


title: CF_U_24HR

description: Library name: Sample 6


title: 7_shSMRT_RNAseq_1

description: Library name: Sample 7


title: 2_shGFP_RNAseq_2

description: Library name: Sample 2


title: DPSCs, APE, 24hrs, Biolrep4

city: Sakaka

first: Saeed

last: Alqahtani

country: Saudi Arabia

institute: Jouf University-College of Dentistry

description:
Library name: Sample16
column name in raw_counts_all_samples.txt: APE_24h4

data_processing:
Bioinformatic analysis was performed by Novogene using in-house Perl scripts (Novogene Co., LTD, Cambridge, UK).
Assembly: Human Genome Assembly GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Dental pulp

growth_protocol: DPSCs were maintained in Knock-out DMEM supplemented with 10 % Foetal bovine serum, 1 % L-Glutamine, and 1 % Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). 2.65 μg of total RNA was used for the construction of sequencing libraries.
RNA library preparation by polyA capture using the NEB Next® Ultra™ RNA Library Prep Kit.

treatment_protocol: Treated DPSCs were stimulated with 100 μM APE for 4 and 24 h. Untreated DPSCs were maintained in normal culture media.

value: Dental pulp

value: Primary human dental pulp stem cells (DPSCs)

value: Mesenchymal stem cell

value: APE treated

tag: time


title: enriched nuclei_DRLU102018A_3083

value: Oligo


title: 1_shGFP_RNAseq_1

description: Library name: Sample 1

value: monocyte


title: enriched nuclei_DRLU102018A_3084


title: BMDM_shSMRT_3

description: Library name: Sample 21

data_processing:
RNA-seq raw files (fastq, PE150) were aligned to the GRCm38/mm10 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided (tab-delimited file).

source_name: BMDM

growth_protocol: C57BL/6 mice were maintained under standard housing conditions and received a regular diet. The RAW264.7 cells, lentivirus-medicated knockdown cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
Total cellular RNA was extracted using the E.Z.N.A.® Total RNA Kit I(E.Z.N.A.® Total RNA Kit I) according to the reagent instructions.
The RNA-seq library preparation was followed by the instructions of LC Bio Technology CO., Ltd.

treatment_protocol: We knocked down NCOR and SMRT in BMDM-derived cells using the same virus and conducted transcriptome RNA-seq sequencing (TRCN0000238140 for SMRT and TRCN0000350169 for NCOR).  We also used siRNA sequences to knock down NCOR and SMRT in RAW264.7 cells to verify the reproducibility and stability of our results. The verified sequences were transfected into RAW264.7 cells and treated with 10 ng/mL LPS for 6 hours, followed by RNA extraction and RNA sequencing.

value: BMDM

tag: strain

value: shSMRT


title: DPSCs, APE, 24hrs, Biolrep3

description:
Library name: Sample15
column name in raw_counts_all_samples.txt: APE_24h3


title: enriched nuclei_DRLU041818C_2699


title: enriched nuclei_DRLU030918A_4282


title: enriched nuclei_DRLU041818C_2154


title: DPSCs, APE, 24hrs, Biolrep2

description:
Library name: Sample14
column name in raw_counts_all_samples.txt: APE_24h2


title: enriched nuclei_DRLU030918A_2773


title: enriched nuclei_DRLU041818C_2698


title: DPSCs, APE, 24hrs, Biolrep1

description:
Library name: Sample13
column name in raw_counts_all_samples.txt: APE_24h1


title: BMDM_shSMRT_2

description: Library name: Sample 20


title: enriched nuclei_DRLU030918A_2717


title: 3_shGFP_RNAseq_3

description: Library name: Sample 3

value: Macrophages

value: BALB/c


title: DPSCs, APE, 4hrs, Biolrep4

description:
Library name: Sample12
column name in raw_counts_all_samples.txt: APE_4h4


title: enriched nuclei_DRLU030918A_2754

value: OPC


title: 5_shNCOR_RNAseq_2

description: Library name: Sample 5


title: enriched nuclei_DRLU030918A_2412


title: BMDM_shNCOR_3

description: Library name: Sample 18

value: shNCOR


title: DPSCs, APE, 4hrs, Biolrep3

description:
Library name: Sample11
column name in raw_counts_all_samples.txt: APE_4h3


title: enriched nuclei_DRLU030819A_11105


title: BMDM_shNCOR_2

description: Library name: Sample 17


title: enriched nuclei_DB_1900_9677


title: enriched nuclei_DB_1900_9672

value: Purkinje


title: BMDM_shNCOR_1

description: Library name: Sample 16


title: DPSCs, APE, 4hrs, Biolrep2

description:
Library name: Sample10
column name in raw_counts_all_samples.txt: APE_4h2


title: DPSCs, APE, 4hrs, Biolrep1

description:
Library name: Sample9
column name in raw_counts_all_samples.txt: APE_4h1


title: BMDM_shGFP_s_3

description: Library name: Sample 15


title: enriched nuclei_CY_7630


title: enriched nuclei_DB_1900_9607


title: enriched nuclei_CY_1845


title: BMDM_shGFP_s_2

description: Library name: Sample 14


title: DPSCs, control, 24hrs, Biolrep4

description:
Library name: Sample8
column name in raw_counts_all_samples.txt: Ctrl_24h4

value: untreated


title: enriched nuclei_CY_1844


title: enriched nuclei_CW_40


title: enriched nuclei_CY_1613


title: BMDM_shSMRT_1

description: Library name: Sample 19


title: BMDM_shGFP_s_1

description: Library name: Sample 13


title: enriched nuclei_CW_37


title: DPSCs, control, 24hrs, Biolrep2

description:
Library name: Sample6
column name in raw_counts_all_samples.txt: Ctrl_24h2


title: enriched nuclei_DRLU030918A_2484


title: enriched nuclei_CW_286


title: BMDM_shGFP_n_3

description: Library name: Sample 12


title: DPSCs, control, 24hrs, Biolrep1

description:
Library name: Sample5
column name in raw_counts_all_samples.txt: Ctrl_24h1


title: enriched nuclei_CW_270


title: enriched nuclei_CH_635


title: DPSCs, control, 4hrs, Biolrep4

description:
Library name: Sample4
column name in raw_counts_all_samples.txt: Ctrl_4h4


title: enriched nuclei_CH_1429


title: BMDM_shGFP_n_1

description: Library name: Sample 10


title: DPSCs, control, 4hrs, Biolrep3

description:
Library name: Sample3
column name in raw_counts_all_samples.txt: Ctrl_4h3


title: RAW_siSMRT_3

description: Library name: Sample 9

value: macrophages

value: siSMRT


title: BMDM_shGFP_n_2

description: Library name: Sample 11


title: DPSCs, control, 24hrs, Biolrep3

description:
Library name: Sample7
column name in raw_counts_all_samples.txt: Ctrl_24h3


title: enriched nuclei_CA_160

value: Cerebellum


title: enriched nuclei_CA_162


title: DPSCs, control, 4hrs, Biolrep2

description:
Library name: Sample2
column name in raw_counts_all_samples.txt: Ctrl_4h2

value: Dental pulp


title: enriched nuclei_CA_158


title: DPSCs, control, 4hrs, Biolrep1

description:
Library name: Sample1
column name in raw_counts_all_samples.txt: Ctrl_4h1

value: Primary human dental pulp stem cells (DPSCs)


title: RAW_siSMRT_1

description: Library name: Sample 7


title: enriched nuclei_C9/194_3549

value: Microglia


title: RAW_siNCOR_3

description: Library name: Sample 6

value: siNCOR


title: enriched nuclei_C9/194_3548


title: D HF3

city: London

first: Chloe

middle: Emily

last: Jang

state: Ontario

address: 1151 Richmond St

country: Canada

institute: Western University

description: Library name: sample 12

data_processing:
Data were analyzed using Partek Flow (St. Louis, MO) and aligned to the human genome (hg38) using STAR 2.7.8a and annotated using hg38 Ensembl transcripts release 110. Features with fewer than 8 reads were filtered out, and normalization was done by counts per million (cpm) Plus 1.0. Differentially expressed genes (DEGs) were identified with an adjusted p-value < 0.05 and Log2FC ≥ 1. Pathway analysis was performed using iPathway Guide
Assembly: hg38 Ensembl transcripts release 110.
Supplementary files format and content: matrix table with raw or normalized gene counts for every gene and every sample; in text file

source_name: endometrium

growth_protocol: Human endometrial stromal cells  (ABM T0533) were grown in DMEM F/12 media supplemented with 10% Fetal Bovine Serum, 100 U/mL Penicillin and 100 mg/mL Streptomycin in a humidified atmosphere at 5% CO2 and 37C

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer's instructions
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment and library preparation were performed using the Illumina Stranded mRNA Prep Kit (Illumina), as per the manufacturer’s recommendations. Libraries were quantified using the KAPA Library Quantification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a Fragment Analyzer (Agilent) instrument.

treatment_protocol: Human endometrial stromal cells cultured in phenol red-free DMEM/F12 with 2% dextran-coated charcoal-stripped FBS, 100 U/mL penicillin and 100 mg/mL streptomycin were decidualized in vitro using 0.5 mM 8-bromo-camp (Cayman) and 1 uM Medroxyprogesterone acetate (Cayman) for 4 days in the presence or absence of 100 nM Halofuginone (Cayman)

value: endometrium

value: ABM T0533 (t-HESC)

value: endometrial stromal cells

value: WT

value: differentiated with halofuginone (HF)


title: D HF2

description: Library name: sample 11


title: enriched nuclei_C9/194_3546


title: enriched nuclei_CH_634

value: Oligo


title: RAW_siNCOR_2

description: Library name: Sample 5

value: BALB/c


title: enriched nuclei_CH_1970

value: OPC


title: D HF1

description: Library name: sample 10


title: RAW_siNCOR_1

description: Library name: Sample 4


title: enriched nuclei_C11/97_3534


title: enriched nuclei_C11/97_3533


title: enriched nuclei_CA_233

value: Astrocyte


title: enriched nuclei_C11/97_3495


title: enriched nuclei_C11/97_3497


title: UD HF3

description: Library name: sample 9

value: undifferentiated with halofuginone (HF)


title: UD HF2

description: Library name: sample 8


title: RAW_siCtrl_3

description: Library name: Sample 3

value: macrophages

value: siCtrl


title: RAW_siSMRT_2

description: Library name: Sample 8

value: siSMRT


title: enriched nuclei_BV_620

value: Cerebellum


title: enriched nuclei_C11/97_12688


title: enriched nuclei_CA_159


title: enriched nuclei_BV_619


title: enriched nuclei_BV_1499


title: RAW_siCtrl_1

description: Library name: Sample 1


title: RAW_siCtrl_2

description: Library name: Sample 2


title: enriched nuclei_BN2_3843

value: Purkinje


title: enriched nuclei_C9/194_3547


title: D3

description: Library name: sample 6

value: differentiated


title: UD HF1

description: Library name: sample 7


title: 5/6 Nx animal 4 fed a 0.3% phosphorus and 2.5% protein diet

city: New Haven

first: Yujun

last: Cai

address: 310 Cedar St.

institute: Yale University

description:
Library name: Nx_LP_Lpi_4
Column name in gene_count.txt and gene_fpkm.csv

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Aorta

extract_protocol:
Animals fed one of four different diets for 30 days. These diets were: HPi-Lp diet (TD.180077) containing 2% phosphorus and 2.5% protein, HPi-Hp diet (TD.220202) containing 2% phosphorus and 18% protein, LPi-Lp diet (TD.230207) containing 0.3% phosphorus and 2.5% protein, and LPi-Hp diet (TD.230584) containing 0.3% phosphorus and 18% protein. All diets were purchased from Inotiv Envigo. The aorta was collected and total RNA was isolated using RNeasy Mini Kit.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesizedusing random hexamer primers, followed by the second strand cDNAsynthesis using either dUTP for directional library or dTTP for non-directional library.

value: Aorta

value: Sham and 5/6 Nx with different diet


title: D2

description: Library name: sample 5

value: endometrium

value: ABM T0533 (t-HESC)


title: 5/6 Nx animal 3 fed a 0.3% phosphorus and 2.5% protein diet

description:
Library name: Nx_LP_Lpi_3
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BN2_1803


title: enriched nuclei_BN2_1660


title: D1

description: Library name: sample 4

value: endometrial stromal cells

value: WT


title: enriched nuclei_BN2_3744

value: Microglia


title: enriched nuclei_BN2_1659


title: 5/6 Nx animal 2 fed a 0.3% phosphorus and 2.5% protein diet

description:
Library name: Nx_LP_Lpi_2
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BN2_1655

value: Oligo


title: UD3

description: Library name: sample 3

value: undifferentiated


title: 5/6 Nx animal 1 fed a 0.3% phosphorus and 2.5% protein diet

description:
Library name: Nx_LP_Lpi_1
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BN1_694


title: UD2

description: Library name: sample 2


title: enriched nuclei_BN1_692

value: OPC


title: enriched nuclei_BN1_690


title: enriched nuclei_BN1_691


title: 5/6 Nx animal 4 fed a 2% phosphorus and 18% protein diet

description:
Library name: Nx_HP_Hpi_4
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BE_252


title: UD1

description: Library name: sample 1


title: 5/6 Nx animal 3 fed a 2% phosphorus and 18% protein diet

description:
Library name: Nx_HP_Hpi_3
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BE_154


title: enriched nuclei_BN2_3745

value: Astrocyte


title: enriched nuclei_BE_152


title: enriched nuclei_BBN110.29570_141


title: enriched nuclei_BBN110.28970_535


title: Control_3

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description:
Library name: Control_3
HIVEseq

data_processing:
Fastqs were processed into gene and transcript counts ising beenet v1.1 (Honeycomb Biotechnologies, Inc)
Assembly: Human hg38
Supplementary files format and content: ensembl build 104
Supplementary files format and content: tab separated values and qc files

source_name: RBC depleted leukocytes

extract_protocol:
venous blood samples were collected for testing in PAXgene™ blood RNA tubes (Qiagen, Hilden, Germany) and Acid Citric Dextrose tubes (BD).  Red blood cells were depleted from whole blood by immunomagnetic negative selection, using the EasySep™ RBC depletion reagent protocol (catalog #18000), preserving all leukocyte populations, including granulocytes. HIVE devices were each loaded with cells in 1 mL of DPBS + 1% FBS, followed by 3mL of cell media. The leukocytes were loaded into the HIVE system within an hour of blood sampling from all individuals to minimise neutrophil activation. Single-cells settled into picowells of the HIVE containing 3’ transcript-capture beads. HIVEs were then placed onto a spin plate and spun at 30 x G for 3 minutes. Media was removed from the HIVE, and 2mL sample wash solution (provided by PerkinElmer) was added to each. Sample wash solution was removed, and the cell-loaded HIVE™ were frozen at -80°C after the addition of cell preservation solution.
Following standard protocol, cell-loaded HIVE devices were sealed with a semi-permeable membrane, allowing for the use of the strong lysis solution followed by the addition of hybridization solution. After collection with or without storage, beads with captured transcripts were extracted from the HIVE device by centrifugation. The remaining HIVE library preparation steps were conducted in a 96-well plate format. PerkinElmer’s LabChip® GX TouchTM nucleic acid analyzer was used for accurate assessment of individual library sizes, and the concentration of final pooled libraries was determined by qPCR. HIVE scRNAseq libraries were sequenced using specific primers contained in the kit on an Illumina® NovaSeq® 6000 sequencer

treatment_protocol: Single-cell RNA sequencing in children with Paediatric Acute-Onset Neuropsychiatric syndrome before and after IVIg treatment and healthy controls

value: RBC depleted leukocytes

tag: condition

value: Pt

tag: cohort


title: enriched nuclei_BBN110.28970_2150


title: enriched nuclei_BBN110.28668_304


title: 5/6 Nx animal 4 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Nx_LP_Hpi_4
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BBN110.28668_180


title: enriched nuclei_BBN110.28649_753


title: Control_1

description:
Library name: Control_1
HIVEseq

value: Ctrl


title: 5/6 Nx animal 3 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Nx_LP_Hpi_3
Column name in gene_count.txt and gene_fpkm.csv


title: Patient_5_post

description:
Library name: Patient_5_post
HIVEseq


title: enriched nuclei_BBN110.28649_436

value: Cerebellum


title: Control_2

description:
Library name: Control_2
HIVEseq


title: 5/6 Nx animal 2 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Nx_LP_Hpi_2
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BBN110.28649_435


title: Patient_4_post

description:
Library name: Patient_4_post
HIVEseq


title: enriched nuclei_BBN110.26146_249


title: 5/6 Nx animal 1 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Nx_LP_Hpi_1
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BBN110.28649_177


title: Patient_3_post

description:
Library name: Patient_3_post
HIVEseq


title: Sham animal 4 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Sha_LP_Hpi_4
Column name in gene_count.txt and gene_fpkm.csv


title: 5/6 Nx animal 2 fed a 2% phosphorus and 18% protein diet

description:
Library name: Nx_HP_Hpi_2
Column name in gene_count.txt and gene_fpkm.csv


title: Patient_2_post

description:
Library name: Patient_2_post
HIVEseq


title: enriched nuclei_BBN110.26146_247


title: enriched nuclei_BBN110.26146_176


title: enriched nuclei_BBN110.28649_490


title: Sham animal 3 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Sha_LP_Hpi_3
Column name in gene_count.txt and gene_fpkm.csv


title: Control_4

description:
Library name: Control_4
HIVEseq


title: enriched nuclei_BBN110.26146_245


title: 5/6 Nx animal 1 fed a 2% phosphorus and 18% protein diet

description:
Library name: Nx_HP_Hpi_1
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BBN_23801_137


title: Sham animal 2 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Sha_LP_Hpi_2
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BBN110.26146_174


title: enriched nuclei_BBN_23801_135


title: enriched nuclei_BBN_23801_134


title: Patient_5_pre

description:
Library name: Patient_5_pre
HIVEseq


title: Sham animal 1 fed a 2% phosphorus and 2.5% protein diet

description:
Library name: Sha_LP_Hpi_1
Column name in gene_count.txt and gene_fpkm.csv


title: enriched nuclei_BBN_23801_133


title: Patient_1_post

description:
Library name: Patient_1_post
HIVEseq


title: enriched nuclei_AY_677


title: enriched nuclei_AY_675


title: Lung IM, EC-SOD SMC KO, 14d hypoxia, rep2

city: Aurora

first: Caitlin

middle: Vanessa

last: Lewis

state: Colorado

address: University of Colorado Denver AMC, 12700 East 19th Avenue, Mail Stop B131

department: Pediatrics

institute: University of Colorado

description: Library name: Sample 18

data_processing:
FastQC v0.11.9 for quality control and UMI-tools v1.1.1 for UMI extraction
Trim Galore! V0.6.6 to trim adapter and low-quality sequences
Alignment to mm10 genome and BAM file filtering using STAR v2.6.1d, SAMtools v1.9 and UMI-tools
Genes assigned using featureCounts v2.0.1
Differential gene expression analyzed using DESeq2
Assembly: mm10
Supplementary files format and content: excel spreadsheet of normalized read count matrix

source_name: lung

extract_protocol:
RNA was harvested from FACS isolated IMs using the Qiagen RNeasy Micro Kit. 20 ng total RNA was used for library preparation
RNA libraries prepared using Illumina Novaseq protocol

treatment_protocol: Mice exposed to 4 or 14 days of hypobaric hypoxia (FiO2 10%) vs normoxia

value: lung

value: intersitial macrophage

value: EC-SODloxp/loxp x Tgcre/SMMHC

value: 14 day hypoxia


title: Patient_3_pre

description:
Library name: Patient_3_pre
HIVEseq


title: Lung IM, EC-SOD SMC KO, 14d hypoxia, rep3

description: Library name: Sample 19


title: enriched nuclei_2012-033_4261


title: Lung IM, EC-SOD SMC KO, 14d hypoxia, rep1

description: Library name: Sample 17


title: Patient_2_pre

description:
Library name: Patient_2_pre
HIVEseq


title: enriched nuclei_2012-033_4260

value: Purkinje


title: enriched nuclei_2012-005_4391


title: Lung IM, EC-SOD SMC KO, 4d hypoxia, rep4

description: Library name: Sample 16

value: 4 day hypoxia


title: Patient_1_pre

description:
Library name: Patient_1_pre
HIVEseq


title: Lung IM, EC-SOD SMC KO, 4d hypoxia, rep3

description: Library name: Sample 15


title: enriched nuclei_2012-005_4390


title: enriched nuclei_2012-005_4344


title: enriched nuclei_2012-005_4347


title: HRMECs, 10mM APX2009 normoxia, replicate 5, 6 hours

city: Indianapolis

first: Kelley

last: Mark

state: Indiana

institute: Herman B Wells Center for Pediatric Research

description: Library name: 2009_10_5_Nor

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE 31 genes using featureCounts (from subread v1.6.5) with the following parameters: “-s0 –p –Q 10”.
Raw count were subject to differential expression analysis using EdgeR
Assembly: hg38
Supplementary files format and content: raw counts file

source_name: retinal endothelial cells

extract_protocol:
Total RNA was extracted with QIAGEN RNA Isolation Kit.
KAPA mRNA Hyperprep Kit (KK8581).

value: retinal endothelial cells

value: HRMECs

value: endothelial cells

value: 6 hours 10mM APX2009 normoxia


title: Lung IM, EC-SOD SMC KO, 4d hypoxia, rep2

description: Library name: Sample 14


title: enriched nuclei_2012-005_4343

value: Microglia


title: HRMECs, 10mM APX2009 normoxia, replicate 3, 6 hours

description: Library name: 2009_10_3_Nor

value: WT


title: HRMECs, 10mM APX2009 normoxia, replicate 4, 6 hours

description: Library name: 2009_10_4_Nor


title: enriched nuclei_2012-005_4345


title: Lung IM, EC-SOD SMC KO, 4d hypoxia, rep1

description: Library name: Sample 13


title: Patient_4_pre

description:
Library name: Patient_4_pre
HIVEseq


title: HRMECs, 10mM APX2009 normoxia, replicate 2, 6 hours

description: Library name: 2009_10_2_Nor


title: enriched nuclei_2012-005_4342

value: Oligo


title: enriched nuclei_AY_676


title: enriched nuclei_2012-001_7653


title: Lung IM, EC-SOD SMC KO, normoxia, rep3

description: Library name: Sample 12

value: untreated/normoxia


title: enriched nuclei_2012-001_7651

value: OPC


title: HRMECs, 10mM APX2009 normoxia, replicate 1, 6 hours

description: Library name: 2009_10_1_Nor


title: Lung IM, EC-SOD SMC KO, normoxia, rep2

description: Library name: Sample 11


title: enriched nuclei_2012-001_7323


title: enriched nuclei_2012-001_7322

value: Astrocyte


title: enriched nuclei_2012-005_4346

value: Cerebellum


title: HRMECs, 1% DMSO normoxia replicate 5, 6 hours

description: Library name: DMSO_5_Nor

value: 6 hours 1% DMSO normoxia


title: Lung IM, EC-SOD SMC KO, normoxia, rep1

description: Library name: Sample 10

value: lung

value: intersitial macrophage


title: enriched nuclei_2012-001_7320


title: enriched nuclei_2012-001_7319


title: enriched nuclei_2011-111_4286


title: enriched nuclei_2011-111_4285


title: Lung IM, Floxed WT, 14d hypoxia, rep3

description: Library name: Sample 9

value: EC-SODloxp/loxp (Floxed WT)

value: 14 day hypoxia


title: HRMECs, 1% DMSO normoxia replicate 4, 6 hours

description: Library name: DMSO_4_Nor


title: HRMECs, 1% DMSO normoxia replicate 3, 6 hours

description: Library name: DMSO_3_Nor


title: enriched nuclei_2012-001_7318


title: Lung IM, Floxed WT, 14d hypoxia, rep2

description: Library name: Sample 8


title: HRMECs, 1% DMSO normoxia replicate 2, 6 hours

description: Library name: DMSO_2_Nor


title: Lung IM, Floxed WT, 14d hypoxia, rep1

description: Library name: Sample 7


title: HRMECs, 1% DMSO normoxia replicate 1, 6 hours

description: Library name: DMSO_1_Nor


title: enriched nuclei_2011-111_4284


title: enriched nuclei_2011-111_4277


title: Lung IM, Floxed WT, 4d hypoxia, rep3

description: Library name: Sample 6

value: 4 day hypoxia


title: enriched nuclei_2011-111_4273


title: enriched nuclei_2011-111_4275


title: enriched nuclei_2011-111_4274


title: Lung IM, Floxed WT, 4d hypoxia, rep2

description: Library name: Sample 5


title: enriched nuclei_2011-090_4308


title: enriched nuclei_2011-111_4252

value: Purkinje


title: enriched nuclei_2011-090_4203


title: DE48NGSUKBR129386_Control, no depressive symptomes [postpartum sample]

city: Uppsala

first: Alkistis

last: Skalkidou

address: Dag Hammarskjölds väg 14 B

department: Women's and Children's Health

country: Sweden

institute: Uppsala university

description: Library name: DE48NGSUKBR129386

data_processing:
UCSC Genome Browser hg38 using Spliced Transcripts Alignment to a Reference (STAR) with standard parameters
Count matrix per gene obtained for each sample using htseq-count function from HTSeq
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count number for each sample

source_name: blood

extract_protocol:
RNA was extracted using the PAXgene 96 Blood RNA Kit (Qiagen GmbH)
RNA libraries for RNA sequencing were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen)

tag: age (years)

tag: pre-pregnancy bmi_(kg/m2)

tag: ssri user_(yes/no)

value: Yes

value: blood

tag: subject group

value: Control

tag: time point

value: postpartum sample


title: enriched nuclei_2011-090_4204

value: Microglia


title: DE95NGSUKBR129413_Control, no depressive symptomes [postpartum sample]

description: Library name: DE95NGSUKBR129413


title: DE19NGSUKBR129423_Control, no depressive symptomes [postpartum sample]

description: Library name: DE19NGSUKBR129423


title: enriched nuclei_2011-090_4200


title: enriched nuclei_2011-090_4312


title: Lung IM, Floxed WT, normoxia, rep2

description: Library name: Sample 2


title: enriched nuclei_2011-090_4199


title: DE81NGSUKBR129374_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE81NGSUKBR129374


title: Lung IM, Floxed WT, normoxia, rep1

description: Library name: Sample 1


title: DE54NGSUKBR129375_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE54NGSUKBR129375


title: enriched nuclei_2011-090_4198

value: Oligo


title: enriched nuclei_2011-082_7302


title: MEF, SODWT, biol rep 3

first: Joseph

last: Schell

address: 4939 Charles Katz

institute: UT Health San Antonio

description:
Mouse Embryo Fibroblasts isolated from SOD2WT mice with a C57BL/6 background on day E13.5.
MEFSODWT3r
MEFSODWT3r_S35

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm39) using HISAT2 (v2.2.1) default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts (v2.0.6) to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: mm39
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. There are twelve (12) columns total. The first six are: Geneid; Chr; Start; End; Strand; Length; The remaining columns give the raw counts and are named with the bamfile name.

source_name: Mouse Embryo Fibroblast

extract_protocol:
RNA was extracted by Triazol and Qiagen RNeasy Plus Mini kit. RNA quality was determined by BioAnalyzer and RIN > 4. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq library preparation by following the NEB stranded mRNA sample preparation guide

tag: mouse strain

value: Mouse Embryo Fibroblast

value: WT


title: enriched nuclei_2011-082_7730

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for initial quality control. Adapter trimming was performed with Cutadapt v1.12 (Dobin et al., 2013). Reads were aligned to the hg38 human genome build (NCBI primary analysis set) using STAR aligner v2.5.2b (Wang et al., 2012) with splice junction files generated from Gencode release 27 and RefSeq GRCh38.p10. Post-alignment quality control was performed by examination of the STAR alignment metrics, Picard tools v2.8.2 (CollectRNASeqMetrics) (https://broadinstitute.github.io/picard/) and RSeQC v2.6.4 (tin.py) (Anders et al., 2015). Expression quantitation was performed with htseq-count v0.6.1p1 (Anders et al., 2015) using a custom annotation file based on RefSeq where both exonic and intronic reads are counted for each gene.  The read counts table from each sample was imported into RStudio (version 1.1.423; R version 3.4.3) running under CentOS Linux 7. Using edgeR (version 3.20.9), the read counts were normalized into Counts Per Million (TPM), log transformed, and batch corrected. For each individual cell type, we removed technical variance associated with batch effect using sva R package. Hierarchal clustering analysis was performed using the pheatmap R package (Kolde R et al., 2018). Principal component analysis was performed using pcaMethods R package. Metabolic flux analysis was computed using scFEA R package (https://github.com/changwn/scFEA, Alghamdi N et al., 2021). Cell type specific genes were identified using the specificity index algorithm previous described in (Xu et al., 2018) and (Dougherty et al., 2010). log2(TPM) values were used as gene expression input and ranks were averaged across 1,000 iterations.
Assembly: Gencode release 27 and RefSeq GRCh38.p10
Supplementary files format and content: fastq file containing raw data
Supplementary files format and content: txt files with raw counts

source_name: Cerebellum

extract_protocol:
RNA extractions from sorted nuclei were carried out with FFPE RNA Purification kits (Norgen: Product # 25300) using the manufacturer’s protocol from Step 2 (Lysate Preparation) with the following modifications: The On-column DNA removal Protocol was omitted. RNA binding and Column Wash centrifuge steps were carried out at 1,789×g for 2 min, followed by 1,789×g for 5 min to dry the resin. Elution was carried out in two steps, with 25 µL Elution Solution A added to each column followed by a 1 min room temperature incubation and centrifugation at 200×g for 2 min, then a further 15 µL Elution Solution A was added to each column with centrifugation at 1,789×g for 5 min. For samples containing >2,000 nuclei, the final 30 µL elution was split into two 15 µL aliquots. Purified RNA was vacuum dried in a CentriVap Benchtop Vacuum Concentrator (Labconco) for 40 min (or until no liquid was visible) at 4˚C and either used directly for library preparation or stored at -20˚C.
Sequencing library generation was carried out using the Trio RNA-Seq, Human rRNA Library Preparation Kit (Tecan: Product # 0506-A01) using the manufacturer’s protocol with the following modifications: Lyophilized RNA was resuspended in 12.5 µL DNAse mix and incubated at 37˚C for 30 min followed by 60˚C for 5 min and 4˚C Hold. Library Amplification I was carried out as 72˚C 2 min/95˚C 2 min/2×(95˚C 30 s/ 60˚C 60 s)/6×(95˚C 30 s/ 65˚C 60 s)/65˚C 5 min/4˚C Hold Library Amplification II was carried out as 95˚C 2 min/2×(95˚C 30 s/ 60˚C 60 s)/6×(95˚C 30 s/ 65˚C 60 s)/65˚C 5 min/4˚C Hold Final Libraries eluted in 30 µL DNA Resuspension Buffer (DR1) were checked on Agilent Bioanalyzer DNA 1000 chips, then measured on a Nanodrop 8000 and 32 sample pools (normalized to 500 ng/sample then diluted to 5 ng/µL) were sent for sequencing on an Illumina NextSeq High Output platform.


title: enriched nuclei_2011-082_4211


title: DE21NGSUKBR129387_Control, no depressive symptomes [postpartum sample]

description: Library name: DE21NGSUKBR129387


title: enriched nuclei_2011-082_4192

value: Astrocyte


title: MEF, SODWT, biol rep 2

description:
Mouse Embryo Fibroblasts isolated from SOD2WT mice with a C57BL/6 background on day E13.5.
MEFSODWT2r
MEFSODWT2r_S34


title: enriched nuclei_2011-082_4193

value: Cerebellum


title: DE10NGSUKBR129391_Control, no depressive symptomes [postpartum sample]

description: Library name: DE10NGSUKBR129391


title: enriched nuclei_2011-090_4233


title: Lung IM, Floxed WT, 4d hypoxia, rep1

description: Library name: Sample 4


title: Lung IM, Floxed WT, normoxia, rep3

description: Library name: Sample 3

value: untreated/normoxia


title: enriched nuclei_2011-082_4191

value: OPC


title: enriched nuclei_2011-082_4190


title: MEF, SODWT, biol rep 1

description:
Mouse Embryo Fibroblasts isolated from SOD2WT mice with a C57BL/6 background on day E13.5.
MEFSODWT1r
MEFSODWT1r_S33


title: DE59NGSUKBR129382_Control, no depressive symptomes [postpartum sample]

description: Library name: DE59NGSUKBR129382


title: enriched nuclei_2011-082_4189


title: enriched nuclei_2011-017_4547


title: DE91NGSUKBR129388_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE91NGSUKBR129388

value: Depressive symptomes only postpartum

value: postpartumy sample


title: DE32NGSUKBR129383_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE32NGSUKBR129383


title: MEF, SODK68R, biol rep 3

description:
Mouse Embryo Fibroblasts isolated from SOD2K68R mice with a C57BL/6 background on day E13.5.
MEFSOD68R3
MEFSOD68R3_S38


title: enriched nuclei_2011-017_4388


title: MEF, SODK68R, biol rep 1

description:
Mouse Embryo Fibroblasts isolated from SOD2K68R mice with a C57BL/6 background on day E13.5.
MEFSOD68R1
MEFSOD68R1_S36


title: enriched nuclei_2011-017_4396


title: DE35NGSUKBR129426_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE35NGSUKBR129426


title: MEF, SODK68R, biol rep 2

description:
Mouse Embryo Fibroblasts isolated from SOD2K68R mice with a C57BL/6 background on day E13.5.
MEFSOD68R2
MEFSOD68R2_S37


title: enriched nuclei_2009-096_7642


title: DE63NGSUKBR129407_Control, no depressive symptomes [postpartum sample]

description: Library name: DE63NGSUKBR129407


title: enriched nuclei_2009-096_4594


title: enriched nuclei_2009-096_4581


title: enriched nuclei_2009-096_4563


title: D7-GFP_plus_EPZ

city: NY

first: Yang

last: Bai

state: NY

address: 1300 York Ave

department: Cardiothoracic Surgery

institute: Weill Cornell Medicine

data_processing:
Sequencing quality was evaluated using FastQC (Andrews S. FastQC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned via STAR v2.7.6a against the mouse genome build mm39 and counted using the `htseq-count` tool . DEseq2 package in R was used for differential expression analysis. A Wald test was applied for mRNA differential analysis, and p-values were corrected for multiple testing using the Benjamini and Hochberg method. Genes with adjusted p-value ≤0.05 and fold-change >= 1.5 were considered significantly differentially expressed. Gene clusters across sample groups were identified using the DEGreport  package in R.
Assembly: mm39
Supplementary files format and content: bigwig

source_name: breast

growth_protocol: DMEM + 10% FBS + 1X Pen-Strep in 100 mm dish (Corning™ 100 mm TC-Treated Culture Dishes)

extract_protocol:
As described in the protocol for Rneasy Plus Mini Kit (Qiagen 74134)
TruSeq RNA library prep kit (Illumina)

treatment_protocol: 5ul of DMSO or 5uM EPZ-6438 for 7 days

value: breast

value: 5uM EZH2


title: D7-GFP_plus_EPZ replicate 2


title: DE85NGSUKBR129399_Control, no depressive symptomes [postpartum sample]

description: Library name: DE85NGSUKBR129399


title: enriched nuclei_2009-096_4565

last: Stirparo


title: D7-GFP_plus_EPZ replicate 3


title: DE41NGSUKBR129415_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE41NGSUKBR129415


title: enriched nuclei_2009-039_4311


title: enriched nuclei_2009-039_4245

value: Purkinje


title: enriched nuclei_2009-005_7648


title: DE68NGSUKBR129414_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE68NGSUKBR129414

value: Yes


title: D7-GFP_plus_DMSO replicate 3

value: DMSO


title: enriched nuclei_2011-017_4546


title: DE25NGSUKBR129412_Control, no depressive symptomes [postpartum sample]

description: Library name: DE25NGSUKBR129412

value: blood

value: Control


title: enriched nuclei_2009-005_7325


title: enriched nuclei_2009-005_4318


title: enriched nuclei_2012-001_7652

value: Microglia


title: enriched nuclei_2009-005_4317


title: DE15NGSUKBR129398_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE15NGSUKBR129398


title: enriched nuclei_2009-005_4307


title: DE57NGSUKBR129418_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE57NGSUKBR129418

value: postpartum sample


title: enriched nuclei_2009-005_4316


title: D7-GFP-_EPZ replicate 3


title: D7-GFP_plus_DMSO


title: enriched nuclei_2009-005_4241


title: DE37NGSUKBR129390_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE37NGSUKBR129390


title: D7-GFP-_EPZ replicate 2


title: U2OS_DRB_20minR_rep2_batch2

city: Copenhagen

first: Haiyue

last: Liu

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Sequencing reads of the two sequencing batches from the same sample were merged into one single fastq file.
The UMI sequences were extracted from R2 files and attached to the read headers of R1 files using UMI_tools v1.1.4.
The UMI attched single-end reads (R1) were trimmed for sequencing adaptors and low quality sequences using trimgalore v0.6.6.
The trimmed reads were aligned to a human and yeast hybrid reference genome using STAR 2.7.9a with options:--outSAMattributes NH HI AS NM MD XS --outSAMstrandField intronMotif --outSAMmultNmax 1.
The uniquely mapped reads were extracted from the alignments using samtools v1.15.1 with options: -q 255 -F 0x2.
PCR duplicates were removed from the uniquely mapped reads using UMI_tools v1.1.4.
The reads were further cleaned up by removing those mapped to exon-exon junctions using samtools v1.15.1 with options: -he '[XS]'.
The reads containing genes originated from the forward and reverse strands were split using samtools v1.15.1.
Uniquely assigned features (i.e. genes) to each sample were counted using featureCounts from Subread v2.0.3.
The bigwig files were generated from the forward and reverse strand mapped reads using  UCSC GenomeToolset and bedtools. The scaling factors were calculated from the yeast spike-ins using DESeq2.
The transcription elongation rates for individual genes were calculated from the forward and reverse strands split reads using self-developed script as described here: https://github.com/haiyueliu/elongation_rate.
Assembly: GRCh38, Saccharomyces_cerevisiae.R64-1-1
Supplementary files format and content: bigwig format contain the coverage profiles that can be viewed in a genome browser or IGV
Library strategy: DRB/TTchem-seq2

extract_protocol:
Total RNA was harvested using TRIzol including an additional chloroform cleanup and isopropanol precipitated.
20 ug of total RNA were spiked in with 0.2 ug of yeast spike-ins (Saccharomyces cerevisiae W303a cells labeled with 5mM 4-thiouracil (4tU, Sigma, 440736) for 5 min, see Gregersen et al., 2022 for detailed procedure). RNA was fragmented for 20 min on ice by base hydrolysis and returned to a neutral pH buffer prior to biotinylation as previously described (Gregersen et al., 2020a). For addition of biotin to 4sU residues we used the MTSEA Biotin-XX linker (Biotium, BT90066). Biotinylated RNA was purified by phenol:chloroform and isopropanol precipitation, heat denatured and used for purification with uMACS Streptavidin microbeads (Miltenyi, 130-074-101). 4sU-RNA was eluted from beads using 2 rounds of 100 mM DTT and cleaned-up with the RNeasy MinElute Cleanup Kit (Qiagen, 74204) using 1.5x excess of ethanol for the RNA precipitation compared to the supplied protocol to ensure recovery of small RNA fragments. Concentration of 4sU-RNA was measured by Qubit (RNA high sensitivity assay, ThermoFisher Q32852) and the size range determined by high sensitivity RNA assay on a TapeStation (high sensitivity RNA ScreenTape, Agilent, 5067-5579). 4 ng of 4sU RNA was used for next-generation sequencing library preparation with the NEBNext Ultra II directional RNA kit (NEB, E7760) using Unique Dual Index UMI Adaptors (NEB, E7416) following the protocol for degraded RNA (RIN 1-2) without additional RNA fragmentation. Libraries were amplified using 12 PCR cycles, concentration measured by Qubit (DNA high sensitivity assay) and size distribution assessed using TapeStation (high sensitivity D5000 ScreenTape, Agilent, 5067-5592). The final library size distribution peaked at 390 nt, corresponding to an insert size of 260 nt. Libraries were sequenced on two P3 v100 flow cells (130 cycles) in paired-end mode on a NextSeq2000 (Illumina).

treatment_protocol: DRB/TTchem-seq2 was developed based on the previous protocol from (Gregersen et al, 2020a) with the major modifications being (1) the RNA labelling time, (2) shorter DRB release time points (3) inclusion of UMI adapters and (4) addition of a no DRB released sample for background subtraction.  For RNAPII synchronization close to the TSS USO2 cells were incubated with 100 uM DRB (5,6-dichlorobenzimidazole 1-β-D-ribofuranoside; Sigma-Aldrich, D1916) for 3.5 hrs and DRB inhibition released for 5, 10, 15 and 40 min by 3 washes pre-warmed PBS. For each time point newly synthesized RNA was labeled with 1 mM 4-thiourudine (4sU, Biosynth Carbosynth, NT06186) for 5 min immediately prior to harvest by addition of TRIzol (Thermo Fisher, 15596026) directly on top of the cell monolayer. Samples were prepared in duplicates for all time points.

value: Human osteosarcoma

value: DRB 3.5 hours, DRB release 20 minutes and 4sU labeling for the last 5 minutes


title: U2OS_DRB_10minR_rep2_batch2

value: WT

value: DRB 3.5 hours, DRB release 10 minutes and 4sU labeling for the last 5 minutes


title: enriched nuclei_2009-005_7327

first: Giuliano

institute: Cerevance ltd

value: Cerebellum

value: Astrocyte


title: DE46NGSUKBR129422_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE46NGSUKBR129422


title: D7-GFP-_EPZ


title: U2OS_DRB_5minR_rep2_batch2

value: DRB 3.5 hours, DRB release 5 minutes and 4sU labeling at the same time for 5 minutes


title: DE96NGSUKBR129298_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE96NGSUKBR129298

value: No

value: Depressive symptomes only postpartum

value: postpartumy sample


title: U2OS_DRB_noR_rep2_batch2

value: DRB 3.5 hours, and 4sU labeling for the last 5 minutes


title: D7-GFP-_DMSO replicate 3

value: breast


title: U2OS_DRB_15minR_rep1_batch2

value: DRB 3.5 hours, DRB release 15 minutes and 4sU labeling for the last 5 minutes


title: D7-GFP_plus_DMSO replicate 2

value: DMSO


title: U2OS_DRB_20minR_rep1_batch2


title: DE43NGSUKBR129282_Control, no depressive symptomes [postpartum sample]

description: Library name: DE43NGSUKBR129282

value: Yes

value: blood

value: Control


title: U2OS_DRB_10minR_rep1_batch2

value: Human osteosarcoma


title: U2OS_DRB_5minR_rep1_batch2


title: DE21NGSUKBR129290_Control, no depressive symptomes [postpartum sample]

description: Library name: DE21NGSUKBR129290

value: postpartum sample


title: U2OS_DRB_20minR_rep2_batch1

value: WT

value: DRB 3.5 hours, DRB release 20 minutes and 4sU labeling for the last 5 minutes


title: D7-GFP-_DMSO


title: U2OS_DRB_noR_rep1_batch2


title: H3K27me3_GFPneg_EPZ_Day7 replicate 4

data_processing:
Sequencing quality was validated by FastQC, and adapters were trimmed by Trimmomatic.
Trimmed sequences were aligned to the mm10 genome by Bowtie2, and filtered for mapping reads with proper pairs and duplicate marked using samtools.
Read fragments of all lengths were utilized during the analysis of histone marks. Resulting alignments were converted into track files by RPGC normalization using deepTools . Narrow peaks were called using seacr with stringent method and 1% threshold, and broad peaks for histones were called using MACS3. Consensus peaks between different replicates and conditions were merged by taking the union of all peaks and combining any overlapping peaks, then filtering to merged peaks that have at least 3 replicates as called peaks.
Reads within the peaks were quantified using featureCounts and normalized using variance-stabilizing transform in DESeq2 for visualization purposes, such as heatmaps, unsupervised clustering, t-SNE and PCA.
Differential peak binding was calculated with a negative binomial model and TMM normalization using DESeq2. Genes were assigned to H3K27me3 peaks by taking the closest peak to the TSS within 25 kb distance and comparing log2 fold-change in RNAseq as a function of the significance and direction of the differential H3K27me3 peaks.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
The CUT&RUN protocol was modified based on EpiCypher CUTANA™ CUT&RUN Protocol. EO771.50,000 cells per group were pelleted and washed with PBS. Cells were washed with wash buffer twice and concanavalin A beads were activated and added into cells at RT for 10 mins. Supernatant was discarded post nuclei binding, and the bead-bound nuclei were blocked with antibody buffer. H3K27me3 antibody and IgG were added in (5µL antibody per sample) and incubated at 4°C overnight. Supernatant was discarded and Digitonin buffer were added followed by pAG-MNase binding and cleavage. Samples were incubated with rotation at RT for 10 mins and washed twice afterwards. 100mM CaCl2 was added to initiate the cleavage. After two hours, reactions were stopped with the addition of stop buffer. Samples were incubated at 37°C for 10 minutes to digest RNA and release DNA fragments. Samples were centrifuged at 16,000g for 5 minutes and supernatants were used to extract DNA with DNA extraction kit from Zymo research.
The library was prepared with NEBNext Ultra II DNA Library Prep Kit (NEB) and sequenced on Illumina platform.


title: U2OS_DRB_10minR_rep2_batch1

value: DRB 3.5 hours, DRB release 10 minutes and 4sU labeling for the last 5 minutes


title: U2OS_DRB_5minR_rep2_batch1


title: U2OS_DRB_15minR_rep2_batch1


title: DE71NGSUKBR129360_Control, no depressive symptomes [postpartum sample]

description: Library name: DE71NGSUKBR129360


title: DE39NGSUKBR129354_Control, no depressive symptomes [postpartum sample]

description: Library name: DE39NGSUKBR129354


title: U2OS_DRB_15minR_rep2_batch2


title: U2OS_DRB_noR_rep2_batch1


title: U2OS_DRB_15minR_rep1_batch1


title: U2OS_DRB_20minR_rep1_batch1


title: U2OS_DRB_10minR_rep1_batch1


title: U2OS_DRB_5minR_rep1_batch1


title: DE17NGSUKBR129362_Control, no depressive symptomes [postpartum sample]

description: Library name: DE17NGSUKBR129362


title: DE22NGSUKBR129369_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE22NGSUKBR129369


title: H3K27me3_GFPneg_EPZ_Day7


title: H3K27me3_GFPneg_Untreated_Day7 replicate 3


title: U2OS_DRB_noR_rep1_batch1


title: DE96NGSUKBR129104_Control, no depressive symptomes [postpartum sample]

description: Library name: DE96NGSUKBR129104


title: H3K27me3_GFPneg_EPZ_Day7 replicate 2


title: Ly6C+CXCR3+ cells, CD103Tg rep 4

city: Bethesda

first: Can

last: Li

state: Maryland

address: 9000 Rockville Pike

institute: NIH

description:
Library name: sample8
Column name in CPM_TMM_genes_filtered.txt: X8_Tg_2_4

data_processing:
Basecalling was done using Illumina instrument real time analysis software
Demultiplexing was performed using Bcl2fastq v2.17
Sequence reads were trmmed for adaptor sequence/low-quality sequence using Cutadapt 1.18
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR 2.7.0f
Read count extraction and normalization were performed using STAR/RSEM tools
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: Lymph node

extract_protocol:
RNA was harvested using RNeasy Plus Mini kit (Qiagen), and the quality of total RNA samples was checked on Agilent 2200 Tapestation system
RNA labraries for RNA-seq were prepared using Clonetech SMART-Seq v4 Ultra Low Input RNA and Nextera XT DNA Library Prep Kits following manufacturer's protocols

value: Lymph node

value: CD8 T cells


title: Ly6C+CXCR3+ cells, CD103Tg rep 3

description:
Library name: sample7
Column name in CPM_TMM_genes_filtered.txt: X7_Tg_2_3


title: Ly6C+CXCR3+ cells, CD103Tg rep 2

description:
Library name: sample6
Column name in CPM_TMM_genes_filtered.txt: X6_Tg_2_2


title: D7-GFP-_DMSO replicate 2


title: H3K27me3_GFPneg_EPZ_Day7 replicate 3


title: Ly6C+CXCR3+ cells, CD103Tg rep 1

description:
Library name: sample5
Column name in CPM_TMM_genes_filtered.txt: X5_Tg_2_1


title: Ly6C+CXCR3+ cells, B6 rep 4

description:
Library name: sample4
Column name in CPM_TMM_genes_filtered.txt: X4_B6_1_4


title: DE92NGSUKBR129370_Control, no depressive symptomes [postpartum sample]

description: Library name: DE92NGSUKBR129370

value: No


title: DE52NGSUKBR129120_Control, no depressive symptomes [postpartum sample]

description: Library name: DE52NGSUKBR129120


title: H3K27me3_GFPpos_EPZ_Day7 replicate 4


title: H3K27me3_GFPneg_Untreated_Day7


title: DE30NGSUKBR129322_Control, no depressive symptomes [postpartum sample]

description: Library name: DE30NGSUKBR129322


title: Ly6C+CXCR3+ cells, B6 rep 2

description:
Library name: sample2
Column name in CPM_TMM_genes_filtered.txt: X2_B6_1_2


title: DE74NGSUKBR129112_Control, no depressive symptomes [postpartum sample]

description: Library name: DE74NGSUKBR129112


title: H3K27me3_GFPpos_EPZ_Day7 replicate 3


title: Ly6C+CXCR3+ cells, B6 rep 3

description:
Library name: sample3
Column name in CPM_TMM_genes_filtered.txt: X3_B6_1_3


title: Ly6C+CXCR3+ cells, B6 rep 1

description:
Library name: sample1
Column name in CPM_TMM_genes_filtered.txt: X1_B6_1_1


title: Ly6C-CXCR3- cells, CD103KO rep 3

description:
Library name: sample6
Column name in RawCountFile_rsemgenes.txt: 2KO_3

data_processing:
Basecalling was done using Illumina instrument RTA 3.9.25 software
Demultiplexing was performed using Bcl2fastq v2.20
Sequence reads were trmmed for adaptor sequence/low-quality sequence using Cutadapt 1.18
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR 2.7.0f
Read count extraction and normalization were performed using STAR/RSEM tools
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using RNeasy Plus Mini kit (Qiagen), and the quality of total RNA samples was checked on Agilent 2200 Tapestation system.
RNA labraries for RNA-seq were prepared using Illumina® Stranded mRNA Ligation Prep Kits following manufacturer's protocols.


title: Ly6C-CXCR3- cells, CD103KO rep 2

description:
Library name: sample5
Column name in RawCountFile_rsemgenes.txt: 2KO_2


title: Ly6C-CXCR3- cells, CD103KO rep 1

description:
Library name: sample4
Column name in RawCountFile_rsemgenes.txt: 2KO_1


title: H3K27me3_GFPpos_EPZ_Day7 replicate 2


title: DE44NGSUKBR129167_Control, no depressive symptomes [postpartum sample]

description: Library name: DE44NGSUKBR129167


title: H3K27me3_GFPneg_Untreated_Day7 replicate 2


title: DE22NGSUKBR129175_Control, no depressive symptomes [postpartum sample]

description: Library name: DE22NGSUKBR129175


title: Ly6C-CXCR3- cells, WT rep 2

description:
Library name: sample2
Column name in RawCountFile_rsemgenes.txt: 2WT_2


title: H3K27me3_GFPpos_Untreated_Day7 replicate 3


title: DE43NGSUKBR129088_Control, no depressive symptomes [postpartum sample]

description: Library name: DE43NGSUKBR129088


title: 72_shSMRT_LPS_H3K27ac_CUT_Tag_2

description: Library name: Sample 72

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
RNA-seq raw files (fastq, PE150) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Library strategy: CUT&Tag

value: monocyte

value: Macrophages

value: BALB/c

value: CUT&Tag


title: Ly6C-CXCR3- cells, WT rep 1

description:
Library name: sample1
Column name in RawCountFile_rsemgenes.txt: 2WT_1


title: H3K27me3_GFPpos_Untreated_Day7 replicate 2

value: breast


title: DE21NGSUKBR129096_Control, no depressive symptomes [postpartum sample]

description: Library name: DE21NGSUKBR129096


title: 71_shSMRT_LPS_H3K27ac_CUT_Tag_1

description: Library name: Sample 71


title: 70_shSMRT_IL4_H3K27ac_CUT_Tag_2

description: Library name: Sample 70


title: H3K27me3_GFPpos_Untreated_Day7


title: 69_shSMRT_IL4_H3K27ac_CUT_Tag_1

description: Library name: Sample 69


title: DE35NGSUKBR129135_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE35NGSUKBR129135

value: Depressive symptomes only postpartum

value: postpartumy sample


title: 68_shSMRT_H3K27ac_CUT_Tag_2

description: Library name: Sample 68


title: DE88NGSUKBR129151_Control, no depressive symptomes [postpartum sample]

description: Library name: DE88NGSUKBR129151

value: blood


title: 67_shSMRT_H3K27ac_CUT_Tag_1

description: Library name: Sample 67


title: CC011_MAIT

first: Liyen

last: Loh

address: 12800 E 19th Ave, Research 1 North, P18-8401K

description: BD Rhapsody

data_processing:
Quality control, demultiplexing, and read mapping were performed using the BD Rhapsody WTA Analysis Pipeline (v1.0) on the Seven Bridges server.
Assembly: mm10
Supplementary files format and content: MolsPerCell.csv

source_name: spleen (SP), colon (Co_LP)

extract_protocol:
Spleen and Colon tissues were stained with MR1-5-OP-RU-APC tetramer, in the spleen enrichment with APC-magnetic beads from single cell suspensions was proformed. MAIT cells (Live Tetramer+ TCRb+) cells from each animal and tissue were simultaneously labeled with the cell surface sorting panel an oligonucleotide-tagged antibody sample tag (BD Biosciences) prior to cell sorting on a FACSAria3 (BD Biosciences).
BD Rhapsody mRNA whole, WTA Kit with sample tags

value: spleen (SP), colon (Co_LP)

value: MAIT cells


title: Aged1to1pt8

city: Charlestown

first: Fabrisia

last: Ambrosio

state: MA

institute: Harvard Medical School

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Cell Ranger processed files were imported into Partek Flow (Partek Gemonics, Inc.), and the genome was mapped to assembly mm10B49.
Single cell counts (cells) were filtered based on mitochondrial read percentage (excluded if >20%) and ribosomal read percentage (excluded in <5%)
Reads (gene counts) were filtered based on low expression across cells (genes expressed in >1% of cells)
Normalization was performed using CPM (counts per million), add 1.0, and Log 2.0 transform.
Cells expressing markers of non-myogenic stromal cells (i.e., fibroadipoprogenitor cells [PDGFRa], macrophages [Adgre1], and tenocytes [Tnmd]) were also excluded prior to downstream analyses.
For dynamo analyses, preprocessing steps remained the same, while veloctyo was used to generate pre- and mature gene counts.
Assembly: mm10B49
Supplementary files format and content: tab-delimited .txt files are provided with expression values for each sample.

source_name: Skeletal muscle

growth_protocol: Muscle stem cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in a humidified incubator with 5% CO2 at 37C for a period of seven days

extract_protocol:
Following treatment, cells were tyrpsinized from PDMS substrates and subjected to single cell RNA sequencing using the 10X Chromium Controller
Library reconstruction was done using the Single Cell 3’ Reagent kit v3 per manufacturer’s instructions

treatment_protocol: Young and old mouse muscle stem cells were exposed to both soft (12 kPa) and stiff (29 kPa) polydimethysiloxane (PDMS) substrates for a period of seven days

value: Skeletal muscle

value: Muscle stem cells

value: WT, C57BL/6

value: cell culture on stiff (29 kPa) polydimethylsiloxane substrates


title: DE13NGSUKBR129143_Control, no depressive symptomes [postpartum sample]

description: Library name: DE13NGSUKBR129143

value: Control

value: postpartum sample


title: DE66NGSUKBR129159_Control, no depressive symptomes [postpartum sample]

description: Library name: DE66NGSUKBR129159

value: No


title: 66_shSMRT_GW_H3K27ac_CUT_Tag_2

description: Library name: Sample 66

extract_protocol:
Fresh cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) for 30 minutes, followed by 1% formaldehyde for 10 minutes at room temperature. Nuclei were isolated, sonicated, and incubated with magnetic bead-antibody complexes.  Antibodies to NCOR (bethyl, A301-145A), SMRT (bethyl, A301-147A), and GPS2 (homemade) were used.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×105 cells one day before the experiments. Cells were washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
2×105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

value: monocyte


title: H3K27me3_GFPpos_EPZ_Day7


title: 64_shNCOR_LPS_H3K27ac_CUT_Tag_2

description: Library name: Sample 64

value: Macrophages


title: 63_shNCOR_LPS_H3K27ac_CUT_Tag_1

description: Library name: Sample 63

value: BALB/c


title: DE57NGSUKBR129127_Control, no depressive symptomes [postpartum sample]

description: Library name: DE57NGSUKBR129127


title: Ly6C-CXCR3- cells, WT rep 3

description:
Library name: sample3
Column name in RawCountFile_rsemgenes.txt: 2WT_3

value: Lymph node

value: CD8 T cells

value: WT


title: Young1to1pt8


title: 61_shNCOR_IL4_H3K27ac_CUT_Tag_1

description: Library name: Sample 61

value: CUT&Tag


title: 60_shNCOR_H3K27ac_CUT_Tag_2

description: Library name: Sample 60


title: DE29NGSUKBR129340_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE29NGSUKBR129340

value: Yes

value: blood


title: 59_shNCOR_H3K27ac_CUT_Tag_1

description: Library name: Sample 59


title: Young1to1

value: cell culture on soft (12 kPa) polydimethylsiloxane substrates


title: DE96NGSUKBR129395_Control, no depressive symptomes [postpartum sample]

description: Library name: DE96NGSUKBR129395


title: 65_shSMRT_GW_H3K27ac_CUT_Tag_1

description: Library name: Sample 65