title: Scn2a, WT, Fluoxetine, male, replicate2

description: Library name: Scn_WfM_2


status: Public on Jul 28 2026

type: SRA

city: New Haven

first: Ramanaiah

last: Mamillapalli

state: CT

address: 310 Cedar Street

department: OBGYN

country: USA

institute: Yale University

description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S18-12619_01-01
Differential gene expression in human endometriosis, Sample S18-12619_01-01

library_source: transcriptomic

data_processing:
Low quality reads were trimmed, and adaptor contamination were removed using Trim Galore (v. 0.5.0) with a minimum Phred score cutoff of 20 and automatic adapter detection. Trimmed reads were mapped to the human reference genome GRCh38/hg38) using HISAT2 (v. 2.1.0).(Kim et al., 2019; O'Leary et al., 2024) Gene expression quantification was performed using StringTie (v. 1.3.3b) with GENCODE gene annotations (release v.27), utilizing a minimum transcript coverage of 1 TPM. Differential gene expression analysis was conducted using DESeq2 (v. 1.22.1) in R (v.1.66) with Benjamini-Hochberg correction for multiple hypothesis testing (Love et al., 2014). Genes found to be differentially expressed with adjusted p-value < 0.05 were deemed significant. Functional enrichment analysis was performed using Gene Set Enrichment Analysis (GSEA). Genes were ranked by fold change to search the Molecular Signatures Database (MSigDB) C5 Gene ontology collection (Liberzon et al., 2011; Subramanian et al., 2005) The analysis was conducted with 1000 permutations and gene sets with False Discovery Rate (FDR) adjusted q-value < 0.25 or nominal p-value < 0.01 were deemed significant. Weighted Gene Correlation Network Analysis (WGCNA) was conducted to identify gene modules associated with clinical traits (Langfelder & Horvath, 2008). WGCNA was performed using the R package (v. 1.66), with a soft-thresholding power of 6 determined by the scale-free topology criterion. The minimum module size was set to 30 genes, and dynamic tree cut with a deep split of 2 was used to define gene modules. Module-trait relationships were calculated by correlating the module eigengenes with symptomaticity, and significant modules were selected based on a correlation threshold of |r| > 0.3 and a nominal p-value < 0.05. Significant modules were then queried using GSEA, ranking member genes by module membership. Weighted Gene Correlation Network Analysis (WGCNA) was conducted to identify gene modules associated with clinical traits (Langfelder & Horvath, 2008). WGCNA was performed using the R package (v. 1.66), with a soft-thresholding power of 6 determined by the scale-free topology criterion. The minimum module size was set to 30 genes, and dynamic tree cut with a deep split of 2 was used to define gene modules. Module-trait relationships were calculated by correlating the module eigengenes with symptomaticity, and significant modules were selected based on a correlation threshold of |r| > 0.3 and a nominal p-value < 0.05. Significant modules were then queried using GSEA, ranking member genes by module membership.
Assembly: GRCh38/hg38
Supplementary files format and content: Xslx file containing each gene with its Size, ES, NES, NOM p-val, and FDR q-val.

molecule: total RNA

organism: Homo sapiens

source_name: Ectopic Endometrium

extract_protocol:
Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue samples using the FormaPure XL RNA Kit (Beckman Coulter Life Sciences, Brea, CA, Cat. No. A33342). Briefly, 10-micron curls were deparaffinized with two washes of 100% xylene, followed by sequential rehydration in 100%, 95%, and 70% ethanol. Samples were then digested with 1 mg/mL proteinase K at 56°C for 15 minutes, followed by an additional digestion at 80°C for 15 minutes to reverse formaldehyde crosslinking. RNA was purified using paramagnetic bead-based capture and 80% ethanol washes to remove contaminants. Residual genomic DNA was eliminated using on-bead DNase I treatment. Purified RNA was eluted in ≥20 µL nuclease-free water, and its concentration and integrity were assessed using a NanoDrop spectrophotometer (Thermo Fisher, Waltham, MA) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNAseq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche, Pleasanton, CA, Cat. No. KR1351). Briefly, 25–1000 ng of total RNA was subjected to ribosomal RNA (rRNA) depletion via hybridization to complementary DNA oligonucleotides, followed by RNase H digestion at 45°C for 30 minutes followed by DNase treatment at 37°C for 30 minutes to degrade rRNA-DNA hybrids. rRNA-depleted RNA was then fragmented via incubation in divalent magnesium cation buffer at 65°C for 1 min to target a 100-200 bp insert size. First-strand cDNA synthesis was performed using random hexamer priming, followed by second-strand synthesis incorporating dUTP in place of dTTP to mark the second strand. Following double-stranded cDNA synthesis, sequencing adapters were ligated, and libraries underwent strand-specific PCR-amplification. Indexed libraries meeting quality and yield thresholds were quantified using qRT-PCR with the KAPA Library Quantification Kit (Roche) and assessed for insert size distribution using either the LabChip GX (PerkinElmer, Waltham, MA) or Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries with a final concentration of ≥0.5 ng/µL were used for sequencing. Final sequencing libraries were normalized to a concentration of 2 nM and denatured according to Illumina’s standard protocol. Libraries were then diluted to a final loading concentration optimized for cluster density, targeting 40 million passing filter clusters per sample. Sequencing was performed on the Illumina NovaSeq X system (Illumina, San Diego, CA) using 100 bp paired-end reads.

tag: tissue

value: Ectopic Endometrium

tag: severity

value: Severe

tag: asrm stage

value: II

tag: hormones

value: OCPs (microgestin)


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S18-07087_11-01
Differential gene expression in human endometriosis, Sample S18-07087_11-01


title: Scn2a, WT, Fluoxetine, female, replicate4

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

description: Library name: Scn_WfF_5

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.

organism: Mus musculus

source_name: prefrontal cortex

growth_protocol: Mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning.

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: prefrontal cortex

tag: strain

tag: genotype

value: Wildtype


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S17-18492_03-01
Differential gene expression in human endometriosis, Sample S17-18492_03-01

value: III


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S17-18492_02-01
Differential gene expression in human endometriosis, Sample S17-18492_02-01


title: Scn2a, WT, Fluoxetine, female, replicate3

description: Library name: Scn_WfF_3


title: Scn2a, WT, Fluoxetine, female, replicate2

description: Library name: Scn_WfF_2


title: hiPSC MNase-seq, 10 U

city: Darlinghurst

first: David

middle: Thomas

last: Humphreys

address: 405 Liverpool Street

department: Genome core

country: Australia

institute: Victor Chang Cardiac Research Institute

description: Library name: hiPSC_MNase_10U

library_source: genomic

data_processing:
Paired-end reads were adapter- and quality-trimmed with Trimmomatic v0.40 (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 with orphan-read retention :1:true; LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:33).
For 150 bp NovaSeq X reads, reads were additionally cropped to 50 bp where required to recover subnucleosomal fragments and harmonize fragment-size classification across platforms.
Reads were processed with the nucMACC pipeline v3.1 (Nextflow v25.10.4), running the MNaseQC and nucMACC analysis modules; reads were aligned to GRCh38.
ENCODE blacklist regions (636 intervals) were excluded. The internal read-depth filtering threshold in get_nucMACC_scores.R was adjusted to 14 (values of 8 and 11 also evaluated) to enable recovery of mono-nucleosomal outputs from high-depth libraries.
nucMACC scores were computed across the MNase titration to classify mono- and subnucleosomal fragments, derive hyper- and hypo-accessible nucleosome classes (LOESS-slope cutoffs on rank-normalized scores), and generate TSS-centered occupancy and accessibility profiles.
Assembly: GRCh38
Supplementary files format and content: bigWig: genome-wide normalized MNase coverage tracks (GRCh38).
Supplementary files format and content: BED/bedGraph: nucMACC nucleosome positions with accessibility scores, including hyper- and hypo-accessible nucleosome classifications.

molecule: genomic DNA

source_name: not applicable (cell line)

growth_protocol: hiPSC line PB010.5 (MCRIi010-A; RRID:CVCL_UK91) was maintained under feeder-free conditions on hESC-qualified Matrigel (Corning 354277) in mTeSR Plus (STEMCELL 100-0276) with 0.5% (v/v) penicillin-streptomycin, passaged with ReLeSR (STEMCELL 100-0483), and used between passages 30-45. Cells were dissociated to single cells with TrypLE (Thermo 12604013) and counted prior to digestion.

extract_protocol:
RNA was removed with RNase A (42°C, 30 min) and protein digested with 20% SDS plus Proteinase K (55°C, 15 min). MNase-digested DNA was purified with the GeneJET PCR Purification Kit (Thermo K0701) and quantified by NanoDrop. Saccharomyces cerevisiae (BY4742) mononucleosomal spike-in DNA — prepared by Zymolyase spheroplasting and 60 U MNase digestion (10 min, 37°C) of log-phase cells followed by GeneJET purification — was added to each sample at 0.5 ng per 10 ng hiPSC DNA (~5% of total) immediately before library preparation.
Libraries were prepared from 10 ng MNase-digested hiPSC DNA plus 0.5 ng BY4742 spike-in DNA using the Active Motif DNA Library Kit for Illumina (53220): end repair, indexed Illumina adapter ligation, SPRI bead cleanup, 12-cycle PCR enrichment, and SPRI size selection. Library quality and size distribution were assessed by capillary electrophoresis (Agilent TapeStation, D1000 ScreenTape).

treatment_protocol: Single-cell hiPSC suspensions (typically 250,000-500,000 cells) were permeabilized in MNase digestion Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.1% (v/v) NP-40, 1 mM β-mercaptoethanol) for 10 min at 22°C, supplemented with CaCl2 to 2 mM, and digested with micrococcal nuclease (Thermo EN0181) at 0.5, 1, 3, 6, or 10 U for 5 min at 37°C with shaking (450 rpm). Digestion was stopped with ice-cold 50 mM EDTA / 50 mM EGTA.

value: not applicable (cell line)

tag: cell line

value: hiPSCs RRID:CVCL_UK91

value: Human


title: Scn2a, WT, Fluoxetine, female, replicate1

description: Library name: Scn_WfF_1


title: Scn2a, HT, Vehicle, male, replicate5

description: Library name: Scn_HvM_5

value: Heterozygous


title: hiPSC MNase-seq, 3 U

description: Library name: hiPSC_MNase_3U


title: Scn2a, HT, Vehicle, male, replicate3

description: Library name: Scn_HvM_3


title: hiPSC MNase-seq, 0.5 U

description: Library name: hiPSC_MNase_0.5U


title: Scn2a, HT, Vehicle, male, replicate4

description: Library name: Scn_HvM_4


title: Scn2a, HT, Vehicle, male, replicate2

description: Library name: Scn_HvM_2


title: Kasumi-1, PinA1 #3, 24h

city: Seongnam-si

first: Kyeongmi

state: Gyeonggi-do

address: 4th floor, 46, Wiryeseoil-ro, Sujeong-gu

institute: Pin Therapeutics

description:
Library name: Kasumi-1_PinA1_rep3
Column name in norm.count.txt: N_Kas-1uM_rep3

data_processing:
Raw sequencing reads were processed to remove adaptor sequences and low-quality bases using Trimmomatic (v0.38).
Trimmed reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.1.0).
Gene expression levels were quantified using StringTie (v2.1.3b).
Expression values were normalized using DESeq2 (v1.38.3) in R (v4.2.2).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized gene expression values for all samples

growth_protocol: MV4-11 and Kasumi-1 human acute myeloid leukemia (AML) cell lines were obtained from ATCC and cultured under recommended conditions. MV4-11 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (PS), whereas Kasumi-1 cells were cultured in RPMI1640 supplemented with 20% FBS and 1% PS. Cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated from MV4-11 or Kasumi-1 cells using TRIzol® RNA Isolation Reagent (Life Technologies) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyzer with the RNA 6000 Pico Kit (Agilent Technologies).
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following the manufacturer’s instructions. Briefly, poly(A)+ RNA was enriched from total RNA and fragmented, followed by first- and second-strand cDNA synthesis. After end repair, A-tailing, and adaptor ligation, indexed libraries were amplified and quality-checked using the Agilent Bioanalyzer.

treatment_protocol: Cells were treated with the CK1α degrader PinA1 at a final concentration of 1 μM or vehicle control (DMSO) for 24 hours prior to RNA extraction.

tag: cell type

value: acute myeloid leukemia cell line

value: TP53 mutant

tag: treatment

value: CK1α degrader (PinA1, 1 µM)


title: Kasumi-1, PinA1 #2, 24h

description:
Library name: Kasumi-1_PinA1_rep2
Column name in norm.count.txt: N_Kas-1uM_rep2


title: Scn2a, HT, Vehicle, female, replicate5

description: Library name: Scn_HvF_5


title: Kasumi-1, PinA1 #1, 24h

description:
Library name: Kasumi-1_PinA1_rep1
Column name in norm.count.txt: N_Kas-1uM_rep1


title: Scn2a, HT, Vehicle, female, replicate4

description: Library name: Scn_HvF_4


title: Kasumi-1 DMSO Control #3, 24h

description:
Library name: Kasumi-1_DMSO_rep3
Column name in norm.count.txt: N_Kas-DMSO_rep3

value: DMSO control


title: Kasumi-1, DMSO Control #2, 24h

description:
Library name: Kasumi-1_DMSO_rep2
Column name in norm.count.txt: N_Kas-DMSO_rep2


title: Scn2a, HT, Vehicle, female, replicate2

description: Library name: Scn_HvF_2


title: Kasumi-1, DMSO Control #1, 24h

description:
Library name: Kasumi-1_DMSO_rep1
Column name in norm.count.txt: N_Kas-DMSO_rep1


title: Scn2a, HT, Lithium, male, replicate5

description: Library name: Scn_HLM_5


title: MV4-11, PinA1 #2, 24h

description:
Library name: MV4-11_PinA1_rep2
Column name in norm.count.txt: N_MV_1uM_rep2

value: TP53 wild-type


title: Scn2a, HT, Lithium, male, replicate4

description: Library name: Scn_HLM_4


title: MV4-11, PinA1 #1, 24h

description:
Library name: MV4-11_PinA1_rep1
Column name in norm.count.txt: N_MV_1uM_rep1


title: Scn2a, HT, Lithium, male, replicate3

description: Library name: Scn_HLM_3


title: MV4-11, DMSO Control #3, 24h

description:
Library name: MV4-11_DMSO_rep3
Column name in norm.count.txt: N_MV4-11DMSO_rep3


title: Scn2a, HT, Lithium, male, replicate2

description: Library name: Scn_HLM_2


title: MV4-11, DMSO Control #2, 24h

description:
Library name: MV4-11_DMSO_rep2
Column name in norm.count.txt: N_MV4-11DMSO_rep2


title: Scn2a, HT, Lithium, male, replicate1

description: Library name: Scn_HLM_1


title: MV4-11, DMSO Control #1, 24h

description:
Library name: MV4-11_DMSO_rep1
Column name in norm.count.txt: N_MV4-11DMSO_rep1


title: Scn2a, HT, Lithium, female, replicate5

description: Library name: Scn_HLF_5


title: AF22, COMMD3-BMI1_multiplex, 3

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

country: Japan

institute: Hiroshima University

description: Library name: Human_COMBMI_3

data_processing:
Adaptor and imcomplete sequences were removed by Trim Galore (ver. 0.6.6)
Human and mouse short reads were mapped to the COMMD3–BMI1 locus on human chromosome 10 and mouse chromosome 2, respectively, using TopHat2 to visualize junction reads.
For the quantification of junction reads, BMI1 exon 2–containing reads were mapped to COMMD3 exons using Bowtie2, and the read ends opposite to the BMI1 exon 2–containing sequences were assigned to their corresponding COMMD3 exons.
Assembly: hg38, mm10
Supplementary files format and content: BED file includes read data for each COMMD3 exon.

extract_protocol:
RNA was extracted using Sepazol Super G RNA (Nakarai Tesque) by the phenol-chloroform method.
Total RNA was reverse‑transcribed using the ReverTra Ace® qPCR RT Master Mix with gDNA Remover (Toyobo, FSQ‑301), following the manufacturer’s instructions. Multiplex PCR was performed using KOD‑Multi & Epi‑ (Toyobo) under the following conditions: 94 °C for 2 min, followed by 40 cycles of 98 °C for 10 s and 65 °C for 30 s. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: neural stem cells

value: WT


title: Scn2a, HT, Lithium, female, replicate4

description: Library name: Scn_HLF_4


title: AF22, COMMD3-BMI1_multiplex, 1

description: Library name: Human_COMBMI_1


title: Scn2a, HT, Lithium, female, replicate2

description: Library name: Scn_HLF_2


title: AF22, COMMD3/COMMD3-BMI1_KD 3

description: Library name: COMMD3/COMMD3-BMI1_KD_3

data_processing:
Adaptor and imcomplete sequences were removed by Trim Galore (ver. 0.6.6)
Short-read sequences were mapped on the human reference genome hg38 by STAR (ver. 2.7.10a)
mapped reads were counted by bedtools (ver. v2.29.2)
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
RNA was extracted with Sepazol Super G RNA (Nakarai Tesque), followed by Dnase digestion with NucleoSpin RNA column kit. 700 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: COMMD3/COMMD3-BMI1 knockdown


title: Scn2a, HT, Lithium, female, replicate1

description: Library name: Scn_HLF_1


title: AF22, COMMD3/COMMD3-BMI1_KD 2

description: Library name: COMMD3/COMMD3-BMI1_KD_2


title: Scn2a, HT, Fluoxetine, male, replicate5

description: Library name: Scn_HfM_5


title: AF22, COMMD3/COMMD3-BMI1_KD 1

description: Library name: COMMD3/COMMD3-BMI1_KD_1


title: Scn2a, HT, Fluoxetine, male, replicate4

description: Library name: Scn_HfM_4


title: AF22, shControl 3

description: Library name: shControl_3


title: Scn2a, HT, Fluoxetine, male, replicate3

description: Library name: Scn_HfM_3


title: AF22, shControl 2

description: Library name: shControl_2


title: AF22, shControl 1

description: Library name: shControl_1


title: Scn2a, HT, Fluoxetine, male, replicate1

description: Library name: Scn_HfM_1


title: AF22, COMMD3-BMI1_multiplex, 2

description: Library name: Human_COMBMI_2


title: Scn2a, HT, Lithium, female, replicate3

description: Library name: Scn_HLF_3


title: AF22, BMI1/COMMD3-BMI1_KD, 3

description: Library name: BMI1/COMMD3-BMI1_KD_3

value: BMI1/COMMD3-BMI1 knockdown


title: Scn2a, HT, Fluoxetine, female, replicate4

description: Library name: Scn_HfF_4


title: AF22, BMI1/COMMD3-BMI1_KD, 2

description: Library name: BMI1/COMMD3-BMI1_KD_2


title: Scn2a, HT, Fluoxetine, female, replicate3

description: Library name: Scn_HfF_3


title: AF22, shControl, 3

description: Library name: shControl_3


title: Scn2a, HT, Fluoxetine, female, replicate2

description: Library name: Scn_HfF_2


title: AF22, shControl, 2

description: Library name: shControl_2


title: Scn2a, HT, Fluoxetine, female, replicate1

description: Library name: Scn_HfF_1


title: Bioreplicate 1 Cfh KO control

city: Hamburg

first: Christina

last: Mayer

address: Falkenried 94

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Library name: Bio1_KO_Ctrl

data_processing:
Reads were aligned to the mouse reference genome GRCm38 (mm10)  with STAR v.2.5.2b
Gene counts were calculated with featureCounts v.1.5.1
DESeq2 for differential expression analysis
Assembly: Assembly: mouse reference genome GRCm38 (mm10)
Supplementary files format and content: Supplementary files format and content: Tab-delimited text file containing raw gene counts with genes in rows and samples in columns.

source_name: Cortex

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen)
RNA sequencing libraries were prepared using the TruSeq stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions. After pooling, libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) generating 150 bp paired-end reads.

value: Cortex

value: primary cortical neurons

value: neuronal Cfh conditional knockout

value: no treatment


title: Hepatocytes co-cultured with Phgdh KO cancer cells and CXCR2i rep2

city: New York

first: Jason

middle: Rodencal

last: Terrell

state: NY

address: 530 1st Avenue

institute: NYU Langone Health

description: Library name: Hepato_14

data_processing:
The .txt file was generated using the standard Novogene RNA-seq analysis pipeline. Raw paired-end reads were produced on an Illumina NovaSeq 6000 platform. Adapter sequences and low-quality reads were removed to obtain clean reads. Clean reads were aligned to the reference genome using HISAT2, and gene-level read counts were quantified. Gene expression levels were normalized and reported as FPKM values.
Assembly: GRCm38 (mm10)
Supplementary files format and content: excel sheet with fpkm

source_name: mouse hepatocytes

extract_protocol:
RNA was extracted using RNeasy mini kit per manufacturer's protcols and RNA quality was validated.
As per Novogene protocols

value: mouse hepatocytes

value: cocultured with KO cancer cells and CXCR2 inhibitor


title: OPM-2 cells, ATRA+POM (Input)

city: Chengdu

first: Ling

last: Zhong

state: Please Select

address: No. 32, Section 2, West First Ring Road, Qingyang District

country: China

institute: Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital

description: Library name: Sample 8

data_processing:
The DNBs were loaded into patterned nanoarray and SE50 bases reads were generated on DNBseq-G400 platform.
Assembly: hg38
Supplementary files format and content: bed (peaks) files for four groups

extract_protocol:
1 × 106 cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched by the addition of glycine to a final concentration of 125 mM for 5 min. After washing twice with ice-cold PBS, the cells were collected by scraping. Chromatin fragments of 200 bp to 500 bp in length were generated using Chromatin Prep Kit according to the manufacture (Millipore sigma, 17-375). After sonication, samples were diluted 10 times with buffer [1% Triton X-100, 2 mM EDTA, 20 mM tris-HCl (pH 8.1), and150 mM NaCl] and centrifuged. A portion of supernatants was taken out as input. The remaining supernatants were immunoprecipitated using antibody at 4°C overnight. Enzymatic Chromatin IP Kit (CST, 9002S) was used to perform ChIP.
Library preparation was performed using MGIEasy Universal DNA Library Prep Set. Firstly, a certain amount of purified DNA sample was taken and converted into blunt-end DNA through end repair reaction. Then adenosine was added to the 3′ ends of the end DNA repaired through A-tailing reaction. Later, library adaptors were connected through adaptor ligation process. The single-stranded library products were produced via denaturation. The reaction system for circularization was set up to get single-stranded cyclized DNA products. The final single strand circularized library was amplified with phi29 and rolling circle amplification to make DNA nanoball (DNB) which carried more than 300 copies of the initial single stranded circularized library molecule.

value: multiple myeloma cell line

value: 1 μM ATRA + 1 μM POM for 72 hours


title: Naa15,WT, Vehicle, male, replicate5

description: Library name: Na_WvM_5

value: prefrontal cortex

value: Wildtype


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-10905_06-01
Differential gene expression in human endometriosis, Sample S19-10905_06-01

value: Ectopic Endometrium


title: OPM-2 cells, ATRA+POM (ChIP)

description: Library name: Sample 7


title: Scn2a, WT, Lithium, male, replicate2

description: Library name: Scn_WLM_2


title: Naa15,WT, Vehicle, male, replicate4

description: Library name: Na_WvM_4


title: Hepatocytes co-cultured with Phgdh KO cancer cells and CXCR2i rep3

description: Library name: Hepato_15


title: OPM-2 cells, POM (Input)

description: Library name: Sample 6

value: 1 μM POM for 72 hours


title: Naa15,WT, Vehicle, male, replicate3

description: Library name: Na_WvM_3


title: Naa15,WT, Vehicle, male, replicate2

description: Library name: Na_WvM_2


title: Scn2a, HT, Fluoxetine, male, replicate2

description: Library name: Scn_HfM_2

value: Heterozygous


title: OPM-2 cells, POM (ChIP)

description: Library name: Sample 5


title: Naa15,WT, Vehicle, male, replicate1

description: Library name: Na_WvM_1


title: OPM-2 cells, ATRA (ChIP)

description: Library name: Sample 3

value: 1 μM ATRA for 72 hours


title: OPM-2 cells, ATRA (Input)

description: Library name: Sample 4


title: Scn2a, WT, Fluoxetine, male, replicate1

description: Library name: Scn_WfM_1


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S18-09141_03-01
Differential gene expression in human endometriosis, Sample S18-09141_03-01

value: MIld

value: III


title: Naa15,WT, Vehicle, female, replicate5

description: Library name: Na_WvF_5


title: OPM-2 cells, DMSO (Input)

description: Library name: Sample 2

value: DMSO for 72 hours


title: Naa15,WT, Vehicle, female, replicate4

description: Library name: Na_WvF_4


title: OPM-2 cells, DMSO (ChIP)

description: Library name: Sample 1


title: Naa15,WT, Vehicle, female, replicate3

description: Library name: Na_WvF_3


title: 3390

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

description: Library name: 3390

data_processing:
The nf-core/rnaseq v3.12.0 (https://nf-co.re/rnaseq) pipeline was used to process the data.
The pipeline was executed with nf-core tools v2.10 and Nextflow v23.04.4.
STAR v2.7.10a alignment and RSEM v1.3.1 transcript quantification were performed.
Assembly: Sscrofa11.1 (Ensembl Pig release-110)
Supplementary files format and content: tab-delimited text file includes expected raw counts for each sample

organism: Sus scrofa

source_name: Heart

growth_protocol: Female Ossabaw swines were fed high fat diet as of 2 months of age (heart failure cohorts) or normal chow (control cohort).

extract_protocol:
Total RNA extracted  via RNeasy mini kit (Qiagen #74104)
The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) was utilized according to the manufacturer's recommendations. ERCC RNA Spike-In Mix (ThermoFisher, #4456740) was added to normalized total RNA prior to library preparation following manufacturer’s protocol.

treatment_protocol: Obese female Ossabaw swines (Heart failure cohorts) were subjected to aortic banding and immediately treated by peripheral intravenous infusion with 8e12 vg/kg (3 e14 vg total) AAV9sc.KBD. Heart tissue were collected 6 months after treatment.

value: Heart

value: Ossabaw

value: strain

value: wildtype

value: AAV9sc.KBD-treated Heart Failure

tag: batch


title: Naa15,WT, Vehicle, female, replicate2

description: Library name: Na_WvF_2


title: Naa15,WT, Vehicle, female, replicate1

description: Library name: Na_WvF_1


title: 3380

description: Library name: 3380


title: 3340

description: Library name: 3340


title: Naa15,WT, Lithium, male, replicate4

description: Library name: Na_WLM_4


title: Naa15,WT, Lithium, male, replicate5

description: Library name: Na_WLM_5


title: 3389

description: Library name: 3389

value: Saline-treated Heart Failure


title: hiPSC MNase-seq, 6 U

description: Library name: hiPSC_MNase_6U

value: not applicable (cell line)

value: hiPSCs RRID:CVCL_UK91

value: Human


title: 3335

description: Library name: 3335


title: hiPSC MNase-seq, 1 U

description: Library name: hiPSC_MNase_1U


title: Naa15,WT, Lithium, male, replicate3

description: Library name: Na_WLM_3

value: prefrontal cortex

value: Wildtype


title: 3388

description: Library name: 3388


title: Naa15,WT, Lithium, male, replicate2

description: Library name: Na_WLM_2


title: Naa15,WT, Lithium, male, replicate1

description: Library name: Na_WLM_1


title: Scn2a, HT, Vehicle, male, replicate1

description: Library name: Scn_HvM_1


title: 3369

description: Library name: 3369


title: 3367

description: Library name: 3367


title: Control (NT) replicate 3

first: Morgan

last: Huse

address: 417 E 68th St

institute: Sloan Kettering Institute

description:
Library name: NT3
Bulk RNA-seq of non-targeting control cells (biological replicate 3)

data_processing:
CutAdapt (v1.6) was used to trim adapter sequences with a minimum overlap of 10 bases. Reads shorter than half the original read length were removed.
Reads were aligned to the mouse reference genome (mm10) using STAR (v2.5.0a) in two-pass mode.
Gene-level counts were generated using HTSeq (v0.5.3) with parameters: -m intersection-strict -s reverse -t exon.
Count matrices were normalized and analyzed for differential expression using DESeq.
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing normalized gene expression counts.
Supplementary files format and content: Rows correspond to genes and columns correspond to samples (NT and KO replicates).

molecule: polyA RNA

growth_protocol: Cells were cultured under standard conditions appropriate for the experimental system.

extract_protocol:
Total RNA was extracted using standard RNA isolation methods according to manufacturer protocols.
RNA-seq libraries were prepared using standard Illumina-compatible protocols for polyA-selected RNA and sequenced using paired-end sequencing.

treatment_protocol: Knockout samples were generated using CRISPR cas9. Control samples (NT) were processed in parallel without targeting.

value: Melanoma cells

value: Non-targeting control

value: batch 1


title: Naa15,WT, Lithium, female, replicate5

description: Library name: Na_WLF_5


title: Naa15,WT, Lithium, female, replicate4

description: Library name: Na_WLF_4


title: 3449

description: Library name: 3449

value: control


title: Naa15,WT, Lithium, female, replicate3

description: Library name: Na_WLF_3


title: 3448

description: Library name: 3448


title: 3453

description: Library name: 3453


title: 3443

description: Library name: 3443


title: Naa15,WT, Lithium, female, replicate1

description: Library name: Na_WLF_1


title: Naa15,WT, Lithium, female, replicate2

description: Library name: Na_WLF_2


title: Scn2a, HT, Vehicle, female, replicate3

description: Library name: Scn_HvF_3

value: Heterozygous


title: OP768

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description: Library name: N2414_X7

data_processing:
Raw POD5 signal files were basecalled using Dorado (version 0.8.1) from Oxford Nanopore Technologies with the R10.4.1 high-accuracy model (dna_r10.4.1_e8.2_400bps_hac@v5.0.0). Basecalling was performed on an NVIDIA A40 GPU. Basecalled reads were demultiplexed using dorado demux (kit SQK-NBD114-24) with barcode trimming enabled, yielding per-barcode read sets corresponding to the analyzed strains.
Assembly: ce11
Supplementary files format and content: tab-delimited text file with coordinates of identified integrations

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Mixed-stage animals were grown on a 10 cm NGM plate and washed three times with M9 buffer, pelleted and frozen in a dry ice-ethanol bath for 10 minutes.

extract_protocol:
DNA extraction from frozen worm pellets for Oxford Nanopore Sequencing, based on https://nanoporetech.com/document/extraction-method/c-elegans-dna QIAGEN Puregene Cell Kit (158043) and Proteinase K (19131). DNA was eluted in 200 µl water per sample.
4µg of genomic DNA was fragmented to a target size of 15kb using G-Tubes (Covaris). Library preparation was performed using the Native barcoding kit v14 (SQK-NBD114.24) from Oxford Nanopore Technologies, following the manufacturer recommendations. Pooled libraries were sequenced on a PromethION flowcell (R10.4.1) using a P2 solo device.

value: whole animals


title: Scn2a, HT, Vehicle, female, replicate1

description: Library name: Scn_HvF_1


title: PE255

description: Library name: N2414_X6

value: feIs5 [sur-5p::luciferase::GFP + rol-6(su1006)] X


title: Naa15,WT, Fluoxetine, male, replicate3

description: Library name: Na_WfM_3


title: PE254

description: Library name: N2414_X5

value: feIs4 [sur-5p::luciferase::GFP + rol-6(su1006)] V.


title: Naa15,WT, Fluoxetine, male, replicate5

description: Library name: Na_WfM_5


title: Naa15,WT, Fluoxetine, male, replicate4

description: Library name: Na_WfM_4


title: MRS387

description: Library name: N2414_X4

value: sevIs1[Psur-5::luc+::gfp] X


title: VT3855

description: Library name: N2414_X3


title: Naa15,WT, Fluoxetine, male, replicate2

description: Library name: Na_WfM_2


title: Naa15,WT, Fluoxetine, female, replicate5

description: Library name: Na_WfF_5


title: SX346

description: Library name: N2414_X2


title: Naa15,WT, Fluoxetine, male, replicate1

description: Library name: Na_WfM_1


title: HW143

description: Library name: N2414_X1

value: wIs79[ajm-1::gfp, scm::gfp]


title: Naa15,WT, Fluoxetine, female, replicate3

description: Library name: Na_WfF_3


title: MV4-11, PinA1 #3, 24h

description:
Library name: MV4-11_PinA1_rep3
Column name in norm.count.txt: N_MV_1uM_rep3

value: acute myeloid leukemia cell line

value: TP53 wild-type

value: CK1α degrader (PinA1, 1 µM)


title: GR1395

description: Library name: N2401

value: mgIs49 [mlt-10p::gfp::pest; ttx-3::gfp]


title: Naa15,WT, Fluoxetine, female, replicate4

description: Library name: Na_WfF_4


title: WT_12_3

city: Kunming

first: Xuewei

last: Yang

state: Yunnan

address: Chenggong District

institute: Yunnan University

description: Library name: Sample 12

data_processing:
Date was analyzed using OmicShare tools (https://www.omicshare.com/).
Assembly: HiSat2 and StringTie
Supplementary files format and content: FPKM, count value for each sample

organism: Fungi

source_name: hypha

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The WT and ΔAohal4b mutant strains were pre-cultured in liquid TG medium at 28ºC for 48 h. Next, mycelia were transferred to the WA medium, a low-nutrient environment, to induce trap formation. Approximately 300 nematodes were added to each well. Mycelial samples were harvested immediately before nematode addition (0 h post-induction) and 12 h post-induction.

value: hypha

value: Fungal hyphae cells

value: wild type

value: Trap induction with nematode


title: Naa15,WT, Fluoxetine, female, replicate2

description: Library name: Na_WfF_2

value: prefrontal cortex

value: Wildtype


title: Naa15,WT, Fluoxetine, female, replicate1

description: Library name: Na_WfF_1


title: WT_0_3

description: Library name: Sample 9

growth_protocol: The WT and ΔAohal4b mutant strains were pre-cultured in liquid TG medium at 28ºC for 48 h

value: no treatment


title: WT_12_1

description: Library name: Sample 10


title: Naa15,HT, Vehicle, male, replicate4

description: Library name: Na_HvM_5

value: Heterozygous


title: Naa15,HT, Vehicle, male, replicate3

description: Library name: Na_HvM_4


title: WT_12_2

description: Library name: Sample 11


title: WT_0_1

description: Library name: Sample 7


title: Naa15,HT, Vehicle, male, replicate1

description: Library name: Na_HvM_1


title: Naa15,HT, Vehicle, male, replicate2

description: Library name: Na_HvM_2


title: Hal4b_12_3

description: Library name: Sample 6

value: mutant strain


title: WT_0_2

description: Library name: Sample 8


title: Hal4b_12_1

description: Library name: Sample 4


title: Naa15,HT, Vehicle, female, replicate5

description: Library name: Na_HvF_5


title: Naa15,HT, Vehicle, female, replicate3

description: Library name: Na_HvF_3


title: Naa15,HT, Vehicle, female, replicate4

description: Library name: Na_HvF_4


title: Hal4b_12_2

description: Library name: Sample 5


title: Hal4b_0_3

description: Library name: Sample 3


title: Naa15,HT, Vehicle, female, replicate2

description: Library name: Na_HvF_2


title: Hal4b_0_2

description: Library name: Sample 2


title: Naa15,HT, Vehicle, female, replicate1

description: Library name: Na_HvF_1


title: Hal4b_0_1

description: Library name: Sample 1


title: Naa15,HT, Lithium, male, replicate5

description: Library name: Na_HLM_5


title: Naa15,HT, Lithium, male, replicate4

description: Library name: Na_HLM_4


title: Naa15,HT, Lithium, male, replicate2

description: Library name: Na_HLM_2


title: Naa15,HT, Lithium, male, replicate3

description: Library name: Na_HLM_3


title: Naa15,HT, Lithium, male, replicate1

description: Library name: Na_HLM_1


title: Naa15,HT, Lithium, female, replicate4

description: Library name: Na_HLF_4


title: Naa15,HT, Lithium, female, replicate5

description: Library name: Na_HLF_5


title: NK cells co-cultured with tumor cells(KYSE-150) and Tetra-Ab(46.3), replicate 3

city: Zhengzhou

first: Yafei

last: Liu

address: East Jianshe Road NO.1

institute: The first affiliated hospital of zhengzhou university

description: Library name: P46_3

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file include FPKM values including all samples
Supplementary files format and content: raw fq files for each sample

source_name: innate lymphoid cells

growth_protocol: NK cells were maintained in TAKARA  GT-T551 H3 supplemented with IL-2 (1000U/ml) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

treatment_protocol: K cells were co-cultured with KYSE-150 tumor cells at an E/T ratio of 5:1 in the presence of 25 nM antibodies for 4 hours.

value: innate lymphoid cells

value: NK cells

value: Immune cells

value: WT


title: NK cells co-cultured with tumor cells(KYSE-150) and Tetra-Ab(46.3), replicate 2

description: Library name: P46_2


title: NK cells co-cultured with tumor cells(KYSE-150) and Tetra-Ab(30.1), replicate 2

description: Library name: P30_2


title: NK cells co-cultured with tumor cells(KYSE-150) and Tri-Ab, replicate 3

description: Library name: Tri_3


title: NK cells co-cultured with tumor cells(KYSE-150) and Tetra-Ab(30.1), replicate 1

description: Library name: P30_1


title: NK cells co-cultured with tumor cells(KYSE-150) and Tetra-Ab(46.3), replicate 1

description: Library name: P46_1


title: Naa15,HT, Lithium, female, replicate3

description: Library name: Na_HLF_3


title: NK cells co-cultured with tumor cells(KYSE-150) and Tetra-Ab(30.1), replicate 3

description: Library name: P30_3


title: NK cells co-cultured with tumor cells(KYSE-150) and Tri-Ab, replicate 2

description: Library name: Tri_2


title: Naa15,HT, Lithium, female, replicate2

description: Library name: Na_HLF_2


title: NK cells co-cultured with tumor cells(KYSE-150) and Tri-Ab, replicate 1

description: Library name: Tri_1


title: Naa15,HT, Lithium, female, replicate1

description: Library name: Na_HLF_1


title: NK cells co-cultured with tumor cells(KYSE-150) and amivantamab, replicate 3

description: Library name: Ami_3


title: Naa15,HT, Fluoxetine, male, replicate5

description: Library name: Na_HfM_5


title: NK cells co-cultured with tumor cells(KYSE-150) and amivantamab, replicate 2

description: Library name: Ami_2


title: Naa15,HT, Fluoxetine, male, replicate4

description: Library name: Na_HfM_4


title: NK cells co-cultured with tumor cells(KYSE-150) and amivantamab, replicate 1

description: Library name: Ami_1


title: Naa15,HT, Fluoxetine, male, replicate3

description: Library name: Na_HfM_3


title: Naa15,HT, Fluoxetine, male, replicate1

description: Library name: Na_HfM_1


title: NK cells co-cultured with tumor cells(KYSE-150), replicate 2

description: Library name: NC_2


title: NK cells co-cultured with tumor cells(KYSE-150), replicate 3

description: Library name: NC_3


title: HEK Expi293F™ cells transfected with triple plasmids at composition 3 (Triple 3), replicate 3

city: Dublin

first: Mark

last: Smales

state: Co. Dublin

address: Fosters Avenue

department: Advanced Biotherapies and Cell Factory

country: Ireland

institute: National Institute for Bioprocessing Research and Training

description:
Library name: Triple 3_3
Column name in gene_count_matrix.xlsx: Triple 3_3

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1
Reads were quality filtered using FastP v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Quality-filtered reads were aligned to Homo sapiens reference genome GRCh38_114 using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads
Coordinate sorting of BAM files using samtools v1.22.1
UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0
Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RSeQC v5.0.4 and Qualimap v2.3
Generation of comprehensive QC report using MultiQC v1.32
Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file
Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation
Differential expression using edgeR v4.0.16 with filtering for low-expressed genes with edgeR::filterByExpr with absolute (log2 fold change >0.5585 and adjusted p-value=<0.05
Assembly: GRCh38, Ensemble release 114
Supplementary files format and content: Excel workbook gene_count_matrix.xlsx containing gene-level processed expression and count per million (cpm) values across twenty-one samples.

source_name: Kidney (Embryonic)

growth_protocol: Human embryonic kidney (HEK) Expi293FTM cells were maintained in suspension culture in chemically defined, serum-free BalanCD HEK293 medium supplemented with 4 mM L-glutamine.  The cells were cultured in Erlenmeyer flasks at 37 °C, 5% CO2 with agitation at 120 rpm in a humidified atmosphere.

extract_protocol:
Total RNA extraction from cultured HEK Expi293F™ cells was performed using automated bead-based extraction approach from cells preserved in Zymo DNA/RNA Shield following the manufacturer’s standard protocol. Briefly, the pellet of 1m viable HEK cells was homogenized in 100 µL Zymo DNA/RNA Shield solution, followed by magnetic bead binding, washing, and eluting of the RNA using RNase-free water. Post-extraction RNA concentration was assessed via a fluorescence-based plate reader assay.
For sequencing library preparation, the mRNA was converted into complementary DNA (cDNA) using a poly(dT)VN primer via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification. A single end sequencing toward the 3’ end counting approach was used to capture differential gene expression, which allowed for extremely efficient and accurate counts of mRNA transcripts. Unique molecular identifiers (UMIs) to was used to deduplicate and unique dual indices (UDIs) was used to prevent index hopping.

treatment_protocol: This study systemically investigated the transcriptional changes of single, dual and the prevailing triple plasmid transfection process for rAAV production in HEK293 cells, with three independent biological replicates per condition

value: Kidney (Embryonic)

value: Human embryonic kidney cells

value: Triple plasmids transfection composition 3


title: Naa15,HT, Fluoxetine, female, replicate4

description: Library name: Na_HfF_4


title: HEK Expi293F™ cells transfected with triple plasmids at composition 3 (Triple 3), replicate 2

description:
Library name: Triple 3_2
Column name in gene_count_matrix.xlsx: Triple 3_2


title: Naa15,HT, Fluoxetine, female, replicate5

description: Library name: Na_HfF_5


title: Naa15,HT, Fluoxetine, male, replicate2

description: Library name: Na_HfM_2


title: NK cells co-cultured with tumor cells(KYSE-150), replicate 1

description: Library name: NC_1


title: Naa15,HT, Fluoxetine, female, replicate3

description: Library name: Na_HfF_3


title: HEK Expi293F™ cells transfected with triple plasmids at composition 3 (Triple 3), replicate 1

description:
Library name: Triple 3_1
Column name in gene_count_matrix.xlsx: Triple 3_1


title: Naa15,HT, Fluoxetine, female, replicate2

description: Library name: Na_HfF_2


title: HEK Expi293F™ cells transfected with triple plasmids at composition 2 (Triple 2), replicate 3

description:
Library name: Triple 2_3
Column name in gene_count_matrix.xlsx: Triple 2_3

value: Triple plasmids transfection composition 2


title: Naa15,HT, Fluoxetine, female, replicate1

description: Library name: Na_HfF_1


title: HEK Expi293F™ cells transfected with triple plasmids at composition 2 (Triple 2), replicate 2

description:
Library name: Triple 2_2
Column name in gene_count_matrix.xlsx: Triple 2_2


title: Dyrk1a, WT, Vehicle, male, replicate5

description: Library name: Dyrk_WvM_5


title: HEK Expi293F™ cells transfected with triple plasmids at composition 2 (Triple 2), replicate 1

description:
Library name: Triple 2_1
Column name in gene_count_matrix.xlsx: Triple 2_1


title: Dyrk1a, WT, Vehicle, male, replicate4

description: Library name: Dyrk_WvM_4


title: HEK Expi293F™ cells transfected with triple plasmids at composition 1 (Triple 1), replicate 3

description:
Library name: Triple 1_3
Column name in gene_count_matrix.xlsx: Triple 1_3

value: Triple plasmids transfection composition 1


title: Dyrk1a, WT, Vehicle, male, replicate3

description: Library name: Dyrk_WvM_3


title: HEK Expi293F™ cells transfected with triple plasmids at composition 1 (Triple 1), replicate 2

description:
Library name: Triple 1_2
Column name in gene_count_matrix.xlsx: Triple 1_2


title: Dyrk1a, WT, Vehicle, male, replicate1

description: Library name: Dyrk_WvM_1


title: HEK Expi293F™ cells transfected with triple plasmids at composition 1 (Triple 1), replicate 1

description:
Library name: Triple 1_1
Column name in gene_count_matrix.xlsx: Triple 1_1


title: HEK Expi293F™ cells transfected with dual plasmids (Dual), replicate 2

description:
Library name: Dual_2
Column name in gene_count_matrix.xlsx: Dual_2

value: Dual plasmids transfection


title: HEK Expi293F™ cells transfected with dual plasmids (Dual), replicate 3

description:
Library name: Dual_3
Column name in gene_count_matrix.xlsx: Dual_3


title: Dyrk1a, WT, Vehicle, male, replicate2

description: Library name: Dyrk_WvM_2


title: Dyrk1a, WT, Vehicle, female, replicate5

description: Library name: Dyrk_WvF_5


title: HEK Expi293F™ cells transfected with dual plasmids (Dual), replicate 1

description:
Library name: Dual_1
Column name in gene_count_matrix.xlsx: Dual_1


title: Dyrk1a, WT, Vehicle, female, replicate4

description: Library name: Dyrk_WvF_4


title: Dyrk1a, WT, Vehicle, female, replicate3

description: Library name: Dyrk_WvF_3


title: Tanc2, WT, Vehicle, female, replicate5

description: Library name: Tanc_WvF_5


title: Tanc2, WT, Vehicle, male, replicate4

description: Library name: Tanc_WvM_5


title: Dyrk1a, WT, Vehicle, female, replicate2

description: Library name: Dyrk_WvF_2


title: HEK Expi293F™ cells transfected with single plasmid at higher concentration (Single H), replicate 3

description:
Library name: Single H_3
Column name in gene_count_matrix.xlsx: Single H_3

value: Single plasmid transfection at higher concentration


title: HEK Expi293F™ cells transfected with single plasmid at higher concentration (Single H), replicate 2

description:
Library name: Single H_2
Column name in gene_count_matrix.xlsx: Single H_2


title: Dyrk1a, WT, Vehicle, female, replicate1

description: Library name: Dyrk_WvF_1


title: Dyrk1a, WT, Lithium, male, replicate5

description: Library name: Dyrk_WLM_5


title: HEK Expi293F™ cells transfected with single plasmid at higher concentration (Single H), replicate 1

description:
Library name: Single H_1
Column name in gene_count_matrix.xlsx: Single H_1


title: HEK Expi293F™ cells transfected with single plasmid at lower concentration (Single L), replicate 3

description:
Library name: Single L_3
Column name in gene_count_matrix.xlsx: Single L_3

value: Single plasmid transfection at lower concentration


title: Dyrk1a, WT, Lithium, male, replicate4

description: Library name: Dyrk_WLM_4

value: prefrontal cortex


title: HEK Expi293F™ cells transfected with single plasmid at lower concentration (Single L), replicate 2

description:
Library name: Single L_2
Column name in gene_count_matrix.xlsx: Single L_2


title: Dyrk1a, WT, Lithium, male, replicate3

description: Library name: Dyrk_WLM_3

value: Wildtype


title: HEK Expi293F™ cells transfected with single plasmid at lower concentration (Single L), replicate 1

description:
Library name: Single L_1
Column name in gene_count_matrix.xlsx: Single L_1


title: Dyrk1a, WT, Lithium, male, replicate2

description: Library name: Dyrk_WLM_2


title: HEK Expi293F™ cells without transfection (Control), replicate 2

description:
Library name: Control_2
Column name in gene_count_matrix.xlsx: Control_2

value: Control without transfection


title: HEK Expi293F™ cells without transfection (Control), replicate 1

description:
Library name: Control_1
Column name in gene_count_matrix.xlsx: Control_1


title: Dyrk1a, WT, Lithium, female, replicate5

description: Library name: Dyrk_WLF_5


title: Dyrk1a, WT, Lithium, female, replicate4

description: Library name: Dyrk_WLF_4


title: HEK Expi293F™ cells without transfection (Control), replicate 3

description:
Library name: Control_3
Column name in gene_count_matrix.xlsx: Control_3


title: Dyrk1a, WT, Lithium, male, replicate1

description: Library name: Dyrk_WLM_1


title: IDHO08 oligodendroglioma

city: Rehovot

first: Itay

last: Tirosh

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
Library name: IDHO08
fresh frozen spatial transcriptomics (10X Visium)

data_processing:
FASTQs were generated by the SpaceRanger pipeline (version 1.0 and 1.1, 10X Genomics).
Alignment of FASTQs with human reference genome GRCh38, UMI counting, and spot barcode filtering were performed using SpaceRanger.
Assembly: human reference genome GRCh38
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression data, list of genes, and spatial barcodes in compressed HDF5 format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_lowres_image.png: low-res tissue image
Supplementary files format and content: tissue_positions_list.csv: spatial barcodes and their positional coordinates
Supplementary files format and content: metrics.csv: sample QC metrics
Library strategy: Spatial Transcriptomics

source_name: IDH mutant glioma

extract_protocol:
Fresh frozen tumor samples with RIN >7 were embedded in OCT and 10 micron sections were cut on cryostat and placed on Visium capture slides.
Spatial transcriptomics libraries were prepared with the 10x Visium Spatial Gene Expression slides and reagent kit according to the manufacturer's instructions.

value: IDH mutant glioma

tag: tumor stage

tag: tumor region

value: unannotated


title: IDHO06 oligodendroglioma

description:
Library name: IDHO06
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a, WT, Lithium, female, replicate3

description: Library name: Dyrk_WLF_3


title: Dyrk1a, WT, Lithium, female, replicate2

description: Library name: Dyrk_WLF_2


title: IDHO03 oligodendroglioma

description:
Library name: IDHO03
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a, WT, Lithium, female, replicate1

description: Library name: Dyrk_WLF_1


title: IDHO02 oligodendroglioma

description:
Library name: IDHO02
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a, WT, Fluoxetine, male, replicate4

description: Library name: Dyrk_WfM_4


title: IDHO01 oligodendroglioma

description:
Library name: IDHO01
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a, WT, Fluoxetine, male, replicate3

description: Library name: Dyrk_WfM_3


title: Dyrk1a, WT, Fluoxetine, male, replicate1

description: Library name: Dyrk_WfM_1


title: IDHA14 astrocytoma

description:
Library name: IDHA14
fresh frozen spatial transcriptomics (10X Visium)


title: IDHA13 astrocytoma

description:
Library name: IDHA13
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a, WT, Fluoxetine, male, replicate2

description: Library name: Dyrk_WfM_2


title: Dyrk1a, WT, Fluoxetine, female, replicate5

description: Library name: Dyrk_WfF_5


title: IDHA12 astrocytoma

description:
Library name: IDHA12
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a, WT, Fluoxetine, female, replicate4

description: Library name: Dyrk_WfF_4


title: IDHA10 astrocytoma

description:
Library name: IDHA10
fresh frozen spatial transcriptomics (10X Visium)


title: IDHA11 astrocytoma

description:
Library name: IDHA11
fresh frozen spatial transcriptomics (10X Visium)


title: IDHA09 astrocytoma

description:
Library name: IDHA09
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a, WT, Fluoxetine, female, replicate3

description: Library name: Dyrk_WfF_3


title: IDHA08 astrocytoma

description:
Library name: IDHA08
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a+/I48X, Vehicle, male, replicate5

description: Library name: Dyrk_HvM_5

value: Heterozygous


title: Dyrk1a, WT, Fluoxetine, female, replicate1

description: Library name: Dyrk_WfF_1


title: Dyrk1a+/I48X, Vehicle, male, replicate4

description: Library name: Dyrk_HvM_4


title: IDHA06 astrocytoma

description:
Library name: IDHA06
fresh frozen spatial transcriptomics (10X Visium)


title: Dyrk1a+/I48X, Vehicle, male, replicate3

description: Library name: Dyrk_HvM_3


title: IDHA03 astrocytoma

description:
Library name: IDHA03
fresh frozen spatial transcriptomics (10X Visium)


title: IDHA01 astrocytoma

description:
Library name: IDHA01
fresh frozen spatial transcriptomics (10X Visium)


title: Healthy_002_1853818_2_1_3

city: Tarrytown

first: William

last: Galbavy

address: 777 Old Saw Mill River Road

institute: Regeneron

description:
Library name: 1853818_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment

data_processing:
CellRanger (v.6.1.1, 10X Genomics) with GRCh38.100 reference was performed on the processed cells to align the reads, to calculate gene expression levels, and to make raw count matrix, gene/barcode list. Quality control has been done on the data to filter out abnormalities, empty droplets, and multiplets. In each sample, cells with the total number of molecules detected within a cell higher than 20,000 and lower than 2,000, and the total number of genes per cell higher than 4500 and lower than 800 were filtered out. Then Python module Scanpy (v1.7.1) was used to normalize the data. There were 3 steps for the normalization: 1. For every cell, scale total counts sum up to 10,000. 2. Log-normalization with log1p function. 3.Unit scaling the counts between 0 and 10.
Assembly: GRCh38.100
Supplementary files format and content: Tab-separated matrix files (scRNA-seq)
Supplementary files format and content: contig_annotations.csv (BCR-Seq)
Library strategy: BCR-Seq

source_name: Peripheral Blood Cells

extract_protocol:
Blood was diluted 1:1 with PBS then added to SepMate-50 tubes filled with 15 mL of Ficoll-Paque PLUS (Cytiva, #17144003) and centrifuged at 1,200 g for 10 minutes. PBMCs and plasma layers were poured in a new tube, pelleted at 300 g for 10 minutes, and resuspended with 5 mL of ACK lysing buffer (Gibco, # A10492-01) for 3 minutes to eliminate red blood cells. PBS was added to 50 mL and PBMCs were pelleted at 300 g for 10 minutes. If necessary, the red blood cell lysis step was repeated. Portions of resuspended PBMCs were then used for single cell OMICs (scRNA/BCRseq) and high parameter flow cytometry.
10x 5prime NextGEM v2

value: Peripheral Blood Cells

tag: age

tag: Sex

value: Female

tag: disease state

value: Healthy


title: Dyrk1a+/I48X, Vehicle, male, replicate2

description: Library name: Dyrk_HvM_2


title: Dyrk1a+/I48X, Vehicle, female, replicate4

description: Library name: Dyrk_HvF_4


title: Dyrk1a+/I48X, Vehicle, female, replicate3

description: Library name: Dyrk_HvF_3


title: Dyrk1a+/I48X, Vehicle, female, replicate2

description: Library name: Dyrk_HvF_2


title: Dyrk1a+/I48X, Vehicle, female, replicate1

description: Library name: Dyrk_HvF_1


title: APECED_005_1853817_1_1_3

description:
Library name: 1853817_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment

value: APECED


title: Healthy_010_1841000_2_1_3

description:
Library name: 1841000_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment

value: Male


title: Dyrk1a+/I48X, Lithium, male, replicate5

description: Library name: Dyrk_HLM_5


title: Healthy_010_1841000_1_1_3

description:
Library name: 1841000_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, male, replicate4

description: Library name: Dyrk_HLM_4


title: APECED_010_1840999_2_1_3

description:
Library name: 1840999_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, male, replicate3

description: Library name: Dyrk_HLM_3


title: APECED_010_1840999_1_1_3

description:
Library name: 1840999_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, male, replicate2

description: Library name: Dyrk_HLM_2


title: Healthy_009_1831047_2_1_3

description:
Library name: 1831047_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, male, replicate1

description: Library name: Dyrk_HLM_1


title: Dyrk1a+/I48X, Lithium, female, replicate5

description: Library name: Dyrk_HLF_5


title: Healthy_009_1831047_1_1_3

description:
Library name: 1831047_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Healthy_006_1824142_2_1_2

description:
Library name: 1824142_2_1_2
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, female, replicate4

description: Library name: Dyrk_HLF_4


title: Healthy_006_1824142_1_1_2

description:
Library name: 1824142_1_1_2
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, female, replicate3

description: Library name: Dyrk_HLF_3


title: Healthy_008_1823420_2_1_3

description:
Library name: 1823420_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, female, replicate2

description: Library name: Dyrk_HLF_2


title: Healthy_008_1823420_1_1_3

description:
Library name: 1823420_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Healthy_007_1823419_2_1_3

description:
Library name: 1823419_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Lithium, female, replicate1

description: Library name: Dyrk_HLF_1


title: Pten, WT, Lithium, female, replicate4

description: Library name: Pten_WLF_4


title: Healthy_007_1823419_1_1_3

description:
Library name: 1823419_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Fluoxetine, male, replicate3

description: Library name: Dyrk_HfM_3


title: APECED_008_1797330_1_1_4

description:
Library name: 1797330_1_1_4
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Fluoxetine, male, replicate4

description: Library name: Dyrk_HfM_4


title: Healthy_005_1797329_2_1_4

description:
Library name: 1797329_2_1_4
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Fluoxetine, male, replicate2

description: Library name: Dyrk_HfM_2


title: Dyrk1a+/I48X, Fluoxetine, male, replicate1

description: Library name: Dyrk_HfM_1


title: Dyrk1a+/I48X, Fluoxetine, female, replicate5

description: Library name: Dyrk_HfF_5


title: Healthy_003_1780203_2_1_2

description:
Library name: 1780203_2_1_2
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Healthy_005_1797329_1_1_4

description:
Library name: 1797329_1_1_4
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Healthy_003_1780203_1_1_2

description:
Library name: 1780203_1_1_2
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Fluoxetine, female, replicate4

description: Library name: Dyrk_HfF_4


title: APECED_007_1780202_2_1_3

description:
Library name: 1780202_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Fluoxetine, female, replicate3

description: Library name: Dyrk_HfF_3


title: Healthy_004_1767712_2_1_3

description:
Library name: 1767712_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Fluoxetine, female, replicate1

description: Library name: Dyrk_HfF_1


title: Healthy_004_1767712_1_1_3

description:
Library name: 1767712_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: APECED_006_1767709_2_1_2

description:
Library name: 1767709_2_1_2
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Tbl1xr1, WT, Vehicle, male, replicate4

description: Library name: Tbl_WvM_4


title: APECED_006_1767709_1_1_2

description:
Library name: 1767709_1_1_2
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Tbl1xr1, WT, Vehicle, male, replicate3

description: Library name: Tbl_WvM_3


title: APECED_004_1767708_2_1_3

description:
Library name: 1767708_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: APECED_004_1767708_1_1_3

description:
Library name: 1767708_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Tbl1xr1, WT, Vehicle, male, replicate1

description: Library name: Tbl_WvM_1


title: APECED_002_1760324_2_1_1

description:
Library name: 1760324_2_1_1
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Tbl1xr1, WT, Vehicle, female, replicate5

description: Library name: Tbl_WvF_5


title: Tbl1xr1, WT, Vehicle, female, replicate4

description: Library name: Tbl_WvF_4


title: APECED_002_1760324_1_1_1

description:
Library name: 1760324_1_1_1
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Vehicle, male, replicate1

description: Library name: Dyrk_HvM_1


title: APECED_001_1753268_2_1_2

description:
Library name: 1753268_2_1_2
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Tbl1xr1, WT, Vehicle, female, replicate3

description: Library name: Tbl_WvF_3


title: Tbl1xr1, WT, Vehicle, female, replicate2

description: Library name: Tbl_WvF_2


title: APECED_003_1749854_1_1_3

description:
Library name: 1749854_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Healthy_001_1749853_2_1_3

description:
Library name: 1749853_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Tbl1xr1, WT, Lithium, male, replicate3

description: Library name: Tbl_WLM_4


title: Healthy_001_1749853_1_1_3

description:
Library name: 1749853_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Tbl1xr1, WT, Lithium, male, replicate4

description: Library name: Tbl_WLM_5


title: Healthy_002_1853818_2_1_1

description:
Library name: 1853818_2_1_1
10x 5prime NextGEM v2

library_source: transcriptomic single cell

data_processing:
CellRanger (v.6.1.1, 10X Genomics) with GRCh38.100 reference was performed on the processed cells to align the reads, to calculate gene expression levels, and to make raw count matrix, gene/barcode list. Quality control has been done on the data to filter out abnormalities, empty droplets, and multiplets. In each sample, cells with the total number of molecules detected within a cell higher than 20,000 and lower than 2,000, and the total number of genes per cell higher than 4500 and lower than 800 were filtered out. Then Python module Scanpy (v1.7.1) was used to normalize the data. There were 3 steps for the normalization: 1. For every cell, scale total counts sum up to 10,000. 2. Log-normalization with log1p function. 3.Unit scaling the counts between 0 and 10.
Assembly: GRCh38.100
Supplementary files format and content: Tab-separated matrix files (scRNA-seq)
Supplementary files format and content: contig_annotations.csv (BCR-Seq)


title: Tbl1xr1, WT, Lithium, male, replicate2

description: Library name: Tbl_WLM_2

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.


title: Healthy_002_1853818_1_1_1

description:
Library name: 1853818_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Lithium, male, replicate1

description: Library name: Tbl_WLM_1


title: APECED_005_1853817_2_1_1

description:
Library name: 1853817_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Lithium, female, replicate4

description: Library name: Tbl_WLF_4


title: APECED_005_1853817_1_1_1

description:
Library name: 1853817_1_1_1
10x 5prime NextGEM v2


title: Healthy_010_1841000_2_1_1

description:
Library name: 1841000_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Lithium, female, replicate2

description: Library name: Tbl_WLF_2


title: Tbl1xr1, WT, Lithium, female, replicate3

description: Library name: Tbl_WLF_3


title: Healthy_010_1841000_1_1_1

description:
Library name: 1841000_1_1_1
10x 5prime NextGEM v2


title: APECED_010_1840999_2_1_1

description:
Library name: 1840999_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Lithium, female, replicate1

description: Library name: Tbl_WLF_1


title: APECED_010_1840999_1_1_1

description:
Library name: 1840999_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Fluoxetine, male, replicate5

description: Library name: Tbl_WfM_5


title: Healthy_009_1831047_2_1_1

description:
Library name: 1831047_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Fluoxetine, male, replicate4

description: Library name: Tbl_WfM_4


title: Tbl1xr1, WT, Fluoxetine, male, replicate2

description: Library name: Tbl_WfM_2


title: Healthy_006_1824142_2_1_1

description:
Library name: 1824142_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Fluoxetine, male, replicate3

description: Library name: Tbl_WfM_3


title: Tbl1xr1, WT, Fluoxetine, male, replicate1

description: Library name: Tbl_WfM_1


title: APECED_009_1824141_2_1_1

description:
Library name: 1824141_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Fluoxetine, female, replicate4

description: Library name: Tbl_WfF_4


title: Healthy_008_1823420_1_1_1

description:
Library name: 1823420_1_1_1
10x 5prime NextGEM v2


title: Healthy_006_1824142_1_1_1

description:
Library name: 1824142_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Vehicle, female, replicate1

description: Library name: Tbl_WvF_1


title: APECED_003_1749854_2_1_3

description:
Library name: 1749854_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Healthy_008_1823420_2_1_1

description:
Library name: 1823420_2_1_1
10x 5prime NextGEM v2


title: APECED_009_1824141_1_1_1

description:
Library name: 1824141_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, WT, Fluoxetine, female, replicate1

description: Library name: Tbl_WfF_1


title: Tbl1xr1, WT, Fluoxetine, female, replicate5

description: Library name: Tbl_WfF_5


title: Tbl1xr1, WT, Fluoxetine, female, replicate2

description: Library name: Tbl_WfF_2


title: Tbl1xr1, HT, Vehicle, male, replicate4

description: Library name: Tbl_HvM_4


title: Tanc, Hippocampus, HT, male,replicate2

description: Library name: Tanc_HPC_HvM_2

source_name: Hippocampus

growth_protocol: Mice were maintained under standard laboratory conditions and analyzed at postnatal day 25 (P25)

value: Hippocampus

value: male


title: Healthy_007_1823419_2_1_1

description:
Library name: 1823419_2_1_1
10x 5prime NextGEM v2


title: APECED_008_1797330_1_1_1

description:
Library name: 1797330_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Vehicle, male, replicate2

description: Library name: Tbl_HvM_2


title: APECED_008_1797330_2_1_1

description:
Library name: 1797330_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Vehicle, male, replicate5

description: Library name: Tbl_HvM_5


title: Tbl1xr1, HT, Vehicle, male, replicate3

description: Library name: Tbl_HvM_3


title: Healthy_005_1797329_2_1_1

description:
Library name: 1797329_2_1_1
10x 5prime NextGEM v2


title: Dyrk1a, WT, Fluoxetine, female, replicate2

description: Library name: Dyrk_WfF_2


title: Tbl1xr1, HT, Vehicle, female, replicate4

description: Library name: Tbl_HvF_4


title: APECED_007_1780202_1_1_1

description:
Library name: 1780202_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Vehicle, female, replicate3

description: Library name: Tbl_HvF_3


title: Healthy_005_1797329_1_1_1

description:
Library name: 1797329_1_1_1
10x 5prime NextGEM v2


title: IDHA02 astrocytoma

description:
Library name: IDHA02
fresh frozen spatial transcriptomics (10X Visium)


title: IDHA07 astrocytoma

description:
Library name: IDHA07
fresh frozen spatial transcriptomics (10X Visium)


title: Tbl1xr1, HT, Vehicle, male, replicate1

description: Library name: Tbl_HvM_1


title: Healthy_004_1767712_1_1_1

description:
Library name: 1767712_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Vehicle, female, replicate2

description: Library name: Tbl_HvF_2


title: Healthy_009_1831047_1_1_1

description:
Library name: 1831047_1_1_1
10x 5prime NextGEM v2


title: APECED_007_1780202_2_1_1

description:
Library name: 1780202_2_1_1
10x 5prime NextGEM v2


title: Healthy_003_1780203_2_1_1

description:
Library name: 1780203_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Vehicle, female, replicate5

description: Library name: Tbl_HvF_5


title: Tbl1xr1, HT, Lithium, male, replicate5

description: Library name: Tbl_HLM_5


title: Healthy_002_1853818_1_1_3

description:
Library name: 1853818_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Healthy_004_1767712_2_1_1

description:
Library name: 1767712_2_1_1
10x 5prime NextGEM v2


title: APECED_006_1767709_1_1_1

description:
Library name: 1767709_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Lithium, male, replicate3

description: Library name: Tbl_HLM_3


title: APECED_004_1767708_1_1_1

description:
Library name: 1767708_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Lithium, male, replicate1

description: Library name: Tbl_HLM_1


title: APECED_004_1767708_2_1_1

description:
Library name: 1767708_2_1_1
10x 5prime NextGEM v2


title: IDHA04 astrocytoma

description:
Library name: IDHA04
fresh frozen spatial transcriptomics (10X Visium)


title: Trip12, HT, Vehicle, female, replicate2

description: Library name: T12_HvF_2


title: Tbl1xr1, HT, Vehicle, female, replicate1

description: Library name: Tbl_HvF_1


title: APECED_005_1853817_2_1_3

description:
Library name: 1853817_2_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: Dyrk1a+/I48X, Vehicle, female, replicate5

description: Library name: Dyrk_HvF_5


title: Tbl1xr1, HT, Lithium, male, replicate2

description: Library name: Tbl_HLM_2


title: APECED_002_1760324_1_1_2

description:
Library name: 1760324_1_1_2
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Lithium, female, replicate4

description: Library name: Tbl_HLF_4


title: APECED_001_1753268_2_1_1

description:
Library name: 1753268_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Lithium, female, replicate2

description: Library name: Tbl_HLF_2


title: Healthy_003_1780203_1_1_1

description:
Library name: 1780203_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Lithium, male, replicate4

description: Library name: Tbl_HLM_4


title: Tbl1xr1, HT, Lithium, female, replicate5

description: Library name: Tbl_HLF_5


title: APECED_006_1767709_2_1_1

description:
Library name: 1767709_2_1_1
10x 5prime NextGEM v2


title: Healthy_001_1749853_1_1_1

description:
Library name: 1749853_1_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Lithium, female, replicate3

description: Library name: Tbl_HLF_3


title: APECED_003_1749854_1_1_1

description:
Library name: 1749854_1_1_1
10x 5prime NextGEM v2


title: Healthy_001_1749853_2_1_1

description:
Library name: 1749853_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Fluoxetine, male, replicate4

description: Library name: Tbl_HfM_4


title: Tbl1xr1, HT, Fluoxetine, male, replicate5

description: Library name: Tbl_HfM_5


title: APECED_002_1760324_2_1_2

description:
Library name: 1760324_2_1_2
10x 5prime NextGEM v2


title: APECED_003_1749854_2_1_1

description:
Library name: 1749854_2_1_1
10x 5prime NextGEM v2


title: Tbl1xr1, HT, Fluoxetine, female, replicate5

description: Library name: Tbl_HfF_5


title: Tbl1xr1, HT, Fluoxetine, male, replicate1

description: Library name: Tbl_HfM_1


title: Tbl1xr1, HT, Fluoxetine, female, replicate4

description: Library name: Tbl_HfF_4


title: Tbl1xr1, HT, Fluoxetine, female, replicate2

description: Library name: Tbl_HfF_2


title: Tbl1xr1, WT, Vehicle, male, replicate5

description: Library name: Tbl_WvM_5


title: Tbl1xr1, HT, Fluoxetine, female, replicate1

description: Library name: Tbl_HfF_1


title: SSc subject 2 terazosin

first: Genta

last: Ishikawa

state: Connecticut

address: 300 Cedar Street

department: Pulmonary, Critical Care, and Sleep Medicine

description: Library name: ssc_4_248_329_S10_L001

data_processing:
Raw sequencing reads (FASTQ files) were first assessed for quality using FastQC. No adapter trimming was performed as overall sequence quality was acceptable.
Reads were aligned to the human reference genome (GRCh38 and GENCODE release 43) using STAR aligner
Gene-level read counts were generated using STAR. Raw count matrices were constructed by extracting unstranded counts from STAR output files for each sample. Gene counts from all samples were merged into a single gene-by-sample count matrix.
STAR v2.7.11a
featureCounts
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: primary lung fibroblast

extract_protocol:
Total RNA was extracted using a silica column–based purification kit with on-column DNase digestion, and RNA integrity was confirmed using a microfluidics-based bioanalyzer.
RNA-seq libraries were prepared at the Yale Center for Genome Analysis (YCGA) using the Illumina TruSeq Stranded mRNA Library Prep Kit (poly(A) selection) according to the manufacturer’s protocol.

tag: disease

value: SSc-ILD

value: primary lung fibroblast

value: terazosin


title: SSc subject 4 terazosin

description: Library name: ssc_8_200_377_S14_L001


title: Dyrk1a+/I48X, Fluoxetine, male, replicate5

description: Library name: Dyrk_HfM_5

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)


title: SSc subject 1 terazosin

description: Library name: ssc_2_272_305_S8_L001


title: Tbl1xr1, HT, Fluoxetine, female, replicate3

description: Library name: Tbl_HfF_3


title: IPF subject 4 terazosin

description: Library name: ipf_8_199_378_S22_L001

value: IPF


title: Tbl1xr1, WT, Vehicle, male, replicate2

description: Library name: Tbl_WvM_2

value: prefrontal cortex


title: IPF subject 3 terazosin

description: Library name: ipf_6_223_354_S20_L001


title: IPF subject 3 control

description: Library name: ipf_5_235_342_S19_L001

value: control


title: Tbl1xr1, HT, Fluoxetine, male, replicate3

description: Library name: Tbl_HfM_3


title: IPF subject 2 terazosin

description: Library name: ipf_4_247_330_S18_L001


title: Arid1b, WT, Vehicle, female, replicate5

description: Library name: Arid_WvF_5

value: Wildtype


title: SSc subject 3 control

description: Library name: ssc_5_236_341_S11_L001


title: Tbl1xr1, HT, Fluoxetine, male, replicate2

description: Library name: Tbl_HfM_2


title: SSc subject 3 terazosin

description: Library name: ssc_6_224_353_S12_L001


title: SSc subject 4 control

description: Library name: ssc_7_212_365_S13_L001


title: SSc subject 1 control

description: Library name: ssc_1_284_293_S7_L001


title: Tbl1xr1, HT, Lithium, female, replicate1

description: Library name: Tbl_HLF_1


title: SSc subject 2 control

description: Library name: ssc_3_260_317_S9_L001


title: APECED_007_1780202_1_1_3

description:
Library name: 1780202_1_1_3
10x 5prime NextGEM v2 with Connect BCR Enrichment


title: IPF subject 2 control

description: Library name: ipf_3_259_318_S17_L001


title: IPF subject 1 control

description: Library name: ipf_1_283_294_S15_L001


title: Arid1b, WT, Vehicle, male, replicate3

description: Library name: Arid_WvM_4


title: IPF subject 4 control

description: Library name: ipf_7_211_366_S21_L001


title: Arid1b, WT, Vehicle, male, replicate1

description: Library name: Arid_WvM_2


title: Arid1b, WT, Vehicle, male, replicate4

description: Library name: Arid_WvM_5


title: Dyrk1a+/I48X, Fluoxetine, female, replicate2

description: Library name: Dyrk_HfF_2


title: OPM-2 cells, ATRA+POM

description: Library name: AP

data_processing:
Raw sequencing data were processed to map reads to a reference genome. Peaks of enrichment indicate regions of open chromatin.
Assembly: hg38
Supplementary files format and content: BED files (peaks), BED files (summits)

extract_protocol:
MM cells were prepared, and nuclei were isolated. Tn5 transposase, loaded with sequencing adapters, was added to the nuclei. DNA fragments tagged by Tn5 were purified to remove proteins and other cellular debris.
The adapter-tagged DNA was amplified using PCR to generate a sequencing-ready library. The DNA library was sequenced using next-generation sequencing platforms (Illumina Novaseq 6000).

value: multiple myeloma cell line

value: 1 μM ATRA + 1 μM POM for 72 hours


title: Arid1b, WT, Vehicle, male, replicate2

description: Library name: Arid_WvM_3


title: Arid1b, WT, Vehicle, female, replicate1

description: Library name: Arid_WvF_1


title: OPM-2 cells, POM

description: Library name: P

value: 1 μM POM for 72 hours


title: Arid1b, WT, Vehicle, female, replicate4

description: Library name: Arid_WvF_4


title: IPF subject 1 terazosin

description: Library name: ipf_2_271_306_S16_L001


title: Arid1b, WT, Vehicle, female, replicate3

description: Library name: Arid_WvF_3


title: Arid1b, WT, Vehicle, female, replicate2

description: Library name: Arid_WvF_2


title: Arid1b, WT, Lithium, male, replicate5

description: Library name: Arid_WLM_5


title: OPM-2 cells, DMSO

description: Library name: NC

value: DMSO for 72 hours


title: OPM-2-POM

description: Library name: Sample 7

data_processing:
After quality control and adaptor trimming, sequencing reads were mapped to the UCSC human genome. The featureCounts (version 1.6.4) function was used to determine the expression level of each annotated gene. Differentially expressed genes were identified using DESeq2 (version 1.2.4) as those with a cutoff Benjamini-Hochberg adjusted p value of 0.05 and an absolute fold change of greater than 1.5 (|Log2FC| > 0.58).
Assembly: hg38
Supplementary files format and content: NCI-H929-fpkm.xlsx: Contains FPKM values for the NCI-H929 cells in 4 groups.
Supplementary files format and content: OPM-2-fpkm.txt: Contains FPKM values for the OPM-2 cells in 4 groups.

extract_protocol:
Total RNA from treated MM cells was extracted using TRIzol RNA isolation reagents (Invitrogen).
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.


title: OPM-2-ATRA

description: Library name: Sample 6

value: 1 μM ATRA for 72 hours


title: OPM-2-DMSO

description: Library name: Sample 5


title: Arid1b, WT, Lithium, female, replicate5

description: Library name: Arid_WLF_5


title: NCI-H929-ATRA

description: Library name: Sample 2


title: OPM-2 cells, ATRA

description: Library name: A


title: Arid1b, WT, Lithium, male, replicate1

description: Library name: Arid_WLM_1


title: OPM-2-ATRA+POM

description: Library name: Sample 8


title: Arid1b, WT, Lithium, female, replicate1

description: Library name: Arid_WLF_1


title: Arid1b, WT, Fluoxetine, male, replicate5

description: Library name: Arid_WfM_5


title: NCI-H929-POM

description: Library name: Sample 3


title: Arid1b, WT, Lithium, female, replicate3

description: Library name: Arid_WLF_3


title: Arid1b, WT, Lithium, female, replicate2

description: Library name: Arid_WLF_2


title: Arid1b, WT, Lithium, male, replicate3

description: Library name: Arid_WLM_3


title: Arid1b, WT, Lithium, male, replicate4

description: Library name: Arid_WLM_4


title: Arid1b, WT, Lithium, female, replicate4

description: Library name: Arid_WLF_4


title: NCI-H929-DMSO

description: Library name: Sample 1


title: Arid1b, WT, Fluoxetine, male, replicate2

description: Library name: Arid_WfM_2


title: NCI-H929-ATRA+POM

description: Library name: Sample 4


title: BEAS-2B cells with PR8 and erucic acid, rep3

city: Guangzhou

first: liu

last: lifu

state: Guangdong

address: Panyu xinzao NO.1 Road

institute: Guangzhou Medical University

description:
Library name: V+EA-3
Virus-Erucic_Acid-3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 1.5 or fold change <2/3.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and tpm values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Lung

value: epithelial cells

value: PR8+erucic acid


title: Arid1b, WT, Fluoxetine, male, replicate4

first: Eunjoon

address: Kuseong-dong

description: Library name: Arid_WfM_4


title: Tbl1xr1, WT, Fluoxetine, female, replicate3

description: Library name: Tbl_WfF_3


title: BEAS-2B cells with PR8 and erucic acid, rep2

description:
Library name: V+EA-2
Virus-Erucic_Acid-2


title: BEAS-2B cells with PR8, rep2

description:
Library name: V-2
Virus-2


title: Arid1b, WT, Fluoxetine, male, replicate1

description: Library name: Arid_WfM_1


title: BEAS-2B cells with PR8, rep3

description:
Library name: V-3
Virus-3


title: BEAS-2B cells without treatment, rep3

description:
Library name: NC-3
Control-3

value: without treatment


title: BEAS-2B cells without treatment, rep1

description:
Library name: NC-1
Control-1


title: BEAS-2B cells with PR8 and erucic acid, rep1

description:
Library name: V+EA-1
Virus-Erucic_Acid-1


title: 3D culture from T47D cells at day 6 replicate

city: CDMX

first: Stephanie Iraiz

last: Nuñez Olvera

address: Circuito, Mario de La Cueva s/n

country: Mexico

institute: Universidad Nacional Autónoma de México

description: Library name: T4-C3D2

data_processing:
Sequencing reads were aligned to the human reference genome (hg38) using Bowtie2 within the pipe4C analysis pipeline. The assembly version used was hg38. Supplementary files format and content: .bedgraph files. The library preparation strategy corresponded to 4C-seq.
Assembly: hg38
Supplementary files format and content: .bedGraph
Library strategy: 4C-Seq

source_name: cell line

growth_protocol: 2D culture of BT-474 and T47D cell lines (ATCC) were cultured in Hybri-Care or RPMI medium (Gibco) supplemented with 10% FBS. To establish 3D cultures, 120 µL of Geltrex (Thermo Fisher) was dispensed into 24-well plates and incubated at 37 °C for 30 minutes to solidify. Then, 3.1 × 10⁴ cells from 2D cultures were seeded in 250 µL of medium and incubated for another 30 minutes. An additional 250 µL of medium containing 5% Geltrex was added. From the following day, 3D cultures were maintained by replacing the medium with 500 µL of fresh complete medium every three days.

extract_protocol:
A total of 15 million BT-474 and T47D cells were fixed with 2% formaldehyde in PBS for 10 minutes at room temperature to crosslink chromatin. The reaction was stopped by adding glycine (0.125 M), followed by a 5-minute incubation at 4 °C. Cells were then washed twice with cold PBS to remove residual formaldehyde. Lysis was performed in 5 mL of buffer containing Tris-HCl (50 mM, pH 8.0), NaCl (150 mM), EDTA (5 mM), Igepal CA-630 (0.5%), and Triton X-100 (1%) for 30 minutes on ice. For 3D cultures, cells were additionally dissociated with cold TrypLE™ Express to ensure single-cell suspension prior to lysis. Nuclei were isolated and 10 million were resuspended in 500 µL of 1X NEBuffer r2.1, followed by heat inactivation steps (60 °C for 10 min, then 37 °C for 50 min). Chromatin was digested using 200 U of EcoRI at 37 °C for 6 hours in a thermomixer (900 rpm), with a second enzyme dose added for overnight digestion. Subsequently, proximity ligation was carried out overnight at 16 °C using 100 U of T4 DNA ligase in 7 mL final volume with 5% PEG. To reverse crosslinking, samples were treated with Proteinase K (30 µL, 10 mg/mL) at 65 °C for 6 hours, followed by RNase A (30 µL, 10 mg/mL) at 37 °C for 45 minutes. DNA was purified by phenol–chloroform–isoamyl alcohol extraction and ethanol precipitation. The resulting DNA was then digested overnight with the secondary restriction enzyme Csp6I, purified again, and circularized via a second ligation step (overnight at 16 °C, then 1 hour at room temperature). Circular DNA was purified once more and used as template for 4C library amplification via inverse PCR.
Circularized DNA was used as a template for 4C library amplification via PCR, employing the primers CTD-2566J3.1-Reading (5′-ATGAACTAGGCACAGTGTAC-3′) and CTD-2566J3.1-Non-reading (5′-TTCCAGGGAAACTGCAAATTG-3′). Eight parallel reactions were performed using 100–200 ng of DNA each and amplified with Hot Start Phusion II High-Fidelity DNA Polymerase. PCR products were pooled and purified using the Qiagen PCR Purification Kit. Final 4C libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) and subjected to high-throughput sequencing on the Illumina platform.

value: cell line

value: Breast cancer


title: Arid1b, WT, Fluoxetine, male, replicate3

last: Kim

institute: IBS/KAIST

description: Library name: Arid_WfM_3


title: Arid1b, HT, Vehicle, male, replicate4

description: Library name: Arid_HvM_4

value: Heterozygous


title: Arid1b, WT, Lithium, male, replicate2

description: Library name: Arid_WLM_2


title: Arid1b, WT, Fluoxetine, female, replicate5

description: Library name: Arid_WfF_5


title: 3D culture from T47D cells at day 6

description: Library name: T4-C3D1


title: BEAS-2B cells with PR8, rep1

description:
Library name: V-1
Virus-1


title: 2D culture from T47D cells at day 6 replicate

description: Library name: T4-C2D2


title: Arid1b, WT, Fluoxetine, female, replicate2

description: Library name: Arid_WfF_2


title: Arid1b, WT, Fluoxetine, female, replicate4

description: Library name: Arid_WfF_4


title: 4_HW7KJBGXT.4.CGGAGCCT_TACTCCTT

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: 4_SM-NBWB8_plate2
DHMT_48hr_NT_698_d

data_processing:
To identify cell-type-specific gene expression profiles, the fastq files of the bulk RNA-seq data were aligned to a mixed human-mouse reference genome (GRCh37/hg19 and GRCm38/mm10, GSE63269) using STAR65 (v.2.5). As quality control, Illumina adapters and low-quality base bares were trimmed using Trimmomatic66 (v.0.36) and short reads (< 36 base pairs) were removed. Next the reads were annotated with GENCODE GTF annotation version 19 and a custom GTF file for the mixed genome (GSE63269) for the mixed genome. A raw counts matrix was generated using featureCounts67 by Rsubread (v.1.32). Genes with a total read count less than 10 were filtered using filterByExpr function in edgeR68 (v. 4.2.0). Read counts were then normalized for library size (method = TMM) and transformed to log2 counts-per-million (logCPM) estimates using the voom function by limma69 (v. 3.60.3) package. The normalized logCPM gene expression matrices were used as input for all the following analyses.
Assembly: GRCh37/hg19 and GRCm38/mm10, GSE63269
Supplementary files format and content: counts_raw_all.txt contain raw counts for each sample (link: barcode).
Supplementary files format and content: counts_logCPM_human.txt contain logCPM values for all iPCS WT samples.
Supplementary files format and content: counts_logCPM_mouse.txt contain logCPM values for all astrocyte samples that have not been co-cultured CRISPRi-neurons.
Supplementary files format and content: counts_logCPM_CRISPRi_human.txt contain logCPM values for all CRISPRi-edited iPCS  samples.
Supplementary files format and content: counts_logCPM_CRISPRi_mouse.txt contain logCPM values for all astrocyte samples that have been co-cultured with CRISPRi-neurons.

extract_protocol:
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow

value: iPSC-derived excitatory neuron, astrocyte

value: Non-targeting knockdown

tag: day

tag: guide rna

tag: barcode


title: BEAS-2B cells without treatment, rep2

description:
Library name: NC-2
Control-2

tag: tissue


title: 2D culture from T47D cells at day 6

description: Library name: T4-C2D1


title: Arid1b, WT, Fluoxetine, female, replicate3

city: Daejeon

description: Library name: Arid_WfF_3

value: prefrontal cortex


title: Arid1b, HT, Vehicle, male, replicate1

description: Library name: Arid_HvM_1


title: Arid1b, HT, Vehicle, male, replicate5

description: Library name: Arid_HvM_5


title: Arid1b, HT, Vehicle, male, replicate2

description: Library name: Arid_HvM_2


title: Arid1b, WT, Fluoxetine, female, replicate1

description: Library name: Arid_WfF_1


title: 2_HW7KJBGXT.2.CGGAGCCT_TACTCCTT

description:
Library name: 2_SM-NBWB8_plate2
DHMT_48hr_NT_698_d


title: Arid1b, HT, Vehicle, male, replicate3

description: Library name: Arid_HvM_3


title: Arid1b, HT, Vehicle, female, replicate3

description: Library name: Arid_HvF_3


title: Arid1b, HT, Vehicle, female, replicate4

description: Library name: Arid_HvF_4


title: 3_HW7KJBGXT.3.CGGAGCCT_TACTCCTT

description:
Library name: 3_SM-NBWB8_plate2
DHMT_48hr_NT_698_d


title: Arid1b, HT, Vehicle, female, replicate2

description: Library name: Arid_HvF_2


title: Arid1b, HT, Vehicle, female, replicate1

description: Library name: Arid_HvF_1


title: 1_HW7KJBGXT.1.CGGAGCCT_TACTCCTT

description:
Library name: 1_SM-NBWB8_plate2
DHMT_48hr_NT_698_d


title: 4_HW7KJBGXT.4.GCGTAGTA_TACTCCTT

description:
Library name: 4_SM-NBWB7_plate2
DHMT_48hr_NT_698_c


title: 3_HW7KJBGXT.3.GCGTAGTA_TACTCCTT

description:
Library name: 3_SM-NBWB7_plate2
DHMT_48hr_NT_698_c


title: 2_HW7KJBGXT.2.GCGTAGTA_TACTCCTT

description:
Library name: 2_SM-NBWB7_plate2
DHMT_48hr_NT_698_c


title: Arid1b, HT, Lithium, male, replicate5

description: Library name: Arid_HLM_5


title: 4_HW7KJBGXT.4.GGAGCTAC_TACTCCTT

description:
Library name: 4_SM-NBWB6_plate2
DHMT_48hr_NT_698_b


title: Arid1b, HT, Lithium, male, replicate4

description: Library name: Arid_HLM_4


title: Arid1b, HT, Lithium, female, replicate5

description: Library name: Arid_HLF_5


title: 1_HW7KJBGXT.1.GCGTAGTA_TACTCCTT

description:
Library name: 1_SM-NBWB7_plate2
DHMT_48hr_NT_698_c


title: 2_HW7KJBGXT.2.GGAGCTAC_TACTCCTT

description:
Library name: 2_SM-NBWB6_plate2
DHMT_48hr_NT_698_b


title: 1_HW7KJBGXT.1.GGAGCTAC_TACTCCTT

description:
Library name: 1_SM-NBWB6_plate2
DHMT_48hr_NT_698_b


title: Arid1b, HT, Lithium, male, replicate3

description: Library name: Arid_HLM_3


title: Arid1b, HT, Lithium, female, replicate4

description: Library name: Arid_HLF_4


title: 3_HW7KJBGXT.3.GGAGCTAC_TACTCCTT

description:
Library name: 3_SM-NBWB6_plate2
DHMT_48hr_NT_698_b


title: Arid1b, HT, Lithium, male, replicate1

description: Library name: Arid_HLM_1


title: 4_HW7KJBGXT.4.ACTCGCTA_TACTCCTT

description:
Library name: 4_SM-NBWB5_plate2
DHMT_48hr_NT_698_a


title: Arid1b, HT, Lithium, male, replicate2

description: Library name: Arid_HLM_2


title: Arid1b, HT, Lithium, female, replicate3

description: Library name: Arid_HLF_3


title: 3_HW7KJBGXT.3.ACTCGCTA_TACTCCTT

description:
Library name: 3_SM-NBWB5_plate2
DHMT_48hr_NT_698_a


title: 2_HW7KJBGXT.2.ACTCGCTA_TACTCCTT

description:
Library name: 2_SM-NBWB5_plate2
DHMT_48hr_NT_698_a


title: Arid1b, HT, Lithium, female, replicate2

description: Library name: Arid_HLF_2


title: Arid1b, HT, Lithium, female, replicate1

description: Library name: Arid_HLF_1


title: 1_HW7KJBGXT.1.ACTCGCTA_TACTCCTT

description:
Library name: 1_SM-NBWB5_plate2
DHMT_48hr_NT_698_a


title: Arid1b, HT, Fluoxetine, male, replicate5

description: Library name: Arid_HfM_5


title: 4_HW7KJBGXT.4.CGGAGCCT_TATGCAGT

description:
Library name: 4_SM-NBWAV_plate2
DHMT_48hr_NT_637_d


title: 2_HW7KJBGXT.2.CGGAGCCT_TATGCAGT

description:
Library name: 2_SM-NBWAV_plate2
DHMT_48hr_NT_637_d


title: Arid1b, HT, Fluoxetine, male, replicate2

description: Library name: Arid_HfM_2


title: Arid1b, HT, Fluoxetine, female, replicate5

description: Library name: Arid_HfF_5


title: Arid1b, HT, Fluoxetine, male, replicate1

description: Library name: Arid_HfM_1


title: 4_HW7KJBGXT.4.GCGTAGTA_TATGCAGT

description:
Library name: 4_SM-NBWAU_plate2
DHMT_48hr_NT_637_c


title: Arid1b, HT, Fluoxetine, female, replicate3

description: Library name: Arid_HfF_3


title: 2_HW7KJBGXT.2.GCGTAGTA_TATGCAGT

description:
Library name: 2_SM-NBWAU_plate2
DHMT_48hr_NT_637_c


title: Arid1b, HT, Fluoxetine, female, replicate4

description: Library name: Arid_HfF_4


title: 1_HW7KJBGXT.1.GCGTAGTA_TATGCAGT

description:
Library name: 1_SM-NBWAU_plate2
DHMT_48hr_NT_637_c


title: Arid1b, HT, Fluoxetine, female, replicate1

description: Library name: Arid_HfF_1


title: 4_HW7KJBGXT.4.GGAGCTAC_TATGCAGT

description:
Library name: 4_SM-NBWAT_plate2
DHMT_48hr_NT_637_b


title: Arid1b, HT, Fluoxetine, female, replicate2

description: Library name: Arid_HfF_2