title: SNI_rep3

city: Guangzhou

first: yao

last: shan

state: Guangdong

address: Xinzao

institute: guangzhou

data_processing:
For transcriptome analysis, fastp software (https://github.com/OpenGene/fastp) was used to exclude the reads containing adaptor contamination, base with low quality, and undetermined bases with default parameters and verify the quality of the sequence. The reads were mapped with HISAT2 (https://ccb.jhu.edu/software/hisat2) and assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. All transcriptomes from all samples were then merged to reconstruct a comprehensive transcriptome with gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts.
Assembly: GRCm38
Supplementary files format and content: gene count for each Sample

source_name: brain

extract_protocol:
In brief, total RNA was extracted from PrL tissue using TRIzol reagent (Invitrogen, Carlsbad, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: brain


title: DE12NGSUKBR129355_Depressive symptomes only postpartum [postpartumy sample]

status: Public on Sep 24 2025

type: SRA

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: DE12NGSUKBR129355

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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: No

tag: tissue

value: blood

tag: subject group

value: Depressive symptomes only postpartum

tag: time point

value: postpartumy sample


title: 56_shGFP_LPS_H3K27ac_CUT_Tag_2

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

description: Library name: Sample 56

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.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

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

tag: cell line

tag: cell type

value: Macrophages

tag: genotype

value: BALB/c

tag: batch

value: CUT&Tag


title: 57_shNCOR_GW_H3K27ac_CUT_Tag_1

description: Library name: Sample 57


title: SNI_rep4


title: 55_shGFP_LPS_H3K27ac_CUT_Tag_1

description: Library name: Sample 55


title: 54_shGFP_IL4_H3K27ac_CUT_Tag_2

description: Library name: Sample 54


title: SNI_rep2


title: SNI_rep1


title: 53_shGFP_IL4_H3K27ac_CUT_Tag_1

description: Library name: Sample 53


title: 51_shGFP_H3K27ac_CUT_Tag_1

description: Library name: Sample 51


title: 52_shGFP_H3K27ac_CUT_Tag_2

description: Library name: Sample 52


title: 62_shNCOR_IL4_H3K27ac_CUT_Tag_2

description: Library name: Sample 62


title: Aged1to1

city: Charlestown

first: Fabrisia

last: Ambrosio

state: MA

country: USA

institute: Harvard Medical School

library_source: transcriptomic single cell

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

tag: treatment

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


title: 50_shGFP_GW_H3K27ac_CUT_Tag_2

description: Library name: Sample 50


title: Sham_rep4


title: DE82NGSUKBR129356_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE82NGSUKBR129356


title: DE42NGSUKBR129300_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE42NGSUKBR129300


title: 40_2nd_RAW_shSMRT_SMRT_CUT_Tag_rp2

description: Library name: Sample 40


title: 39_2nd_RAW_shSMRT_SMRT_CUT_Tag_rp1

description: Library name: Sample 39


title: 58_shNCOR_GW_H3K27ac_CUT_Tag_2

description: Library name: Sample 58


title: DE30NGSUKBR129419_Control, no depressive symptomes [postpartum sample]

description: Library name: DE30NGSUKBR129419

value: Control

value: postpartum sample


title: Sham_rep3


title: Sham_rep2


title: 37_2nd_RAW_shNCOR_SMRT_CUT_Tag_rp1

description: Library name: Sample 37


title: DE58NGSUKBR129400_Control, no depressive symptomes [postpartum sample]

description: Library name: DE58NGSUKBR129400


title: DE34NGSUKBR129347_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE34NGSUKBR129347


title: 38_2nd_RAW_shNCOR_SMRT_CUT_Tag_rp2

description: Library name: Sample 38


title: DE87NGSUKBR129363_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE87NGSUKBR129363


title: Sham_rep1


title: 36_2nd_RAW_shGFP_SMRT_CUT_Tag_rp2

description: Library name: Sample 36


title: 35_2nd_RAW_shGFP_SMRT_CUT_Tag_rp1

description: Library name: Sample 35


title: 34_1st_ChIPseq_shSMRT_rp2_SMRT

description: Library name: Sample 34

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.

value: ChIP-seq


title: 33_1st_ChIPseq_shSMRT_rp1_SMRT

description: Library name: Sample 33


title: DE65NGSUKBR129371_Control, no depressive symptomes [postpartum sample]

description: Library name: DE65NGSUKBR129371


title: 32_1st_ChIPseq_shNCOR_SMRT_rp2

description: Library name: Sample 32


title: 49_shGFP_GW_H3K27ac_CUT_Tag_1

description: Library name: Sample 49


title: coro1a-DsRed cells, WT, 24 hpf,scRNA-seq, rep4

city: Chongqing

first: he

last: yuepeng

state: Chongqing

address: No.266 Fangzheng Avenue,Shuitu Hi-tech Industrial Park, Shuitu Town, Beibei District, Chongqing

institute: Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences

description:
Library name: sample20
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
RNA-seq was performed using the PE100 strategy on the Illumina HiSeq 2500 (Anoroda Corporation). Reads were aligned to the zebrafish reference genome (Danio rerio, GRCz11), and differentially expressed genes (DEGs) were identified with DESeq2 (v1.32.0) using P < 0.05. Functional enrichment of DEGs was analyzed with ClusterProfiler.  For ATAC-seq, adapters and low-quality bases (phred < 10) were removed with Trimmomatic (v0.38). Clean reads were aligned to the reference genome using Bowtie2 (v2.4.3), and properly paired reads (MAPQ ≥ 30) were retained with Samtools (v1.9). PCR duplicates were removed with Picard, and organelle contamination was excluded. Chromatin integrity was evaluated by insertion size distribution (R v3.5.1) and TSS enrichment scores following ENCODE guidelines. Peaks were called with MACS2 using parameters --nomodel --shift 75 --extsize 150. Reproducibility was assessed with pseudo-replicates, and differential peaks were analyzed with DiffBind (v3.4.5) and DESeq2.  For scRNA-seq, low-quality cells were filtered out (200–6,000 genes, UMI > 1,000, mitochondrial content < 10%). Data were normalized with Seurat (LogNormalize), and the top 2,000 variable genes were identified with the vst method. After regressing out nCount_RNA and percent.mito, PCA was performed, followed by UMAP and t-SNE using the top 50 PCs. Clustering was performed with Seurat (resolution = 1.2) using the Louvain algorithm on a shared nearest-neighbor graph. Cell trajectory and pseudotime analyses were performed with Monocle 2.
Assembly: GRCz11
Supplementary files format and content: Matrix Market format files (.mtx) containing gene-by-cell UMI count matrix, accompanied by cell annotation file (.tsv) with cell barcodes, and gene annotation file (.tsv) with gene IDs and names.

organism: Danio rerio

source_name: coro1a-DsRed cells, WT, 24 hpf

extract_protocol:
Tg(coro1a:DsRed) embryos from WT, Tg(coro1a:HA-ikzf1), Tg(coro1a:FLAG-myb), and ikzf1Δ4+3/Δ4+3; mybhkz3/hkz3 (DM) embryos were collected at 24–30 hpf. Embryos were dissociated with a Papain Dissociation Kit (Worthington) in DPBS at 37 °C for 20–30 minutes to obtain single-cell suspensions, which were generated by gentle trituration, filtered through 40–70 μm strainers, and sorted by FACS. Sorted coro1a-DsRed+ cells (about 5,000 for ATAC-seq, larger pools for Smart-seq) were subsequently processed using established protocols, with single-cell suspensions loaded onto Single Cell G Chips (v3.1 chemistry, PN1000120).
RNA-seq libraries were prepared from total RNA extracted with the TRIzol Reagent Kit (Invitrogen) following the manufacturer’s protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer and agarose gel electrophoresis. Eukaryotic mRNA was enriched with Oligo(dT) beads, and prokaryotic mRNA by rRNA depletion (Ribo-Zero Magnetic Kit, Epicentre). Enriched mRNA was fragmented, reverse-transcribed, and converted to double-stranded cDNA. After end repair, A-tailing, and adapter ligation, libraries were size-selected, PCR-amplified, and sequenced on an Illumina NovaSeq 6000 (Gene Denovo, Guangzhou, China).  For ATAC-seq, nuclei were isolated with cell lysis buffer, and Tn5 transposase was used to fragment accessible DNA. After PCR amplification, libraries were sequenced on the Illumina platform using a PE150 strategy, generating ~20 Gb of raw data.  Single-cell RNA-seq libraries were generated using the Chromium Single Cell Gene Expression system (10x Genomics) with the v3.1 reagent kit (PN-1000121). Single-cell suspensions were loaded onto Chromium Chips, processed on the Chromium Controller to form GEM partitions, and libraries were prepared according to the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5 (PN-20028312).

value: embryos coro1a-DsRed positive myeloid cells

value: myeloid cell

value: WT


title: DE64NGSUKBR129292_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE64NGSUKBR129292

value: No

value: blood


title: 31_1st_ChIPseq_shNCOR_SMRT_rp1

description: Library name: Sample 31


title: DE07NGSUKBR129348_Control, no depressive symptomes [postpartum sample]

description: Library name: DE07NGSUKBR129348


title: coro1a-DsRed cells, WT, 24 hpf,scRNA-seq, rep2

description:
Library name: sample18
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz


title: 30_1st_ChIPseq_shGFP_SMRT_rp2

description: Library name: Sample 30


title: 29_1st_ChIPseq_shGFP_SMRT_rp1

description: Library name: Sample 29


title: coro1a-DsRed cells, WT, 24 hpf,scRNA-seq, rep1

description:
Library name: sample17
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz


title: DE60NGSUKBR129364_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE60NGSUKBR129364

value: Depressive symptomes only postpartum

value: postpartumy sample


title: 28_2nd_batch_ChIPseq_shSMRT_NCOR_rp2

description: Library name: Sample 28

value: monocyte

value: Macrophages


title: DE26NGSUKBR129103_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE26NGSUKBR129103


title: 27_2nd_batch_ChIPseq_shSMRT_NCOR_rp1

description: Library name: Sample 27

value: BALB/c


title: E40

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: 10x Genomics

data_processing:
FASTQ files were aligned to the improved pig genome and pre-processed using the CellRanger 10x Genomics software for downstream analyses.
Assembly: ensembl v101
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: Pancreas

extract_protocol:
Freshly dissected pancreata were minced into fine pieces and digested with collagenase V (0.5 mg/mL for E20-50, 1 mg/mL for E60-85, Sigma-Aldrich) for 5 mins followed by dissociation with TrypLE™ Express (Gibco) for 10-15 mins at 37°C. Cell suspension was filtered through a 40 µm cell strainer, and stained with EpCAM antibody in 1% BSA + PBS (1:200, Invitrogen) for 30 mins at 4°C. Cells were then washed and filtered into a tube through a 35 µm filter. 7-AAD (Invitrogen) was used to distinguish dead cells. The resulting cell suspension was loaded onto a FACSAria III (BD) for sorting. 7-AAD-/EpCAM+ cells from pancreata were collected and pancreata of INS-eGFP embryos at specified ages were used to enrich eGFP+/7-AAD-/EpCAM+ endocrine cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, SC-islet cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Pancreas

value: Wild-type

tag: age

tag: enrichment

value: EpCAM


title: 26_2nd_batch_ChIPseq_shGFP_NCOR_rp2

description: Library name: Sample 26


title: DE04NGSUKBR129111_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE04NGSUKBR129111

value: Yes


title: 25_2nd_batch_ChIPseq_shGFP_NCOR_rp1

description: Library name: Sample 25


title: E22

description: 10x Genomics


title: 24_1st_ChIPseq_shSMRT_NCOR_rp2

description: Library name: Sample 24


title: 23_1st_ChIPseq_shSMRT_NCOR_rp1

description: Library name: Sample 23


title: E33

description: 10x Genomics


title: 20_1st_ChIPseq_shGFP_NCOR_rp2

description: Library name: Sample 20


title: 22_1st_ChIPseq_shNCOR_NCOR_rp2

description: Library name: Sample 22


title: DE11NGSUKBR129373_Control, no depressive symptomes [postpartum sample]

description: Library name: DE11NGSUKBR129373

value: Control


title: coro1a-DsRed cells, WT, 24 hpf,scRNA-seq, rep3

description:
Library name: sample19
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz


title: ADH1_G4 mutant strain, biological replicate 3

city: Umeå

first: Nasim

last: Sabouri

address: Linnaeus vag

institute: Umeå University

description:
Library name: Sample 9
Column name in gene_count.xls ADH1_G4_MUT_rep3

data_processing:
The sequenced data, referred to as Raw Data or Raw Reads, were obtained in FASTQ format files. The sequencing reads were filtered to remove those with adapter contamination, low-quality nucleotides, and uncertain nucleotides.
The filtered reads were aligned to the yeast reference genome using HISAT2 v2.0.5. Mapped regions were classified as exonic, intronic, or intergenic and were annotated accordingly. Gene expression levels were estimated based on the abundance of transcripts that mapped to the genome or exons, using the FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) method.
Assembly: 972h- Genome assembly ASM294v2
Supplementary files format and content: excel spreadsheet (.xlsx) include raw gene counts for all the samples together

organism: Schizosaccharomyces pombe

source_name: yeast cell

growth_protocol: One million cells/mL wild-type (ADH1_G4_WT), and CRISPR/Cas9-mediated mutant (ADH1_G4-TATA_MUT and ADH1_G4_MUT) strains were grown in Yeast extract supplement (YES) media for 16 hours to exponential phase. Cell number after this time is about 8 million cells/mL

extract_protocol:
RNA was isolated from the exponentially growing S. pombe cells using NucleoSpin RNA kit (Macherey Nagel). The quality and integrity of the isolated RNA  was checked using absorbance (260/280 nm) and agarose gel electrophoresis. Small aliquot of the isolated RNA was taken to check for genomic DNA contamination by performing quantitative PCR using primers amplifying coding regions of act1 and tdh1 genes.
Messenger RNA was then purified from the total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, the first strand of cDNA was synthesized using random hexamer primers. This was followed by the synthesis of the second strand cDNA, utilizing either dUTP for the creation of a directional library or dTTP for a non-directional library. The constructed library was assessed using Qubit and real-time PCR for quantification, as well as a bioanalyzer to determine the size distribution. Quantified libraries were subsequently pooled and sequenced on high-throughput Illumina sequencing platforms in Novogene.

value: yeast cell

value: bfr1::hygr  pmd::natr cdc20+::cdc20-3HA-kanmx6 pfh1::ura4+-nmt-pfh1-GFP ura4-D18? leu1-32 his3-D1? adh1GGG..GGG..GGG..GGG::adh1 GTG..GTG..GTG..GTG

value: CRISPR/Cas9 mutagenesis


title: 21_1st_ChIPseq_shNCOR_NCOR_rp1

description: Library name: Sample 21

value: ChIP-seq


title: DE42NGSUKBR129397_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE42NGSUKBR129397


title: ADH1_G4 mutant strain, biological replicate 1

description:
Library name: Sample 7
Column name in gene_count.xls ADH1_G4_MUT_rep1


title: 19_1st_ChIPseq_shGFP_NCOR_rp1

description: Library name: Sample 19


title: DE43NGSUKBR129379_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE43NGSUKBR129379


title: DE38NGSUKBR129372_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE38NGSUKBR129372


title: ADH1_G4-TATA box mutant strain, biological replicate 3

description:
Library name: Sample 6
Column name in gene_count.xls ADH1_G4-TATA_MUT_rep3

value: bfr1::hygr  pmd::natr cdc20+::cdc20-3HA-kanmx6 pfh1::ura4+-nmt-pfh1-GFP ura4-D18? leu1-32 his3-D1? adh1TATAAATA::adh1TAAATATA adh1GGG..GGG..GGG..AGG..GGG::adh1 GTG..GTG..GTG..ACG..GTG


title: monoculture neurons A

city: Cambridge

first: Benjamin

last: James

address: 32 Vassar St

institute: Massachusetts Institute of Technology

description:
Library name: D23-6473
monoculture neurons

data_processing:
Mapping to GRCh38.p13/GENCODE v43 using STAR 2.7.9a
Feature quantification using featureCounts from Subread 1.6.2
Assembly: GRCh38.p13
Supplementary files format and content: Counts matrix (TSV, featureCounts output)
Supplementary files format and content: Counts matrix (TSV, featureCounts output, aggregated into one TSV)

molecule: polyA RNA

source_name: monoculture neurons

growth_protocol: miBrains were cultured for 2 weeks prior to cell isolation and RNA sequencing. Corresponding cell monocultures were maintained in parallel for 2 weeks and then sorted using the same parameters as the miBrains. To minimize batch-dependent effects, the same batch of differentiated cells was used for the monoculture condition and the miBrain condition in each RNAseq experiment.

extract_protocol:
To dissociate miBrains, samples were washed with PBS, then were incubated for 5-10 minutes in a mixture of accutase, collagenase IV (1:20), and dextranase (1:20). These were triturated 15-20 times with a P1000 pipette to form a homogeneous suspension, then pelleted and washed with DPBS twice. Astrocytes, iMG, and neuron monocultures grown in parallel were dissociated using accutase, then washed with DPBS prior to proceeding with antibody labeling and sorting. Oligodendroglia were fixed with 4% PFA on ice for 20 minutes prior to dissociation to ensure stability. iMG were incubated with CD45-Cy7 alongside isotype controls at 1:200 on ice for 25 minutes before proceeding with sorting. Dissociated miBrains and monocultures were resuspended in FACS buffer (DPBS, BSA, EDTA) with DAPI and filtered through a 40 μm strainer. Samples were sorted on a BD FACSAria equipped with a 70 μm nozzle. Neurons were FACS-isolated based on tdTomato expression, astrocytes and oligodendroglia based on mCherry, and iMG based on CD45 expression. RNA was harvested in triplicate and in parallel from 20K neurons, 50K astrocytes, 50K oligodendroglia, or 2K CD45-positive iMG per replicate. Cells were gated on FSC-A vs SSC-A to separate intact cells from debris, then FSC-H vs FSC-W and SSC-H vs SSC-W to separate single cells from doublets, then DAPI to exclude dead cells, and then the channel corresponding to the antibody used. Cells were sorted into 96-well plates containing 50 μl RNAprotect per well. For live samples, RNA was isolated from sorted cells using the Qiagen RNeasy isolation kit according to the manufacturer’s protocol. For fixed samples, sorted cells were spun down and resuspended in 200 μL digestion buffer (RecoverAll kit) supplemented with 1:50 Proteinase K, incubated at 50°C for 15 minutes, and then at 80°C for 15 minutes with no agitation to de-crosslink RNA from fixed tissue. 800 μL Trizol was added to the sample and incubated for 5 minutes, then 215 μl chloroform was added and the sample was vortexed vigorously for 30 seconds. Sample was transferred to a 5-prime phase lock heavy gel tube and centrifuged for 15 minutes at 12,000 g. The upper layer containing RNA was transferred to a fresh 1.5 ml microcentrifuge tube and an equal volume of 100% ethanol before proceeding with RNA isolation using Zymo Direct-zol RNA microprep kit according to the manufacturer’s protocols. Standard RNA quality control was performed using AATI fragment analyzer.
RNA sequencing libraries were prepared using NEB Ultra II PolyA stranded library and sequenced using Illumina NextSeq500.

treatment_protocol: Neurons were isolated by first virally labeling neurons from the same batch with pAAV-CAG-tdTomato for 24 hours (1:50 dilution, Addgene 59462-AAV1) prior to incorporation into miBrain or monoculture, a subset of which were incorporated into miBrains and a subset of which were maintained in monoculture. To ensure sufficient capture of target cell populations, 15 individual miBrains were pooled per replicate, and three replicates were isolated per experiment. After 2 weeks, tdTomato-neuron miBrains and monoculture samples were harvested. Astrocytes and oligodendroglia were isolated using a similar approach, but by utilizing endogenously mCherry-expressing astrocytes. iMG were incorporated into 2-week old miBrains, while a subset from the same batch were maintained in monoculture, and after an additional four days, sorted based on CD45-Cy7.

value: monoculture neurons

value: monoculture


title: monoculture neurons C

description:
Library name: D23-6475
monoculture neurons


title: miBrain neurons B

description:
Library name: D23-6477
miBrain neurons

source_name: miBrain neurons

value: miBrain neurons

value: miBrain


title: miBrain neurons A

description:
Library name: D23-6476
miBrain neurons


title: DE95NGSUKBR129316_Control, no depressive symptomes [postpartum sample]

description: Library name: DE95NGSUKBR129316

value: No

value: blood

value: postpartum sample


title: monoculture oligo C

description:
Library name: D23-3785
monoculture oligo

source_name: monoculture oligo

value: monoculture oligo


title: miBrain neurons C

description:
Library name: D23-6478
miBrain neurons


title: monoculture neurons B

description:
Library name: D23-6474
monoculture neurons


title: monoculture oligo B

description:
Library name: D23-3784
monoculture oligo


title: ADH1_G4-TATA box mutant strain, biological replicate 2

description:
Library name: Sample 5
Column name in gene_count.xls ADH1_G4-TATA_MUT_rep2


title: monoculture oligo A

description:
Library name: D23-3783
monoculture oligo


title: DE51NGSUKBR129429_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE51NGSUKBR129429

value: Depressive symptomes only postpartum

value: postpartumy sample


title: DE35NGSUKBR129232_Control, no depressive symptomes [postpartum sample]

description: Library name: DE35NGSUKBR129232


title: ADH1_G4-TATA box mutant strain, biological replicate 1

description:
Library name: Sample 4
Column name in gene_count.xls ADH1_G4-TATA_MUT_rep1


title: ADH1_G4_wild-type strain, biological replicate 3

description:
Library name: Sample 3
Column name in gene_count.xls ADH1_G4_WT_rep3

value: bfr1::hygr  pmd::natr cdc20+::cdc20-3HA-kanmx6, pfh1::ura+nmt81-pfh1-GFP, leu1-32

value: No treatment


title: DE20NGSUKBR129308_Control, no depressive symptomes [postpartum sample]

description: Library name: DE20NGSUKBR129308

value: Control


title: ADH1_G4 mutant strain, biological replicate 2

description:
Library name: Sample 8
Column name in gene_count.xls ADH1_G4_MUT_rep2

value: yeast cell

value: bfr1::hygr  pmd::natr cdc20+::cdc20-3HA-kanmx6 pfh1::ura4+-nmt-pfh1-GFP ura4-D18? leu1-32 his3-D1? adh1GGG..GGG..GGG..GGG::adh1 GTG..GTG..GTG..GTG


title: monoculture astrocyte C

description:
Library name: D23-2991
monoculture astrocyte

source_name: monoculture astrocyte

value: monoculture astrocyte


title: DE73NGSUKBR129324_Control, no depressive symptomes [postpartum sample]

description: Library name: DE73NGSUKBR129324


title: miBrain oligo B

description:
Library name: D23-3781
miBrain oligo

source_name: miBrain oligo

value: miBrain oligo


title: miBrain oligo A

description:
Library name: D23-3780
miBrain oligo


title: ADH1_G4_wild-type strain, biological replicate 2

description:
Library name: Sample 2
Column name in gene_count.xls ADH1_G4_WT_rep2


title: monoculture astrocyte B

description:
Library name: D23-2990
monoculture astrocyte


title: ADH1_G4_wild-type strain, biological replicate 1

description:
Library name: Sample 1
Column name in gene_count.xls ADH1_G4_WT_rep1


title: miBrain astrocyte C

description:
Library name: D23-2988
miBrain astrocyte

source_name: miBrain astrocyte

value: miBrain astrocyte


title: monoculture astrocyte A

description:
Library name: D23-2989
monoculture astrocyte

value: monoculture


title: DE86NGSUKBR129381_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE86NGSUKBR129381


title: DE73NGSUKBR129421_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE73NGSUKBR129421

value: Yes


title: miBrain astrocyte B

description:
Library name: D23-2987
miBrain astrocyte

value: miBrain


title: monoculture BMEC C

description:
Library name: D23-2115
monoculture BMEC

source_name: monoculture BMEC

value: monoculture BMEC


title: monoculture BMEC A

description:
Library name: D23-2113
monoculture BMEC


title: larval trachea, w1118, rep4

city: Kiel

first: Judith

last: Bossen

address: Am Botanischen Garten 3-9

department: Molecular Physiology

institute: CAU Kiel, Zoological Institute

description: Library name: w1118_BR4

data_processing:
transcriptomic analysis was performed with CLC workbench 9.5.2, Illumina files (fastq) were importet and failed reads were removed
the reads were mapped to gene regions only using the Drosophila melanogaster genome (assembly Release 6 plus ISO1 MT) using the following parameters: mismatch cost = 2, insertion cost = 2, deletion cost = 2, length fraction = 0.8, similarity fraction = 0.85, global alignment = no, strand specific = both, maximum number of hits for a read = 10, count paired reads as two = no, expression value = RPKM, calculate RPKM for genes without transcripts = no, use EM estimation = yes
Differential expression for RNA-Seq was perfomed by compairing against a control group (Trabid-KO; w1118)
Assembly: Drosophila melanogaster Release 6 plus ISO1 MT
Supplementary files format and content: xlsx files include differential expression values based on comparison to the control group

organism: Drosophila melanogaster

source_name: larval trachea

extract_protocol:
whole RNA from dissected trachea was extracted using RNAmagic (Bio-Budget Technologies GmbH, Germany)
Samples were quantified with a fluorometric dye (Quant-IT, Thermofisher, USA) and between 187 and 500 ng per sample were used as input for the TruSeq stranded mRNA library kit (Illumina, USA) following the manufacturers manual. Resulting libraries showed a fragment size distribution of around 350 bp and were sequenced on a HiSeq 4000 (Illumina, USA) with 50bp single-end reads

value: larval trachea


title: miBrain astrocyte A

description:
Library name: D23-2986
miBrain astrocyte


title: miBrain oligo C

description:
Library name: D23-3782
miBrain oligo


title: larval trachea, w1118, rep1

description: Library name: w1118_BR1


title: monoculture BMEC B

description:
Library name: D23-2114
monoculture BMEC


title: DE16NGSUKBR129380_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE16NGSUKBR129380

value: blood


title: monoculture microglia B

description:
Library name: D21-10374
monoculture microglia

source_name: monoculture microglia

value: monoculture microglia


title: monoculture microglia A

description:
Library name: D21-10373
monoculture microglia


title: monoculture microglia C

description:
Library name: D21-10375
monoculture microglia


title: larval trachea, w1118, rep3

description: Library name: w1118_BR3


title: larval trachea, Trabid-KO, rep5

description: Library name: Trabid-KO_BR5

value: trabid-KO


title: DE27NGSUKBR129376_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE27NGSUKBR129376

value: Depressive symptomes only postpartum

value: postpartumy sample


title: miBrain microglia B

description:
Library name: D21-10371
miBrain microglia

source_name: miBrain microglia

value: miBrain microglia


title: larval trachea, Trabid-KO, rep4

description: Library name: Trabid-KO_BR4


title: miBrain microglia A

description:
Library name: D21-10370
miBrain microglia


title: DE78NGSUKBR129428_Control, no depressive symptomes [postpartum sample]

description: Library name: DE78NGSUKBR129428

value: No

value: Control

value: postpartum sample


title: DE20NGSUKBR129405_Control, no depressive symptomes [postpartum sample]

description: Library name: DE20NGSUKBR129405


title: miBrain microglia C

description:
Library name: D21-10372
miBrain microglia


title: DE52NGSUKBR129411_Control, no depressive symptomes [postpartum sample]

description: Library name: DE52NGSUKBR129411


title: larval trachea, Trabid-KO, rep3

description: Library name: Trabid-KO_BR3


title: HeLa cells : DTP selected following IC90 Etopiside drug treatment for 7 days_2

city: Brookline

first: Maria

last: Davern

state: Massachusetts

address: 440 Brookline avenue / Mayer Building

institute: Dana-Farber Cancer Institute

description:
Library name: Etop_DTPs_2
Etop_DTPs_2

data_processing:
RNA-Seq
Assembly: The final pool was sequenced with paired-end 150bp reads on an Illumina NovaSeq 6000
Supplementary files format and content: Sequenced reads were aligned to the UCSC hg38 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)
Supplementary files format and content: MDAVERNGeneCounts.txt.csv

source_name: Uterus; Cervix

growth_protocol: Standard culture conditions

extract_protocol:
total RNA was extracted using RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol
Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation reagents on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance

treatment_protocol: Parental samples are untreated HeLa cells. IPC are HeLa cells treated for 3 weeks with EGFR CAR T-cells. 5-FU, OX and ETOP DTPs are HeLa cells treated for 7 days respectively with IC90 concentrations of 5-Fluorouracil (5-FU), Oxaliplatin (Ox) and Etopiside (Etop).

value: Uterus; Cervix

value: HeLa

value: epithelial

value: Cells were treated with IC90 concentration of Etopiside for 7 days


title: HeLa cells : DTP selected following IC90 Etopiside drug treatment for 7 days_1

description:
Library name: Etop_DTPs_1
Etop_DTPs_1


title: DE89NGSUKBR129424_Control, no depressive symptomes [postpartum sample]

description: Library name: DE89NGSUKBR129424

source_name: blood


title: HeLa cells : DTP selected following IC90 Oxaliplatin drug treatment for 7 days_3

description:
Library name: Ox_DTPs_3
Ox_DTPs_3

value: Cells were treated with IC90 concentration of Oxaliplatin for 7 days


title: SKOV3_KDM1A shRNA_Cisplatin_2

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description: SKOV3 KDM1A knockdown cells treated with cisplatin

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the genes using htseq-count

growth_protocol: SKOV3 cells were cultured in McCoy's 5a Medium Modified, supplemented with 10% FBS.

extract_protocol:
SKOV3-control and SKOV3-KDM1A knockdown cells were treated with vehicle or cisplatin (2.5 µM) for 72 hours. RNA was isolated using RNeasy mini kit and subjected to RNA-seq on illumina HiSeq 3000 system using Illumina TruSeq stranded mRNA-seq library preparation kit
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

value: ovarian cancer cell line

value: KDM1A shRNA

value: Cisplatin


title: HeLa cells : DTP selected following IC90 Oxaliplatin drug treatment for 7 days_2

description:
Library name: Ox_DTPs_2
Ox_DTPs_2


title: DE74NGSUKBR129403_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE74NGSUKBR129403

value: Yes

value: blood


title: SKOV3_KDM1A shRNA_Cisplatin_1

treatment_protocol: SKOV3-control and SKOV3-KDM1A knockdown cells were treated with vehicle or cisplatin (2.5 µM) for 72 hours.


title: HeLa cells : DTP selected following IC90 5-FU drug treatment for 7 days_3

description:
Library name: 5-FU_DTPs_3
5-FU_DTPs_3

value: Cells were treated with IC90 concentration of 5-FU for 7 days


title: DE53NGSUKBR129393_Control, no depressive symptomes [postpartum sample]

description: Library name: DE53NGSUKBR129393


title: SKOV3_KDM1A shRNA_Vehicle_2

description: SKOV3 KDM1A knockdown cells

value: Vehicle


title: HeLa cells : DTP selected following IC90 5-FU drug treatment for 7 days_2

description:
Library name: 5-FU_DTPs_2
5-FU_DTPs_2


title: DE25NGSUKBR129315_Control, no depressive symptomes [postpartum sample]

description: Library name: DE25NGSUKBR129315


title: HeLa cells : DTP selected following IC90 Oxaliplatin drug treatment for 7 days_1

description:
Library name: Ox_DTPs_1
Ox_DTPs_1


title: SKOV3_KDM1A shRNA_Vehicle_1

description: SKOV3 KDM1A knockdown cells


title: HeLa cells : DTP selected following IC90 Etopiside drug treatment for 7 days_3

description:
Library name: Etop_DTPs_3
Etop_DTPs_3


title: DE04NGSUKBR129402_Control, no depressive symptomes [postpartum sample]

description: Library name: DE04NGSUKBR129402


title: HeLa cells : IPC population selected with EGFR CAR T-cells for 3 weeks_2

description:
Library name: IPC_2
IPC_2

value: Co-culture with EGFR CAR T-cells for 3 weeks to select the population


title: HeLa cells : IPC population selected with EGFR CAR T-cells for 3 weeks_3

description:
Library name: IPC_3
IPC_3


title: DE18NGSUKBR129344_Control, no depressive symptomes [postpartum sample]

description: Library name: DE18NGSUKBR129344


title: HeLa cells : IPC population selected with EGFR CAR T-cells for 3 weeks_1

description:
Library name: IPC_1
IPC_1


title: SKOV3_Control shRNA_Cisplatin_2

description: SKOV3 control cells treated with cisplatin

value: ShControl


title: HeLa cells : no treatment_2

description:
Library name: Parental_2
Parental_2

value: No treatment


title: HeLa cells : DTP selected following IC90 5-FU drug treatment for 7 days_1

description:
Library name: 5-FU_DTPs_1
5-FU_DTPs_1


title: HeLa cells : no treatment_1

description:
Library name: Parental_1
Parental_1


title: HeLa cells : no treatment_3

description:
Library name: Parental_3
Parental_3


title: DE05NGSUKBR129384_Control, no depressive symptomes [postpartum sample]

description: Library name: DE05NGSUKBR129384

value: No

value: Control


title: SKOV3_Control shRNA_Cisplatin_1


title: DE31NGSUKBR129401_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE31NGSUKBR129401

value: postpartum sample


title: SKOV3_Control shRNA_Vehicle_2

description: SKOV3 control cells


title: larval trachea, Trabid-KO, rep2

description: Library name: Trabid-KO_BR2

value: larval trachea

value: trabid-KO


title: WT, Pan, 100, 24hr, D9, 0dpi, Rep3 ATAC

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Fastq read files for each sample were obtained and then aligned using the Computational Suite for Bioinformaticians and Biologists version 3.0 (CSBB-v3.0) to remove low quality bases and potential adapter contamination. Open chromatin region and transcription factor binding sites (NEUROG3) were then called, filtered, and annotated to the nearest gene using MACS2 and HOMER
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

extract_protocol:
Samples were collected on differentiation day 9 and day 12 with or without 8-hour or 24-hour NEUROG3 induction. Cells were dissociated with Accutase into single cell suspension. 50,000 cells were collected for lysis and transposition based on Omni-ATAC protocol. Briefly, cells were lysed with Lysis buffer (10mM Tris-HCL, 10mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin), washed with washing buffer (10mM Tris-HCL, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20), and incubated with Transposition buffer (Nextra) for at 1000 rpm 37°C for 30 minutes. DNA was purified (Qiagen MinElute) for library construction
Library was prepared and sequenced at Kottyan lab, CCHMC. 5ul of the amplified DNA was then used to perform qPCR to determine the optimal number of additional cycles to prevent amplification saturation of DNA libraries. Double size selection of amplified libraries (0.5x – left sided, 1.8x – right sided) was performed using AMPure XP beads and the DNdA was eluted in a final volume of 20ul in 0.1x TE buffer. Purified libraries were sequenced on an Illumina NextSeq 500 instrument with a 2 3 75bp read length.

value: WA01 hESC:NEUROG3-/- ; NEUROG3-TetON

value: Endocrine progenitors day 9

value: 24-hour Dox


title: KO, Pan, 0, 24hr, D9, 0dpi, Rep3, ATAC

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

value: no Dox


title: WT, Pan, 100, 8hr, D9, 0dpi, Rep3 ATAC

value: 8-hour Dox


title: SKOV3_Control shRNA_Vehicle_1

description: SKOV3 control cells

value: ovarian cancer cell line


title: WT, Pan, 100, 24hr, D12, 3dpi, Rep3 ATAC

value: Endocrine progenitors day 12


title: WT, Pan, 100, 8hr, D9, 0dpi, Rep2, ATAC


title: WT, Pan, 100, 8hr, D12, 3dpi, Rep3 ATAC


title: DE70NGSUKBR129378_Control, no depressive symptomes [postpartum sample]

description: Library name: DE70NGSUKBR129378

value: blood


title: DE47NGSUKBR129307_Control, no depressive symptomes [postpartum sample]

description: Library name: DE47NGSUKBR129307


title: KO, Pan, 0, 24hr, D12, 3dpi, Rep3 ATAC


title: S_9_cells_CD19Jurkat_bulk_JH0025

city: Vienna

first: Jakob

last: Huemer

state: Vienna

address: Zimmermannpl. 10

country: Austria

institute: Children’s Cancer Research Institute

description:
9 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

data_processing:
Raw reads were trimmed using trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using HISAT2 (version 2.1.0)
Uniquely mapped reads for each exon were counted using the function summarizeOverlaps from the Ge-nomicAlignments package (version 1.12.0) in R (version 3.4.0)
Gene and exon annotations were obtained from the Ensembl GENCODE Basic set (genome-build GRCh38)
Assembly: hg38
Supplementary files format and content: csv file of read counts

source_name: Jurkat cells

growth_protocol: Human primary NK cells (‘primary NK cells’) were isolated from buffe coat and enriched using RosetteSep Human NK Cell Enrichment Cocktail (Stemcell technologies) according to manufacturer’s instructions. Enriched NK cells were resuspended in PBS supplemented with 3% heat-inactivated fetal bovine serum and 10mM ultrapure EDTA, pH 8.0 (Invitrogen) and further purified with MagniSort Human NK cell Enrichment Kit (Invitrogen) according to manufacturer’s instructions. CD19-specific human CAR T cells (‘aCD19CAR cells’) were generated similarly as described before (Salzer et.al., 2020). Normal donor derived T cells were lentivirally transduced following 24 hours of stimulation with T Cell TransAct (Miltenyi Biotec) according to manufacturer’s protocol. Lentiviral supernatant was added at a final dilution of 1:4. Stimulation reagent was removed by centrifugation after 72 hours of activation. Transduced T cells were cultivated in AIM V medium (Thermo Scientific) with 2.5% 1M HEPES (Gibco), 2% heat-inactivated octaplas SD blood type AB (Vienna Red Cross), 1% L-Glutamine was supplemented with 10 ng/ml rh IL- 7 (Miltenyi Biotec) and 5 ng/ml rh IL-15 (Miltenyi Biotec) instead of 200 rh U/ml IL-2. CD19 specific CAR T cells were enriched for CD8+ population using MagniSort Human CD8 T cell Enrichment Kit (Invitrogen) according to manufacturer’s instructions. CAFs (‘CAF cells’) were isolated from a liver metastasis of an individual with colorectal cancer. The tumor metastasis was dissociated with 100 U/ml collagenase IV (Gibco) in DMEM supplemented with 10% fetal bovine serum for 1 hour at 37°C. Cells were strained through 0.45µm filter and grown for 2 hours in EGM-MV2 (PromoCell). Thereafter, cells were cultured in EGM-MV2 supplemented with 0.25 μg/ml amphotericin B (Gibco), 20 mg/ml gentamycin (Gibco), 100 U/ml penicillin/streptomycin (Sigma) with a daily 5 hours antibiotic free incubation period. From passage 2 onwards fibroblast were grown in EGM-MV2 without antibiotics. NK-92 cells (‘NK92 cells’) were cultured in alphaMEM (Sigma) supplemented with 12.5% heat-inactivated fetal bovine serum (Sigma), 12.5% heat-inactivated horse serum (Sigma), 0.2 mM myo-inositol, 0.02 mM folic acid, 10 mM HEPES (Gibco), 100 U/ml Penicillin-Streptomycin (Gibco), 2 mM L-glutamine (Sigma), and 20 U/ml rh IL-2 (Novartis). NK-92 cells were passaged every 2-3 days and given fresh medium 1 day before the experiments. K562 cells (‘K562 cells’) were grown in RPMI-1640 (Gibco) supplemented with 2 mM L-glutamine, 10 mM HEPES, 100 U/ml Penicillin-Streptomycin, and 10% heat-inactivated fetal bovine serum (further described as ‘full RPMI’). Jurkat cells (‘Jurkat cells’) were grown in full RPMI. CD19+ Jurkat cells were generated by CD19 mRNA electroporation similar to the previously described method (Zajc et. al., 2020).

extract_protocol:
RNA was isolated according to Smart-seq2 was performed as described previously (Picelli et.  al., 2014). In brief, cells were lysed in 0.2% Triton X-100 in the presence of RNase inhibitor 40 U/µl RNase inhibitor (Takara) and stored at -80°C until ready to proceed.
RNA was denatured, reverse transcribed and amplified for 22 cycles. After reverse transcription, 1 ng cDNA was tagmented, amplified and barcoded following the Illumina Nextera indexing strategy. Final libraries were pooled to 4 nM for sequencing on HiSeq3000/4000. cDNA and library quality was assessed using TapeStation 4150 instrument and D5000HS or D1000 screening tapes (Agilent), respectively. DNA concentration was determined using Qubit dsDNA HS kit and instrument (Invitrogen). cDNA and Illumina Nextera indexed samples were purified using Ampure XP beads (Beckman Coulter) at 1:1 ratio. Sequencing was performed by the Biomedical Sequencing Facility at CeMM at 50bp single-end configuration.

treatment_protocol: For CIPS application: Cells were brought to high viability and density by spinning at 100 rcf for 3 minutes and subsequent elution in full RPMI. 1 million cells were stained with Hoechst 3334 (Invitrogen) and to discriminate GFP-expressing K562 from NK-92 cells, NK-92 cells were in addition counterstained with CD56-PE (N901, Beckman Coulter) for 30 minutes in full RPMI. Cells were washed with PBS and brought to a density of 1000 cells per µl in full RPMI for loading on a DEPArray Cartridge V2 (Silicon Biosystems). Cells were scanned for brightfield, the corresponding fluorescent markers and Hoechst (DAPI) for doublet/multicell exclusion. For further use, cells were defined with the following parameters: (i) in ‘grid’ (one cell per DEP cage), (ii) Hoechst positive, and (iii) cell size. Cell fulfilling criteria (i) to (iii) were categorized as NK-92: smaller cells, GFP negative, PE positive or K562: bigger cells, GFP positive, PE negative. From this pool, approximately 50-60 cells each were moved the Cartridge ‘park area’, where cells were aligned, collided and separated by changing the electric potential of DEP cages. Cells were assigned and moved to RNase/DNase-free 0.2 ml PCR-tubes (Applied Biosystems). After total four hours of cell-cell interactions cells were washed by adding RNase-free PBS up to a total of 100 µl per sample. Cells were spun and the total volume was reduced to approximately 1 µl using the VRNxT/Silicon Biosystems (‘DEPArray OUT‘ program) according to the manufacturer’s instructions. Enriched primary human NK cells with K562 partner cell were stained and processed the same in the CIPS procedure as described above for NK-92 and K562 cells. Enriched CD8+ CD19 specific CAR T cells with Jurkat partner cell and CAFs processed with following adaptations. Enriched CD8+ CD19 specific CAR T were stained with Hoechst 3334, CD4-APC (clone RPA-T4, BD Biosciences), CD8-PE (clone SK1, BD Biosciences) and GFP-expressing Jurkat cells with Hoechst 3334. Cells were categorized as CD8+ T cells as: smaller cells, APC negative, PE positive or Jurkat: bigger cells, GFP positive, APC negative, PE negative. CAFs were stained with Hoechst 3334, CD90-APC (clone 5E10, Biolegend), FAP-AF488 (clone # 427819, R&D) and categorized as: bigger cells, APC positive, GFP dim. Cell manipulation, recovery was done as described before with longer routing times for primary human NK cells and CD8+ T cells. For FACS application: Enrichment of human primary NK cells, CD8+ CD19 specific CAR T cells and expression of CD19 on Jurkat cells was assessed using 100-200*10^3 cells and controls each. Cells were washed in 2% heat-inactivated fetal bovine serum in PBS after blocking for 10min, 4°C in 10% heat-inactivated fetal bovine serum in PBS. Cells were stained with the following antibodies at 4°C for 30min. Primary human NK cells: CD56-AF700 (clone B159, BD Biosciences) and CD3-FITC (clone SK7, BD Biosciences). CD19 specific CAR T cells: CD3-FITC (clone SK7, BD Biosciences), CD4-APC (clone RPA-T4, BD Biosciences), CD8-V450 (clone RPA-T8, BD Biosciences), and DYKDDDDK (Flag) Tag-PE (clone L5, Biolegend), the latter for CAR expression. CD19+ Jurkat cells: CD19-PECy7 (clone SJ25C1, BD Bioscience). Cells were washed and analyzed as well as  500 cell per well sorted for following populations. Primary NK cells: ‘CD56hi’, ‘CD56dim’; Jurkat cells: ‘Jurkat’, ‘CD19Jurkat’; CD19-specific human CAR T cells: ‘CD4pos’, ‘CD8pos’ using Aria Fusion. Following a degranulation assay NK-92 and K562 cells stained with stained with a CD56-AF700 and CD107a-PE antibody cells were washed, re-suspended, and filtered in 0.5% BSA in PBS. 500 cells of unresponsive NK-92 (CD56+, CD107a-), granule releasing NK-92 (CD56+, CD107a+) and K562 (GFP+) were sorted with Aria Fusion into a 96-well plate for follow-up Smart-seq2 processing. CD107a positivity was defined by NK-92 cells stimulated for two hours with 250 ng/ml Phorbol 12-myristate 13-acetate (PMA) and 1 µg/ml Ionomycin. NK-92 and K562 cells incubated alone were processed as negative controls. For both, CIPS and FACS application cells were further processed with the Smart-Seq2 protocol.

value: Jurkat cells

tag: number of cells

tag: interaction duration

tag: experiment id

tag: phenotype

value: GFP


title: DE94NGSUKBR129140_Control, no depressive symptomes [postpartum sample]

description: Library name: DE94NGSUKBR129140

tag: age (years)


title: S_9_cells_Monocytes_bulk_JH0030

description:
9 monocyte cells that did not interact
processed data file: Counts_CAR.csv

source_name: monocyte cells

value: monocyte cells


title: KO, Pan, 0, 24hr, D9, 0dpi, Rep2, ATAC


title: S_9_cells_CAF_bulk_JH0030

description:
9 CAF cells that did not interact
processed data file: Counts_CAR.csv

source_name: CAF cells

value: CAF cells


title: DE08NGSUKBR129427_Control, no depressive symptomes [postpartum sample]

description: Library name: DE08NGSUKBR129427

tag: pre-pregnancy bmi_(kg/m2)

value: No

value: Control


title: WT, Pan, 100, 24hr, D9, 0dpi, Rep2, ATAC


title: S_6_cells_primNKSG_bulk_JH0020

description:
6 primary NK cells that did not interact
processed data file: Counts_PrimNK.csv

source_name: primary NK cells

value: primary NK cells

value: SG


title: WT, Pan, 100, 8hr, D12, 3dpi, Rep2, ATAC

value: WA01 hESC:NEUROG3-/- ; NEUROG3-TetON


title: KO, Pan, 0, 24hr, D12, 3dpi, Rep2, ATAC


title: KO, Pan, 0, 24hr, D9, 0dpi, Rep1, ATAC

value: Endocrine progenitors day 9


title: WT, Pan, 100, 24hr, D9, 0dpi, Rep1, ATAC

value: 24-hour Dox


title: DE09NGSUKBR129409_Control, no depressive symptomes [postpartum sample]

description: Library name: DE09NGSUKBR129409

tag: ssri user_(yes/no)

value: postpartum sample


title: DE97NGSUKBR129377_Control, no depressive symptomes [postpartum sample]

description: Library name: DE97NGSUKBR129377

tag: tissue


title: KO, Pan, 0, 24hr, D12, 3dpi, Rep1, ATAC

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

value: no Dox


title: DE69NGSUKBR129396_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE69NGSUKBR129396

tag: subject group

value: Depressive symptomes only postpartum

value: postpartumy sample


title: WT, Pan, 100, 24hr, D12, 3dpi, Rep1 ATAC

value: Endocrine progenitors day 12


title: S_5_cells_K562_bulk_JH0021

description:
5 K562 cells that did not interact
processed data file: Counts_PrimNK.csv

source_name: K562 cells

value: K562 cells

value: WT


title: WT, Pan, 100, 8hr, D9, 0dpi, Rep1, ATAC

value: 8-hour Dox


title: S_20_cells_NK92_WT_Jhbatch_S61473

description:
20 NK92 cells that did not interact
processed data file: Counts_NK92.csv

source_name: NK92 cells

value: NK92 cells

value: Jhbatch


title: DE62NGSUKBR129425_Control, no depressive symptomes [postpartum sample]

description: Library name: DE62NGSUKBR129425

value: No

value: blood

value: Control

tag: time point


title: WT, Pan, 100, 8hr, D12, 3dpi, Rep1 ATAC

tag: cell line

value: WA01 hESC:NEUROG3-/- ; NEUROG3-TetON


title: DE30NGSUKBR129128_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE30NGSUKBR129128


title: Heart, heart failure

city: Shinjuku-ku

first: Toshiomi

last: Katsuki

state: Tokyo

address: Shinanomachi 35

department: Cardiology

country: Japan

institute: Keio University Hospital

description: Library name: Heart failure

data_processing:
A Hiseq2500 platform (Illumina, CA, US) was used to sequence 26 and 98 base
Sequenced reads were aligned to the reference genome (mm10) using Cell Ranger v2.0.0 software (10× Genomics).
Assembly: mm10
Supplementary files format and content: Filtered raw counts output by Cell Ranger count

source_name: heart

growth_protocol: Mice care was performed according to the standard method.

extract_protocol:
Type II collagenase (Worthington, CA, USA) (13.5 g) and DNase I (Qiagen) (2 mg) were dissolved in 30 mL of F12Ham medium (Thermo Fisher Scientific, MA, USA). The heart was minced using scissors in an ice-cold Petri dish and mixed with a collagenase solution. The solution was poured into an Erlenmeyer flask soaked in a 38 °C warm bath with a magnetic stirrer for 30 min. After a 30-min incubation, the mixture was repeatedly cannulated using an 18G needle with a 10 mL syringe. After cannulation, a 30-minute reaction was performed. Ice-cold PBS (20 mL PBS to stop the reaction. This solution was centrifuged at 450 × g and 4 ℃. The supernatant was removed, and 5 mL of 1X RBC Lysis Buffer (Thermo Fisher Scientific, MA, USA) was added on ice with gentle shaking. Ice cold PBS (45 mL) was added and the mixture was passed through 70-µm and 40-µm filters (pluriSelect, Leipzig, Germany) consecutively. The solution was centrifuged as previously described and the supernatant was removed. CellCover (Anacyte Laboratories, Hamburg, Germany) (3 mL) was added on ice for 5 min. Ice-cold PBS (47 mL) was added and centrifuged as described previously. The supernatant was removed, and 4 mL of ice-cold PBS was added. This solution and Percoll was stacked in the tube, and was centrifuged for 25 minutes at 3000 × g and 25 ℃. The debris layer and Percoll were swiftly aspirated. The cell layer were washed by ice-cold PBS up to 50 mL and centrifuged for 6 min at 450 × g and 4 ℃. The precipitate was washed again in the same manner. Finally, 1mL of CellCover was added before application to the single-cell analysis apparatus.
Libraries were constructed using a commercial microdroplet-based platform, Chromium Single Cell 3’ v2 (10×Genomics) according to the manufacturer’s instructions.

treatment_protocol: After inducing anesthesia, approximately 2 cm midline skin incision was made on the chest. The second rib was opened and the thymus was pushed towards the head. Fat and connective tissues were carefully detached from the aortic arch. The arch was ligated twice using a 10-0 nylon thread (Natsume, Tokyo, Japan) with 29-gauge needle (Nipro, Osaka, Japan) spacer. The opened ribs and skin were sutured using 5-0 silk thread (Natsume, Tokyo, Japan).

value: heart

value: ventricles

tag: cell type

value: non-cardiomyocytes

value: wild-type

value: TAC


title: S_20_cells_NK92_RAB27A_KO_MF239_S61512

tag: genotype


title: Heart, adaptive hypertrophy

description: Library name: Adaptive hypertrophy


title: WT, Pan, 100, 24hr, D12, 3dpi, Rep2, ATAC

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

value: 24-hour Dox


title: S_20_cells_K562_Jhbatch_S61471

description:
20 K562 cells that did not interact
processed data file: Counts_NK92.csv


title: DE16NGSUKBR129283_Control, no depressive symptomes [postpartum sample]

description: Library name: DE16NGSUKBR129283

value: postpartum sample


title: Heart, healty

description: Library name: Healty


title: GPR43 KO_EOS_4

city: Daejeon

first: Jihyun

last: Yu

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

data_processing:
Galaxy (https://usegalaxy.org/)
Sequence reads were trimmed for adaptor sequence / low-quality sequence using fastp
Trimmed sequence reads were mapped to mm10 using STAR in the default setting
Read count extraction was performed using FeatureCounts
TPM value was calculated manually
Assembly: mm10
Supplementary files format and content: csv file includes the raw counts for each sample
Supplementary files format and content: csv file includes TPM values for each sample

source_name: Lung

extract_protocol:
To isolate asthmatic lung cells, lungs were chopped into small fragments and enzymatically digested with Collagenase D and DNase I at 37 °C for 30 minutes. The enzyme reaction was stopped by adding EDTA. After vigorous resuspension, cells were filtered through 100 µm strainers, and red blood cells were lysed with ACK lysis buffer. Eosinophils were purified using fluorescence-activated cell sorting (FACS). Purified eosinophils were lysed with Qiazol and chloroform was added in a 5:1 ratio. Following centrifugation, the clear upper phase was collected, and RNA was precipitated by adding an equal volume of 100% isopropanol along with 20 µg of glycogen. After another round of centrifugation, the resulting pellet was washed with 75% ethanol and allowed to air-dry. Lastly, RNA was dissolved in nuclease-free water.
Ribosomal RNAs were removed using NEBNext rRNA Depletion Kit v2, and the cDNA library was synthesized using NEBNext Ultra II Directional RNA Library Prep kit according to the manufacturer’s protocols.

value: Lung

value: eosinophil

value: HDM-induced asthma


title: GPR43 KO_EOS_3


title: DE84NGSUKBR129417_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE84NGSUKBR129417


title: S_18_cells_K562_MF239_S61510

description:
18 K562 cells that did not interact
processed data file: Counts_NK92.csv

value: K562 cells


title: GPR43 KO_EOS_2


title: DE36NGSUKBR129408_Control, no depressive symptomes [postpartum sample]

description: Library name: DE36NGSUKBR129408


title: GPR43 KO_EOS_1


title: S_12_cells_aCD19CAR_bulk_JH0024

description:
12 aCD19CAR cells that did not interact
processed data file: Counts_CAR.csv

source_name: aCD19CAR cells

value: aCD19CAR cells


title: S_6_cells_K562_bulk_JH0020

description:
6 K562 cells that did not interact
processed data file: Counts_PrimNK.csv

value: WT

value: GFP


title: Ctrl_EOS_5

value: Epx-Cre/+


title: Ctrl_EOS_3


title: Ctrl_EOS_1


title: DE69NGSUKBR129299_Control, no depressive symptomes [postpartum sample]

description: Library name: DE69NGSUKBR129299

value: No

value: blood

value: Control


title: Ctrl_EOS_2


title: S_12_cells_Jurkat_bulk_JH0024

description:
12 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

value: Jurkat cells


title: S_10_cells_NK92_RAB27A_KO_MF247_S61481

description:
10 NK92 cells that did not interact
processed data file: Counts_NK92.csv

value: NK92 cells


title: Sample 6-IP

city: Xinxiang

first: chengbiao

last: Lu

address: 601 Jinsui Avenue

institute: xinxiang medicial university

description:
Methylated_RNA_sites.mRNA.xlsx
O3-H.mRNA.m5C.bed

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Assembly: mm10
Supplementary files format and content: XLS sheet "Methylated_RNA_sites.mRNA.xlsx" illustrated the m5A methylation sites information,  including m5A peak start site, peak stop site, peak ID, m5C peak score, peak length, generated by MACS software(see column B to column F). BED files that illustrated the m6A peak start site, peak stop site, peak ID, m6A peak score, generated by MACS software.

source_name: Hippocampus

extract_protocol:
Total RNA was subjected to immunoprecipitation with the GenSeq® m5C-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m5C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified.
Both the input samples without immunoprecipitation and the m5C IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit.  Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

tag: strain

tag: Sex

value: female

value: Hippocampus

value: natural aging

tag: time


title: S_10_cells_Monocytes_bulk_JH0029

description:
10 monocyte cells that did not interact
processed data file: Counts_CAR.csv

value: monocyte cells

tag: treatment


title: Sample 5-Input

description:
Methylated_RNA_sites.mRNA.xlsx
O2-H.mRNA.m5C.bed


title: S_11_cells_CAF_bulk_JH0022

description:
11 CAF cells that did not interact
processed data file: Counts_CAR.csv

value: CAF cells

tag: number of cells


title: DE26NGSUKBR129394_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE26NGSUKBR129394

value: Depressive symptomes only postpartum

value: postpartumy sample


title: DE56NGSUKBR129339_Control, no depressive symptomes [postpartum sample]

description: Library name: DE56NGSUKBR129339

value: postpartum sample


title: Sample 5-IP


title: Sample 4-Input

description:
Methylated_RNA_sites.mRNA.xlsx
O1-H.mRNA.m5C.bed


title: DE03NGSUKBR129323_Control, no depressive symptomes [postpartum sample]

description: Library name: DE03NGSUKBR129323


title: DE93NGSUKBR129352_Control, no depressive symptomes [postpartum sample]

description: Library name: DE93NGSUKBR129352


title: Sample 4-IP


title: DE14NGSUKBR129416_Control, no depressive symptomes [postpartum sample]

description: Library name: DE14NGSUKBR129416


title: S_10_cells_K562_MF247_S61497

description:
10 K562 cells that did not interact
processed data file: Counts_NK92.csv

value: K562 cells

tag: interaction duration


title: Ctrl_EOS_4

value: Lung

value: eosinophil

value: HDM-induced asthma


title: DE28NGSUKBR129358_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE28NGSUKBR129358

value: No


title: Sample 3-Input

description:
Methylated_RNA_sites.mRNA.xlsx
Y3-H.mRNA.m5C.bed

value: WT

value: young


title: S_10_cells_K562_bulk_JH0017

description:
10 K562 cells that did not interact
processed data file: Counts_PrimNK.csv

tag: experiment id

value: GFP


title: Sample 1-IP

description:
Methylated_RNA_sites.mRNA.xlsx
Y1-H.mRNA.m5C.bed


title: Sample 3-IP


title: Sample 2-IP

description:
Methylated_RNA_sites.mRNA.xlsx
Y2-H.mRNA.m5C.bed


title: S_10_cells_Jurkat_bulk_JH0028

description:
10 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

value: Jurkat cells

tag: phenotype


title: DE78NGSUKBR129331_Control, no depressive symptomes [postpartum sample]

description: Library name: DE78NGSUKBR129331

tag: age (years)

value: blood

value: Control


title: Sample 1-Input

value: female

value: Hippocampus


title: S_10_cells_CD19Jurkat_bulk_JH0026


title: Sample 6-Input

value: natural aging


title: S_10_cells_aCD19CAR_bulk_JH0026

description:
10 aCD19CAR cells that did not interact
processed data file: Counts_CAR.csv

value: aCD19CAR cells


title: DE71NGSUKBR129263_Control, no depressive symptomes [postpartum sample]

description: Library name: DE71NGSUKBR129263

tag: pre-pregnancy bmi_(kg/m2)


title: DE91NGSUKBR129291_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE91NGSUKBR129291

tag: ssri user_(yes/no)

value: Depressive symptomes only postpartum

value: postpartumy sample


title: S_10_cells_aCD19CAR_bulk_JH0025


title: Sample 2-Input

tag: tissue


title: C1498_45deg_15h_14

city: Kobe

first: Katsuyuki

last: Shiroguchi

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

description: Library name: Cell_ID_353

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Each library was sequenced twice, and the generated fastq files were merged for each library.
Reads were aligned to the mm10 genome assembly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: Mouse mm10
Supplementary files format and content: The calculated copy number of RNA moelcules per cell for each gene is listed.

extract_protocol:
RNAs from cell lysate was directly used for library preparation.
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Microscopically observed headted cells were picked with ALPS.


title: S_10_cells_CAF_bulk_JH0029

description:
10 CAF cells that did not interact
processed data file: Counts_CAR.csv

value: CAF cells


title: C1498_45deg_15h_18

description: Library name: Cell_ID_357


title: C1498_45deg_15h_17

description: Library name: Cell_ID_356


title: C1498_45deg_15h_16

description: Library name: Cell_ID_355


title: S_10_cells_aCD19CAR_bulk_JH0028


title: C1498_45deg_15h_19

description: Library name: Cell_ID_358


title: C1498_45deg_15h_20

description: Library name: Cell_ID_359


title: C1498_45deg_15h_12

description: Library name: Cell_ID_351


title: DE05NGSUKBR129287_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE05NGSUKBR129287

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

tag: subject group

value: postpartum sample


title: DE50NGSUKBR129350_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE50NGSUKBR129350

tag: time point


title: C1498_45deg_15h_15

description: Library name: Cell_ID_354

tag: cell line


title: DE57NGSUKBR129224_Control, no depressive symptomes [postpartum sample]

description: Library name: DE57NGSUKBR129224


title: S_1_cell_NK92_WT_3241_0min_JH00014_S65131

description:
1 NK92 cells that did not interact
processed data file: Counts_NK92.csv

tag: cell type

value: NK92 cells


title: C1498_45deg_15h_11

description: Library name: Cell_ID_350


title: C1498_45deg_15h_13

description: Library name: Cell_ID_352


title: DE19NGSUKBR129326_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE19NGSUKBR129326


title: C1498_45deg_15h_9

description: Library name: Cell_ID_348


title: C1498_45deg_15h_8

description: Library name: Cell_ID_347


title: C1498_45deg_15h_10

description: Library name: Cell_ID_349


title: DE63NGSUKBR129310_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE63NGSUKBR129310


title: DE80NGSUKBR129295_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE80NGSUKBR129295

value: Yes


title: C1498_45deg_15h_6

description: Library name: Cell_ID_345


title: S_1_cell_NK92_WT_3204_0min_JH00014_S65132

tag: genotype


title: S_1_cell_NK92_RAB27A_KO_6561_0min_JH00011_S65191


title: S_1_cell_NK92_WT_4812_0min_JH00010_S65245


title: C1498_45deg_15h_5

description: Library name: Cell_ID_344


title: C1498_45deg_15h_3

description: Library name: Cell_ID_342


title: S_1_cell_NK92_RAB27A_KO_6136_0min_JH00011_S65192


title: C1498_45deg_15h_1

description: Library name: Cell_ID_340


title: C1498_45deg_15h_2

description: Library name: Cell_ID_341


title: C1498_45deg_15h_4

description: Library name: Cell_ID_343


title: S_1_cell_NK92_RAB27A_KO_5155_0min_JH00013_S65158


title: DE58NGSUKBR129303_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE58NGSUKBR129303


title: S_1_cell_K562_5144_0min_JH00011_S65209

description:
1 K562 cells that did not interact
processed data file: Counts_NK92.csv

value: K562 cells


title: C1498_45deg_10h_52

description: Library name: Cell_ID_339


title: S_1_cell_NK92_RAB27A_KO_5242_0min_JH00013_S65157


title: DE41NGSUKBR129318_Control, no depressive symptomes [postpartum sample]

description: Library name: DE41NGSUKBR129318

value: No


title: C1498_45deg_10h_50

description: Library name: Cell_ID_337


title: DE67NGSUKBR129335_Control, no depressive symptomes [postpartum sample]

description: Library name: DE67NGSUKBR129335


title: C1498_45deg_10h_47

description: Library name: Cell_ID_334


title: DE94NGSUKBR129334_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE94NGSUKBR129334


title: C1498_45deg_10h_51

description: Library name: Cell_ID_338


title: S_1_cell_K562_4579_0min_JH00011_S65215


title: C1498_45deg_10h_49

description: Library name: Cell_ID_336


title: DE27NGSUKBR129279_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE27NGSUKBR129279


title: C1498_45deg_10h_48

description: Library name: Cell_ID_335


title: C1498_45deg_10h_44

description: Library name: Cell_ID_331


title: DE97NGSUKBR129280_Control, no depressive symptomes [postpartum sample]

description: Library name: DE97NGSUKBR129280


title: C1498_45deg_15h_7

description: Library name: Cell_ID_346


title: DE36NGSUKBR129311_Control, no depressive symptomes [postpartum sample]

description: Library name: DE36NGSUKBR129311


title: C1498_45deg_10h_41

description: Library name: Cell_ID_328


title: C1498_45deg_10h_42

description: Library name: Cell_ID_329


title: C1498_45deg_15h_21

description: Library name: Cell_ID_360


title: S_1_cell_K562_4024_0min_JH00013_S65178


title: C1498_45deg_10h_46

description: Library name: Cell_ID_333


title: DE06NGSUKBR129366_Control, no depressive symptomes [postpartum sample]

description: Library name: DE06NGSUKBR129366


title: DE98NGSUKBR129359_Control, no depressive symptomes [postpartum sample]

description: Library name: DE98NGSUKBR129359


title: C1498_45deg_10h_43

description: Library name: Cell_ID_330


title: S_1_cell_K562_3333_0min_JH00013_S65171


title: C1498_45deg_10h_39

description: Library name: Cell_ID_326


title: DE62NGSUKBR129328_Control, no depressive symptomes [postpartum sample]

description: Library name: DE62NGSUKBR129328


title: R2_S_15_cells_NK92_WT_JH0008

description:
15 NK92 cells that did not interact
processed data file: Counts_NK92.csv

value: WT


title: R2_S_20_cells_NK92_RAB27A_KO_JH0002

description:
20 NK92 cells that did not interact
processed data file: Counts_NK92.csv


title: C1498_45deg_10h_37

description: Library name: Cell_ID_324


title: C1498_45deg_10h_36

description: Library name: Cell_ID_323


title: R2_S_18_cells_K562_JH0002

description:
18 K562 cells that did not interact
processed data file: Counts_NK92.csv


title: DE40NGSUKBR129336_Control, no depressive symptomes [postpartum sample]

description: Library name: DE40NGSUKBR129336


title: DE53NGSUKBR129296_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE53NGSUKBR129296


title: C1498_45deg_10h_45

description: Library name: Cell_ID_332


title: C1498_45deg_10h_35

description: Library name: Cell_ID_322


title: C1498_45deg_10h_34

description: Library name: Cell_ID_321


title: R2_S_15_cells_NK92_WT_JH0006


title: C1498_45deg_10h_33

description: Library name: Cell_ID_320


title: R2_S_15_cells_K562_JH0007

description:
15 K562 cells that did not interact
processed data file: Counts_NK92.csv


title: C1498_45deg_10h_40

description: Library name: Cell_ID_327


title: C1498_45deg_10h_32

description: Library name: Cell_ID_319


title: C1498_45deg_10h_31

description: Library name: Cell_ID_318


title: DE89NGSUKBR129327_Control, no depressive symptomes [postpartum sample]

description: Library name: DE89NGSUKBR129327


title: R2_S_15_cells_K562_JH0006


title: C1498_45deg_10h_29

description: Library name: Cell_ID_316


title: R2_S_11_cells_no2_K562_JH0004

description:
11 K562 cells that did not interact
processed data file: Counts_NK92.csv


title: DE72NGSUKBR129342_Control, no depressive symptomes [postpartum sample]

description: Library name: DE72NGSUKBR129342


title: R2_S_15_cells_no2_NK92_WT_JH0004


title: C1498_45deg_10h_38

description: Library name: Cell_ID_325


title: R2_S_11_cells_K562_JH0004


title: C1498_45deg_10h_27

description: Library name: Cell_ID_314


title: C1498_45deg_10h_26

description: Library name: Cell_ID_313


title: C1498_45deg_10h_28

description: Library name: Cell_ID_315


title: DE31NGSUKBR129304_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE31NGSUKBR129304


title: C1498_45deg_10h_25

description: Library name: Cell_ID_312


title: R2_NK92_WT_906_p10_2min_JH0005

description:
1 NK92 cells that interacted for 2min
processed data file: Counts_NK92.csv


title: C1498_45deg_10h_22

description: Library name: Cell_ID_309


title: R2_NK92_WT_8634_t1_5min_30min_5min_JH0008

description:
1 NK92 cells that interacted for 5min30min5min
processed data file: Counts_NK92.csv


title: C1498_45deg_10h_20

description: Library name: Cell_ID_307


title: DE23NGSUKBR129351_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE23NGSUKBR129351


title: C1498_45deg_10h_23

description: Library name: Cell_ID_310


title: C1498_45deg_10h_30

description: Library name: Cell_ID_317


title: R2_NK92_WT_944_p12_10min_JH0007

description:
1 NK92 cells that interacted for 10min
processed data file: Counts_NK92.csv


title: C1498_45deg_10h_19

description: Library name: Cell_ID_306


title: DE09NGSUKBR129312_Control, no depressive symptomes [postpartum sample]

description: Library name: DE09NGSUKBR129312


title: R2_NK92_WT_8316_p15_2min_JH0007


title: DE75NGSUKBR129288_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE75NGSUKBR129288


title: DE84NGSUKBR129320_Control, no depressive symptomes [postpartum sample]

description: Library name: DE84NGSUKBR129320


title: R2_NK92_WT_8087_t2_5min_30min_5min_JH0008


title: DE59NGSUKBR129188_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE59NGSUKBR129188


title: C1498_45deg_10h_18

description: Library name: Cell_ID_305


title: R2_NK92_WT_7061_p1_5min_JH0006

description:
1 NK92 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: DE76NGSUKBR129367_Control, no depressive symptomes [postpartum sample]

description: Library name: DE76NGSUKBR129367


title: C1498_45deg_10h_16

description: Library name: Cell_ID_303


title: C1498_45deg_10h_13

description: Library name: Cell_ID_300


title: C1498_45deg_10h_14

description: Library name: Cell_ID_301


title: DE02NGSUKBR129341_Control, no depressive symptomes [postpartum sample]

description: Library name: DE02NGSUKBR129341


title: C1498_45deg_10h_15

description: Library name: Cell_ID_302


title: DE14NGSUKBR129319_Control, no depressive symptomes [postpartum sample]

description: Library name: DE14NGSUKBR129319


title: DE60NGSUKBR129267_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE60NGSUKBR129267


title: R2_NK92_WT_6743_p1_5min_JH0007


title: C1498_45deg_10h_24

description: Library name: Cell_ID_311


title: C1498_45deg_10h_12

description: Library name: Cell_ID_299


title: C1498_45deg_10h_11

description: Library name: Cell_ID_298


title: R2_NK92_WT_6728_p2_5min_JH0007


title: C1498_45deg_10h_21

description: Library name: Cell_ID_308


title: C1498_45deg_10h_10

description: Library name: Cell_ID_297


title: C1498_45deg_10h_9

description: Library name: Cell_ID_296


title: DE82NGSUKBR129259_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE82NGSUKBR129259


title: R2_NK92_WT_6419_t3_5min_30min_5min_JH0008


title: DE38NGSUKBR129275_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE38NGSUKBR129275


title: R2_NK92_WT_5685_p3_5min_JH0007


title: C1498_45deg_10h_8

description: Library name: Cell_ID_295


title: C1498_45deg_10h_6

description: Library name: Cell_ID_293


title: DE37NGSUKBR129196_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE37NGSUKBR129196


title: C1498_45deg_10h_17

description: Library name: Cell_ID_304


title: C1498_45deg_10h_4

description: Library name: Cell_ID_291


title: C1498_45deg_10h_7

description: Library name: Cell_ID_294


title: R2_NK92_WT_5683_t4_5min_30min_5min_JH0008


title: C1498_45deg_10h_5

description: Library name: Cell_ID_292


title: C1498_45deg_10h_2

description: Library name: Cell_ID_289


title: C1498_45deg_10h_3

description: Library name: Cell_ID_290


title: R2_NK92_WT_5662_p4_5min_JH0007


title: C1498_45deg_5h_223

description: Library name: Cell_ID_287


title: C1498_45deg_5h_222

description: Library name: Cell_ID_286


title: C1498_45deg_5h_221

description: Library name: Cell_ID_285


title: R2_NK92_WT_4806_p5_5min_JH0008


title: C1498_45deg_10h_1

description: Library name: Cell_ID_288


title: DE15NGSUKBR129301_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE15NGSUKBR129301


title: R2_NK92_WT_5210_p5_10min_JH0007


title: DE07NGSUKBR129251_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE07NGSUKBR129251


title: C1498_45deg_5h_220

description: Library name: Cell_ID_284


title: C1498_45deg_5h_219

description: Library name: Cell_ID_283


title: R2_NK92_WT_4279_p4_2min_JH0006


title: DE68NGSUKBR129220_Control, no depressive symptomes [postpartum sample]

description: Library name: DE68NGSUKBR129220


title: C1498_45deg_5h_218

description: Library name: Cell_ID_282


title: C1498_45deg_5h_217

description: Library name: Cell_ID_281


title: DE24NGSUKBR129236_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE24NGSUKBR129236


title: R2_NK92_WT_2921_p6_5min_JH0008


title: R2_NK92_WT_3498_p6_20min_JH0007

description:
1 NK92 cells that interacted for 20min
processed data file: Counts_NK92.csv


city: Houston

first: Oluwadara

last: Coker

state: Texas

address: 6767 Bertner Ave

department: GI Medical Oncology

institute: MD Anderson Cancer Center

description:
Library name: Sample 50
C1144, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 4
Column name in C1144_rawcounts.csv and VST_C1144R.csv: combo_clone4

data_processing:
Xenome v1.0.1
Human reads in the form of BAM files were aligned to the human reference genome (GRCh38) using STAR aligner (v2.7.2b), with duplicated reads marked using biobambam (v0.0.191)
Reads were annotated using GENCODE (v22). Un-normalized genes counts were generated using HTseq (v0.11.0) and subsequently filtered to keep only protein-coding genes
Counts were then processed through the R software package, DESeq2 (v1.41.4), to generate differentially expressed genes for pathway analysis.
Pathway analysis was conducted using GSEA (fgsea R package v1.26.0)
Assembly: GRCh38
Supplementary files format and content: raw counts are stored in .csv files
Supplementary files format and content: processed data show RNA expression as VST values stored in .csv files

source_name: mCRC PDX

growth_protocol: human CRC tumors were implanted into nude female mice and allowed to grow to a size of 300-400cm3

extract_protocol:
Mice were euthanised at the end of the treatment period and tumors were harveste, snap-frozen using liquid nitrogen and then submitted to Admera Health for processing and sequencing
RNA libraries for RNA-seq were prepared by Admera Health

treatment_protocol: Mice were treated with G12Ci or G12Ci/EGFRi until resistance was achieved. In experiments involving TEADi, mice were treated for 21 days

value: mCRC PDX

value: KRAS p.G12C

value: Day 21


title: DE46NGSUKBR129228_Control, no depressive symptomes [postpartum sample]

city: Uppsala

first: Alkistis

last: Skalkidou

institute: Uppsala university

description: Library name: DE46NGSUKBR129228

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)

value: blood

value: Control


title: C1498_45deg_5h_215

description: Library name: Cell_ID_279


title: DE77NGSUKBR129252_Control, no depressive symptomes [postpartum sample]

description: Library name: DE77NGSUKBR129252


title: C1498_45deg_5h_216

description: Library name: Cell_ID_280


title: DE15NGSUKBR129204_Control, no depressive symptomes [postpartum sample]

description: Library name: DE15NGSUKBR129204


description:
Library name: Sample 49
C1144, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 3
Column name in C1144_rawcounts.csv and VST_C1144R.csv: combo_clone3


title: R2_NK92_WT_2905_p8_10min_JH0007


description:
Library name: Sample 48
C1144, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 2
Column name in C1144_rawcounts.csv and VST_C1144R.csv: combo_clone2


title: R2_NK92_WT_2813_p8_5min_JH0006


title: C1498_45deg_5h_214

description: Library name: Cell_ID_278


title: R2_NK92_WT_2123_p10_5min_JH0006


description:
Library name: Sample 47
C1144, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 1
Column name in C1144_rawcounts.csv and VST_C1144R.csv: combo_clone1


title: DE77NGSUKBR129349_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE77NGSUKBR129349


title: C1498_45deg_5h_213

description: Library name: Cell_ID_277


title: R2_NK92_WT_1926_p9_10min_JH0007


title: DE24NGSUKBR129333_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE24NGSUKBR129333


title: C1498_45deg_5h_212

description: Library name: Cell_ID_276


title: DE55NGSUKBR129357_Control, no depressive symptomes [postpartum sample]

description: Library name: DE55NGSUKBR129357


description:
Library name: Sample 46
B8026, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 5
Column name in B8026_rawcounts.csv and VST_B8026R.csv: combo_clone5


title: R2_NK92_WT_1887_p7_5min_JH0008


description:
Library name: Sample 45
B8026, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 4
Column name in B8026_rawcounts.csv and VST_B8026R.csv: combo_clone4


title: C1498_45deg_5h_211

description: Library name: Cell_ID_275


title: DE11NGSUKBR129276_Control, no depressive symptomes [postpartum sample]

description: Library name: DE11NGSUKBR129276


description:
Library name: Sample 44
B8026, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 3
Column name in B8026_rawcounts.csv and VST_B8026R.csv: combo_clone3


description:
Library name: Sample 43
B8026, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 2
Column name in B8026_rawcounts.csv and VST_B8026R.csv: combo_clone2


title: C1498_45deg_5h_209

description: Library name: Cell_ID_273


title: R2_NK92_WT_1789_p10_10min_JH0007


title: DE02NGSUKBR129244_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE02NGSUKBR129244


title: R2_NK92_WT_1246_t9_5min_30min_5min_JH0008


title: DE85NGSUKBR129302_Control, no depressive symptomes [postpartum sample]

description: Library name: DE85NGSUKBR129302


title: DE10NGSUKBR129294_Control, no depressive symptomes [postpartum sample]

description: Library name: DE10NGSUKBR129294


title: C1498_45deg_5h_208

description: Library name: Cell_ID_272


title: DE55NGSUKBR129260_Control, no depressive symptomes [postpartum sample]

description: Library name: DE55NGSUKBR129260


title: R2_NK92_RAB27A_KO_7854_p3_15min_JH0002

description:
1 NK92 cells that interacted for 15min
processed data file: Counts_NK92.csv


description:
Library name: Sample 42
B8026, resistant to G12Ci/EGFRi, G12Ci/EGFRi/TEADi tx, clone 1
Column name in B8026_rawcounts.csv and VST_B8026R.csv: combo_clone1


description:
Library name: Sample 41
C1144, resistant to G12Ci/EGFRi, TEADi tx, clone 5
Column name in C1144_rawcounts.csv and VST_C1144R.csv: teadi_clone5

value: TEADi monotherapy


title: R2_NK92_WT_1156_p11_10min_JH0006


title: DE37NGSUKBR129293_Control, no depressive symptomes [postpartum sample]

description: Library name: DE37NGSUKBR129293


title: C1498_45deg_5h_207

description: Library name: Cell_ID_271


title: R2_NK92_RAB27A_KO_7846_p2_10min_JH0002


title: C1498_45deg_5h_206

description: Library name: Cell_ID_270


title: DE33NGSUKBR129365_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE33NGSUKBR129365


description:
Library name: Sample 38
C1144, resistant to G12Ci/EGFRi, TEADi tx, clone 2
Column name in C1144_rawcounts.csv and VST_C1144R.csv: teadi_clone2


title: DE46NGSUKBR129325_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE46NGSUKBR129325


title: R2_NK92_RAB27A_KO_3041_p13_10min_JH0002


description:
Library name: Sample 39
C1144, resistant to G12Ci/EGFRi, TEADi tx, clone 3
Column name in C1144_rawcounts.csv and VST_C1144R.csv: teadi_clone3


title: C1498_45deg_5h_205

description: Library name: Cell_ID_269


title: R2_NK92_RAB27A_KO_2585_p12_5min_JH0002


title: C1498_45deg_5h_204

description: Library name: Cell_ID_268


title: C1498_45deg_5h_210

description: Library name: Cell_ID_274


title: DE30NGSUKBR129225_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE30NGSUKBR129225


description:
Library name: Sample 37
C1144, resistant to G12Ci/EGFRi, TEADi tx, clone 1
Column name in C1144_rawcounts.csv and VST_C1144R.csv: teadi_clone1


title: R2_NK92_RAB27A_KO_1532_p10_5min_JH0002


title: C1498_45deg_5h_203

description: Library name: Cell_ID_267


title: DE90NGSUKBR129309_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE90NGSUKBR129309


title: C1498_45deg_5h_202

description: Library name: Cell_ID_266


description:
Library name: Sample 36
B8026, resistant to G12Ci/EGFRi, TEADi tx, clone 5
Column name in B8026_rawcounts.csv and VST_B8026R.csv: teadi_clone5


title: DE83NGSUKBR129241_Control, no depressive symptomes [postpartum sample]

description: Library name: DE83NGSUKBR129241


description:
Library name: Sample 35
B8026, resistant to G12Ci/EGFRi, TEADi tx, clone 4
Column name in B8026_rawcounts.csv and VST_B8026R.csv: teadi_clone4


title: C1498_45deg_5h_201

description: Library name: Cell_ID_265


description:
Library name: Sample 34
B8026, resistant to G12Ci/EGFRi, TEADi tx, clone 3
Column name in B8026_rawcounts.csv and VST_B8026R.csv: teadi_clone3