title: DE33NGSUKBR129268_Control, no depressive symptomes [postpartum sample]

description: Library name: DE33NGSUKBR129268


title: R2_NK92_RAB27A_KO_1344_p6_5min_JH0002

status: Public on Sep 24 2025

type: SRA

city: Vienna

first: Jakob

last: Huemer

state: Vienna

address: Zimmermannpl. 10

country: Austria

institute: Children’s Cancer Research Institute

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

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: NK92 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.

tag: cell type

value: NK92 cells

tag: number of cells

tag: interaction duration

tag: experiment id

tag: genotype

tag: phenotype

tag: treatment


city: Houston

first: Oluwadara

last: Coker

state: Texas

address: 6767 Bertner Ave

department: GI Medical Oncology

country: USA

institute: MD Anderson Cancer Center

description:
Library name: Sample 40
C1144, resistant to G12Ci/EGFRi, TEADi tx, clone 4
Column name in C1144_rawcounts.csv and VST_C1144R.csv: teadi_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

tag: tissue

value: mCRC PDX

value: KRAS p.G12C

value: TEADi monotherapy

tag: time

value: Day 21


title: DE54NGSUKBR129278_Control, no depressive symptomes [postpartum sample]

city: Uppsala

first: Alkistis

last: Skalkidou

address: Dag Hammarskjölds väg 14 B

department: Women's and Children's Health

country: Sweden

institute: Uppsala university

description: Library name: DE54NGSUKBR129278

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

source_name: blood

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

tag: age (years)

tag: pre-pregnancy bmi_(kg/m2)

tag: ssri user_(yes/no)

value: No

value: blood

tag: subject group

value: Control

tag: time point

value: postpartum sample


title: C1498_45deg_5h_200

city: Kobe

first: Katsuyuki

last: Shiroguchi

state: Hyogo

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

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

description: Library name: Cell_ID_264

library_source: transcriptomic single cell

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.

molecule: polyA RNA

organism: Mus musculus

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.

tag: cell line


title: R2_NK92_RAB27A_KO_1328_p18_10min_JH0002

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


title: R2_NK92_RAB27A_KO_1017_p19_5min_JH0002


title: C1498_45deg_5h_199

description: Library name: Cell_ID_263


title: R2_K562_918_p7_2min_JH0005

description:
1 K562 cells that interacted for 2min
processed data file: Counts_NK92.csv

source_name: K562 cells

value: K562 cells

value: WT


title: DE32NGSUKBR129286_Control, no depressive symptomes [postpartum sample]

description: Library name: DE32NGSUKBR129286


title: R2_K562_716_p10_2min_JH0005


description:
Library name: Sample 31
F3008, resistant to G12Ci/EGFRi, clone 4
Column name in F3008_rawcounts.csv and VST_F3008R.csv: g12ci_egfri_clone4

value: not applicable


description:
Library name: Sample 32
B8026, resistant to G12Ci/EGFRi, TEADi tx, clone 1
Column name in B8026_rawcounts.csv and VST_B8026R.csv: teadi_clone1


title: R2_K562_6320_p16_2min_JH0005


title: C1498_45deg_5h_197

description: Library name: Cell_ID_261


description:
Library name: Sample 30
F3008, resistant to G12Ci/EGFRi, clone 3
Column name in F3008_rawcounts.csv and VST_F3008R.csv: g12ci_egfri_clone3


title: DE96NGSUKBR129201_Control, no depressive symptomes [postpartum sample]

description: Library name: DE96NGSUKBR129201


title: R2_K562_5298_p7_10min_JH0007

description:
1 K562 cells that interacted for 10min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_196

description: Library name: Cell_ID_260


title: DE08NGSUKBR129233_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE08NGSUKBR129233

value: Depressive symptomes only postpartum

value: postpartumy sample


description:
Library name: Sample 29
F3008, resistant to G12Ci/EGFRi, clone 2
Column name in F3008_rawcounts.csv and VST_F3008R.csv: g12ci_egfri_clone2


title: R2_K562_52_p19_5min_JH0002

description:
1 K562 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_195

description: Library name: Cell_ID_259


description:
Library name: Sample 33
B8026, resistant to G12Ci/EGFRi, TEADi tx, clone 2
Column name in B8026_rawcounts.csv and VST_B8026R.csv: teadi_clone2


title: DE16NGSUKBR129186_Control, no depressive symptomes [postpartum sample]

description: Library name: DE16NGSUKBR129186


description:
Library name: Sample 28
F3008, resistant to G12Ci/EGFRi, clone 1
Column name in F3008_rawcounts.csv and VST_F3008R.csv: g12ci_egfri_clone1


title: R2_K562_5174_p12_5min_JH0002


title: R2_K562_4920_p11_10min_JH0002


description:
Library name: Sample 27
C1144, resistant to G12Ci/EGFRi, clone 5
Column name in C1144_rawcounts.csv and VST_C1144R.csv: g12ci_egfri_clone5


title: C1498_45deg_5h_194

description: Library name: Cell_ID_258


title: DE91NGSUKBR129194_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE91NGSUKBR129194


title: R2_K562_480_p5_5min_JH0005


title: DE17NGSUKBR129265_Control, no depressive symptomes [postpartum sample]

description: Library name: DE17NGSUKBR129265


description:
Library name: Sample 26
C1144, resistant to G12Ci/EGFRi, clone 4
Column name in C1144_rawcounts.csv and VST_C1144R.csv: g12ci_egfri_clone4


title: DE47NGSUKBR129210_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE47NGSUKBR129210


title: C1498_45deg_5h_193

description: Library name: Cell_ID_257


title: C1498_45deg_5h_198

description: Library name: Cell_ID_262


title: C1498_45deg_5h_192

description: Library name: Cell_ID_256


title: DE56NGSUKBR129242_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE56NGSUKBR129242


description:
Library name: Sample 25
C1144, resistant to G12Ci/EGFRi, clone 3
Column name in C1144_rawcounts.csv and VST_C1144R.csv: g12ci_egfri_clone3


title: R2_K562_4674_p5_5min_JH0008


description:
Library name: Sample 24
C1144, resistant to G12Ci/EGFRi, clone 2
Column name in C1144_rawcounts.csv and VST_C1144R.csv: g12ci_egfri_clone2


title: R2_K562_4559_t2_c2_5min_JH0008


title: C1498_45deg_5h_190

description: Library name: Cell_ID_254


description:
Library name: Sample 23
C1144, resistant to G12Ci/EGFRi, clone 1
Column name in C1144_rawcounts.csv and VST_C1144R.csv: g12ci_egfri_clone1


title: DE69NGSUKBR129202_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE69NGSUKBR129202


title: R2_K562_4290_t3_c2_5min_JH0008


title: C1498_45deg_5h_189

description: Library name: Cell_ID_253


title: DE86NGSUKBR129187_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE86NGSUKBR129187

value: Yes


description:
Library name: Sample 22
B8026, resistant to G12Ci/EGFRi, clone 8
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone8


title: DE87NGSUKBR129266_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE87NGSUKBR129266


title: C1498_45deg_5h_188

description: Library name: Cell_ID_252


title: R2_K562_3986_t4_c2_5min_JH0008


description:
Library name: Sample 21
B8026, resistant to G12Ci/EGFRi, clone 7
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone7


title: C1498_45deg_5h_187

description: Library name: Cell_ID_251


title: DE03NGSUKBR129226_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE03NGSUKBR129226


title: R2_K562_3858_t3_c1_5min_JH0008


title: C1498_45deg_5h_186

description: Library name: Cell_ID_250


description:
Library name: Sample 20
B8026, resistant to G12Ci/EGFRi, clone 6
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone6


description:
Library name: Sample 19
B8026, resistant to G12Ci/EGFRi, clone 5
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone5


title: DE65NGSUKBR129274_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE65NGSUKBR129274


title: R2_K562_3855_t9_c2_5min_JH0008


title: C1498_45deg_5h_185

description: Library name: Cell_ID_249


title: C1498_45deg_5h_191

description: Library name: Cell_ID_255


title: DE12NGSUKBR129258_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE12NGSUKBR129258


title: DE78NGSUKBR129234_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE78NGSUKBR129234


title: C1498_45deg_5h_184

description: Library name: Cell_ID_248


title: R2_K562_3697_t1_c2_5min_JH0008


title: DE42NGSUKBR129203_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE42NGSUKBR129203


description:
Library name: Sample 18
B8026, resistant to G12Ci/EGFRi, clone 4
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone4


title: C1498_45deg_5h_183

description: Library name: Cell_ID_247


description:
Library name: Sample 17
B8026, resistant to G12Ci/EGFRi, clone 3
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone3


title: R2_K562_3502_p13_10min_JH0006


title: C1498_45deg_5h_182

description: Library name: Cell_ID_246


description:
Library name: Sample 16
B8026, resistant to G12Ci/EGFRi, clone 2
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone2


title: DE73NGSUKBR129227_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE73NGSUKBR129227


title: R2_K562_4064_t4_c1_5min_JH0008


description:
Library name: Sample 15
B8026, resistant to G12Ci/EGFRi, clone 1
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_egfri_clone1


title: C1498_45deg_5h_181

description: Library name: Cell_ID_245


title: R2_K562_3323_p6_20min_JH0007

description:
1 K562 cells that interacted for 20min
processed data file: Counts_NK92.csv


title: DE20NGSUKBR129211_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE20NGSUKBR129211


title: F3008, resistant to G12Ci, clone 3

description:
Library name: Sample 14
F3008, resistant to G12Ci, clone 3
Column name in F3008_rawcounts.csv and VST_F3008R.csv: g12ci_clone3

value: G12Ci monotherapy


title: C1498_45deg_5h_180

description: Library name: Cell_ID_244


title: DE64NGSUKBR129195_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE64NGSUKBR129195


title: C1498_45deg_5h_179

description: Library name: Cell_ID_243


title: R2_K562_3306_p6_5min_JH0002

description:
1 K562 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: R2_K562_3131_p18_10min_JH0002

description:
1 K562 cells that interacted for 10min
processed data file: Counts_NK92.csv


title: DE44NGSUKBR129264_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE44NGSUKBR129264


title: F3008, resistant to G12Ci, clone 1

description:
Library name: Sample 12
F3008, resistant to G12Ci, clone 1
Column name in F3008_rawcounts.csv and VST_F3008R.csv: g12ci_clone1


title: R2_K562_3512_p10_5min_JH0002


title: DE13NGSUKBR129240_Control, no depressive symptomes [postpartum sample]

description: Library name: DE13NGSUKBR129240


title: R2_K562_284_t2_c1_5min_JH0008


title: DE95NGSUKBR129219_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE95NGSUKBR129219


title: C1047, resistant to G12Ci, clone 6

description:
Library name: Sample 11
C1047, resistant to G12Ci, clone 6
Column name in C1047_rawcounts.csv and VST_C1047R.csv: g12ci_clone6


title: C1498_45deg_5h_178

description: Library name: Cell_ID_242


title: C1498_45deg_5h_177

description: Library name: Cell_ID_241


title: C1047, resistant to G12Ci, clone 5

description:
Library name: Sample 10
C1047, resistant to G12Ci, clone 5
Column name in C1047_rawcounts.csv and VST_C1047R.csv: g12ci_clone5


title: DE21NGSUKBR129193_Depressive symptomes only postpartum [postpartumy sample]

description: Library name: DE21NGSUKBR129193


title: R2_K562_2584_p12_10min_JH0007


title: C1498_45deg_5h_176

description: Library name: Cell_ID_240


title: R2_K562_2576_p15_2min_JH0007

description:
1 K562 cells that interacted for 2min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_175

description: Library name: Cell_ID_239


title: DE66NGSUKBR129256_Control, no depressive symptomes [postpartum sample]

description: Library name: DE66NGSUKBR129256


title: DE43NGSUKBR129185_Depressive symptomes during pregnancy and postpartum [postpartum sample]

description: Library name: DE43NGSUKBR129185


title: R2_K562_2565_p1_5min_JH0007


title: F3008, resistant to G12Ci, clone 2

description:
Library name: Sample 13
F3008, resistant to G12Ci, clone 2
Column name in F3008_rawcounts.csv and VST_F3008R.csv: g12ci_clone2


title: C1498_45deg_5h_174

description: Library name: Cell_ID_238


title: C1047, resistant to G12Ci, clone 2

description:
Library name: Sample 7
C1047, resistant to G12Ci, clone 2
Column name in C1047_rawcounts.csv and VST_C1047R.csv: g12ci_clone2


title: R2_K562_3211_p3_5min_JH0007


title: C1498_45deg_5h_173

description: Library name: Cell_ID_237


title: DE88NGSUKBR129248_Control, no depressive symptomes [postpartum sample]

description: Library name: DE88NGSUKBR129248


title: DE70NGSUKBR129184_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE70NGSUKBR129184

value: pregnancy sample


title: R2_K562_2329_p6_5min_JH0008


title: C1047, resistant to G12Ci, clone 1

description:
Library name: Sample 6
C1047, resistant to G12Ci, clone 1
Column name in C1047_rawcounts.csv and VST_C1047R.csv: g12ci_clone1


title: R2_K562_2046_p5_10min_JH0007


title: DE93NGSUKBR129255_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE93NGSUKBR129255


title: C1498_45deg_5h_172

description: Library name: Cell_ID_236


title: C1498_45deg_5h_171

description: Library name: Cell_ID_235


title: R2_K562_2103_p4_5min_JH0007


title: B8026, resistant to G12Ci, clone 5

description:
Library name: Sample 5
B8026, resistant to G12Ci, clone 5
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_clone5


title: B8026, resistant to G12Ci, clone 3

description:
Library name: Sample 3
B8026, resistant to G12Ci, clone 3
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_clone3


title: R2_K562_1754_p9_10min_JH0007


title: C1047, resistant to G12Ci, clone 4

description:
Library name: Sample 9
C1047, resistant to G12Ci, clone 4
Column name in C1047_rawcounts.csv and VST_C1047R.csv: g12ci_clone4


title: DE49NGSUKBR129271_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE49NGSUKBR129271


title: DE04NGSUKBR129208_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE04NGSUKBR129208


title: C1498_45deg_5h_169

description: Library name: Cell_ID_233


title: C1498_45deg_5h_170

description: Library name: Cell_ID_234


title: C1047, resistant to G12Ci, clone 3

description:
Library name: Sample 8
C1047, resistant to G12Ci, clone 3
Column name in C1047_rawcounts.csv and VST_C1047R.csv: g12ci_clone3


title: DE40NGSUKBR129239_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE40NGSUKBR129239


title: B8026, resistant to G12Ci, clone 2

description:
Library name: Sample 2
B8026, resistant to G12Ci, clone 2
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_clone2


title: R2_K562_1573_p7_5min_JH0008


title: B8026, resistant to G12Ci, clone 4

description:
Library name: Sample 4
B8026, resistant to G12Ci, clone 4
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_clone4


title: C1498_45deg_5h_168

description: Library name: Cell_ID_232


title: DE48NGSUKBR129192_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE48NGSUKBR129192


title: R2_K562_2036_p8_10min_JH0007


title: B8026, resistant to G12Ci, clone 1

description:
Library name: Sample 1
B8026, resistant to G12Ci, clone 1
Column name in B8026_rawcounts.csv and VST_B8026R.csv: g12ci_clone1


title: DE18NGSUKBR129247_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE18NGSUKBR129247


title: R2_K562_1298_p10_10min_JH0007


title: C1498_45deg_5h_166

description: Library name: Cell_ID_230


title: R2_K562_1254_t1_c1_5min_JH0008


title: C1498_45deg_5h_167

description: Library name: Cell_ID_231


title: DE26NGSUKBR129297_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE26NGSUKBR129297


title: C1498_45deg_5h_165

description: Library name: Cell_ID_229


title: R2_K562_1182_p13_5min_JH0005


title: IgG pulldown, Replicate 3, Saline-treated

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: SAL-IGG-3

library_source: genomic

data_processing:
FASTQ files were processed with the NGS-Data-Charmer pipeline (https://github.com/shenlab-sinai/NGS-Data-Charmer). In brief, adapter trimming was performed, forllowed by alignment to the mm10 genome build using HISAT2, and duplicate alignments were removed using the Picard ‘MarkDuplicates’ module.
Bigwig files were generated after duplicate removal using Deeptools "bamCoverage", with the parameters "--binSize 10 --normalizeUsing RPKM".
Assembly: mm10
Supplementary files format and content: Narrowpeak files were annotated with ChIPSeekeR. Each annotated file contains peak locations and the associated genomic annotations of the peaks.
Library strategy: CUT&Run

molecule: genomic DNA

source_name: brain

extract_protocol:
DNA was extracted via phenol-cholorform precipitation
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) based on manufacturer instructions.

value: brain

value: astrocyte


title: IgG pulldown, Replicate 4, Saline-treated

description: Library name: SAL-IGG-4


title: R2_K562_1155_t9_c1_5min_JH0008


title: C1498_45deg_5h_164

description: Library name: Cell_ID_228


title: IgG pulldown, Replicate 2, Saline-treated

description: Library name: SAL-IGG-2


title: DE35NGSUKBR129329_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE35NGSUKBR129329


title: C1498_45deg_5h_163

description: Library name: Cell_ID_227


title: DE13NGSUKBR129337_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE13NGSUKBR129337


title: primNKWG_CD56hi_4

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

source_name: primary NK cells

value: primary NK cells

value: WG


title: CREB pulldown, Replicate 4, Saline-treated

description: Library name: SAL-CREB-4


title: C1498_45deg_5h_162

description: Library name: Cell_ID_226


title: DE66NGSUKBR129353_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE66NGSUKBR129353


title: CREB pulldown, Replicate 3, Saline-treated

description: Library name: SAL-CREB-3


title: primNKWG_CD56hi_2


title: C1498_45deg_5h_161

description: Library name: Cell_ID_225


title: primNKWG_CD56hi_3


title: C1498_45deg_5h_160

description: Library name: Cell_ID_224


title: primNKWG_CD56hi_1


title: CREB pulldown, Replicate 2, Saline-treated

description: Library name: SAL-CREB-2


title: DE88NGSUKBR129345_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE88NGSUKBR129345


title: DE04NGSUKBR129305_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE04NGSUKBR129305


title: primNKWG_CD56dim_4


title: C1498_45deg_5h_159

description: Library name: Cell_ID_223


title: DE79NGSUKBR129313_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE79NGSUKBR129313


title: DE70NGSUKBR129281_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE70NGSUKBR129281


title: IgG pulldown, Replicate 4, Cocaine-treated

description: Library name: COC-IGG-4


title: C1498_45deg_5h_158

description: Library name: Cell_ID_222


title: DE48NGSUKBR129289_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE48NGSUKBR129289


title: IgG pulldown, Replicate 3, Cocaine-treated

description: Library name: COC-IGG-3


title: IgG pulldown, Replicate 1, Saline-treated

description: Library name: SAL-IGG-1


title: primNKWG_CD56dim_3


title: C1498_45deg_5h_157

description: Library name: Cell_ID_221


title: IgG pulldown, Replicate 2, Cocaine-treated

description: Library name: COC-IGG-2


title: DE31NGSUKBR129207_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE31NGSUKBR129207


title: primNKWG_CD56dim_1


title: DE53NGSUKBR129199_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE53NGSUKBR129199


title: primNKWG_6944_single_0min_JH0018

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


title: IgG pulldown, Replicate 1, Cocaine-treated

description: Library name: COC-IGG-1


title: C1498_45deg_5h_155

description: Library name: Cell_ID_219


title: CREB pulldown, Replicate 4, Cocaine-treated

description: Library name: COC-CREB-4


title: DE98NGSUKBR129262_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE98NGSUKBR129262


title: DE23NGSUKBR129254_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE23NGSUKBR129254


title: CREB pulldown, Replicate 3, Cocaine-treated

description: Library name: COC-CREB-3


title: primNKWG_5793_p5_15min_JH0017

description:
1 primary NK cells that interacted for 15min
processed data file: Counts_PrimNK.csv


title: primNKWG_32705_p4_8min_JH0017

description:
1 primary NK cells that interacted for 8min
processed data file: Counts_PrimNK.csv


title: CREB pulldown, Replicate 1, Saline-treated

description: Library name: SAL-CREB-1


title: DE76NGSUKBR129270_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE76NGSUKBR129270


title: CREB pulldown, Replicate 1, Cocaine-treated

description: Library name: COC-CREB-1


title: CREB pulldown, Replicate 2, Cocaine-treated

description: Library name: COC-CREB-2


title: primNKWG_10617_single_0min_JH0017


title: C1498_45deg_5h_151

description: Library name: Cell_ID_215


title: primNKWG_19546_p3_6min_JH0017

description:
1 primary NK cells that interacted for 6min
processed data file: Counts_PrimNK.csv


title: primNKWG_CD56dim_2


title: DE45NGSUKBR129246_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE45NGSUKBR129246


title: C1498_45deg_5h_156

description: Library name: Cell_ID_220


title: primNKSG_CD56hi_4

value: SG


title: C1498_45deg_5h_150

description: Library name: Cell_ID_214


title: Cyfip2, 7week, Hippocampus, WT_replicate 4

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro

country: South Korea

institute: Korea University

description: Library name: 7w-HP-WT4

data_processing:
Transcript abundance was estimated with Salmon(v0.11.2) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Hippocampus

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

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

value: Hippocampus

tag: strain

value: Wildtype

tag: age

value: 7 week


title: C1498_45deg_5h_149

description: Library name: Cell_ID_213


title: primNKSG_CD56hi_3

tag: cell type


title: primNKSG_CD56hi_2

tag: number of cells


title: C1498_45deg_5h_154

description: Library name: Cell_ID_218


title: DE14NGSUKBR129222_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE14NGSUKBR129222

value: No

value: blood

value: Control


title: DE58NGSUKBR129206_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE58NGSUKBR129206


title: C1498_45deg_5h_147

description: Library name: Cell_ID_211


title: C1498_45deg_5h_148

description: Library name: Cell_ID_212


title: primNKSG_CD56hi_1

tag: interaction duration


title: C1498_45deg_5h_153

description: Library name: Cell_ID_217


title: Cyfip2, 7week, Hippocampus, KI, replicate 4

description: Library name: 7w-HP-KI4

value: Knock-in


title: DE05NGSUKBR129190_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE05NGSUKBR129190


title: Cyfip2, 7week, Hippocampus, WT_replicate 1

description: Library name: 7w-HP-WT1


title: primNKSG_CD56dim_4

tag: experiment id


title: DE27NGSUKBR129182_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE27NGSUKBR129182


title: DE67NGSUKBR129238_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE67NGSUKBR129238

value: Depressive symptomes only postpartum


title: C1498_45deg_5h_146

description: Library name: Cell_ID_210


title: C1498_45deg_5h_152

description: Library name: Cell_ID_216


title: Cyfip2, 7week, Hippocampus, KI, replicate 3

description: Library name: 7w-HP-KI3

tag: genotype


title: Cyfip2, 7week, Hippocampus, WT_replicate 3

description: Library name: 7w-HP-WT3


title: Cyfip2, 7week, Hippocampus, KI, replicate 2

description: Library name: 7w-HP-KI2


title: DE06NGSUKBR129269_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE06NGSUKBR129269


title: DE89NGSUKBR129230_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE89NGSUKBR129230


title: primNKSG_CD56dim_2

tag: phenotype


title: C1498_45deg_5h_144

description: Library name: Cell_ID_208

tag: treatment


title: DE84NGSUKBR129223_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE84NGSUKBR129223

tag: tissue


title: Cyfip2, 7week, Hippocampus, WT_replicate 2

description: Library name: 7w-HP-WT2


title: primNKSG_CD56dim_1


title: Cyfip2, 7week, Hippocampus, KI, replicate 1

description: Library name: 7w-HP-KI1


title: C1498_45deg_5h_143

description: Library name: Cell_ID_207


title: Cyfip2, 7week, Cortex, WT, replicate 4

description: Library name: 7w-CTX-WT4

source_name: Cortex

value: Cortex


title: DE28NGSUKBR129261_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE28NGSUKBR129261


title: primNKSG_8602_p4_5min_JH0021

description:
1 primary NK cells that interacted for 5min
processed data file: Counts_PrimNK.csv


title: Cyfip2, 7week, Cortex, WT, replicate 3

description: Library name: 7w-CTX-WT3


title: C1498_45deg_5h_141

description: Library name: Cell_ID_205


title: DE72NGSUKBR129245_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE72NGSUKBR129245


title: DE62NGSUKBR129231_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE62NGSUKBR129231


title: primNKSG_8587_single_0min_JH0021


title: Cyfip2, 7week, Cortex, WT, replicate 2

description: Library name: 7w-CTX-WT2


title: primNKSG_8535_p3_20min_JH0021

description:
1 primary NK cells that interacted for 20min
processed data file: Counts_PrimNK.csv


title: C1498_45deg_5h_145

description: Library name: Cell_ID_209


title: Cyfip2, 7week, Cortex, WT, replicate 1

description: Library name: 7w-CTX-WT1


title: primNKSG_814_p2_10_5min_JH0020

description:
1 primary NK cells that interacted for 10.5minn
processed data file: Counts_PrimNK.csv


title: C1498_45deg_5h_139

description: Library name: Cell_ID_203


title: C1498_45deg_5h_140

description: Library name: Cell_ID_204


title: DE50NGSUKBR129253_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE50NGSUKBR129253


title: Cyfip2, 7week, Cortex, KI, replicate 4

description: Library name: 7w-CTX-KI4


title: DE19NGSUKBR129229_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE19NGSUKBR129229


title: Cyfip2, 7week, Cortex, KI, replicate 3

description: Library name: 7w-CTX-KI3


title: C1498_45deg_5h_142

description: Library name: Cell_ID_206


title: C1498_45deg_5h_138

description: Library name: Cell_ID_202


title: primNKSG_7769_p1_18min_JH0021

description:
1 primary NK cells that interacted for 18min
processed data file: Counts_PrimNK.csv


title: DE10NGSUKBR129197_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE10NGSUKBR129197


title: C1498_45deg_5h_137

description: Library name: Cell_ID_201


title: primNKSG_4265_p5_2_5min_JH0021

description:
1 primary NK cells that interacted for 2.5min
processed data file: Counts_PrimNK.csv


title: C1498_45deg_5h_136

description: Library name: Cell_ID_200


title: primNKSG_2458_p8_13_5min_JH0020

description:
1 primary NK cells that interacted for 13.5min
processed data file: Counts_PrimNK.csv


title: Cyfip2, 7week, Cortex, KI, replicate 2

description: Library name: 7w-CTX-KI2


title: C1498_45deg_5h_134

description: Library name: Cell_ID_198


title: DE32NGSUKBR129189_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE32NGSUKBR129189


title: primNKSG_2949_p5_2min_JH0020

description:
1 primary NK cells that interacted for 2min
processed data file: Counts_PrimNK.csv


title: DE41NGSUKBR129221_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE41NGSUKBR129221


title: primNKSG_2402_p7_15_5min_JH0020

description:
1 primary NK cells that interacted for 15.5min
processed data file: Counts_PrimNK.csv


title: Cyfip2, 7week, Cortex, KI, replicate 1

description: Library name: 7w-CTX-KI1


title: primNKSG_1384_single_0min_JH0021


title: C1498_45deg_5h_135

description: Library name: Cell_ID_199


title: Cyfip2, 28week, Hippocampus, WT_replicate 4

description: Library name: 28w-HP-WT4

value: 28 week


title: DE85NGSUKBR129205_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE85NGSUKBR129205


title: primNKSG_2446_p10_5min_JH0020


title: C1498_45deg_5h_133

description: Library name: Cell_ID_197


title: Cyfip2, 28week, Hippocampus, WT_replicate 3

description: Library name: 28w-HP-WT3


title: C1498_45deg_5h_131

description: Library name: Cell_ID_195


title: DE94NGSUKBR129237_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE94NGSUKBR129237


title: Cyfip2, 28week, Hippocampus, WT_replicate 1

description: Library name: 28w-HP-WT1


title: Cyfip2, 28week, Hippocampus, WT_replicate 2

description: Library name: 28w-HP-WT2


title: Cyfip2, 28week, Hippocampus, KI, replicate 4

description: Library name: 28w-HP-KI4


title: primNKSG_1138_p3_11_5min_JH0020

description:
1 primary NK cells that interacted for 11.5min
processed data file: Counts_PrimNK.csv


title: C1498_45deg_5h_132

description: Library name: Cell_ID_196


title: C1498_45deg_5h_130

description: Library name: Cell_ID_194


title: C1498_45deg_5h_129

description: Library name: Cell_ID_193


title: Cyfip2, 28week, Hippocampus, KI, replicate 3

description: Library name: 28w-HP-KI3


title: DE28NGSUKBR129164_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE28NGSUKBR129164


title: DE06NGSUKBR129172_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE06NGSUKBR129172


title: Cyfip2, 28week, Hippocampus, KI, replicate 2

description: Library name: 28w-HP-KI2


title: primNKSG_1106_p9_2min_JH0020


title: DE63NGSUKBR129213_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE63NGSUKBR129213


title: DE72NGSUKBR129148_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE72NGSUKBR129148


title: primNKSG_CD56dim_3


title: primNKSG_1026_p6_4min_JH0020

description:
1 primary NK cells that interacted for 4min
processed data file: Counts_PrimNK.csv


title: NK92_WT_9825_t6_5min_2h_5min_JH00014_S65134

description:
1 NK92 cells that interacted for 5min2h5min
processed data file: Counts_NK92.csv

value: NK92 cells

value: WT


title: C1498_45deg_5h_127

description: Library name: Cell_ID_191


title: DE54NGSUKBR129181_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE54NGSUKBR129181

value: pregnancy sample


title: C1498_45deg_5h_128

description: Library name: Cell_ID_192


title: primNKSG_1016_p8_5min_JH0021


title: Cyfip2, 28week, Cortex, WT, replicate 4

description: Library name: 28w-CTX-WT4


title: C1498_45deg_5h_126

description: Library name: Cell_ID_190


title: DE47NGSUKBR129404_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE47NGSUKBR129404


title: DE40NGSUKBR129142_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE40NGSUKBR129142


title: DE84NGSUKBR129126_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE84NGSUKBR129126


title: DE50NGSUKBR129156_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE50NGSUKBR129156


title: Cyfip2, 28week, Cortex, WT, replicate 3

description: Library name: 28w-CTX-WT3


title: C1498_45deg_5h_124

description: Library name: Cell_ID_188


title: NK92_WT_9818_t3_5min_2h_5min_JH00014_S65146


title: NK92_WT_845_p11_12min_JH00010_S65239

description:
1 NK92 cells that interacted for 12min
processed data file: Counts_NK92.csv


title: Cyfip2, 28week, Cortex, WT, replicate 2

description: Library name: 28w-CTX-WT2


title: C1498_45deg_5h_125

description: Library name: Cell_ID_189


title: primNKSG_1317_p4_12_5min_JH0020

description:
1 primary NK cells that interacted for 12.5min
processed data file: Counts_PrimNK.csv


title: DE31NGSUKBR129110_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE31NGSUKBR129110


title: DE62NGSUKBR129134_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE62NGSUKBR129134


title: NK92_WT_8281_t1_5min_2h_5min_JH00014_S65148


title: Cyfip2, 28week, Hippocampus, KI, replicate 1

description: Library name: 28w-HP-KI1


title: C1498_45deg_5h_123

description: Library name: Cell_ID_187


title: Cyfip2, 28week, Cortex, WT, replicate 1

description: Library name: 28w-CTX-WT1


title: Cyfip2, 28week, Cortex, KI, replicate 3

description: Library name: 28w-CTX-KI3


title: NK92_WT_7302_p1_tc1_ctrl_5min_JH00014_S65133

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


title: DE53NGSUKBR129102_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE53NGSUKBR129102


title: NK92_WT_7782_t2_5min_2h_5min_JH00014_S65145


title: C1498_45deg_5h_122

description: Library name: Cell_ID_186


title: Cyfip2, 28week, Cortex, KI, replicate 2

description: Library name: 28w-CTX-KI2


title: C1498_45deg_5h_121

description: Library name: Cell_ID_185


title: DE09NGSUKBR129118_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE09NGSUKBR129118


title: Cyfip2, 28week, Cortex, KI, replicate 1

description: Library name: 28w-CTX-KI1


title: DE97NGSUKBR129086_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE97NGSUKBR129086


title: NK92_WT_7295_p2_tc1_ctrl_5min_JH00014_S65140


title: DE75NGSUKBR129094_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE75NGSUKBR129094


title: C1498_45deg_5h_120

description: Library name: Cell_ID_184


title: NK92_WT_649_p2_3min_JH00010_S65230

description:
1 NK92 cells that interacted for 3min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_119

description: Library name: Cell_ID_183


title: C1498_45deg_5h_117

description: Library name: Cell_ID_181


title: Cyfip2, 1week, Hippocampus, WT_replicate 3

description: Library name: 1w-HP-WT3

value: 1 week


title: Cyfip2, 28week, Cortex, KI, replicate 4

description: Library name: 28w-CTX-KI4


title: DE47NGSUKBR129113_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE47NGSUKBR129113


title: NK92_WT_695_p1_7min_JH00010_S65231

description:
1 NK92 cells that interacted for 7min
processed data file: Counts_NK92.csv


title: DE87NGSUKBR129169_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE87NGSUKBR129169


title: Cyfip2, 1week, Hippocampus, WT_replicate 2

description: Library name: 1w-HP-WT2


title: NK92_WT_4703_p3_tc1_ctrl_5min_JH00014_S65139


title: Cyfip2, 1week, Hippocampus, WT_replicate 4

description: Library name: 1w-HP-WT4


title: NK92_WT_468_p3_4min_JH00010_S65229

description:
1 NK92 cells that interacted for 4min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_116

description: Library name: Cell_ID_180


title: DE12NGSUKBR129161_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE12NGSUKBR129161


title: NK92_WT_422_p5_tc2_ctrl_5min_JH00014_S65137


title: C1498_45deg_5h_115

description: Library name: Cell_ID_179


title: NK92_WT_400_p4_2min_JH00010_S65236

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


title: C1498_45deg_5h_114

description: Library name: Cell_ID_178


title: DE03NGSUKBR129129_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE03NGSUKBR129129


title: Cyfip2, 1week, Hippocampus, WT_replicate 1

description: Library name: 1w-HP-WT1


title: DE34NGSUKBR129153_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE34NGSUKBR129153


title: Cyfip2, 1week, Hippocampus, KI, replicate 3

description: Library name: 1w-HP-KI3


title: C1498_45deg_5h_118

description: Library name: Cell_ID_182


title: NK92_WT_3990_p29_12min_JH00010_S65241


title: Cyfip2, 1week, Hippocampus, KI, replicate 2

description: Library name: 1w-HP-KI2


title: C1498_45deg_5h_112

description: Library name: Cell_ID_176


title: NK92_WT_3900_p4_tc2_ctrl_5min_JH00014_S65138


title: C1498_45deg_5h_113

description: Library name: Cell_ID_177


title: DE61NGSUKBR129152_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE61NGSUKBR129152


title: DE65NGSUKBR129177_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE65NGSUKBR129177


title: Cyfip2, 1week, Hippocampus, KI, replicate 1

description: Library name: 1w-HP-KI1


title: Cyfip2, 1week, Cortex, WT, replicate 4

description: Library name: 1w-CTX-WT4


title: NK92_WT_2422_p24_20min_JH00010_S65243

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


title: DE78NGSUKBR129137_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE78NGSUKBR129137


title: C1498_45deg_5h_110

description: Library name: Cell_ID_174


title: NK92_WT_245_p6_5min_JH00010_S65234


title: DE56NGSUKBR129145_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE56NGSUKBR129145


title: C1498_45deg_5h_111

description: Library name: Cell_ID_175


title: DE83NGSUKBR129144_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE83NGSUKBR129144


title: NK92_WT_1526_p6_10min_MF224

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


title: Cyfip2, 1week, Hippocampus, KI, replicate 4

description: Library name: 1w-HP-KI4


title: Cyfip2, 1week, Cortex, WT, replicate 3

description: Library name: 1w-CTX-WT3


title: Cyfip2, 1week, Cortex, WT, replicate 1

description: Library name: 1w-CTX-WT1


title: DE58NGSUKBR129109_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE58NGSUKBR129109


title: NK92_WT_1173_p8_11min_JH00010_S65233

description:
1 NK92 cells that interacted for 11min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_107

description: Library name: Cell_ID_171


title: NK92_WT_1998_p14_15min_JH00010_S65237

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


title: C1498_45deg_5h_109

description: Library name: Cell_ID_173


title: Cyfip2, 1week, Cortex, WT, replicate 2

description: Library name: 1w-CTX-WT2


title: DE92NGSUKBR129176_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE92NGSUKBR129176


title: NK92_WT_10299_t5_5min_2h_5min_JH00014_S65135


title: C1498_45deg_5h_106

description: Library name: Cell_ID_170


title: C1498_45deg_5h_105

description: Library name: Cell_ID_169


title: DE17NGSUKBR129168_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE17NGSUKBR129168


title: Cyfip2, 1week, Cortex, KI, replicate 3

description: Library name: 1w-CTX-KI3


title: Cyfip2, 1week, Cortex, KI, replicate 2

description: Library name: 1w-CTX-KI2


title: NK92_RAB27A_KO_797_p8_4min_JH00011_S65205


title: C1498_45deg_5h_104

description: Library name: Cell_ID_168


title: DE39NGSUKBR129160_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE39NGSUKBR129160


title: NK92_RAB27A_KO_747_p11_5min_JH00011_S65201


title: C1498_45deg_5h_102

description: Library name: Cell_ID_166


title: DE08NGSUKBR129136_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE08NGSUKBR129136


title: Cyfip2, 14week, Hippocampus, WT_replicate 4

description: Library name: 14w-HP-WT4

value: 14 week


title: C1498_45deg_5h_108

description: Library name: Cell_ID_172


title: DE91NGSUKBR129097_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE91NGSUKBR129097


title: C1498_45deg_5h_103

description: Library name: Cell_ID_167


title: DE27NGSUKBR129085_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE27NGSUKBR129085


title: Cyfip2, 1week, Cortex, KI, replicate 1

description: Library name: 1w-CTX-KI1


title: Cyfip2, 14week, Hippocampus, WT_replicate 3

description: Library name: 14w-HP-WT3


title: C1498_45deg_5h_101

description: Library name: Cell_ID_165


title: Cyfip2, 14week, Hippocampus, WT_replicate 2

description: Library name: 14w-HP-WT2


title: NK92_RAB27A_KO_4533_p21_15min_JH00013_S65160


title: Cyfip2, 1week, Cortex, KI, replicate 4

description: Library name: 1w-CTX-KI4


title: C1498_45deg_5h_100

description: Library name: Cell_ID_164


title: Cyfip2, 14week, Hippocampus, WT_replicate 1

description: Library name: 14w-HP-WT1


title: NK92_RAB27A_KO_935_p7_5min_JH00011_S65203


title: C1498_45deg_5h_99

description: Library name: Cell_ID_163


title: NK92_RAB27A_KO_425_p2_3min_JH00011_S65207


title: DE80NGSUKBR129101_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE80NGSUKBR129101


title: Cyfip2, 14week, Hippocampus, KI, replicate 4

description: Library name: 14w-HP-KI4


title: DE98NGSUKBR129165_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE98NGSUKBR129165


title: NK92_RAB27A_KO_4734_p19_14min_JH00013_S65165


title: C1498_45deg_5h_98

description: Library name: Cell_ID_162


title: DE16NGSUKBR129089_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE16NGSUKBR129089


title: NK92_RAB27A_KO_3516_p20_8min_MF247_S61500

description:
1 NK92 cells that interacted for 8min
processed data file: Counts_NK92.csv


title: Cyfip2, 14week, Hippocampus, KI, replicate 3

description: Library name: 14w-HP-KI3


title: NK92_RAB27A_KO_433_p1_2min_JH00011_S65211


title: C1498_45deg_5h_97

description: Library name: Cell_ID_161


title: NK92_RAB27A_KO_3456_p33_20min_JH00011_S65194


title: C1498_45deg_5h_96

description: Library name: Cell_ID_160


title: Cyfip2, 14week, Hippocampus, KI, replicate 2

description: Library name: 14w-HP-KI2


title: NK92_RAB27A_KO_3438_p10_10min_MF239_S61501


title: DE67NGSUKBR129141_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE67NGSUKBR129141


title: DE14NGSUKBR129125_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE14NGSUKBR129125


title: Cyfip2, 14week, Hippocampus, KI, replicate 1

description: Library name: 14w-HP-KI1


title: C1498_45deg_5h_94

description: Library name: Cell_ID_158


title: C1498_45deg_5h_95

description: Library name: Cell_ID_159


title: NK92_RAB27A_KO_3177_p25_30min_JH00013_S65159

description:
1 NK92 cells that interacted for 30min
processed data file: Counts_NK92.csv


title: NK92_RAB27A_KO_3189_p27_30min_JH00011_S65196


title: DE23NGSUKBR129157_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE23NGSUKBR129157


title: Cyfip2, 14week, Cortex, WT, replicate 2

description: Library name: 14w-CTX-WT2


title: DE76NGSUKBR129173_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE76NGSUKBR129173


title: Cyfip2, 14week, Cortex, WT, replicate 3

description: Library name: 14w-CTX-WT3


title: NK92_RAB27A_KO_4035_p7_4min_MF239_S61478


title: NK92_RAB27A_KO_2977_p17_9min_JH00013_S65163

description:
1 NK92 cells that interacted for 9min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_93

description: Library name: Cell_ID_157


title: DE36NGSUKBR129117_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE36NGSUKBR129117


title: Cyfip2, 14week, Cortex, WT, replicate 1

description: Library name: 14w-CTX-WT1


title: DE69NGSUKBR129105_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE69NGSUKBR129105


title: NK92_RAB27A_KO_297_p4_2min_JH00011_S65208


title: DE05NGSUKBR129093_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE05NGSUKBR129093


title: DE45NGSUKBR129149_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE45NGSUKBR129149


title: Cyfip2, 14week, Cortex, KI, replicate 4

description: Library name: 14w-CTX-KI4


title: C1498_45deg_5h_91

description: Library name: Cell_ID_155


title: C1498_45deg_5h_92

description: Library name: Cell_ID_156


title: Cyfip2, 14week, Cortex, WT, replicate 4

description: Library name: 14w-CTX-WT4


title: Cyfip2, 14week, Cortex, KI, replicate 3

description: Library name: 14w-CTX-KI3


title: NK92_RAB27A_KO_2596_p10_6min_MF247_S61493

description:
1 NK92 cells that interacted for 6min
processed data file: Counts_NK92.csv


title: DE89NGSUKBR129133_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE89NGSUKBR129133


title: NK92_RAB27A_KO_2280_p15_9min_JH00013_S65170


title: C1498_45deg_5h_90

description: Library name: Cell_ID_154


title: C1498_45deg_5h_89

description: Library name: Cell_ID_153


title: NK92_RAB27A_KO_2021_p11_5min_JH00013_S65168


title: DE19NGSUKBR129132_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE19NGSUKBR129132


title: Cyfip2, 14week, Cortex, KI, replicate 2

description: Library name: 14w-CTX-KI2


title: C1498_45deg_5h_88

description: Library name: Cell_ID_152


title: Cyfip2, 14week, Cortex, KI, replicate 1

description: Library name: 14w-CTX-KI1


title: Cyfip2, 14week, Hippocampus, WT, replicate4

description: Library name: 14w_HIP_WT4


title: DE90NGSUKBR129115_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE90NGSUKBR129115


title: NK92_RAB27A_KO_1975_p11_9min_MF247_S61494


title: C1498_45deg_5h_87

description: Library name: Cell_ID_151


title: NK92_RAB27A_KO_2003_p10_4min_JH00013_S65167


title: DE70NGSUKBR129087_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE70NGSUKBR129087


title: Cyfip2, 14week, Hippocampus, WT, replicate3

description: Library name: 14w_HIP_WT3


title: C1498_45deg_5h_86

description: Library name: Cell_ID_150


title: NK92_RAB27A_KO_1843_p15_10min_JH00011_S65202


title: DE24NGSUKBR129139_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE24NGSUKBR129139


title: Cyfip2, 14week, Hippocampus, WT, replicate2

description: Library name: 14w_HIP_WT2


title: DE02NGSUKBR129147_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE02NGSUKBR129147

value: Yes


title: C1498_45deg_5h_85

description: Library name: Cell_ID_149


title: NK92_RAB27A_KO_1538_p27_40min_JH00013_S65162

description:
1 NK92 cells that interacted for 40min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_84

description: Library name: Cell_ID_148


title: NK92_RAB27A_KO_1489_p2_2min_JH00013_S65172


title: Cyfip2, 14week, Hippocampus, WT, replicate1

description: Library name: 14w_HIP_WT1


title: Cyfip2, 14week, Hippocampus, HT, replicate4

description: Library name: 14w_HIP_HT4

value: Heterozygous


title: C1498_45deg_5h_83

description: Library name: Cell_ID_147


title: DE18NGSUKBR129150_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE18NGSUKBR129150


title: DE41NGSUKBR129124_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE41NGSUKBR129124


title: NK92_RAB27A_KO_1369_p29_30min_JH00013_S65161


title: DE85NGSUKBR129108_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE85NGSUKBR129108


title: C1498_45deg_5h_82

description: Library name: Cell_ID_146


title: NK92_RAB27A_KO_1231_p16_10min_JH00011_S65199


title: C1498_45deg_5h_81

description: Library name: Cell_ID_145


title: Cyfip2, 14week, Hippocampus, HT, replicate2

description: Library name: 14w_HIP_HT2

value: Hippocampus


title: NK92_RAB27A_KO_1000_p5_2min_JH00013_S65173


title: C1498_45deg_5h_80

description: Library name: Cell_ID_144


title: Cyfip2, 14week, Hippocampus, HT, replicate1

description: Library name: 14w_HIP_HT1


title: Monocyte_14465_single_0min_JH0029

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

source_name: monocyte cells

value: monocyte cells


title: C1498_45deg_5h_79

description: Library name: Cell_ID_143


title: Monocyte_12879_single_0min_JH0029


title: DE63NGSUKBR129116_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE63NGSUKBR129116


title: Cyfip2, 14week, Cortex, WT, replicate4

description: Library name: 14w_CTX_WT4

value: Wildtype


title: DE55NGSUKBR129163_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE55NGSUKBR129163

value: No


title: C1498_45deg_5h_78

description: Library name: Cell_ID_142


title: DE46NGSUKBR129131_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE46NGSUKBR129131

value: blood


title: Cyfip2, 14week, Cortex, WT, replicate3

description: Library name: 14w_CTX_WT3


title: DE68NGSUKBR129123_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE68NGSUKBR129123


title: MF212_NK92_WT_Lamp1_PMA_R3

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

value: PmaIono


title: C1498_45deg_5h_77

description: Library name: Cell_ID_141


title: MF212_NK92_WT_Lamp1_PMA_R2


title: Cyfip2, 14week, Hippocampus, HT, replicate3

description: Library name: 14w_HIP_HT3


title: C1498_45deg_5h_76

description: Library name: Cell_ID_140


title: MF212_NK92_WT_Lamp1_PMA_R1


title: DE07NGSUKBR129154_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE07NGSUKBR129154

value: Control


title: MF212_NK92_WT_Lamp1_5h_R3

description:
500 NK92 cells that interacted for 5h
processed data file: Counts_NK92.csv


title: DE20NGSUKBR129114_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE20NGSUKBR129114


title: Cyfip2, 14week, Cortex, WT, replicate1

description: Library name: 14w_CTX_WT1


title: C1498_45deg_5h_75

description: Library name: Cell_ID_139


title: C1498_45deg_5h_74

description: Library name: Cell_ID_138


title: Cyfip2, 14week, Cortex, HT, replicate4

description: Library name: 14w_CTX_HT4


title: DE77NGSUKBR129155_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE77NGSUKBR129155


title: DE48NGSUKBR129095_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE48NGSUKBR129095

value: Depressive symptomes only postpartum


title: Cyfip2, 14week, Cortex, HT, replicate3

description: Library name: 14w_CTX_HT3

value: Cortex


title: MF212_NK92_WT_Lamp1_5h_R2


title: DE71NGSUKBR129166_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE71NGSUKBR129166


title: Cyfip2, 14week, Cortex, HT, replicate2

description: Library name: 14w_CTX_HT2


title: C1498_45deg_5h_72

description: Library name: Cell_ID_136


title: DE15NGSUKBR129107_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE15NGSUKBR129107


title: Cyfip2, 14week, Cortex, WT, replicate2

description: Library name: 14w_CTX_WT2


title: Cyfip2, 14week, Cortex, HT, replicate1

description: Library name: 14w_CTX_HT1


title: MF212_NK92_WT_Lamp1_4h_R3

description:
500 NK92 cells that interacted for 4h
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_71

description: Library name: Cell_ID_135


title: Cyfip2, 7week, Hippocampus, WT, replicate4

description: Library name: 7w_HIP_WT4

value: 7 week


title: MF212_NK92_WT_Lamp1_4h_R2

value: NK92 cells


title: C1498_45deg_5h_70

description: Library name: Cell_ID_134


title: DE37NGSUKBR129099_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE37NGSUKBR129099


title: MF212_NK92_WT_Lamp1_4h_R1

value: WT


title: C1498_45deg_5h_69

description: Library name: Cell_ID_133


title: DE38NGSUKBR129178_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE38NGSUKBR129178

value: pregnancy sample


title: C1498_45deg_5h_68

description: Library name: Cell_ID_132


title: DE42NGSUKBR129106_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE42NGSUKBR129106


title: C1498_45deg_5h_67

description: Library name: Cell_ID_131


title: DE59NGSUKBR129091_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE59NGSUKBR129091


title: C1498_45deg_5h_73

description: Library name: Cell_ID_137


title: MF212_NK92_WT_Lamp1_5h_R1


title: C1498_45deg_5h_66

description: Library name: Cell_ID_130


title: Cyfip2, 7week, Hippocampus, HT, replicate4

description: Library name: 7w_HIP_HT4


title: Cyfip2, 7week, Hippocampus, HT, replicate3

description: Library name: 7w_HIP_HT3


title: MF212_NK92_WT_Lamp1_2h_R3

description:
500 NK92 cells that interacted for 2h
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_65

description: Library name: Cell_ID_129


title: Cyfip2, 7week, Hippocampus, HT, replicate2

description: Library name: 7w_HIP_HT2


title: DE60NGSUKBR129170_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE60NGSUKBR129170


title: MF212_NK92_WT_Lamp1_2h_R2


title: Cyfip2, 7week, Hippocampus, WT, replicate3

description: Library name: 7w_HIP_WT3


title: Cyfip2, 7week, Hippocampus, HT, replicate1

description: Library name: 7w_HIP_HT1


title: MF212_NK92_WT_Lamp1_3h_R3

description:
500 NK92 cells that interacted for 3h
processed data file: Counts_NK92.csv


title: MF212_NK92_WT_Lamp1_2h_R1


title: C1498_45deg_5h_64

description: Library name: Cell_ID_128


title: Cyfip2, 7week, Hippocampus, WT, replicate1

description: Library name: 7w_HIP_WT1


title: Cyfip2, 7week, Hippocampus, WT, replicate2

description: Library name: 7w_HIP_WT2


title: C1498_45deg_5h_63

description: Library name: Cell_ID_127


title: Cyfip2, 7week, Cortex, WT, replicate4

description: Library name: 7w_CTX_WT4


title: DE95NGSUKBR129122_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE95NGSUKBR129122


title: DE11NGSUKBR129179_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE11NGSUKBR129179


title: C1498_45deg_5h_62

description: Library name: Cell_ID_126


title: MF212_NK92_WT_Lamp1_3h_R1


title: MF212_NK92_WT_Lamp1_1h_R3

description:
500 NK92 cells that interacted for 1h
processed data file: Counts_NK92.csv


title: MF212_NK92_WT_Lamp1_3h_R2


title: DE86NGSUKBR129090_Depressive symptomes during pregnancy and postpartum [pregnancy sample]

description: Library name: DE86NGSUKBR129090


title: DE51NGSUKBR129138_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE51NGSUKBR129138


title: MF212_NK92_WT_Lamp1_1h_R2


title: C1498_45deg_5h_61

description: Library name: Cell_ID_125


title: Cyfip2, 7week, Cortex, WT, replicate3

description: Library name: 7w_CTX_WT3


title: Cyfip2, 7week, Cortex, WT, replicate2

description: Library name: 7w_CTX_WT2


title: DE49NGSUKBR129174_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE49NGSUKBR129174


title: MF212_NK92_WT_Lamp1_1h_R1


title: DE82NGSUKBR129162_Depressive symptomes only during pregnancy [pregnancy sample]

description: Library name: DE82NGSUKBR129162


title: DE73NGSUKBR129130_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE73NGSUKBR129130


title: C1498_45deg_5h_60

description: Library name: Cell_ID_124


title: MF212_NK92_WT_alone_R3


title: C1498_45deg_5h_59

description: Library name: Cell_ID_123


title: Cyfip2, 7week, Cortex, WT, replicate1

description: Library name: 7w_CTX_WT1


title: DE93NGSUKBR129158_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE93NGSUKBR129158


title: Cyfip2, 7week, Cortex, HT, replicate4

description: Library name: 7w_CTX_HT4


title: MF212_NK92_WT_alone_R2


title: C1498_45deg_5h_57

description: Library name: Cell_ID_121


title: C1498_45deg_5h_58

description: Library name: Cell_ID_122


title: MF212_NK92_WT_alone_R1


title: Cyfip2, 7week, Cortex, HT, replicate3

description: Library name: 7w_CTX_HT3


title: DE33NGSUKBR129171_Depressive symptomes only postpartum [pregnancy sample]

description: Library name: DE33NGSUKBR129171


title: Cyfip2, 7week, Cortex, HT, replicate2

description: Library name: 7w_CTX_HT2


title: MF212_NK92_WT_5h_R3


title: C1498_45deg_5h_55

description: Library name: Cell_ID_119


title: LicA_183

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

description: Library name: LicA_183_S60

data_processing:
quality control of the raw sequence data was assessed using FASTQC
Sequence reads were mapped to the reference genome hg38 using STAR.
To evaluate the quality of the RNA-seq data, the number of reads falling into different annotated regions of the reference genes was determined with htseq
To analyze the data, low quality mapped reads were excluded and feature counts were used to quantify the gene level expression. Differential gene expression analysis was performed with edgeR, controlling for patient number as a variable in the analysis.
Assembly: hg38
Supplementary files format and content: differential expression statistics

source_name: breast

growth_protocol: Microstructures were cultured in MammoCult media in the ultra-low adherent plates in incubator (37° C, 5% CO2) for 24 h.

extract_protocol:
The media was removed and the trizol protocol was followed for the RNA extraction. To increase the efficiency, the mixture was passed through an 18 gauge niddle (nuclease-free) mutiple times, before proceeding according to the Direct-Zol RNA Prep kit
Libraries were made using Roche KAPA Biosystems protocol (KAPA RNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17, Roche Corporate)

treatment_protocol: LicA (5 uM) or DMSO were mixed with Mammocult media and added to the cultured microstructures, for another 24 h with incubation in 37

value: breast

value: LicA


title: C1498_45deg_5h_56

description: Library name: Cell_ID_120


title: DE29NGSUKBR129146_Control, no depressive symptomes [pregnancy sample]

description: Library name: DE29NGSUKBR129146


title: LicA_187

description: Library name: LicA_187_S64


title: Cyfip2, 7week, Cortex, HT, replicate1

description: Library name: 7w_CTX_HT1


title: MF212_NK92_WT_4h_R3


title: C1498_45deg_5h_54

description: Library name: Cell_ID_118


title: LicA_182

description: Library name: LicA_182_S56


title: C1498_45deg_5h_53

description: Library name: Cell_ID_117


title: Cyfip2, 1week, Hippocampus, WT, replicate4

description: Library name: 1w_HIP_WT4

value: 1 week


title: MF212_NK92_WT_5h_R1


title: Cyfip2, 1week, Hippocampus, WT, replicate2

description: Library name: 1w_HIP_WT2


title: MF212_NK92_WT_4h_R2


title: LicA_181

description: Library name: LicA_181_S52


title: LicA_178

description: Library name: LicA_178_S48


title: Cyfip2, 1week, Hippocampus, WT, replicate1

description: Library name: 1w_HIP_WT1


title: MF212_NK92_WT_4h_R1


title: C1498_45deg_5h_52

description: Library name: Cell_ID_116


title: MF212_NK92_WT_5h_R2


title: MF212_NK92_WT_3h_R3


title: Cyfip2, 1week, Hippocampus, HT, replicate4

description: Library name: 1w_HIP_HT4

value: Heterozygous


title: Cyfip2, 1week, Hippocampus, HT, replicate3

description: Library name: 1w_HIP_HT3

value: Hippocampus


title: DMSO_187

description: Library name: DMSO_187_S61

value: DMSO


title: C1498_45deg_5h_50

description: Library name: Cell_ID_114


title: C1498_45deg_5h_49

description: Library name: Cell_ID_113


title: DMSO_183

description: Library name: DMSO_183_S57


title: Cyfip2, 1week, Hippocampus, HT, replicate2

description: Library name: 1w_HIP_HT2


title: LicA_173

description: Library name: LicA_173_S44


title: C1498_45deg_5h_51

description: Library name: Cell_ID_115


title: Cyfip2, 1week, Hippocampus, WT, replicate3

description: Library name: 1w_HIP_WT3

value: Wildtype


title: Cyfip2, 1week, Hippocampus, HT, replicate1

description: Library name: 1w_HIP_HT1


title: MF212_NK92_WT_3h_R1


title: DMSO_181

description: Library name: DMSO_181_S49


title: MF212_NK92_WT_30min_R3

description:
500 NK92 cells that interacted for 30min
processed data file: Counts_NK92.csv


title: DMSO_182

description: Library name: DMSO_182_S53


title: C1498_45deg_5h_48

description: Library name: Cell_ID_112


title: C1498_45deg_5h_45

description: Library name: Cell_ID_109


title: C1498_45deg_5h_46

description: Library name: Cell_ID_110


title: C1498_45deg_5h_47

description: Library name: Cell_ID_111


title: Cyfip2, 1week, Cortex, WT, replicate4

description: Library name: 1w_CTX_WT4


title: Cyfip2, 1week, Cortex, WT, replicate2

description: Library name: 1w_CTX_WT2


title: DMSO_178

description: Library name: DMSO_178_S45


title: MF212_NK92_WT_3h_R2


title: Cyfip2, 1week, Cortex, WT, replicate3

description: Library name: 1w_CTX_WT3


title: MF212_NK92_WT_30min_R2


title: MF212_NK92_WT_2h_R3


title: DMSO_173

description: Library name: DMSO_173_S41


title: MF212_NK92_WT_30min_R1


title: Cyfip2, 1week, Cortex, WT, replicate1

description: Library name: 1w_CTX_WT1


title: MF212_NK92_WT_2h_R2


title: C1498_45deg_5h_42

description: Library name: Cell_ID_106


title: MF212_NK92_WT_2h_R1


title: Cyfip2, 1week, Cortex, HT, replicate3

description: Library name: 1w_CTX_HT3


title: HeLa cells, G3BP1-GFP, AS+FA

city: Shanghai

first: Yi

last: Yuan

state: Shanghai

address: Building 13, Room 438, 100 Haike Road, Pudong New Area

department: Interdisciplinary Research Center on Biology and Chemistry

country: China

institute: Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences

description:
Library name: Sample 15
in_FA

data_processing:
All sequencing reads were processed using Trim Galore (1.6.6) with the parameters "-nextseq 30 -paired" to remove adapter sequences, retaining reads longer than 20 bp.
Quality-filtered reads were then mapped to the human genome (GRCh38) using STARv2.7.6a) with default settings.
Uniquely mapped read pairs were counted against gene annotations from Homo sapiens (Ensembl: GRCh38.94) using featureCounts (v2.0.1) with the parameters “-p -B -C" to generate gene-level counts.
Assembly: Ensembl: GRCh38.94
Supplementary files format and content: lcFAX-seq.xlsx for all samples

source_name: HeLa

growth_protocol: HeLa cells were cultured in high-glucose Dulbecco's Modified Eagle's Medium (DMEM, Life Technologies™, C11995500BT), supplemented with 10% fetal bovine serum (FBS, Life Technologies™, 10099141C) and 1% penicillin-streptomycin (Life Technologies™, 15140122), maintained at 37°C in a 5% CO₂ atmosphere.

extract_protocol:
After GFP enrichment, 500 μL TRIzol (Thermo, 15596026) was added to the beads to extract RNA, followed by FA crosslink reversal at 54°C for 2 hours and 70°C for 30 minutes. RNA was subjected to end-repair, reverse transcription, adapter ligation, PCR amplification, and size selection by gel electrophoresis.
Libraries were sequenced on the Illumina platform with a 6G throughput per sample. Fastp was used to trim adapters and filter low-quality reads (Q < 20) to generate the final SG transcriptome dataset.

treatment_protocol: A HeLa cell line stably expressing G3BP1-GFP was treated with 250 μM AS (Innochem, A25410) for 20 minutes, followed by 0.05% FA (Sigma-Aldrich, F8775) for another 20 minutes. The reaction was quenched with 125 mM glycine (Sigma-Aldrich, G7126) for 5 minutes. Cells were then washed with PBS and lysed in NP40 lysis buffer (Beyotime, P0013F) which added recombinant RNase inhibitor (Invitrogen™, 10777-019).  Protein concentration was quantified using a BCA assay (Yeasen, 20201ES90). Lysates were incubated with GFP beads (Bio-LinkedIn, L-1016A) overnight at 4°C with rotation. Beads were washed five times with PBS.

value: HeLa

value: cervical cancer cell

value: AS 20 min, Formaldehyde (FA)+AS 20 min

tag: batch


title: Cyfip2, 1week, Cortex, HT, replicate4

description: Library name: 1w_CTX_HT4


title: C1498_45deg_5h_44

description: Library name: Cell_ID_108


title: MF212_NK92_WT_1h_R3


title: C1498_45deg_5h_43

description: Library name: Cell_ID_107


title: HeLa cells, G3BP1-GFP, AS+FA, rep4

description:
Library name: Sample 12
en_FA4


title: MF212_NK92_WT_1h_R1


title: Cyfip2, 1week, Cortex, HT, replicate2

description: Library name: 1w_CTX_HT2


title: HeLa cells, G3BP1-GFP, AS

description:
Library name: Sample 14
in_AS

value: Arsenite (AS) 40 min


title: HeLa cells, G3BP1-GFP, AS+FA, rep3

description:
Library name: Sample 11
en_FA3


title: C1498_45deg_5h_39

description: Library name: Cell_ID_103


title: C1498_45deg_5h_41

description: Library name: Cell_ID_105


title: C1498_45deg_5h_40

description: Library name: Cell_ID_104


title: C1498_45deg_5h_38

description: Library name: Cell_ID_102


title: HeLa cells, G3BP1-GFP, AS+FA, rep1

description:
Library name: Sample 9
en_FA1


title: Cyfip2, 1week, Cortex, HT, replicate1

description: Library name: 1w_CTX_HT1


title: HeLa cells, G3BP1-GFP, AS+FA, rep2

description:
Library name: Sample 10
en_FA2


title: Cell multiplexed CMOs from 4 males rat at 4 weeks of age 2 (CTRL and 2 OI)

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description:
10X Genomics 3’ CellPlex Reagent Kits v3.1
raw_feature_bc_matrix.tar

library_source: other

data_processing:
Generated libraries were sequenced on an Novaseq6000. UMI deconvolution and CMO demultiplexing for the 4 samples was done using Cell Ranger Multi V5.0.0 (10x Genomics) using reference mRatBN7-1.0.0. The cell ranger multi function was run with the antibody parameter (not Multiplexing Capture) using the CMO feature reference (See feature_reference.csv provided). The matrix file contains thus 2 matrices, one for gene expression and one for antibody (CMO) capture. The sample origin of the cells that remained undetermined after CMO demultiplexing (i.e. negative) was recovered using the VireoSNP package (vireoSNP-0.5.7). The data was further processed with Seurat V5 (see Dumont_Mu_OIM_Seurat_object.rds provided)
Assembly: mRatBN7-1.0.0
Supplementary files format and content: Tab separated value files and matrix files. Seurat object (V5) containing GEX, CMO and Vireo informations.

molecule: other

organism: Rattus norvegicus

source_name: Hindlimb muscles

extract_protocol:
Hindlimb muscles were removed from 4 weeks old CTRL and OI rats and dissociated using the gentleMACS dissociator (Miltenyi Biotech). After the digestion the mononuclear cells were filtered through a 100 μm nylon strainer, washed with FACS buffer (2% FBS in PBS), and the red blood cell were removed (Biolegend, Lysis buffer, 420301). Cells were labelled with Cell Multiplexing Oligos (CMOs 305, 306, 307 and 308), pooled and negative lineage selection was performed by FACS sorting using CD45 (Biolegend, 202205), CD31 (Abcam, ab33858), and CD11B (Biolegend, 201805) FITC conjugated antibodies . Prior to the FACS, cells were washed and passed through 30 µm filters. After the FACS cells were manually count and viability assess through trypan blue coloration to ensure a good viability (75-80%).
Libraries were prepared using the 3’ CellPlex Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. Generated libraries were sequenced on an Novaseq6000. Briefly the cells were resuspended in the master mix and loaded 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 GEM was retrotranscripted to cDNA which contains an illumina primer sequence, unique molecular identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleanup with DynaBeads, amplified by PCR and the appropriate fragments size were seleted with SPRIselect reagant for subsquent library construction. During the library construction adaptor ligation mix and sample index were added.

treatment_protocol: Rat pups (Sprague-Dawnley) were exposed to 80% of oxygen from 3 to 10 days of life to mimics preterm birth-related conditions (OI=oxygen induced-injury). Control (CTRL) pups were maintained in room air.

value: Hindlimb muscles

value: OI and CTRL


title: Cell multiplexed transcripts from 4 males rat at 4 weeks of age 2 (CTRL and 2 OI)


title: MF212_K562_GFP_5h_R2

description:
500 K562 cells that interacted for 5h
processed data file: Counts_NK92.csv

value: K562 cells


title: HeLa cells, G3BP1-GFP, AS, rep4

description:
Library name: Sample 8
en_AS4


title: HeLa cells, G3BP1-GFP, AS, rep3

description:
Library name: Sample 7
en_AS3


title: HeLa cells, GFP, AS

description:
Library name: Sample 13
in_GFP


title: MF212_K562_GFP_5h_R1


title: VitD-1

city: Gyeonggi-do

first: Seong-Hoon

last: Kim

state: Seongnam

address: Pangyo-ro 335

department: Department of Bioconvergence Science

institute: CHA university

data_processing:
The reads were prepared for analysis using the Trimmomatic version 0.38 to remove adapter sequences and trim the low-quality bases.
Subsequently, the processed reads were aligned to the Rattus norvegicus reference genome (rn6) using HISAT version 2.1.0 by incorporating both HISAT and Bowtie2 for alignment. Reference genome sequences and gene annotation data were sourced from the NCBI Genome Assembly and NCBI RefSeq databases.
Following alignment, data formatted in SAM was sorted and indexed using SAMtools version 1.9. Then, the StringTie version 2.1.3b tool was used to assemble and quantify the transcripts. Differential gene expression analysis was performed using edgeR version 3.40.2 with raw count data input.
The exactTest function within edgeR was used to determine the statistical significance of the differentially expressed genes (DEGs) after adjusting the p-values using the Benjamini–Hochberg method to control the false discovery rate. The DEGs were identified based on the criteria: |fold change| ≥ 2 and p < 0.05.
Assembly: rn6 (GCF_000001895.5)
Supplementary files format and content: tab-delimited text files include FPKM, TPM values for each Sample

source_name: multifidus muscle

growth_protocol: The care and use of laboratory animals followed the guidelines of HLB biostep Animal Center (Songdo, Republic of Korea) with approval from the Animal Ethics Committee of the institute (Animal ethical approval No.: IACUC 23-KE-0135).

extract_protocol:
Total RNA was extracted from the multifidus muscles using the easy-spin total RNA extraction kit (iNtRON Biotechnology, Seoul, Republic of Korea).
The Illumina sequencing NovaSeq platform (Illumina, San Diego, CA, USA) was used for generating paired-end sequencing reads.

treatment_protocol: The isolated pMT were injected into the left paraspinal muscles at the L4−L5 and L5−L6 levels using a 29-gauge syringe. Each dose contained 25 µg of pMT in 100 µL of SHE buffer per site (total 50 µg). VitD injections consisted of cholecalciferol at a dose of 150 µg (6,000 IU) for each site (total 300 µg). The combination group received injections containing both 25 µg of pMT and 150 µg of VitD at each site (total 50 µg and 300 µg).

value: multifidus muscle

value: wild type

value: VitD


title: MF212_K562_GFP_4h_R3

description:
500 K562 cells that interacted for 4h
processed data file: Counts_NK92.csv

value: WT


title: C1498_45deg_5h_34

description: Library name: Cell_ID_98


title: C1498_45deg_5h_33

description: Library name: Cell_ID_97


title: C1498_45deg_5h_36

description: Library name: Cell_ID_100


title: VitD-3


title: HeLa cells, G3BP1-GFP, AS, rep1

description:
Library name: Sample 5
en_AS1


title: HeLa cells, GFP, AS, rep4

description:
Library name: Sample 4
en_GFP4


title: VitD-2


title: MF212_K562_GFP_3h_R2

description:
500 K562 cells that interacted for 3h
processed data file: Counts_NK92.csv


title: HeLa cells, GFP, AS, rep3

description:
Library name: Sample 3
en_GFP3


title: C1498_45deg_5h_32

description: Library name: Cell_ID_96


title: MF212_K562_GFP_5h_R3


title: pMT/VitD-2

value: pMT/VitD


title: MF212_K562_GFP_4h_R2


title: pMT/VitD-1


title: C1498_45deg_5h_35

description: Library name: Cell_ID_99


title: pMT-4

value: pMT


title: C1498_45deg_5h_37

description: Library name: Cell_ID_101


title: HeLa cells, GFP, AS, rep1

description:
Library name: Sample 1
en_GFP1


title: HeLa cells, G3BP1-GFP, AS, rep2

description:
Library name: Sample 6
en_AS2


title: MF212_K562_GFP_30min_R2

description:
500 K562 cells that interacted for 30min
processed data file: Counts_NK92.csv


title: pMT/VitD-4


title: C1498_45deg_5h_28

description: Library name: Cell_ID_92


title: MF212_K562_GFP_30min_R1


title: pMT-3


title: MF212_K562_GFP_4h_R1


title: LoVo-HM cell, replicate 2

city: Beijing

first: Shengde

last: Liu

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

description: Library name: LoVo-HM2

data_processing:
CLC Genomics Workbench v 22.0.1
Assembly: Homo_sapiens.GRCh38_release95.genome.fa

source_name: LoVo

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LoVo

value: colorectal cancer cells

value: a high-metastatic subline of LoVo cells

value: no


title: MF212_K562_GFP_2h_R3

description:
500 K562 cells that interacted for 2h
processed data file: Counts_NK92.csv


title: MF212_K562_GFP_3h_R3


title: MF212_K562_GFP_3h_R1


title: MF212_K562_GFP_2h_R2


title: pMT/VitD-3


title: HeLa cells, GFP, AS, rep2

description:
Library name: Sample 2
en_GFP2

value: HeLa


title: C1498_45deg_5h_26

description: Library name: Cell_ID_90


title: wildtype LoVo cell, replicate 3

description: Library name: LoVo-3

value: wildtype


title: MF212_K562_GFP_30min_R3


title: C1498_45deg_5h_30

description: Library name: Cell_ID_94


title: Surgery-1

value: Surgery


title: C1498_45deg_5h_29

description: Library name: Cell_ID_93


title: LoVo-HM cell, replicate 3

description: Library name: LoVo-HM3


title: C1498_45deg_5h_27

description: Library name: Cell_ID_91


title: pMT-2


title: MF212_K562_GFP_1h_R1

description:
500 K562 cells that interacted for 1h
processed data file: Counts_NK92.csv


title: Control-2

value: Control


title: Patient AC-005-107 CLL BTKi responder PD-1-

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

institute: RPM Bioinfo Solutions

description: Library name: AC-005-107

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed reads were aligned to the GRCh38 reference genome (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
RseQC was used to assess strand specificity for all transcripts
HTSeq was used to estimate transcript abundance from unique mapped reads
Raw reads were normalized using DESeq2 v1.26.0
Assembly: GRCh38
Supplementary files format and content: Raw counts
Supplementary files format and content: normalized counts

source_name: Peripheral Blood

extract_protocol:
Previously frozen PBMC samples were thawed and stained with Live/Dead Fixable Near-IR Dead Cell Stain (Invitrogen) followed by antibodies directed against CD3, CD19, CD20, CD5, and PD-1. Cells were sorted into RLT buffer at the Emory University School of Medicine Flow Cytometry core using a BD FACSAria II. RNA isolation, library preparation, and sequencing were performed by the Emory University National Primate Center Nonhuman Primate Genomics Core at Emory University.
SMART-Seq v4 Ultra Low Input RNA Kit with Illumina's Nextera XT DNA Library preparation kit

treatment_protocol: Samples were obtained from patients who were 1) treatment naïve, 2) on BTK inhibitors, or 3) progressing from BTK inhibitors

value: Peripheral Blood

tag: cell

value: CLL cell

value: Tumor cell

tag: condition

value: BTKi responder

tag: disease

value: Chronic Lymphocytic Leukemia

tag: FISH

tag: ighv

value: Unmutated

tag: patient id


title: pMT-1

value: multifidus muscle

value: wild type


title: C1498_45deg_5h_31

description: Library name: Cell_ID_95

tag: cell line


title: C1498_45deg_5h_22

description: Library name: Cell_ID_86


title: MF212_K562_alone_R3

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

value: K562 cells

value: WT


title: Surgery-2


title: Patient AC-002-073 CLL BTKi responder PD-1-

description: Library name: AC-002-073


title: MF212_K562_GFP_1h_R3


title: wildtype LoVo cell, replicate 2

description: Library name: LoVo-2

value: LoVo

value: colorectal cancer cells


title: MF212_K562_GFP_1h_R2


title: C1498_45deg_5h_24

description: Library name: Cell_ID_88


title: C1498_45deg_5h_20

description: Library name: Cell_ID_84


title: C1498_45deg_5h_23

description: Library name: Cell_ID_87


title: LoVo-HM cell, replicate 1

description: Library name: LoVo-HM1

value: a high-metastatic subline of LoVo cells

value: no


title: coro1a-DsRed cells,ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM), 30 hpf, smart-seq, rep2

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: sample5
IK-myb-2
Wt-vs-DM.all.annot.txt

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, ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM), 30 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: ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM)


title: Control-1

value: Control


title: coro1a-DsRed cells,ikzf1Δ4+3/Δ4+3;mybhkz3/hkz3 (DM), 30 hpf,smart-seq, rep3

description:
Library name: sample6
IK-myb-3
Wt-vs-DM.all.annot.txt


title: Patient AC-001-079 CLL BTKi responder PD-1-

description: Library name: AC-001-079

value: Peripheral Blood

value: CLL cell

value: del11q, del17p

value: Mutated


title: C1498_45deg_5h_21

description: Library name: Cell_ID_85


title: coro1a-DsRed cells, WT, 30 hpf,smart-seq, rep3

description:
Library name: sample3
Ctrl-3
Wt-vs-DM.all.annot.txt

source_name: coro1a-DsRed cells, WT, 30 hpf


title: C1498_45deg_5h_18

description: Library name: Cell_ID_82


title: MF212_K562_alone_R2


title: coro1a-DsRed cells, WT, 30 hpf, smart-seq, rep2

description:
Library name: sample2
Ctrl-2
Wt-vs-DM.all.annot.txt


title: Patient AC-002-034 CLL BTKi responder PD-1-

description: Library name: AC-002-034

value: Tumor cell

value: BTKi responder

value: Chronic Lymphocytic Leukemia

value: Unmutated


title: C1498_45deg_5h_25

description: Library name: Cell_ID_89


title: MF212_K562_alone_R1

value: K562 cells

value: WT


title: K562_934_p9_2min_JH0020

description:
1 K562 cells that interacted for 2min
processed data file: Counts_PrimNK.csv

value: GFP


title: coro1a-DsRed cells, WT, 30 hpf, smart-seq, rep1

description:
Library name: sample1
Ctrl-1
Wt-vs-DM.all.annot.txt


title: Patient AC-002-027 CLL BTKi responder PD-1-

description: Library name: AC-002-027


title: wildtype LoVo cell, replicate 1

description: Library name: LoVo-1

value: LoVo

value: colorectal cancer cells

value: wildtype


title: C1498_45deg_5h_17

description: Library name: Cell_ID_81


title: K562_9869_t1_c2_5min_JH00014_S65129

description:
1 K562 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: K562_868_p1_7min_JH00010_S65247

description:
1 K562 cells that interacted for 7min
processed data file: Counts_NK92.csv


title: Patient AC-001-110 CLL Progression PD-1-

description: Library name: AC-001-110_PD1lo

value: Progressor


title: K562_892_p12_15min_JH00010_S65256

description:
1 K562 cells that interacted for 15min
processed data file: Counts_NK92.csv


title: Patient AC-001-038 CLL Progression PD-1-

description: Library name: AC-001-038_PD1lo

value: del13q, del11q, Trisomy.12


title: K562_853_p11_5min_JH00011_S65212