title: 3_HW7KJBGXT.3.GGAGCTAC_TATGCAGT

description:
Library name: 3_SM-NBWAT_plate2
DHMT_48hr_NT_637_b


title: Grin2b, WT, Vehicle, male, replicate5

status: Public on Jul 28 2026

type: SRA

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: G2b_WvM_5

library_source: transcriptomic

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.

molecule: total RNA

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)

tag: tissue

value: prefrontal cortex

tag: strain

tag: genotype

value: Wildtype


title: Grin2b, WT, Vehicle, male, replicate4

description: Library name: G2b_WvM_4


title: 1_HW7KJBGXT.1.GGAGCTAC_TATGCAGT

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: 1_SM-NBWAT_plate2
DHMT_48hr_NT_637_b

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.

organism: Homo sapiens

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

tag: cell line

tag: cell type

value: iPSC-derived excitatory neuron, astrocyte

value: Non-targeting knockdown

tag: day

tag: guide rna

tag: barcode


title: 4_HW7KJBGXT.4.ACTCGCTA_TATGCAGT

description:
Library name: 4_SM-NBWAS_plate2
DHMT_48hr_NT_637_a


title: Grin2b, WT, Vehicle, male, replicate3

description: Library name: G2b_WvM_3


title: Grin2b, WT, Vehicle, male, replicate2

description: Library name: G2b_WvM_2


title: 2_HW7KJBGXT.2.ACTCGCTA_TATGCAGT

description:
Library name: 2_SM-NBWAS_plate2
DHMT_48hr_NT_637_a


title: Grin2b, WT, Vehicle, female, replicate5

description: Library name: G2b_WvF_5


title: Grin2b, WT, Vehicle, male, replicate1

description: Library name: G2b_WvM_1


title: 1_HW7KJBGXT.1.ACTCGCTA_TATGCAGT

description:
Library name: 1_SM-NBWAS_plate2
DHMT_48hr_NT_637_a


title: Grin2b, WT, Vehicle, female, replicate3

description: Library name: G2b_WvF_3


title: Grin2b, WT, Vehicle, female, replicate4

description: Library name: G2b_WvF_4


title: Grin2b, WT, Vehicle, female, replicate2

description: Library name: G2b_WvF_2


title: 2_HW7KJBGXT.2.CGGAGCCT_CTCCTTAC

description:
Library name: 2_SM-NBWAJ_plate2
DHMT_48hr_NT_545_d


title: 1_HW7KJBGXT.1.CGGAGCCT_CTCCTTAC

description:
Library name: 1_SM-NBWAJ_plate2
DHMT_48hr_NT_545_d


title: 3_HW7KJBGXT.3.CGGAGCCT_CTCCTTAC

description:
Library name: 3_SM-NBWAJ_plate2
DHMT_48hr_NT_545_d


title: 3_HW7KJBGXT.3.ACTCGCTA_TATGCAGT

description:
Library name: 3_SM-NBWAS_plate2
DHMT_48hr_NT_637_a


title: Grin2b, WT, Lithium, male, replicate5

description: Library name: G2b_WLM_5


title: Grin2b, WT, Vehicle, female, replicate1

description: Library name: G2b_WvF_1


title: Grin2b, WT, Lithium, male, replicate4

description: Library name: G2b_WLM_4


title: 3_HW7KJBGXT.3.GCGTAGTA_CTCCTTAC

description:
Library name: 3_SM-NBWAI_plate2
DHMT_48hr_NT_545_c


title: 1_HW7KJBGXT.1.GCGTAGTA_CTCCTTAC

description:
Library name: 1_SM-NBWAI_plate2
DHMT_48hr_NT_545_c


title: Grin2b, WT, Lithium, male, replicate1

description: Library name: G2b_WLM_1


title: Grin2b, WT, Lithium, female, replicate5

description: Library name: G2b_WLF_5


title: 4_HW7KJBGXT.4.GGAGCTAC_CTCCTTAC

description:
Library name: 4_SM-NBWAH_plate2
DHMT_48hr_NT_545_b


title: 3_HW7KJBGXT.3.GGAGCTAC_CTCCTTAC

description:
Library name: 3_SM-NBWAH_plate2
DHMT_48hr_NT_545_b


title: Grin2b, WT, Lithium, female, replicate4

description: Library name: G2b_WLF_4


title: 1_HW7KJBGXT.1.GGAGCTAC_CTCCTTAC

description:
Library name: 1_SM-NBWAH_plate2
DHMT_48hr_NT_545_b


title: Grin2b, WT, Lithium, female, replicate2

description: Library name: G2b_WLF_2


title: 4_HW7KJBGXT.4.ACTCGCTA_CTCCTTAC

description:
Library name: 4_SM-NBWAG_plate2
DHMT_48hr_NT_545_a


title: Grin2b, WT, Lithium, female, replicate1

description: Library name: G2b_WLF_1


title: 2_HW7KJBGXT.2.ACTCGCTA_CTCCTTAC

description:
Library name: 2_SM-NBWAG_plate2
DHMT_48hr_NT_545_a


title: Grin2b, WT, Fluoxetine, male, replicate4

description: Library name: G2b_WfM_4


title: 1_HW7KJBGXT.1.ACTCGCTA_CTCCTTAC

description:
Library name: 1_SM-NBWAG_plate2
DHMT_48hr_NT_545_a


title: Grin2b, WT, Fluoxetine, male, replicate3

description: Library name: G2b_WfM_3


title: 4_HW7KJBGXT.4.CGGAGCCT_AGAGGATA

description:
Library name: 4_SM-NBWA7_plate2
DHMT_48hr_Neuron_Mono_d

value: iPSC-derived excitatory neuron

value: WT

value: no guide


title: Grin2b, WT, Fluoxetine, male, replicate2

description: Library name: G2b_WfM_2


title: 3_HW7KJBGXT.3.CGGAGCCT_AGAGGATA

description:
Library name: 3_SM-NBWA7_plate2
DHMT_48hr_Neuron_Mono_d


title: Grin2b, WT, Fluoxetine, male, replicate1

description: Library name: G2b_WfM_1


title: 2_HW7KJBGXT.2.CGGAGCCT_AGAGGATA

description:
Library name: 2_SM-NBWA7_plate2
DHMT_48hr_Neuron_Mono_d


title: 1_HW7KJBGXT.1.CGGAGCCT_AGAGGATA

description:
Library name: 1_SM-NBWA7_plate2
DHMT_48hr_Neuron_Mono_d


title: Grin2b, WT, Fluoxetine, female, replicate3

description: Library name: G2b_WfF_3


title: Grin2b, WT, Fluoxetine, female, replicate5

description: Library name: G2b_WfF_5


title: 4_HW7KJBGXT.4.GCGTAGTA_AGAGGATA

description:
Library name: 4_SM-NBWA6_plate2
DHMT_48hr_Neuron_Mono_c


title: Grin2b,  WT, Fluoxetine, female, replicate4

description: Library name: G2b_WfF_4


title: 3_HW7KJBGXT.3.GCGTAGTA_AGAGGATA

description:
Library name: 3_SM-NBWA6_plate2
DHMT_48hr_Neuron_Mono_c


title: 2_HW7KJBGXT.2.GCGTAGTA_AGAGGATA

description:
Library name: 2_SM-NBWA6_plate2
DHMT_48hr_Neuron_Mono_c


title: Grin2b, WT, Fluoxetine, female, replicate1

description: Library name: G2b_WfF_1


title: 1_HW7KJBGXT.1.GCGTAGTA_AGAGGATA

description:
Library name: 1_SM-NBWA6_plate2
DHMT_48hr_Neuron_Mono_c


title: Grin2b+/C456Y, Vehicle, male, replicate5

description: Library name: G2b_HvM_5

value: Heterozygous


title: 3_HW7KJBGXT.3.GGAGCTAC_AGAGGATA

description:
Library name: 3_SM-NBWA5_plate2
DHMT_48hr_Neuron_Mono_b


title: Grin2b+/C456Y, Vehicle, male, replicate4

description: Library name: G2b_HvM_4


title: 4_HW7KJBGXT.4.GGAGCTAC_AGAGGATA

description:
Library name: 4_SM-NBWA5_plate2
DHMT_48hr_Neuron_Mono_b


title: Grin2b+/C456Y, Vehicle, male, replicate3

description: Library name: G2b_HvM_3


title: Ash1l, WT, Fluoxetine, female, replicate3

description: Library name: ASH_WfF_3


title: 2_HW7KJBGXT.2.GGAGCTAC_AGAGGATA

description:
Library name: 2_SM-NBWA5_plate2
DHMT_48hr_Neuron_Mono_b


title: Grin2b+/C456Y, Vehicle, male, replicate2

description: Library name: G2b_HvM_2


title: 4_HW7KJBGXT.4.ACTCGCTA_AGAGGATA

description:
Library name: 4_SM-NBWA4_plate2
DHMT_48hr_Neuron_Mono_a


title: 1_HW7KJBGXT.1.GGAGCTAC_AGAGGATA

description:
Library name: 1_SM-NBWA5_plate2
DHMT_48hr_Neuron_Mono_b


title: Grin2b+/C456Y, Vehicle, male, replicate1

description: Library name: G2b_HvM_1


title: Grin2b+/C456Y, Vehicle, female, replicate5

description: Library name: G2b_HvF_5


title: 3_HW7KJBGXT.3.ACTCGCTA_AGAGGATA

description:
Library name: 3_SM-NBWA4_plate2
DHMT_48hr_Neuron_Mono_a


title: Grin2b+/C456Y, Vehicle, female, replicate4

description: Library name: G2b_HvF_4


title: Grin2b+/C456Y, Vehicle, female, replicate3

description: Library name: G2b_HvF_3


title: Grin2b+/C456Y, Vehicle, female, replicate2

description: Library name: G2b_HvF_2


title: Grin2b+/C456Y, Vehicle, female, replicate1

description: Library name: G2b_HvF_1


title: 4_HKM7VBGXT.4.ACTGAGCG_CGGAGAGA

description:
Library name: 4_SM-NBW9M_plate1
DHMT_D8_d


title: 3_HKM7VBGXT.3.ACTGAGCG_CGGAGAGA

description:
Library name: 3_SM-NBW9M_plate1
DHMT_D8_d


title: 2_HKM7VBGXT.2.ACTGAGCG_CGGAGAGA

description:
Library name: 2_SM-NBW9M_plate1
DHMT_D8_d


title: Grin2b+/C456Y, Lithium, male, replicate4

description: Library name: G2b_HLM_4


title: Ash1l, HT, Vehicle, male, replicate2

description: Library name: ASH_HvM_2


title: Shank3dC, WT, Fluoxetine, female, replicate3

description: Library name: SdC_WfF_3


title: Grin2b+/C456Y, Lithium, male, replicate3

description: Library name: G2b_HLM_3


title: Ash1l, HT, Vehicle, female, replicate1

description: Library name: ASH_HvF_1


title: Grin2b+/C456Y, Lithium, male, replicate2

description: Library name: G2b_HLM_2


title: 1_HKM7VBGXT.1.ACTGAGCG_CGGAGAGA

description:
Library name: 1_SM-NBW9M_plate1
DHMT_D8_d


title: 4_HKM7VBGXT.4.TAGCGCTC_CGGAGAGA

description:
Library name: 4_SM-NBW9L_plate1
DHMT_D8_c


title: Grin2b+/C456Y, Lithium, male, replicate1

description: Library name: G2b_HLM_1


title: 2_HKM7VBGXT.2.TAGCGCTC_CGGAGAGA

description:
Library name: 2_SM-NBW9L_plate1
DHMT_D8_c


title: Grin2b+/C456Y, Lithium, female, replicate5

description: Library name: G2b_HLF_5


title: Grin2b+/C456Y, Lithium, female, replicate4

description: Library name: G2b_HLF_4


title: Grin2b+/C456Y, Lithium, female, replicate3

description: Library name: G2b_HLF_3


title: 1_HKM7VBGXT.1.TAGCGCTC_CGGAGAGA

description:
Library name: 1_SM-NBW9L_plate1
DHMT_D8_c


title: 4_HKM7VBGXT.4.ATGCGCAG_CGGAGAGA

description:
Library name: 4_SM-NBW9K_plate1
DHMT_D8_b


title: 3_HKM7VBGXT.3.ATGCGCAG_CGGAGAGA

description:
Library name: 3_SM-NBW9K_plate1
DHMT_D8_b


title: Grin2b+/C456Y, Lithium, female, replicate2

description: Library name: G2b_HLF_2


title: 2_HKM7VBGXT.2.ATGCGCAG_CGGAGAGA

description:
Library name: 2_SM-NBW9K_plate1
DHMT_D8_b


title: Grin2b+/C456Y, Lithium, female, replicate1

description: Library name: G2b_HLF_1


title: 1_HKM7VBGXT.1.ATGCGCAG_CGGAGAGA

description:
Library name: 1_SM-NBW9K_plate1
DHMT_D8_b


title: 4_HKM7VBGXT.4.TACGCTGC_CGGAGAGA

description:
Library name: 4_SM-NBW9J_plate1
DHMT_D8_a


title: 3_HKM7VBGXT.3.TACGCTGC_CGGAGAGA

description:
Library name: 3_SM-NBW9J_plate1
DHMT_D8_a


title: Ash1l, HT, Lithium, male, replicate5

description: Library name: ASH_HLM_5


title: Grin2b+/C456Y, Fluoxetine, male, replicate4

description: Library name: G2b_HfM_4


title: 2_HKM7VBGXT.2.TACGCTGC_CGGAGAGA

description:
Library name: 2_SM-NBW9J_plate1
DHMT_D8_a


title: 1_HKM7VBGXT.1.TACGCTGC_CGGAGAGA

description:
Library name: 1_SM-NBW9J_plate1
DHMT_D8_a


title: Grin2b+/C456Y, Fluoxetine, male, replicate1

description: Library name: G2b_HfM_1


title: Grin2b+/C456Y, Fluoxetine, male, replicate2

description: Library name: G2b_HfM_2


title: 4_HKM7VBGXT.4.CGGAGCCT_CGGAGAGA

description:
Library name: 4_SM-NBW9I_plate1
DHMT_6hr_d


title: Grin2b+/C456Y, Fluoxetine, female, replicate5

description: Library name: G2b_HfF_5


title: 3_HKM7VBGXT.3.CGGAGCCT_CGGAGAGA

description:
Library name: 3_SM-NBW9I_plate1
DHMT_6hr_d


title: Grin2b+/C456Y, Fluoxetine, female, replicate4

description: Library name: G2b_HfF_4


title: 2_HKM7VBGXT.2.CGGAGCCT_CGGAGAGA

description:
Library name: 2_SM-NBW9I_plate1
DHMT_6hr_d


title: Grin2b+/C456Y, Lithium, male, replicate5

description: Library name: G2b_HLM_5


title: Grin2b+/C456Y, Fluoxetine, female, replicate2

description: Library name: G2b_HfF_2


title: Grin2b+/C456Y, Fluoxetine, female, replicate3

description: Library name: G2b_HfF_3


title: 1_HKM7VBGXT.1.CGGAGCCT_CGGAGAGA

description:
Library name: 1_SM-NBW9I_plate1
DHMT_6hr_d


title: 4_HKM7VBGXT.4.GCGTAGTA_CGGAGAGA

description:
Library name: 4_SM-NBW9H_plate1
DHMT_6hr_c


title: Grin2b+/C456Y, Fluoxetine, female, replicate1

description: Library name: G2b_HfF_1


title: 3_HKM7VBGXT.3.GCGTAGTA_CGGAGAGA

description:
Library name: 3_SM-NBW9H_plate1
DHMT_6hr_c


title: Chd8, WT, Vehicle, male, replicate5

description: Library name: CHN_WvM_5


title: 2_HKM7VBGXT.2.GCGTAGTA_CGGAGAGA

description:
Library name: 2_SM-NBW9H_plate1
DHMT_6hr_c


title: 1_HKM7VBGXT.1.GCGTAGTA_CGGAGAGA

description:
Library name: 1_SM-NBW9H_plate1
DHMT_6hr_c


title: 3_HKM7VBGXT.3.TAGCGCTC_CGGAGAGA

description:
Library name: 3_SM-NBW9L_plate1
DHMT_D8_c


title: Chd8, WT, Vehicle, male, replicate4

description: Library name: CHN_WvM_4


title: Chd8, WT, Vehicle, male, replicate2

description: Library name: CHN_WvM_2


title: Chd8, WT, Vehicle, male, replicate3

description: Library name: CHN_WvM_3


title: 4_HKM7VBGXT.4.GGAGCTAC_CGGAGAGA

description:
Library name: 4_SM-NBW9G_plate1
DHMT_6hr_b


title: 3_HKM7VBGXT.3.GGAGCTAC_CGGAGAGA

description:
Library name: 3_SM-NBW9G_plate1
DHMT_6hr_b


title: Chd8, WT, Vehicle, male, replicate1

description: Library name: CHN_WvM_1


title: 2_HKM7VBGXT.2.GGAGCTAC_CGGAGAGA

description:
Library name: 2_SM-NBW9G_plate1
DHMT_6hr_b


title: Chd8, WT, Vehicle, female, replicate4

description: Library name: CHN_WvF_4


title: 1_HKM7VBGXT.1.GGAGCTAC_CGGAGAGA

description:
Library name: 1_SM-NBW9G_plate1
DHMT_6hr_b


title: Chd8, WT, Vehicle, female, replicate5

description: Library name: CHN_WvF_5


title: Arid1b, HT, Fluoxetine, male, replicate3

description: Library name: Arid_HfM_3


title: 4_HKM7VBGXT.4.ACTCGCTA_CGGAGAGA

description:
Library name: 4_SM-NBW9F_plate1
DHMT_6hr_a


title: Chd8, WT, Vehicle, female, replicate3

description: Library name: CHN_WvF_3


title: 3_HKM7VBGXT.3.ACTCGCTA_CGGAGAGA

description:
Library name: 3_SM-NBW9F_plate1
DHMT_6hr_a


title: Arid1b, HT, Fluoxetine, male, replicate4

description: Library name: Arid_HfM_4


title: 1_HW7KJBGXT.1.CGGAGCCT_TATGCAGT

description:
Library name: 1_SM-NBWAV_plate2
DHMT_48hr_NT_637_d


title: 3_HW7KJBGXT.3.CGGAGCCT_TATGCAGT

description:
Library name: 3_SM-NBWAV_plate2
DHMT_48hr_NT_637_d


title: 3_HW7KJBGXT.3.GCGTAGTA_TATGCAGT

description:
Library name: 3_SM-NBWAU_plate2
DHMT_48hr_NT_637_c


title: Chd8, WT, Vehicle, female, replicate2

description: Library name: CHN_WvF_2


title: Chd8, WT, Vehicle, female, replicate1

description: Library name: CHN_WvF_1


title: Chd8, WT, Lithium, male, replicate5

description: Library name: CHN_WLM_5


title: 2_HKM7VBGXT.2.ACTCGCTA_CGGAGAGA

description:
Library name: 2_SM-NBW9F_plate1
DHMT_6hr_a


title: 2_HW7KJBGXT.2.GGAGCTAC_TATGCAGT

description:
Library name: 2_SM-NBWAT_plate2
DHMT_48hr_NT_637_b


title: Grin2b+/C456Y, Fluoxetine, male, replicate5

description: Library name: G2b_HfM_5


title: Chd8, WT, Lithium, male, replicate3

description: Library name: CHN_WLM_3


title: 2_HKM7VBGXT.2.ACTGAGCG_ATTAGACG

description:
Library name: 2-SM-NBW9A_plate1
DHMT_D7_d


title: Chd8, WT, Lithium, male, replicate2

description: Library name: CHN_WLM_2


title: 4_HKM7VBGXT.4.ACTGAGCG_ATTAGACG

description:
Library name: 4_SM-NBW9A_plate1
DHMT_D7_d


title: Chd8, WT, Lithium, male, replicate4

description: Library name: CHN_WLM_4


title: 3_HKM7VBGXT.3.ACTGAGCG_ATTAGACG

description:
Library name: 3_SM-NBW9A_plate1
DHMT_D7_d


title: 1_HKM7VBGXT.1.ACTGAGCG_ATTAGACG

description:
Library name: 1_SM-NBW9A_plate1
DHMT_D7_d


title: Chd8, WT, Lithium, male, replicate1

description: Library name: CHN_WLM_1


title: Chd8, WT, Lithium, female, replicate5

description: Library name: CHN_WLF_5


title: 3_HKM7VBGXT.3.TAGCGCTC_ATTAGACG

description:
Library name: 3_SM-NBW99_plate1
DHMT_D7_c


title: Chd8, WT, Lithium, female, replicate2

description: Library name: CHN_WLF_2


title: 3_HKM7VBGXT.3.ATGCGCAG_ATTAGACG

description:
Library name: 3_SM-NBW98_plate1
DHMT_D7_b


title: 1_HKM7VBGXT.1.TAGCGCTC_ATTAGACG

description:
Library name: 1_SM-NBW99_plate1
DHMT_D7_c


title: 4_HKM7VBGXT.4.ATGCGCAG_ATTAGACG

description:
Library name: 4_SM-NBW98_plate1
DHMT_D7_b


title: Chd8, WT, Fluoxetine, male, replicate5

description: Library name: CHN_WfM_5


title: Chd8, WT, Fluoxetine, male, replicate4

description: Library name: CHN_WfM_4


title: 1_HKM7VBGXT.1.ATGCGCAG_ATTAGACG

description:
Library name: 1_SM-NBW98_plate1
DHMT_D7_b


title: Chd8, WT, Lithium, female, replicate1

description: Library name: CHN_WLF_1


title: 3_HKM7VBGXT.3.TACGCTGC_ATTAGACG

description:
Library name: 3_SM-NBW97_plate1
DHMT_D7_a


title: 2_HKM7VBGXT.2.TACGCTGC_ATTAGACG

description:
Library name: 2_SM-NBW97_plate1
DHMT_D7_a


title: Chd8, WT, Fluoxetine, male, replicate1

description: Library name: CHN_WfM_1


title: Chd8, WT, Fluoxetine, female, replicate5

description: Library name: CHN_WfF_5


title: 1_HKM7VBGXT.1.TACGCTGC_ATTAGACG

description:
Library name: 1_SM-NBW97_plate1
DHMT_D7_a


title: Chd8, WT, Fluoxetine, female, replicate4

description: Library name: CHN_WfF_4


title: Chd8, WT, Fluoxetine, male, replicate2

description: Library name: CHN_WfM_2


title: 2_HKM7VBGXT.2.CGGAGCCT_ATTAGACG

description:
Library name: 2_SM-NBW96_plate1
DHMT_5hr_d


title: Chd8, WT, Fluoxetine, female, replicate2

description: Library name: CHN_WfF_2


title: Chd8, WT, Fluoxetine, female, replicate3

description: Library name: CHN_WfF_3


title: 3_HKM7VBGXT.3.CGGAGCCT_ATTAGACG

description:
Library name: 3_SM-NBW96_plate1
DHMT_5hr_d


title: Chd8+/N2373K, Vehicle, male, replicate5

description: Library name: CHN_HvM_5


title: 1_HKM7VBGXT.1.CGGAGCCT_ATTAGACG

description:
Library name: 1_SM-NBW96_plate1
DHMT_5hr_d


title: 4_HKM7VBGXT.4.GCGTAGTA_ATTAGACG

description:
Library name: 4_SM-NBW95_plate1
DHMT_5hr_c


title: Chd8+/N2373K, Vehicle, male, replicate4

description: Library name: CHN_HvM_4


title: 3_HKM7VBGXT.3.GCGTAGTA_ATTAGACG

description:
Library name: 3_SM-NBW95_plate1
DHMT_5hr_c


title: Chd8+/N2373K, Vehicle, male, replicate3

description: Library name: CHN_HvM_3


title: 2_HKM7VBGXT.2.GCGTAGTA_ATTAGACG

description:
Library name: 2_SM-NBW95_plate1
DHMT_5hr_c


title: Chd8+/N2373K, Vehicle, male, replicate2

description: Library name: CHN_HvM_2


title: 1_HKM7VBGXT.1.GCGTAGTA_ATTAGACG

description:
Library name: 1_SM-NBW95_plate1
DHMT_5hr_c


title: Chd8+/N2373K, Vehicle, male, replicate1

description: Library name: CHN_HvM_1


title: 3_HKM7VBGXT.3.GGAGCTAC_ATTAGACG

description:
Library name: 3_SM-NBW94_plate1
DHMT_5hr_b


title: Chd8+/N2373K, Vehicle, female, replicate4

description: Library name: CHN_HvF_4


title: Chd8+/N2373K, Vehicle, female, replicate3

description: Library name: CHN_HvF_3


title: 2_HKM7VBGXT.2.GGAGCTAC_ATTAGACG

description:
Library name: 2_SM-NBW94_plate1
DHMT_5hr_b


title: Chd8+/N2373K, Vehicle, female, replicate2

description: Library name: CHN_HvF_2


title: 1_HKM7VBGXT.1.GGAGCTAC_ATTAGACG

description:
Library name: 1_SM-NBW94_plate1
DHMT_5hr_b


title: 4_HKM7VBGXT.4.ACTCGCTA_ATTAGACG

description:
Library name: 4_SM-NBW93_plate1
DHMT_5hr_a


title: Chd8+/N2373K, Vehicle, female, replicate1

description: Library name: CHN_HvF_1


title: 3_HKM7VBGXT.3.ACTCGCTA_ATTAGACG

description:
Library name: 3_SM-NBW93_plate1
DHMT_5hr_a


title: Chd8+/N2373K, Lithium, male, replicate5

description: Library name: CHN_HLM_5


title: 2_HKM7VBGXT.2.ACTCGCTA_ATTAGACG

description:
Library name: 2_SM-NBW93_plate1
DHMT_5hr_a


title: Chd8+/N2373K, Lithium, male, replicate4

description: Library name: CHN_HLM_4


title: 1_HKM7VBGXT.1.ACTCGCTA_ATTAGACG

description:
Library name: 1_SM-NBW93_plate1
DHMT_5hr_a


title: Chd8+/N2373K, Lithium, male, replicate3

description: Library name: CHN_HLM_3


title: 4_HKM7VBGXT.4.TCGACGTC_AGGCTTAG

description:
Library name: 4_SM-NBW92_plate1
DHMT_48hr_LDLR_C_d

value: LDLR knockdown


title: Chd8+/N2373K, Lithium, male, replicate2

description: Library name: CHN_HLM_2


title: 3_HKM7VBGXT.3.TCGACGTC_AGGCTTAG

description:
Library name: 3_SM-NBW92_plate1
DHMT_48hr_LDLR_C_d


title: Chd8+/N2373K, Lithium, male, replicate1

description: Library name: CHN_HLM_1


title: Chd8+/N2373K, Lithium, female, replicate5

description: Library name: CHN_HLF_5


title: 2_HKM7VBGXT.2.TCGACGTC_AGGCTTAG

description:
Library name: 2_SM-NBW92_plate1
DHMT_48hr_LDLR_C_d


title: 1_HKM7VBGXT.1.TCGACGTC_AGGCTTAG

description:
Library name: 1_SM-NBW92_plate1
DHMT_48hr_LDLR_C_d


title: Chd8+/N2373K, Lithium, female, replicate4

description: Library name: CHN_HLF_4


title: 4_HKM7VBGXT.4.TGCAGCTA_AGGCTTAG

description:
Library name: 4_SM-NBW91_plate1
DHMT_48hr_LDLR_C_c


title: Chd8+/N2373K, Lithium, female, replicate3

description: Library name: CHN_HLF_3


title: 3_HKM7VBGXT.3.TGCAGCTA_AGGCTTAG

description:
Library name: 3_SM-NBW91_plate1
DHMT_48hr_LDLR_C_c


title: 2_HKM7VBGXT.2.TGCAGCTA_AGGCTTAG

description:
Library name: 2_SM-NBW91_plate1
DHMT_48hr_LDLR_C_c


title: Chd8+/N2373K, Lithium, female, replicate2

description: Library name: CHN_HLF_2


title: 1_HKM7VBGXT.1.TGCAGCTA_AGGCTTAG

description:
Library name: 1_SM-NBW91_plate1
DHMT_48hr_LDLR_C_c


title: Chd8+/N2373K, Lithium, female, replicate1

description: Library name: CHN_HLF_1


title: Chd8+/N2373K, Fluoxetine, male, replicate5

description: Library name: CHN_HfM_5


title: 4_HKM7VBGXT.4.CGATCAGT_AGGCTTAG

description:
Library name: 4_SM-NBW8Z_plate1
DHMT_48hr_LDLR_C_b


title: Chd8+/N2373K, Fluoxetine, male, replicate4

description: Library name: CHN_HfM_4


title: 3_HKM7VBGXT.3.CGATCAGT_AGGCTTAG

description:
Library name: 3_SM-NBW8Z_plate1
DHMT_48hr_LDLR_C_b


title: Chd8+/N2373K, Fluoxetine, male, replicate3

description: Library name: CHN_HfM_3


title: 1_HKM7VBGXT.1.ACTCGCTA_CGGAGAGA

description:
Library name: 1_SM-NBW9F_plate1
DHMT_6hr_a


title: 4_HKM7VBGXT.4.TAGCGCTC_ATTAGACG

description:
Library name: 4_SM-NBW99_plate1
DHMT_D7_c


title: 2_HKM7VBGXT.2.CGATCAGT_AGGCTTAG

description:
Library name: 2_SM-NBW8Z_plate1
DHMT_48hr_LDLR_C_b


title: Chd8+/N2373K, Fluoxetine, male, replicate2

description: Library name: CHN_HfM_2


title: Chd8+/N2373K, Fluoxetine, male, replicate1

description: Library name: CHN_HfM_1


title: 2_HKM7VBGXT.2.ATGCGCAG_ATTAGACG

description:
Library name: 2_SM-NBW98_plate1
DHMT_D7_b


title: 4_HKM7VBGXT.4.CCTAAGAC_AGGCTTAG

description:
Library name: 4_SM-NBW8Y_plate1
DHMT_48hr_LDLR_C_a


title: Chd8, WT, Lithium, female, replicate3

description: Library name: CHN_WLF_3


title: 2_HKM7VBGXT.2.TAGCGCTC_ATTAGACG

description:
Library name: 2_SM-NBW99_plate1
DHMT_D7_c


title: 1_HKM7VBGXT.1.CGATCAGT_AGGCTTAG

description:
Library name: 1_SM-NBW8Z_plate1
DHMT_48hr_LDLR_C_b


title: Chd8, WT, Lithium, female, replicate4

description: Library name: CHN_WLF_4


title: Chd8+/N2373K, Fluoxetine, female, replicate5

description: Library name: CHN_HfF_5


title: 4_HKM7VBGXT.4.TACGCTGC_ATTAGACG

description:
Library name: 4_SM-NBW97_plate1
DHMT_D7_a


title: 3_HKM7VBGXT.3.CCTAAGAC_AGGCTTAG

description:
Library name: 3_SM-NBW8Y_plate1
DHMT_48hr_LDLR_C_a


title: Chd8+/N2373K, Fluoxetine, female, replicate4

description: Library name: CHN_HfF_4


title: Chd8, WT, Fluoxetine, male, replicate3

description: Library name: CHN_WfM_3


title: 1_HKM7VBGXT.1.CCTAAGAC_AGGCTTAG

description:
Library name: 1_SM-NBW8Y_plate1
DHMT_48hr_LDLR_C_a


title: 4_HKM7VBGXT.4.ACTGAGCG_AGGCTTAG

description:
Library name: 4_SM-NBW8X_plate1
DHMT_D6_d


title: 4_HKM7VBGXT.4.CGGAGCCT_ATTAGACG

description:
Library name: 4_SM-NBW96_plate1
DHMT_5hr_d


title: Chd8+/N2373K, Fluoxetine, female, replicate3

description: Library name: CHN_HfF_3


title: 2_HKM7VBGXT.2.CCTAAGAC_AGGCTTAG

description:
Library name: 2_SM-NBW8Y_plate1
DHMT_48hr_LDLR_C_a


title: Adnp, WT, Vehicle, male, replicate7

description: Library name: ADNP_WvM_7


title: Chd8+/N2373K, Fluoxetine, female, replicate1

description: Library name: CHN_HfF_1


title: 2_HKM7VBGXT.2.ACTGAGCG_AGGCTTAG

description:
Library name: 2_SM-NBW8X_plate1
DHMT_D6_d


title: Chd8+/N2373K, Fluoxetine, female, replicate2

description: Library name: CHN_HfF_2


title: Adnp, WT, Vehicle, male, replicate6

description: Library name: ADNP_WvM_6


title: 3_HKM7VBGXT.3.ACTGAGCG_AGGCTTAG

description:
Library name: 3_SM-NBW8X_plate1
DHMT_D6_d


title: Adnp, WT, Vehicle, male, replicate3

description: Library name: ADNP_WvM_3


title: 1_HKM7VBGXT.1.TAGCGCTC_AGGCTTAG

description:
Library name: 1_SM-NBW8W_plate1
DHMT_D6_c


title: 4_HKM7VBGXT.4.ATGCGCAG_AGGCTTAG

description:
Library name: 4_SM-NBW8V_plate1
DHMT_D6_b


title: Adnp, WT, Vehicle, male, replicate2

description: Library name: ADNP_WvM_2


title: Adnp, WT, Vehicle, male, replicate1

description: Library name: ADNP_WvM_1


title: Adnp, WT, Vehicle, female, replicate7

description: Library name: ADNP_WvF_7


title: 2_HKM7VBGXT.2.ATGCGCAG_AGGCTTAG

description:
Library name: 2_SM-NBW8V_plate1
DHMT_D6_b


title: Adnp, WT, Vehicle, female, replicate6

description: Library name: ADNP_WvF_6


title: 1_HKM7VBGXT.1.ATGCGCAG_AGGCTTAG

description:
Library name: 1_SM-NBW8V_plate1
DHMT_D6_b


title: 1_HKM7VBGXT.1.ACTGAGCG_AGGCTTAG

description:
Library name: 1_SM-NBW8X_plate1
DHMT_D6_d


title: Adnp, WT, Vehicle, male, replicate4

description: Library name: ADNP_WvM_4


title: 4_HKM7VBGXT.4.TAGCGCTC_AGGCTTAG

description:
Library name: 4_SM-NBW8W_plate1
DHMT_D6_c


title: 3_HKM7VBGXT.3.TAGCGCTC_AGGCTTAG

description:
Library name: 3_SM-NBW8W_plate1
DHMT_D6_c


title: Chd8, WT, Fluoxetine, female, replicate1

description: Library name: CHN_WfF_1


title: 2_HKM7VBGXT.2.TAGCGCTC_AGGCTTAG

description:
Library name: 2_SM-NBW8W_plate1
DHMT_D6_c


title: 3_HKM7VBGXT.3.ATGCGCAG_AGGCTTAG

description:
Library name: 3_SM-NBW8V_plate1
DHMT_D6_b


title: Adnp, WT, Vehicle, male, replicate5

description: Library name: ADNP_WvM_5


title: 4_HKM7VBGXT.4.TACGCTGC_AGGCTTAG

description:
Library name: 4_SM-NBW8U_plate1
DHMT_D6_a


title: Chd8+/N2373K, Vehicle, female, replicate5

description: Library name: CHN_HvF_5


title: Adnp, WT, Vehicle, female, replicate3

description: Library name: ADNP_WvF_3


title: 2_HKM7VBGXT.2.TACGCTGC_AGGCTTAG

description:
Library name: 2_SM-NBW8U_plate1
DHMT_D6_a


title: Adnp, WT, Vehicle, female, replicate1

description: Library name: ADNP_WvF_1


title: 3_HKM7VBGXT.3.CGGAGCCT_AGGCTTAG

description:
Library name: 3_SM-NBW8T_plate1
DHMT_4hr_d


title: Grin2b, WT, Lithium, female, replicate3

description: Library name: G2b_WLF_3


title: Adnp, WT, Lithium, male, replicate2

description: Library name: ADNP_WLM_2


title: Adnp, WT, Vehicle, female, replicate5

description: Library name: ADNP_WvF_5


title: Adnp, WT, Vehicle, female, replicate8

description: Library name: ADNP_WvF_8


title: 4_HW7KJBGXT.4.CGGAGCCT_CTCCTTAC

description:
Library name: 4_SM-NBWAJ_plate2
DHMT_48hr_NT_545_d


title: Adnp, WT, Lithium, female, replicate5

description: Library name: ADNP_WLF_5


title: 4_HKM7VBGXT.4.GGAGCTAC_ATTAGACG

description:
Library name: 4_SM-NBW94_plate1
DHMT_5hr_b


title: 1_HKM7VBGXT.1.CGGAGCCT_AGGCTTAG

description:
Library name: 1_SM-NBW8T_plate1
DHMT_4hr_d


title: 1_HKM7VBGXT.1.TACGCTGC_AGGCTTAG

description:
Library name: 1_SM-NBW8U_plate1
DHMT_D6_a


title: 2_HKM7VBGXT.2.CGGAGCCT_AGGCTTAG

description:
Library name: 2_SM-NBW8T_plate1
DHMT_4hr_d


title: 4_HKM7VBGXT.4.GCGTAGTA_AGGCTTAG

description:
Library name: 4_SM-NBW8S_plate1
DHMT_4hr_c


title: Grin2b, WT, Lithium, male, replicate3

description: Library name: G2b_WLM_3


title: 4_HKM7VBGXT.4.CGGAGCCT_AGGCTTAG

description:
Library name: 4_SM-NBW8T_plate1
DHMT_4hr_d


title: Grin2b, WT, Lithium, male, replicate2

description: Library name: G2b_WLM_2


title: Grin2b, WT, Fluoxetine, male, replicate5

description: Library name: G2b_WfM_5


title: Adnp, WT, Lithium, female, replicate4

description: Library name: ADNP_WLF_4


title: 3_HKM7VBGXT.3.TACGCTGC_AGGCTTAG

description:
Library name: 3_SM-NBW8U_plate1
DHMT_D6_a


title: Adnp, WT, Lithium, male, replicate3

description: Library name: ADNP_WLM_3


title: Adnp, WT, Lithium, male, replicate1

description: Library name: ADNP_WLM_1


title: 2_HW7KJBGXT.2.GCGTAGTA_CTCCTTAC

description:
Library name: 2_SM-NBWAI_plate2
DHMT_48hr_NT_545_c


title: Adnp, WT, Vehicle, female, replicate2

description: Library name: ADNP_WvF_2


title: Adnp, WT, Vehicle, female, replicate4

description: Library name: ADNP_WvF_4


title: 3_HKM7VBGXT.3.GCGTAGTA_AGGCTTAG

description:
Library name: 3_SM-NBW8S_plate1
DHMT_4hr_c


title: Adnp, WT, Lithium, female, replicate3

description: Library name: ADNP_WLF_3


title: 2_HKM7VBGXT.2.GCGTAGTA_AGGCTTAG

description:
Library name: 2_SM-NBW8S_plate1
DHMT_4hr_c


title: 1_HKM7VBGXT.1.GCGTAGTA_AGGCTTAG

description:
Library name: 1_SM-NBW8S_plate1
DHMT_4hr_c


title: Adnp, WT, Lithium, female, replicate2

description: Library name: ADNP_WLF_2


title: Adnp, WT, Lithium, female, replicate1

description: Library name: ADNP_WLF_1


title: 4_HKM7VBGXT.4.GGAGCTAC_AGGCTTAG

description:
Library name: 4_SM-NBW8R_plate1
DHMT_4hr_b


title: Grin2b, WT, Fluoxetine, female, replicate2

description: Library name: G2b_WfF_2


title: 1_HKM7VBGXT.1.ACTCGCTA_AGGCTTAG

description:
Library name: 1_SM-NBW8Q_plate1
DHMT_4hr_a


title: Adnp, WT, Fluoxetine, male, replicate4

description: Library name: ADNP_WfM_4


title: Adnp, WT, Fluoxetine, male, replicate2

description: Library name: ADNP_WfM_2


title: 1_HKM7VBGXT.1.GGAGCTAC_AGGCTTAG

description:
Library name: 1_SM-NBW8R_plate1
DHMT_4hr_b


title: 3_HKM7VBGXT.3.ACTCGCTA_AGGCTTAG

description:
Library name: 3_SM-NBW8Q_plate1
DHMT_4hr_a


title: Adnp, WT, Fluoxetine, female, replicate2

description: Library name: ADNP_WfF_2


title: 4_HKM7VBGXT.4.TCGACGTC_TACTCCTT

description:
Library name: 4_SM-NBW8P_plate1
DHMT_48hr_LDLR_B_d


title: Adnp, WT, Fluoxetine, male, replicate5

description: Library name: ADNP_WfM_5


title: 3_HKM7VBGXT.3.GGAGCTAC_AGGCTTAG

description:
Library name: 3_SM-NBW8R_plate1
DHMT_4hr_b


title: 4_HKM7VBGXT.4.ACTCGCTA_AGGCTTAG

description:
Library name: 4_SM-NBW8Q_plate1
DHMT_4hr_a


title: 2_HKM7VBGXT.2.ACTCGCTA_AGGCTTAG

description:
Library name: 2_SM-NBW8Q_plate1
DHMT_4hr_a


title: Adnp, WT, Fluoxetine, female, replicate5

description: Library name: ADNP_WfF_5


title: Adnp, WT, Fluoxetine, male, replicate1

description: Library name: ADNP_WfM_1


title: 2_HKM7VBGXT.2.GGAGCTAC_AGGCTTAG

description:
Library name: 2_SM-NBW8R_plate1
DHMT_4hr_b


title: Adnp, WT, Fluoxetine, female, replicate3

description: Library name: ADNP_WfF_3


title: Adnp, WT, Fluoxetine, female, replicate1

description: Library name: ADNP_WfF_1


title: Adnp, WT, Fluoxetine, male, replicate3

description: Library name: ADNP_WfM_3


title: 2_HKM7VBGXT.2.TCGACGTC_TACTCCTT

description:
Library name: 2_SM-NBW8P_plate1
DHMT_48hr_LDLR_B_d


title: Adnp, HT, Vehicle, male, replicate8

description: Library name: ADNP_HvM_8


title: Adnp, HT, Vehicle, male, replicate7

description: Library name: ADNP_HvM_7


title: Adnp, WT, Fluoxetine, female, replicate4

description: Library name: ADNP_WfF_4


title: 3_HKM7VBGXT.3.TCGACGTC_TACTCCTT

description:
Library name: 3_SM-NBW8P_plate1
DHMT_48hr_LDLR_B_d


title: 2_HKM7VBGXT.2.TGCAGCTA_TACTCCTT

description:
Library name: 2_SM-NBW8O_plate1
DHMT_48hr_LDLR_B_c


title: 4_HKM7VBGXT.4.TGCAGCTA_TACTCCTT

description:
Library name: 4_SM-NBW8O_plate1
DHMT_48hr_LDLR_B_c


title: Adnp, HT, Vehicle, male, replicate5

description: Library name: ADNP_HvM_5


title: 3_HKM7VBGXT.3.TGCAGCTA_TACTCCTT

description:
Library name: 3_SM-NBW8O_plate1
DHMT_48hr_LDLR_B_c


title: 1_HKM7VBGXT.1.TCGACGTC_TACTCCTT

description:
Library name: 1_SM-NBW8P_plate1
DHMT_48hr_LDLR_B_d


title: Adnp, HT, Vehicle, male, replicate6

description: Library name: ADNP_HvM_6


title: 2_HKM7VBGXT.2.CGATCAGT_TACTCCTT

description:
Library name: 2_SM-NBW8N_plate1
DHMT_48hr_LDLR_B_b


title: 3_HKM7VBGXT.3.CGATCAGT_TACTCCTT

description:
Library name: 3_SM-NBW8N_plate1
DHMT_48hr_LDLR_B_b


title: Adnp, HT, Vehicle, female, replicate6

description: Library name: ADNP_HvF_6


title: Adnp, HT, Vehicle, female, replicate5

description: Library name: ADNP_HvF_5


title: 1_HKM7VBGXT.1.TGCAGCTA_TACTCCTT

description:
Library name: 1_SM-NBW8O_plate1
DHMT_48hr_LDLR_B_c


title: 4_HKM7VBGXT.4.CGATCAGT_TACTCCTT

description:
Library name: 4_SM-NBW8N_plate1
DHMT_48hr_LDLR_B_b


title: Adnp, HT, Vehicle, male, replicate3

description: Library name: ADNP_HvM_3


title: Adnp, HT, Vehicle, male, replicate4

description: Library name: ADNP_HvM_4


title: Adnp, HT, Vehicle, male, replicate1

description: Library name: ADNP_HvM_1


title: Adnp, HT, Vehicle, female, replicate8

description: Library name: ADNP_HvF_8


title: Adnp, HT, Vehicle, female, replicate7

description: Library name: ADNP_HvF_7


title: 4_HKM7VBGXT.4.CCTAAGAC_TACTCCTT

description:
Library name: 4_SM-NBW8M_plate1
DHMT_48hr_LDLR_B_a


title: 1_HKM7VBGXT.1.CGATCAGT_TACTCCTT

description:
Library name: 1_SM-NBW8N_plate1
DHMT_48hr_LDLR_B_b


title: 1_HKM7VBGXT.1.CCTAAGAC_TACTCCTT

description:
Library name: 1_SM-NBW8M_plate1
DHMT_48hr_LDLR_B_a


title: 3_HKM7VBGXT.3.CCTAAGAC_TACTCCTT

description:
Library name: 3_SM-NBW8M_plate1
DHMT_48hr_LDLR_B_a


title: 4_HKM7VBGXT.4.ACTGAGCG_TACTCCTT

description:
Library name: 4_SM-NBW8L_plate1
DHMT_D5_d


title: 2_HKM7VBGXT.2.CCTAAGAC_TACTCCTT

description:
Library name: 2_SM-NBW8M_plate1
DHMT_48hr_LDLR_B_a


title: Adnp, HT, Vehicle, female, replicate4

description: Library name: ADNP_HvF_4


title: Adnp, HT, Vehicle, female, replicate3

description: Library name: ADNP_HvF_3


title: Adnp, HT, Vehicle, female, replicate2

description: Library name: ADNP_HvF_2


title: 1_HW7KJBGXT.1.ACTCGCTA_AGAGGATA

description:
Library name: 1_SM-NBWA4_plate2
DHMT_48hr_Neuron_Mono_a


title: 3_HKM7VBGXT.3.ACTGAGCG_TACTCCTT

description:
Library name: 3_SM-NBW8L_plate1
DHMT_D5_d


title: Adnp, HT, Vehicle, female, replicate1

description: Library name: ADNP_HvF_1


title: 2_HKM7VBGXT.2.ACTGAGCG_TACTCCTT

description:
Library name: 2_SM-NBW8L_plate1
DHMT_D5_d


title: Adnp, HT, Lithium, male, replicate5

description: Library name: ADNP_HLM_5


title: 1_HKM7VBGXT.1.ACTGAGCG_TACTCCTT

description:
Library name: 1_SM-NBW8L_plate1
DHMT_D5_d


title: Adnp, HT, Lithium, male, replicate3

description: Library name: ADNP_HLM_3


title: 4_HKM7VBGXT.4.TAGCGCTC_TACTCCTT

description:
Library name: 4_SM-NBW8K_plate1
DHMT_D5_c


title: Adnp, HT, Lithium, male, replicate2

description: Library name: ADNP_HLM_2


title: 1_HKM7VBGXT.1.TAGCGCTC_TACTCCTT

description:
Library name: 1_SM-NBW8K_plate1
DHMT_D5_c


title: 2_HKM7VBGXT.2.TAGCGCTC_TACTCCTT

description:
Library name: 2_SM-NBW8K_plate1
DHMT_D5_c


title: Adnp, HT, Lithium, female, replicate4

description: Library name: ADNP_HLF_5


title: Adnp, HT, Lithium, male, replicate4

description: Library name: ADNP_HLM_4


title: Adnp, HT, Lithium, female, replicate2

description: Library name: ADNP_HLF_2


title: 3_HKM7VBGXT.3.ATGCGCAG_TACTCCTT

description:
Library name: 3_SM-NBW8J_plate1
DHMT_D5_b


title: Adnp, HT, Lithium, female, replicate3

description: Library name: ADNP_HLF_3


title: 1_HKM7VBGXT.1.ATGCGCAG_TACTCCTT

description:
Library name: 1_SM-NBW8J_plate1
DHMT_D5_b


title: Adnp, HT, Lithium, female, replicate1

description: Library name: ADNP_HLF_1


title: 4_HKM7VBGXT.4.ATGCGCAG_TACTCCTT

description:
Library name: 4_SM-NBW8J_plate1
DHMT_D5_b


title: Adnp, HT, Fluoxetine, male, replicate5

description: Library name: ADNP_HfM_5


title: 4_HKM7VBGXT.4.TACGCTGC_TACTCCTT

description:
Library name: 4_SM-NBW8I_plate1
DHMT_D5_a


title: 2_HKM7VBGXT.2.ATGCGCAG_TACTCCTT

description:
Library name: 2_SM-NBW8J_plate1
DHMT_D5_b


title: Adnp, HT, Fluoxetine, male, replicate3

description: Library name: ADNP_HfM_3


title: 3_HKM7VBGXT.3.TACGCTGC_TACTCCTT

description:
Library name: 3_SM-NBW8I_plate1
DHMT_D5_a


title: Adnp, HT, Fluoxetine, male, replicate4

description: Library name: ADNP_HfM_4


title: 2_HKM7VBGXT.2.TACGCTGC_TACTCCTT

description:
Library name: 2_SM-NBW8I_plate1
DHMT_D5_a


title: Adnp, HT, Fluoxetine, male, replicate2

description: Library name: ADNP_HfM_2


title: 1_HKM7VBGXT.1.TACGCTGC_TACTCCTT

description:
Library name: 1_SM-NBW8I_plate1
DHMT_D5_a


title: 4_HKM7VBGXT.4.CGGAGCCT_TACTCCTT

description:
Library name: 4_SM-NBW8H_plate1
DHMT_3hr_d


title: Adnp, HT, Fluoxetine, female, replicate4

description: Library name: ADNP_HfF_4


title: Adnp, HT, Fluoxetine, female, replicate5

description: Library name: ADNP_HfF_5


title: 3_HKM7VBGXT.3.CGGAGCCT_TACTCCTT

description:
Library name: 3_SM-NBW8H_plate1
DHMT_3hr_d


title: 2_HKM7VBGXT.2.CGGAGCCT_TACTCCTT

description:
Library name: 2_SM-NBW8H_plate1
DHMT_3hr_d


title: Adnp, HT, Fluoxetine, male, replicate1

description: Library name: ADNP_HfM_1


title: 4_HKM7VBGXT.4.GCGTAGTA_TACTCCTT

description:
Library name: 4_SM-NBW8G_plate1
DHMT_3hr_c


title: Adnp, HT, Fluoxetine, female, replicate3

description: Library name: ADNP_HfF_3


title: Adnp, HT, Fluoxetine, female, replicate1

description: Library name: ADNP_HfF_1


title: 3_HKM7VBGXT.3.GCGTAGTA_TACTCCTT

description:
Library name: 3_SM-NBW8G_plate1
DHMT_3hr_c


title: Adnp, HT, Fluoxetine, female, replicate2

description: Library name: ADNP_HfF_2


title: 1_HKM7VBGXT.1.CGGAGCCT_TACTCCTT

description:
Library name: 1_SM-NBW8H_plate1
DHMT_3hr_d


title: 4_HW7KJBGXT.4.CGGAGCCT_ATAGAGAG

description:
Library name: 4_SM-NBW9U_plate2
DHMT_48hr_Astrocyte_Mono_d

value: Astrocyte


title: output-XETG00254__0041402__EMBRYO7__20250430__192524

type: RNA

city: New York

first: Jeremy

last: Dasen

state: New York

address: 435 East 30th St NSB 1104

department: Neuroscience

country: USA

institute: NYU School of Medicine

description: Transverse embryonic section containing rostral pectoral, caudal pectoral and pelvic spinal cord and dorsal root ganglia.

hyb_protocol: Tissue sections from Leucoraja erinacea embryos were analyzed using a custom Xenium In Situ panel (10x Genomics) targeting 300 genes associated with sensory neuron identity, spinal cord patterning, neuronal signaling, and development. Hybridization, probe ligation, rolling circle amplification, and sequential imaging were performed according to the manufacturer's Xenium In Situ Gene Expression protocol.

scan_protocol: Samples were imaged using the 10x Genomics Xenium Analyzer following the manufacturer's standard imaging protocol. Fluorescent images were acquired across multiple imaging cycles and decoded to identify individual RNA molecules. High-resolution morphology images were collected for tissue visualization and cell segmentation.

data_processing: Raw image data were processed using Xenium Analyzer software (10x Genomics) with default image processing, transcript decoding, quality filtering, cell segmentation, and transcript assignment parameters. Processed outputs included transcript coordinates, cell-by-gene expression matrices, cell and nuclear segmentation boundaries, and morphology images. Downstream visualization and region-of-interest analyses were performed using Xenium Explorer version 4.1.1.

label: Xenium probe set

organism: Leucoraja erinaceus

source_name: embryonic trunk transverse section

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Skate embryos were fixed for 2 hours in 4% paraformaldehyde, washed with PBS, and placed in 30% sucrose overnight. Skate tissue was embedded on OCT, and sectioned at 10 µm.

value: embryonic trunk transverse section

tag: tissue preservation method

value: 4% paraformaldehyde fixation followed by sucrose cryoprotection and OCT embedding

tag: embryo number

value: c

tag: segments in region

value: Pel, cPec, rPec, pel, cPec, rPec

tag: embryonic stage

tag: fin-ablated side

value: left


title: output-XETG00254__0041402__EMBRYO8__20250430__192524

value: d


title: 2_HKM7VBGXT.2.GCGTAGTA_TACTCCTT

description:
Library name: 2_SM-NBW8G_plate1
DHMT_3hr_c


title: 3_HW7KJBGXT.3.CGGAGCCT_ATAGAGAG

description:
Library name: 3_SM-NBW9U_plate2
DHMT_48hr_Astrocyte_Mono_d


title: output-XETG00254__0041402__EMBRYO6__20250430__192524

value: b


title: output-XETG00254__0041402__EMBRYO5__20250430__192524

value: a

value: right


title: 1_HKM7VBGXT.1.GCGTAGTA_TACTCCTT

description:
Library name: 1_SM-NBW8G_plate1
DHMT_3hr_c

value: iPSC-derived excitatory neuron, astrocyte


title: output-XETG00254__0041370__EMBRYO4__20250430__192524


title: 2_HW7KJBGXT.2.CGGAGCCT_ATAGAGAG

description:
Library name: 2_SM-NBW9U_plate2
DHMT_48hr_Astrocyte_Mono_d


title: output-XETG00254__0041370__EMBRYO3__20250430__192524


title: 4_HKM7VBGXT.4.GGAGCTAC_TACTCCTT

description:
Library name: 4_SM-NBW8F_plate1
DHMT_3hr_b


title: 1_HW7KJBGXT.1.CGGAGCCT_ATAGAGAG

description:
Library name: 1_SM-NBW9U_plate2
DHMT_48hr_Astrocyte_Mono_d


title: 3_HKM7VBGXT.3.GGAGCTAC_TACTCCTT

description:
Library name: 3_SM-NBW8F_plate1
DHMT_3hr_b


title: output-XETG00254__0041370__EMBRYO1__20250430__192524


title: Leucoraja erinacea spinal cord bulk RNA-seq, biological replicate 3

city: Seoul

first: Hanshin

middle: David

last: Shin

address: 1 Gwanak-ro, Gwanak-gu,

department: Interdisciplinary Program in Bioinformatics

institute: Seoul National University

description:
Library name: SC818
Bulk RNA-seq of spinal cord dissected from stage 32 Leucoraja erinacea embryos. Biological replicate 3 (individual pool ID: 818); each replicate consists of pooled tissue from 3-4 embryos. Stranded library with polyA selection. Sequencing barcode: CGGCTATG+CTTCGCCT.

data_processing:
Raw paired-end sequencing reads were demultiplexed by barcode sequence. Quality control and adapter removal were performed using Trimmomatic. Adapter trimming was performed based on the specific barcode sequences for each sample: DRG815 (TAAGATTA), DRG816 (ACGTCCTG), DRG818 (GTCAGTAC), SC815 (AGGATAGG), SC816 (TCAGAGCC), SC818 (CTTCGCCT).
Cleaned paired-end reads were aligned to the Leucoraja erinacea reference genome (NCBI RefSeq assembly: GCF_028641065.1, ASM2654585v1) using HISAT2 (version 2.2.0).
Resulting BAM files were sorted and indexed using SAMtools.
Gene expression levels were quantified by counting fragments mapping to exons using featureCounts, generating a raw count matrix for downstream analysis.
Differential expression analysis between SC and DRG tissues was performed using the edgeR package (version 4.4) in R. Raw counts were normalized using the Trimmed Mean of M-values (TMM) method. Significant DEGs were defined as: adjusted p-value (FDR) < 0.01 and |log2 fold change| > 3. Gene expression levels were additionally quantified as RPKM for visualization using ggplot2.
Assembly: GCF_028641065.1 (Leucoraja erinacea, ASM2654585v1; NCBI RefSeq)
Supplementary files format and content: raw_count_matrix.txt: tab-delimited raw read count matrix generated by featureCounts; 22,111 genes × 6 samples (DRG815, DRG816, DRG818, SC815, SC816, SC818). Rows = genes (RefSeq gene IDs), columns = sample IDs. Header line included.

molecule: polyA RNA

source_name: spinal cord

growth_protocol: Little skate (Leucoraja erinacea) embryos were obtained from the Marine Resources Department at the Marine Biological Laboratory (Woods Hole, MA). Egg cases were maintained in artificial seawater (Instant Ocean, Aquarium Systems) at 16°C. Embryos were anesthetized in seawater containing MS-222 (tricaine methanesulfonate; Sigma-Aldrich) prior to tissue collection.

extract_protocol:
Spinal cord and dorsal root ganglia (DRG) were dissected separately from stage 32 Leucoraja erinacea embryos and stored in TRIzol reagent (Invitrogen) at -80°C. Samples were homogenized by trituration through 18-gauge (20x) and 25-gauge (10x) needles. Following addition of 100 µL chloroform, samples were incubated on ice for 5 minutes and centrifuged at 12,000 rpm for 15 minutes at 4°C. The aqueous layer was transferred to a new tube, mixed with 250 µL isopropanol, incubated on ice for 10 minutes, and centrifuged at 12,000 rpm for 10 minutes at 4°C. RNA pellets were washed twice with 500 µL 75% ethanol (7,000 rpm, 5 minutes, 4°C), air-dried, and resuspended in 25 µL EB buffer. Samples were further purified using the RNA MinElute Cleanup Kit (Qiagen) to remove DNA and small RNA contamination.
Stranded RNA-seq libraries were prepared with polyA selection by the NYU Langone Genome Technology Center (RRID: SCR_017929). Libraries were sequenced on an Illumina NovaSeq 6000 using an SP flow cell (300 cycles, v1.5 chemistry) with paired-end reads.

treatment_protocol: No pharmacological treatment was applied. For fin-ablation experiments (not part of bulk RNA-seq): fin buds were ablated unilaterally near the time of their emergence (stage 27-28) using sharp scissors, and embryos were returned to Instant Ocean and incubated 14-28 days at room temperature. Bulk RNA-seq samples are from untreated (control) wild-type embryos at stage 32.

value: spinal cord

value: mixed (neurons and glia)

value: wild type

tag: batch


title: 4_HW7KJBGXT.4.GCGTAGTA_ATAGAGAG

description:
Library name: 4_SM-NBW9T_plate2
DHMT_48hr_Astrocyte_Mono_c

value: WT

value: no guide


title: Leucoraja erinacea spinal cord bulk RNA-seq, biological replicate 2

description:
Library name: SC816
Bulk RNA-seq of spinal cord dissected from stage 32 Leucoraja erinacea embryos. Biological replicate 2 (individual pool ID: 816); each replicate consists of pooled tissue from 3-4 embryos. Stranded library with polyA selection. Sequencing barcode: CGGCTATG+TCAGAGCC.


title: 3_HW7KJBGXT.3.GCGTAGTA_ATAGAGAG

description:
Library name: 3_SM-NBW9T_plate2
DHMT_48hr_Astrocyte_Mono_c


title: output-XETG00254__0041370__EMBRYO2__20250430__192524


title: Leucoraja erinacea dorsal root ganglion bulk RNA-seq, biological replicate 3

description:
Library name: DRG818
Bulk RNA-seq of dorsal root ganglion dissected from stage 32 Leucoraja erinacea embryos. Biological replicate 3 (individual pool ID: 818); each replicate consists of pooled tissue from 3-4 embryos. Stranded library with polyA selection. Sequencing barcode: CGGCTATG+GTCAGTAC.

source_name: dorsal root ganglion

value: dorsal root ganglion


title: 2_HW7KJBGXT.2.GCGTAGTA_ATAGAGAG

description:
Library name: 2_SM-NBW9T_plate2
DHMT_48hr_Astrocyte_Mono_c

value: Astrocyte


title: Leucoraja erinacea dorsal root ganglion bulk RNA-seq, biological replicate 1

description:
Library name: DRG815
Bulk RNA-seq of dorsal root ganglion dissected from stage 32 Leucoraja erinacea embryos. Biological replicate 1 (individual pool ID: 815); each replicate consists of pooled tissue from 3-4 embryos. Stranded library with polyA selection. Sequencing barcode: CGGCTATG+TAAGATTA.


title: Leucoraja erinacea dorsal root ganglion bulk RNA-seq, biological replicate 2

description:
Library name: DRG816
Bulk RNA-seq of dorsal root ganglion dissected from stage 32 Leucoraja erinacea embryos. Biological replicate 2 (individual pool ID: 816); each replicate consists of pooled tissue from 3-4 embryos. Stranded library with polyA selection. Sequencing barcode: CGGCTATG+ACGTCCTG.


title: Leucoraja erinacea spinal cord bulk RNA-seq, biological replicate 1

description:
Library name: SC815
Bulk RNA-seq of spinal cord dissected from stage 32 Leucoraja erinacea embryos. Biological replicate 1 (individual pool ID: 815); each replicate consists of pooled tissue from 3-4 embryos. Stranded library with polyA selection. Sequencing barcode: CGGCTATG+AGGATAGG.


title: 1_HW7KJBGXT.1.GCGTAGTA_ATAGAGAG

description:
Library name: 1_SM-NBW9T_plate2
DHMT_48hr_Astrocyte_Mono_c


title: 3_HKM7VBGXT.3.ACTCGCTA_TACTCCTT

description:
Library name: 3_SM-NBW8E_plate1
DHMT_3hr_a


title: ptLNPIFN-Y3

city: shenzhen

first: yongfei

last: Zhou

address: Yutang Subdistrict, Guangming District

country: China

institute: Shenzhen Bay Laboratory

description:
Library name: Sample18
ptLNPIFN-Y3

data_processing:
Raw sequencing data were filtered using SOAPnuke to obtain clean reads, which were then aligned to the reference genome with HISAT2.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Gene expression levels were quantified using RSEM. Novel transcripts were predicted with StringTie and Cuffmerge, compared against the reference annotation using Cuffcompare, and evaluated for coding potential by CPC.Differential expression analysis was performed with DESeq2. Genes showing a fold change ≥ 2 and an adjusted P_x001E_value ≤ 0.001 were considered significantly differentially expressed.

source_name: Ovary

growth_protocol: Mouse ovarian tissue samples were snap-frozen and stored in liquid nitrogen prior to RNA extraction.

extract_protocol:
After the addition of a chloroform:isopentanol mixture (24:1) and centrifugation, the supernatant was transferred to a deep_x001E_well plate pre_x001E_loaded with binding solution and magnetic beads. RNA purification was carried out using an automated nucleic acid extractor, and the purified RNA was eluted with RNase_x001E_free water.
For library construction, mRNA was captured using oligo(dT)-conjugated magnetic beads, fragmented, and then reverse_x001E_transcribed into first_x001E_strand and second_x001E_strand cDNA. The resulting double_x001E_stranded cDNA was subjected to end repair, A_x001E_tailing, adaptor ligation, and PCR amplification.Following library quality control, single_x001E_stranded circular DNA was generated and sequenced on a DNBSEQ platform via rolling circle amplification combined with combinatorial Probe_x001E_Anchor Synthesis (cPAS).

treatment_protocol: Tissue specimens were homogenized in lysis buffer.

value: Ovary

tag: treatment

value: ovarian cancer/ptLNPIFN-Y


title: 4_HW7KJBGXT.4.GGAGCTAC_ATAGAGAG

description:
Library name: 4_SM-NBW9S_plate2
DHMT_48hr_Astrocyte_Mono_b


title: ptLNPIFN-Y4

description:
Library name: Sample19
ptLNPIFN-Y4


title: ptLNPIFN-Y1

description:
Library name: Sample16
ptLNPIFN-Y1


title: 2_HKM7VBGXT.2.ACTCGCTA_TACTCCTT

description:
Library name: 2_SM-NBW8E_plate1
DHMT_3hr_a


title: 3_HW7KJBGXT.3.GGAGCTAC_ATAGAGAG

description:
Library name: 3_SM-NBW9S_plate2
DHMT_48hr_Astrocyte_Mono_b


title: LNPIFN-Y5

description:
Library name: Sample15
LNPIFN-Y5

value: ovarian cancer/LNPIFN-Y


title: 1_HKM7VBGXT.1.ACTCGCTA_TACTCCTT

description:
Library name: 1_SM-NBW8E_plate1
DHMT_3hr_a


title: LNPIFN-Y4

description:
Library name: Sample14
LNPIFN-Y4


title: 2_HW7KJBGXT.2.GGAGCTAC_ATAGAGAG

description:
Library name: 2_SM-NBW9S_plate2
DHMT_48hr_Astrocyte_Mono_b


title: LNPIFN-Y3

description:
Library name: Sample13
LNPIFN-Y3


title: 4_HKM7VBGXT.4.TCGACGTC_TATGCAGT

description:
Library name: 4_SM-NBW8D_plate1
DHMT_48hr_LDLR_A_d

value: LDLR knockdown


title: LNPIFN-Y2

description:
Library name: Sample12
LNPIFN-Y2


title: Adnp, HT, Vehicle, male, replicate2

description: Library name: ADNP_HvM_2

value: prefrontal cortex

value: Heterozygous


title: 3_HKM7VBGXT.3.TCGACGTC_TATGCAGT

description:
Library name: 3_SM-NBW8D_plate1
DHMT_48hr_LDLR_A_d


title: LNPIFN-Y1

description:
Library name: Sample11
LNPIFN-Y1


title: Model5

description:
Library name: Sample10
Model5

value: ovarian cancer


title: 1_HKM7VBGXT.1.TCGACGTC_TATGCAGT

description:
Library name: 1_SM-NBW8D_plate1
DHMT_48hr_LDLR_A_d


title: Model2

description:
Library name: Sample7
Model2


title: 2_HKM7VBGXT.2.TCGACGTC_TATGCAGT

description:
Library name: 2_SM-NBW8D_plate1
DHMT_48hr_LDLR_A_d


title: Model1

description:
Library name: Sample6
Model1


title: Model3

description:
Library name: Sample8
Model3


title: 2_HW7KJBGXT.2.ACTCGCTA_ATAGAGAG

description:
Library name: 2_SM-NBW9R_plate2
DHMT_48hr_Astrocyte_Mono_a


title: Control5

description:
Library name: Sample5
Control5


title: 1_HW7KJBGXT.1.ACTCGCTA_ATAGAGAG

description:
Library name: 1_SM-NBW9R_plate2
DHMT_48hr_Astrocyte_Mono_a


title: Control3

description:
Library name: Sample3
Control3


title: 3_HKM7VBGXT.3.TGCAGCTA_TATGCAGT

description:
Library name: 3_SM-NBW8C_plate1
DHMT_48hr_LDLR_A_c


title: 3_HKM7VBGXT.3.TAGCGCTC_TACTCCTT

description:
Library name: 3_SM-NBW8K_plate1
DHMT_D5_c


title: Control2

description:
Library name: Sample2
Control2


title: 2_HKM7VBGXT.2.TGCAGCTA_TATGCAGT

description:
Library name: 2_SM-NBW8C_plate1
DHMT_48hr_LDLR_A_c


title: Adnp, HT, Lithium, male, replicate1

description: Library name: ADNP_HLM_1


title: 1_HKM7VBGXT.1.TGCAGCTA_TATGCAGT

description:
Library name: 1_SM-NBW8C_plate1
DHMT_48hr_LDLR_A_c


title: Postnatal day 22 bio replicate 4 (Male)

city: Bethesda

first: Whitney

last: Heavner

state: MD

address: 35 Convent Drive

department: NINDS

institute: National Institutes of Health

description:
Library name: p22_M_2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v9.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: main olfactory epithelium

growth_protocol: Olfactory epithelium (OE) was dissected from the nasal cavity of wild-type (C57Bl/6) mice at P1, P3, P5, P8, P15, or P22

extract_protocol:
The sensory OE was microdissected from the mouse nasal cavity at P1, P3, P5, P8, P15, and P22, dissociated in 2-3 mL pre-warmed dissociation medium (Worthington) (150 units papain, 100 units DNAse I, 2.5 mM cysteine, and 2.5 mM EDTA in 5 mL Neurobasal), and kept at 37°C for 25 min in a CO2 incubator. Samples were washed 3 times with 10% fetal bovine serum in phosphate-buffered saline (FBS-PBS), gently triturated 5-10 times using a fire-polished glass Pasteur pipette, and strained through a 35 μm nylon filter into a 5 mL polypropylene tube. DAPI, used to identify dead cells, was added at a final concentration of 0.1-1 μg/mL, and live cells (DAPI-low) were collected using a Sony LE-SH-800G cell sorter. At least two biological replicates and at least one female and one male per time point were used for all time points except P5, which only contained males.
Cells were pelleted in a swinging bucket centrifuge at 400g for 5 minutes at 4°C. The cell pellet was resuspended in 43.2 μl FBS-PBS, then 31.8 μl RT master mix was added to the cell pellet before loading the cells onto a Next GEM Chip G. A Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics, PN-1000268) and Dual Index Kit TT Set A (10x Genomics, PN-1000215) were used to generate single-cell whole-transcriptome libraries according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 Dual Index User Guide Rev E).

value: main olfactory epithelium

tag: age

value: postnatal day 22

tag: cell types

value: multipotent progenitors and their progeny

value: wild-type

tag: Sex

value: Male

tag: sequencing batch


title: mouseNSCs, Commd3-Bmi1_multiplex, 1

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

country: Japan

institute: Hiroshima University

description: Library name: Mouse_ComBmi_1

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.

source_name: Forebrain on E11

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.

tag: tissue

value: Forebrain on E11

value: neural stem cells

tag: genotype


title: Nur77_2_5h

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts for each sample

growth_protocol: The RAW264.7 macrophage stable cell lines with doxycyclin-inducible expression of Nur77 or GFP were seeded at a density of 3x10^5 cells/ml and the next day Nur77 or GFP expression was induced by incubation with 50ng/ml doxycyclin for 18 h

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Cells were stimulated with 500 ng/ml LPS for 0, 1 and 5h

tag: cell line

tag: cell type

value: macrophages

value: 5h 500 ng/ml LPS


title: Postnatal day 22 bio replicate 3 (Female)

description:
Library name: p22_F_2
10x Genomics

value: Female


title: Nur77_1_5h


title: Postnatal day 22 bio replicate 2 (Male)

description:
Library name: p22_M
10x Genomics


title: 3_HKM7VBGXT.3.CGATCAGT_TATGCAGT

description:
Library name: 3_SM-NBW8B_plate1
DHMT_48hr_LDLR_A_b

value: iPSC-derived excitatory neuron, astrocyte

tag: day

tag: guide rna


title: Postnatal day 15 bio replicate 2 (Female)

description:
Library name: p15_F
10x Genomics

value: postnatal day 15


title: Nur77_4_1h

value: 1h 500 ng/ml LPS


title: Postnatal day 3 bio replicate 2 (Male)

description:
Library name: p3_M
10x Genomics

value: postnatal day 3


title: Postnatal day 3 bio replicate 1 (Female)

description:
Library name: p3_F
10x Genomics


title: Postnatal day 1 bio replicate 4 (Male)

description:
Library name: p1_M_2
10x Genomics

value: postnatal day 1


title: Postnatal day 1 bio replicate 3 (Female)

description:
Library name: p1_F_2
10x Genomics

value: postnatal  day 1


title: 3_HW7KJBGXT.3.ACTCGCTA_ATAGAGAG

description:
Library name: 3_SM-NBW9R_plate2
DHMT_48hr_Astrocyte_Mono_a

value: Astrocyte

value: WT

value: no guide

tag: barcode


title: Model4

description:
Library name: Sample9
Model4

value: Ovary

value: ovarian cancer


title: Control4

description:
Library name: Sample4
Control4


title: Postnatal day 1 bio replicate 1 (Female)

description:
Library name: p1_F
10x Genomics

value: main olfactory epithelium

value: multipotent progenitors and their progeny

value: wild-type


title: 3_HKM7VBGXT.3.CCTAAGAC_TATGCAGT

description:
Library name: 3_SM-NBW8A_plate1
DHMT_48hr_LDLR_A_a

value: LDLR knockdown


title: Nur77_1_1h

value: macrophages


title: Control1

description:
Library name: Sample1
Control1


title: ASD mouse PFC snRNA-seq [G2b_HLM_2 + G2b_HvF_2 + G2b_HfF_2 + G2b_HLF_2] (4-plex OCM)

description:
Library name: 1209-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

data_processing:
Per-library FASTQ files were demultiplexed in silico into the four constituent mice using the Cell Ranger multi pipeline (10x Genomics), with mouse-specific reads assigned via OCM barcodes and aligned to the mouse reference genome to generate per-nucleus gene count matrices.
Downstream processing was performed in Seurat v5.0. Low-quality nuclei were filtered (<750 or >8000 detected genes, <1000 or >30000 UMI counts, >5% mitochondrial reads). Top 3000 highly variable genes per sample were used; expression values were normalised and scaled.
Principal component analysis was performed and sequencing-batch effects were corrected with Harmony. Visualisation used UMAP and clustering used a shared nearest-neighbour graph at resolution 0.3.
Clusters were annotated by reference-based label transfer using Seurat MapQuery against the Allen Brain Cell Atlas scRNA-seq reference (GSE246717; 3 donors, 64,409 isocortex cells, 12 cell classes), followed by manual curation. The 19 clusters were mapped to 10 major cell classes.
Relative cell-class proportions were computed per mouse, stratified by genotype, sex, treatment, and Group 1 / Group 2 transcriptomic class.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Each GSM (tube) is associated with four per-sample MEX triplets (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) produced by Cell Ranger multi `per_sample_outs/`, one set per multiplexed mouse. File naming convention: <mouse_id>__barcodes.tsv.gz, <mouse_id>__features.tsv.gz, <mouse_id>__matrix.mtx.gz (double underscore between mouse_id and file type).
Supplementary files format and content: 10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing (OCM). Four mouse-specific nuclei suspensions per GEM well; demultiplexed in silico via Cell Ranger multi. OCM barcodes are hardware-encoded in the chip (not antibody-based CMO/HTO), so feature_reference.csv is not applicable. Mouse <-> OCM-slot mapping per tube is provided in mouse_to_pool.tsv.

molecule: nuclear RNA

growth_protocol: All mice were housed under a 12 h light/dark cycle with ad libitum access to food and water. Procedures were approved by the Committee of Animal Research and Ethics at KAIST (KA2024-093-v1) and followed the Korean Laboratory Animal Act.

extract_protocol:
Nuclei were isolated from frozen prefrontal cortex tissue using a lysis buffer of 0.25 M sucrose, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 25 mM KCl, 0.1% Triton X-100, 1 mM DTT and 0.2 U/uL RNAse inhibitor (Protector, Sigma). Tissue was homogenised in 1 mL lysis buffer using a Nano pestle, incubated 5 min on ice and filtered through a 70 um strainer (MACS SmartStrainer, Miltenyi). Filtered samples were centrifuged at 500 g for 5 min at 4 C, resuspended in 1 mL lysis buffer, filtered through a 30 um strainer, centrifuged again at 500 g for 5 min at 4 C, and resuspended in PBS with 0.04% BSA. Nuclei were counted on a Countess 3 (Thermo Fisher).
Four mouse-specific nuclei suspensions were tagged with 10x Genomics On-Chip Multiplexing (OCM) barcodes and pooled prior to loading. Libraries were prepared with the Chromium GEM-X Universal 3' Gene Expression kit v4 with 4-plex On-Chip Multiplexing (10x Genomics) according to the manufacturer's instructions, yielding one paired Gene Expression library per GEM well (tube).

treatment_protocol: From P3 to P25, dams received drinking water containing vehicle (0.2% saccharin), fluoxetine (10 mg/L in saccharin water), or lithium carbonate (600 mg/L in saccharin water). Pups were exposed via maternal milk.

value: prefrontal cortex

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

tag: sex (pool_composition)

value: male; female; female; female

tag: genotype (pool_composition)

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

tag: treatment (pool_composition)

value: lithium; vehicle; fluoxetine; lithium

tag: mouse line_(pool_composition)

value: Grin2b; Grin2b; Grin2b; Grin2b

tag: multiplexed mouse_ids

value: G2b_HLM_2; G2b_HvF_2; G2b_HfF_2; G2b_HLF_2

tag: n samples_per_pool


title: 2_HKM7VBGXT.2.CCTAAGAC_TATGCAGT

description:
Library name: 2_SM-NBW8A_plate1
DHMT_48hr_LDLR_A_a

value: iPSC-derived excitatory neuron, astrocyte


title: ASD mouse PFC snRNA-seq [K5B_HfF_2 + K5B_HLF_2 + G2b_HvM_2 + G2b_HfM_2] (4-plex OCM)

description:
Library name: 1209-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

tag: age

value: female; female; male; male

value: fluoxetine; lithium; vehicle; fluoxetine

value: Kmt5b; Kmt5b; Grin2b; Grin2b

value: K5B_HfF_2; K5B_HLF_2; G2b_HvM_2; G2b_HfM_2


title: Pten, WT, Lithium, male, replicate1

description: Library name: Pten_WLM_1

tag: strain

value: Wildtype


title: 1_HKM7VBGXT.1.CCTAAGAC_TATGCAGT

description:
Library name: 1_SM-NBW8A_plate1
DHMT_48hr_LDLR_A_a


title: ASD mouse PFC snRNA-seq [K5B_HvM_1 + K5B_HfM_1 + K5B_HLM_1 + K5B_HLM_2] (4-plex OCM)

description:
Library name: 1209-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: male; male; male; male

value: vehicle; fluoxetine; lithium; lithium

value: Kmt5b; Kmt5b; Kmt5b; Kmt5b

value: K5B_HvM_1; K5B_HfM_1; K5B_HLM_1; K5B_HLM_2


title: 2_HKM7VBGXT.2.GGAGCTAC_TACTCCTT

description:
Library name: 2_SM-NBW8F_plate1
DHMT_3hr_b

value: WT

value: no guide


title: 1_HKM7VBGXT.1.GGAGCTAC_TACTCCTT

description:
Library name: 1_SM-NBW8F_plate1
DHMT_3hr_b


title: 4_HKM7VBGXT.4.ACTCGCTA_TACTCCTT

description:
Library name: 4_SM-NBW8E_plate1
DHMT_3hr_a


title: ASD mouse PFC snRNA-seq [T12_HfM_2 + T12_HvF_2 + T12_HfF_1 + T12_HfF_2] (4-plex OCM)

description:
Library name: 1203-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: male; female; female; female

value: fluoxetine; vehicle; fluoxetine; fluoxetine

value: Trip12; Trip12; Trip12; Trip12


title: ASD mouse PFC snRNA-seq [Tbl_HfF_2 + Tbl_HLF_2 + T12_HvM_2 + T12_HfM_1] (4-plex OCM)

description:
Library name: 1203-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: female; female; male; male

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: Tbl1xr1; Tbl1xr1; Trip12; Trip12

value: Tbl_HfF_2; Tbl_HLF_2; T12_HvM_2; T12_HfM_1


title: 4_HKM7VBGXT.4.ACTGAGCG_TATGCAGT

description:
Library name: 4_SM-NBW89_plate1
DHMT_96hr_d

value: iPSC-derived excitatory neuron, astrocyte


title: Nur77_1_0h

value: macrophages

tag: treatment

value: untreated


title: ASD mouse PFC snRNA-seq [Tbl_HvM_2 + Tbl_HfM_2 + Tbl_HLM_2 + Tbl_HvF_2] (4-plex OCM)

description:
Library name: 1203-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: male; male; male; female

value: vehicle; fluoxetine; lithium; vehicle

value: Tbl1xr1; Tbl1xr1; Tbl1xr1; Tbl1xr1

value: Tbl_HvM_2; Tbl_HfM_2; Tbl_HLM_2; Tbl_HvF_2

tag: sequencing batch


title: ASD mouse PFC snRNA-seq [L68P_HvF_1 + L68P_HfF_1 + L68P_HLF_1 + L68P_HLF_2] (4-plex OCM)

description:
Library name: 1203-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

tag: tissue

value: prefrontal cortex

value: female; female; female; female

value: vehicle; fluoxetine; lithium; lithium

value: Shank3-L68P; Shank3-L68P; Shank3-L68P; Shank3-L68P


title: GFP4_5h

tag: genotype

value: GFP

value: 5h 500 ng/ml LPS


title: ASD mouse PFC snRNA-seq [Tbl_HLM_1 + Tbl_HvF_1 + Tbl_HfF_1 + Tbl_HLF_1] (4-plex OCM)

description:
Library name: 1201-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: male; female; female; female

value: lithium; vehicle; fluoxetine; lithium

value: Tbl_HLM_1; Tbl_HvF_1; Tbl_HfF_1; Tbl_HLF_1


title: 2_HKM7VBGXT.2.ACTGAGCG_TATGCAGT

description:
Library name: 2_SM-NBW89_plate1
DHMT_96hr_d

tag: cell line

value: iPSC-derived excitatory neuron, astrocyte

value: WT

value: no guide


title: ASD mouse PFC snRNA-seq [T12_HLF_1 + T12_HLF_2 + Tbl_HvM_1 + Tbl_HfM_1] (4-plex OCM)

description:
Library name: 1201-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

tag: cell type

value: female; female; male; male

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: lithium; lithium; vehicle; fluoxetine

value: Trip12; Trip12; Tbl1xr1; Tbl1xr1

value: T12_HLF_1; T12_HLF_2; Tbl_HvM_1; Tbl_HfM_1


title: ASD mouse PFC snRNA-seq [T12_HvM_1 + T12_HLM_1 + T12_HLM_2 + T12_HvF_1] (4-plex OCM)

description:
Library name: 1201-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: male; male; male; female

value: vehicle; lithium; lithium; vehicle

value: Trip12; Trip12; Trip12; Trip12


title: 1_HKM7VBGXT.1.ACTGAGCG_TATGCAGT

description:
Library name: 1_SM-NBW89_plate1
DHMT_96hr_d

tag: day


title: ASD mouse PFC snRNA-seq [L68P_HvM_2 + L68P_HfM_2 + B6J_WvM_4 + B6J_WvF_2] (4-plex OCM)

description:
Library name: 1201-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: heterozygous mutant; heterozygous mutant; wild-type; wild-type

value: vehicle; fluoxetine; vehicle; vehicle

value: Shank3-L68P; Shank3-L68P; C57BL/6J background WT; C57BL/6J background WT


title: GFP2_5h

value: macrophages

value: GFP

value: 5h 500 ng/ml LPS


title: GFP3_5h


title: ASD mouse PFC snRNA-seq [G2b_HLM_1 + G2b_HvF_1 + G2b_HfF_1 + G2b_HLF_1] (4-plex OCM)

description:
Library name: 1124-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: postnatal day 25

value: male; female; female; female

value: lithium; vehicle; fluoxetine; lithium

value: Grin2b; Grin2b; Grin2b; Grin2b

value: G2b_HLM_1; G2b_HvF_1; G2b_HfF_1; G2b_HLF_1


title: 4_HKM7VBGXT.4.TAGCGCTC_TATGCAGT

description:
Library name: 4_SM-NBW88_plate1
DHMT_96hr_c

value: iPSC-derived excitatory neuron, astrocyte

value: WT

tag: guide rna

value: no guide


title: ASD mouse PFC snRNA-seq [L68P_HLM_1 + L68P_HLM_2 + G2b_HvM_1 + G2b_HfM_1] (4-plex OCM)

description:
Library name: 1124-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: male; male; male; male

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: lithium; lithium; vehicle; fluoxetine

value: Shank3-L68P; Shank3-L68P; Grin2b; Grin2b


title: Nur77_3_0h

value: untreated


title: GFP1_5h

value: macrophages


title: ASD mouse PFC snRNA-seq [Scn_HvM_2 + Scn_HfM_2 + L68P_HvM_1 + L68P_HfM_1] (4-plex OCM)

description:
Library name: 1124-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: vehicle; fluoxetine; vehicle; fluoxetine

value: Scn2a; Scn2a; Shank3-L68P; Shank3-L68P

value: Scn_HvM_2; Scn_HfM_2; L68P_HvM_1; L68P_HfM_1


title: 3_HKM7VBGXT.3.TAGCGCTC_TATGCAGT

description:
Library name: 3_SM-NBW88_plate1
DHMT_96hr_c

tag: barcode


title: ASD mouse PFC snRNA-seq [K5B_HvF_1 + K5B_HfF_1 + K5B_HLF_1 + K5B_HvF_2] (4-plex OCM)

description:
Library name: 1209-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: postnatal day 25

tag: sex (pool_composition)

value: female; female; female; female

value: vehicle; fluoxetine; lithium; vehicle

value: Kmt5b; Kmt5b; Kmt5b; Kmt5b

value: K5B_HvF_1; K5B_HfF_1; K5B_HLF_1; K5B_HvF_2


title: ASD mouse PFC snRNA-seq [B6N_WvM_1 + B6N_WvF_1 + Arid_HvF_2 + Arid_HfF_2] (4-plex OCM)

description:
Library name: 1124-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: male; female; female; female

tag: genotype (pool_composition)

value: wild-type; wild-type; heterozygous mutant; heterozygous mutant

value: vehicle; vehicle; vehicle; fluoxetine

value: C57BL/6J background WT; C57BL/6J background WT; Arid1b; Arid1b

value: B6N_WvM_1; B6N_WvF_1; Arid_HvF_2; Arid_HfF_2


title: GFP4_1h

value: GFP

value: 1h 500 ng/ml LPS


title: ASD mouse PFC snRNA-seq [Dyrk_HLM_2 + Dyrk_HvF_2 + Dyrk_HfF_2 + Dyrk_HLF_2] (4-plex OCM)

description:
Library name: 1119-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

tag: treatment (pool_composition)

value: lithium; vehicle; fluoxetine; lithium

value: Dyrk1a; Dyrk1a; Dyrk1a; Dyrk1a

value: Dyrk_HLM_2; Dyrk_HvF_2; Dyrk_HfF_2; Dyrk_HLF_2


title: 2_HKM7VBGXT.2.TAGCGCTC_TATGCAGT

description:
Library name: 2_SM-NBW88_plate1
DHMT_96hr_c

value: iPSC-derived excitatory neuron, astrocyte

value: WT

value: no guide


title: ASD mouse PFC snRNA-seq [Arid_HLF_1 + Arid_HLF_2 + Dyrk_HvM_2 + Dyrk_HfM_2] (4-plex OCM)

description:
Library name: 1119-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: female; female; male; male

value: lithium; lithium; vehicle; fluoxetine

tag: mouse line_(pool_composition)

value: Arid1b; Arid1b; Dyrk1a; Dyrk1a

value: Arid_HLF_1; Arid_HLF_2; Dyrk_HvM_2; Dyrk_HfM_2


title: GFP3_1h

value: macrophages


title: 1_HKM7VBGXT.1.TAGCGCTC_TATGCAGT

description:
Library name: 1_SM-NBW88_plate1
DHMT_96hr_c


title: ASD mouse PFC snRNA-seq [Arid_HfM_2 + Arid_HLM_2 + Arid_HvF_1 + Arid_HfF_1] (4-plex OCM)

description:
Library name: 1119-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: male; male; female; female

value: fluoxetine; lithium; vehicle; fluoxetine

value: Arid1b; Arid1b; Arid1b; Arid1b

tag: multiplexed mouse_ids

value: Arid_HfM_2; Arid_HLM_2; Arid_HvF_1; Arid_HfF_1


title: Nur77_2_0h

value: untreated


title: GFP2_1h

value: GFP

value: 1h 500 ng/ml LPS


title: ASD mouse PFC snRNA-seq [Arid_HvM_1 + Arid_HfM_1 + Arid_HLM_1 + Arid_HvM_2] (4-plex OCM)

description:
Library name: 1119-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: male; male; male; male

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: vehicle; fluoxetine; lithium; vehicle

value: Arid_HvM_1; Arid_HfM_1; Arid_HLM_1; Arid_HvM_2

tag: n samples_per_pool


title: ASD mouse PFC snRNA-seq [Dyrk_HLM_1 + Dyrk_HvF_1 + Dyrk_HfF_1 + Dyrk_HLF_1] (4-plex OCM)

description:
Library name: 1118-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

tag: age

value: postnatal day 25

value: male; female; female; female

value: lithium; vehicle; fluoxetine; lithium

value: Dyrk1a; Dyrk1a; Dyrk1a; Dyrk1a

value: Dyrk_HLM_1; Dyrk_HvF_1; Dyrk_HfF_1; Dyrk_HLF_1


title: ASD mouse PFC snRNA-seq [Mt1_HfF_2 + Mt1_HLF_2 + Dyrk_HvM_1 + Dyrk_HfM_1] (4-plex OCM)

description:
Library name: 1118-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: female; female; male; male

value: fluoxetine; lithium; vehicle; fluoxetine

value: Myt1l; Myt1l; Dyrk1a; Dyrk1a

value: Mt1_HfF_2; Mt1_HLF_2; Dyrk_HvM_1; Dyrk_HfM_1


title: GFP1_1h

value: macrophages

value: GFP


title: ASD mouse PFC snRNA-seq [Mt1_HvF_1 + Mt1_HfF_1 + Mt1_HLF_1 + Mt1_HvF_2] (4-plex OCM)

description:
Library name: 1118-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: female; female; female; female

value: Myt1l; Myt1l; Myt1l; Myt1l

value: Mt1_HvF_1; Mt1_HfF_1; Mt1_HLF_1; Mt1_HvF_2


title: 3_HKM7VBGXT.3.ATGCGCAG_TATGCAGT

description:
Library name: 3_SM-NBW87_plate1
DHMT_96hr_b

value: iPSC-derived excitatory neuron, astrocyte

value: WT

value: no guide


title: 3_HKM7VBGXT.3.ACTGAGCG_TATGCAGT

description:
Library name: 3_SM-NBW89_plate1
DHMT_96hr_d


title: 4_HKM7VBGXT.4.ATGCGCAG_TATGCAGT

description:
Library name: 4_SM-NBW87_plate1
DHMT_96hr_b


title: ASD mouse PFC snRNA-seq [Mt1_HvM_2 + Mt1_HfM_2 + Mt1_HLM_1 + Mt1_HLM_2] (4-plex OCM)

description:
Library name: 1118-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: male; male; male; male

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: vehicle; fluoxetine; lithium; lithium

value: Mt1_HvM_2; Mt1_HfM_2; Mt1_HLM_1; Mt1_HLM_2


title: GFP4_0h

value: untreated


title: 4_HW7KJBGXT.4.GCGTAGTA_CTCCTTAC

description:
Library name: 4_SM-NBWAI_plate2
DHMT_48hr_NT_545_c

value: Non-targeting knockdown


title: ASD mouse PFC snRNA-seq [Scn_HLM_2 + B6J_WvM_3 + Mt1_HvM_1 + Mt1_HfM_1] (4-plex OCM)

description:
Library name: 1117-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: heterozygous mutant; wild-type; heterozygous mutant; heterozygous mutant

value: lithium; vehicle; vehicle; fluoxetine

value: Scn2a; C57BL/6J background WT; Myt1l; Myt1l

value: Scn_HLM_2; B6J_WvM_3; Mt1_HvM_1; Mt1_HfM_1


title: 3_HW7KJBGXT.3.ACTCGCTA_CTCCTTAC

description:
Library name: 3_SM-NBWAG_plate2
DHMT_48hr_NT_545_a


title: 2_HKM7VBGXT.2.ATGCGCAG_TATGCAGT

description:
Library name: 2_SM-NBW87_plate1
DHMT_96hr_b


title: ASD mouse PFC snRNA-seq [ASH_HLM_2 + Scn_HvM_1 + Scn_HfM_1 + Scn_HLM_1] (4-plex OCM)

description:
Library name: 1117-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: lithium; vehicle; fluoxetine; lithium

value: Ash1l; Scn2a; Scn2a; Scn2a

value: ASH_HLM_2; Scn_HvM_1; Scn_HfM_1; Scn_HLM_1


title: GFP3_0h

value: macrophages

value: GFP


title: ASD mouse PFC snRNA-seq [ASH_HfM_1 + ASH_HLM_1 + ASH_HvM_2 + ASH_HfM_2] (4-plex OCM)

description:
Library name: 1117-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: fluoxetine; lithium; vehicle; fluoxetine

value: Ash1l; Ash1l; Ash1l; Ash1l

value: ASH_HfM_1; ASH_HLM_1; ASH_HvM_2; ASH_HfM_2


title: 4_HKM7VBGXT.4.TACGCTGC_TATGCAGT

description:
Library name: 4_SM-NBW86_plate1
DHMT_96hr_a

value: iPSC-derived excitatory neuron, astrocyte

value: WT

value: no guide


title: ASD mouse PFC snRNA-seq [Tanc_HLM_2 + CHN_HvM_1 + CHN_HfM_1 + CHN_HLM_1] (4-plex OCM)

description:
Library name: 1111-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: male; male; male; male

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: Tanc_HLM_2; CHN_HvM_1; CHN_HfM_1; CHN_HLM_1


title: ASD mouse PFC snRNA-seq [CHN_HvM_2 + CHN_HfM_2 + CHN_HLM_2 + ASH_HvM_1] (4-plex OCM)

description:
Library name: 1117-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: vehicle; fluoxetine; lithium; vehicle

value: CHN_HvM_2; CHN_HfM_2; CHN_HLM_2; ASH_HvM_1


title: GFP1_0h

value: untreated


title: GFP2_0h

value: macrophages


title: ASD mouse PFC snRNA-seq [Tanc_HfM_1 + Tanc_HLM_1 + Tanc_HvM_2 + Tanc_HfM_2] (4-plex OCM)

description:
Library name: 1111-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: Tanc2; Tanc2; Tanc2; Tanc2

value: Tanc_HfM_1; Tanc_HLM_1; Tanc_HvM_2; Tanc_HfM_2


title: 2_HW7KJBGXT.2.GGAGCTAC_CTCCTTAC

description:
Library name: 2_SM-NBWAH_plate2
DHMT_48hr_NT_545_b

value: Non-targeting knockdown


title: ASD mouse PFC snRNA-seq [Scn_HvF_1 + Scn_HfF_1 + Scn_HLF_1 + Tanc_HvM_1] (4-plex OCM)

description:
Library name: 1111-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: female; female; female; male

value: Scn2a; Scn2a; Scn2a; Tanc2

value: Scn_HvF_1; Scn_HfF_1; Scn_HLF_1; Tanc_HvM_1


title: 3_HKM7VBGXT.3.TACGCTGC_TATGCAGT

description:
Library name: 3_SM-NBW86_plate1
DHMT_96hr_a

value: iPSC-derived excitatory neuron, astrocyte

value: WT

value: no guide


title: ASD mouse PFC snRNA-seq [CHN_HvF_2 + CHN_HfF_2 + CHN_HLF_1 + CHN_HLF_2] (4-plex OCM)

description:
Library name: 1111-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: female; female; female; female

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: vehicle; fluoxetine; lithium; lithium

value: CHN_HvF_2; CHN_HfF_2; CHN_HLF_1; CHN_HLF_2


title: 2_HW7KJBGXT.2.ACTCGCTA_AGAGGATA

description:
Library name: 2_SM-NBWA4_plate2
DHMT_48hr_Neuron_Mono_a

value: iPSC-derived excitatory neuron


title: 2_HKM7VBGXT.2.TACGCTGC_TATGCAGT

description:
Library name: 2_SM-NBW86_plate1
DHMT_96hr_a


title: 10E_minCHO_rep2_in

city: Barcelona

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

country: Spain

institute: ISGlobal

description:
Library name: 10E_minCHO_rep2_in
10E_minCHO_rep2_in

library_source: genomic

data_processing:
ChIP-seq data analysis was carried out using custom scripts written in Python (v3.7.16), as previously described (Michel-Todó, L., 2023. PMID: 36515553). ChIP-seq reads were trimmed using the bbduk command from BBmap (v36.99) software. The 3' end was trimmed if it had a quality score < 6 and reads shorter than 10 bp after trimming were discarded. Quality control of raw reads was performed using FastQC (v0.11.9) and contamination with non-P. falciparum reads was checked with FastqScreen (v0.14.0).  Bowtie2 (v2.4.5) was used to align reads to the Plasmodium falciparum 3D7 reference genome (PlasmoDB v67) using the parameters: --very-sensitive --local -5 4 -3 4 -I 50 -X 2000, which are different from the default ones. SAMtools (v1.15) was used for compressing, sorting and filtering-out < 5 mapping quality reads, from the alignment files. PCR duplicates were removed using GATK (v4.4.0.0) MarkDuplicates command. Normalized coverage (log₂-transformed enrichment of IP over input) was calculated at 10-bp resolution using the bamCompare function from DeepTools (v3.5.1), with the parameters: --normalizeUsing RPKM -bs 10 --smoothLength 200 --pseudocount 10. Negative values were set to -1 to avoid the detection of apparent differential coverage in non-heterochromatic regions. Normalized log₂(IP/input) coverage values were used to generate bedgraph tracks.
Assembly: Plasmodium falciparum 3D7 reference genome (PlasmoDB v67)
Supplementary files format and content: Bedgraph tracks (.bedgraph): normalized log₂(IP/input) coverage values

molecule: genomic DNA

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in B+ or O+ erythrocytes at a 3% hematocrit under standard conditions in RPMI-1640-based media, supplemented with 0.5% Albumax II (Gibco, 11021037) and 2 mM choline chloride (Sigma-Aldrich, C7527), and maintained in a shaking incubator with a 5% CO₂, 3% O₂, and balance N₂ atmosphere. All cultures were kept at 37ºC, except for parasite lines in which pfap2-hs was disrupted and control cultures grown in parallel , which were maintained at 35ºC because at 37ºC they show reduced growth (Tintó-Font, E., et al., 2021; PMID:34400833). Tight synchronization to a 5 h age window was achieved by purification of late stages in 63% Percoll gradients (GE Healthcare, 17-0891-01) followed by sorbitol lysis 5 h later (Sigma-Aldrich, S3889). For ChIP-seq experiments, erythrocyte were filtered with Plasmodipur (R-Biopharm Nederland B.V., 8011FILTER) to remove leukocytes before using them for parasite cultures.

extract_protocol:
ChIP-seq was performed using tightly synchronized cultures at the mid-trophozoite stage: 33–38 hpi, or 37–42 hpi for the ap2-hs KO line, to account for their slower IDC progression (Tintó-Font, E., et al., 2021; PMID:34400833), unless otherwise stated. Chromatin was extracted from ~30–45 ml at ~2% parasitemia and immunoprecipitated as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). Briefly, after saponin lysis and formaldehyde cross-linking, chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies, 492024). Sonication was performed with a Covaris M220 sonicator to generate ~150–200 bp fragments. For immunoprecipitation, 2 μg of chromatin and 4 μg of anti-H3K9me3 antibody (Diagenode, C15410193) were used. An equal sample was processed in parallel as input, with no immunoprecipitation. The resulting DNA was quantified using Qubit HS before library preparation.
Library preparation was performed using 5 ng of DNA, as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). NEBNext multiplex oligonucleotides for Illumina (NEB, E7335, E7500 and E7710) were used, and 9 cycles of amplification were performed with the Kapa HiFi HotStart PCR kit (Roche, 7958889001). All purification steps were carried out using AMPure XP beads (Beckman Coulter, 082A63881). Quality and concentration of all libraries was determined using a Tapestation 4200 (Agilent). We obtained ~8-19 million 150 bp paired-end reads per sample using a NextSeq500 System (Illumina).

treatment_protocol: Sexual conversion was induced by three different methods: choline depletion, dihydroartemisinin (DHA; Sigma-Aldrich, D7439) treatment or heat shock (HS). For induction by choline depletion, the regular RPMI medium with Albumax II and a 2 mM choline supplement was replaced by the same medium without the choline supplement in cultures at the early ring stage (0-5 h post-invasion, hpi) and cultures were placed in static conditions in a hypoxia chamber for the rest of the experiment. For induction of sexual conversion by DHA or HS, tightly synchronized cultures (0-5 hpi) were placed in static conditions in a hypoxia chamber, and left undisturbed until the early trophozoite stage (25-30 hpi for most experiments; 29-34 hpi for experiments with transgenic lines in which ap2hs was disrupted, to account for their slower growth), when they were exposed to a 3 h of 10 nM DHA pulse or maintained for 3 h at 41.5 ºC (placing the full hypoxia chamber in an incubator at 41.5 ºC), respectively. After exposure, DHA was removed from the medium by centrifugation or cultures were placed back in an incubator at the normal growth temperature. Medium  was refreshed at ~33 hpi to all conditions. A control condition was always kept in parallel until the end of the experiment

value: choline depletion

tag: biological replicate

tag: chip antibody

tag: time


title: ASD mouse PFC snRNA-seq [CHN_HfF_1 + Scn_HvF_2 + Scn_HfF_2 + Scn_HLF_2] (4-plex OCM)

description:
Library name: 1106-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

tag: tissue

value: prefrontal cortex

value: fluoxetine; vehicle; fluoxetine; lithium

value: Chd8-N2373K; Scn2a; Scn2a; Scn2a

value: CHN_HfF_1; Scn_HvF_2; Scn_HfF_2; Scn_HLF_2

tag: sequencing batch


title: ASD mouse PFC snRNA-seq [Tanc_HvF_2 + Tanc_HfF_2 + Tanc_HLF_2 + CHN_HvF_1] (4-plex OCM)

description:
Library name: 1106-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: vehicle; fluoxetine; lithium; vehicle

value: Tanc2; Tanc2; Tanc2; Chd8-N2373K

value: Tanc_HvF_2; Tanc_HfF_2; Tanc_HLF_2; CHN_HvF_1


title: 1_HKM7VBGXT.1.ATGCGCAG_TATGCAGT

description:
Library name: 1_SM-NBW87_plate1
DHMT_96hr_b

tag: cell line

value: iPSC-derived excitatory neuron, astrocyte

tag: genotype

value: WT


title: 10E_minCHO_rep2_IP

description:
Library name: 10E_minCHO_rep2_IP
10E_minCHO_rep2_IP

tag: cell type

tag: treatment

value: H3K9me3 (Diagenode, C15410193)


title: ASD mouse PFC snRNA-seq [TBR1_HLF_1 + Tanc_HvF_1 + Tanc_HfF_1 + Tanc_HLF_1] (4-plex OCM)

description:
Library name: 1106-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: female; female; female; female

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: lithium; vehicle; fluoxetine; lithium

value: Tbr1; Tanc2; Tanc2; Tanc2

value: TBR1_HLF_1; Tanc_HvF_1; Tanc_HfF_1; Tanc_HLF_1


title: 4_HW7KJBGXT.4.ACTCGCTA_ATAGAGAG

description:
Library name: 4_SM-NBW9R_plate2
DHMT_48hr_Astrocyte_Mono_a

value: Astrocyte

tag: day

tag: guide rna

value: no guide

tag: barcode


title: 10E_plusCHO_rep2_in

description:
Library name: 10E_plusCHO_rep2_in
10E_plusCHO_rep2_in

value: control choline


title: 1_HKM7VBGXT.1.TACGCTGC_TATGCAGT

description:
Library name: 1_SM-NBW86_plate1
DHMT_96hr_a


title: 4_HKM7VBGXT.4.CGGAGCCT_TATGCAGT

description:
Library name: 4_SM-NBW85_plate1
DHMT_2hr_d


title: ASD mouse PFC snRNA-seq [ASH_HvF_2 + ASH_HfF_2 + TBR1_HvF_1 + TBR1_HfF_1] (4-plex OCM)

description:
Library name: 1106-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

tag: sex (pool_composition)

tag: genotype (pool_composition)

tag: treatment (pool_composition)

value: vehicle; fluoxetine; vehicle; fluoxetine

value: Ash1l; Ash1l; Tbr1; Tbr1

value: ASH_HvF_2; ASH_HfF_2; TBR1_HvF_1; TBR1_HfF_1


title: 10E_plusCHO_rep2_IP

description:
Library name: 10E_plusCHO_rep2_IP
10E_plusCHO_rep2_IP


title: ASD mouse PFC snRNA-seq [TBR1_HfF_2 + TBR1_HLF_2 + SdC_HvF_1 + SdC_HfF_1] (4-plex OCM)

description:
Library name: 1104-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: fluoxetine; lithium; vehicle; fluoxetine

tag: mouse line_(pool_composition)

value: Tbr1; Tbr1; Shank3-deltaC; Shank3-deltaC

tag: multiplexed mouse_ids

value: TBR1_HfF_2; TBR1_HLF_2; SdC_HvF_1; SdC_HfF_1

tag: n samples_per_pool


title: ASD mouse PFC snRNA-seq [SdC_HLF_1 + SdC_HvF_2 + SdC_HfF_2 + SdC_HLF_2] (4-plex OCM)

description:
Library name: 1104-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

tag: age

value: female; female; female; female

value: Shank3-deltaC; Shank3-deltaC; Shank3-deltaC; Shank3-deltaC

value: SdC_HLF_1; SdC_HvF_2; SdC_HfF_2; SdC_HLF_2


title: 3_HKM7VBGXT.3.CGGAGCCT_TATGCAGT

description:
Library name: 3_SM-NBW85_plate1
DHMT_2hr_d

value: iPSC-derived excitatory neuron, astrocyte

value: WT


title: ASD mouse PFC snRNA-seq [ASH_HvF_1 + ASH_HfF_1 + ASH_HLF_1 + ASH_HLF_2] (4-plex OCM)

description:
Library name: 1104-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: vehicle; fluoxetine; lithium; lithium

value: Ash1l; Ash1l; Ash1l; Ash1l

value: ASH_HvF_1; ASH_HfF_1; ASH_HLF_1; ASH_HLF_2


title: 10E_ap2hsKO_minCHO_rep2_in

description:
Library name: 10E_ap2hsKO_minCHO_rep2_in
10E_ap2hsKO_minCHO_rep2_in

value: ap2-hs knockout

value: choline depletion

tag: biological replicate

tag: chip antibody

tag: time


title: ASD mouse PFC snRNA-seq [B6J_WvF_1 + Na_HvF_2 + Na_HfF_2 + TBR1_HvF_2] (4-plex OCM)

description:
Library name: 1104-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

tag: tissue

value: prefrontal cortex

value: wild-type; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: vehicle; vehicle; fluoxetine; vehicle

value: C57BL/6J background WT; Naa15; Naa15; Tbr1

value: B6J_WvF_1; Na_HvF_2; Na_HfF_2; TBR1_HvF_2

tag: sequencing batch


title: Nur77_4_5h

tag: cell line

tag: cell type

value: macrophages

tag: genotype

value: 5h 500 ng/ml LPS


title: Nur77_3_5h

tag: treatment


title: 2_HKM7VBGXT.2.CGGAGCCT_TATGCAGT

description:
Library name: 2_SM-NBW85_plate1
DHMT_2hr_d

tag: day

tag: guide rna

value: no guide

tag: barcode


title: 10E_ap2hsKO_minCHO_rep2_IP

description:
Library name: 10E_ap2hsKO_minCHO_rep2_IP
10E_ap2hsKO_minCHO_rep2_IP

value: H3K9me3 (Diagenode, C15410193)


title: ASD mouse PFC snRNA-seq [ADNP_HLF_1 + ADNP_HvF_2 + ADNP_HfF_2 + ADNP_HLF_2] (4-plex OCM)

description:
Library name: 1031-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

tag: sex (pool_composition)

value: female; female; female; female

tag: genotype (pool_composition)

tag: treatment (pool_composition)

value: lithium; vehicle; fluoxetine; lithium

value: Adnp; Adnp; Adnp; Adnp

value: ADNP_HLF_1; ADNP_HvF_2; ADNP_HfF_2; ADNP_HLF_2


title: ASD mouse PFC snRNA-seq [Na_HvF_1 + Na_HfF_1 + Na_HLF_1 + Na_HLF_2] (4-plex OCM)

description:
Library name: 1031-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: vehicle; fluoxetine; lithium; lithium

tag: mouse line_(pool_composition)

value: Naa15; Naa15; Naa15; Naa15

tag: multiplexed mouse_ids

value: Na_HvF_1; Na_HfF_1; Na_HLF_1; Na_HLF_2

tag: n samples_per_pool


title: ASD mouse PFC snRNA-seq [P131_HfF_2 + P131_HLF_2 + ADNP_HvF_1 + ADNP_HfF_1] (4-plex OCM)

description:
Library name: 1031-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

tag: age

value: fluoxetine; lithium; vehicle; fluoxetine

value: Pten; Pten; Adnp; Adnp

value: P131_HfF_2; P131_HLF_2; ADNP_HvF_1; ADNP_HfF_1


title: 1_HKM7VBGXT.1.CGGAGCCT_TATGCAGT

description:
Library name: 1_SM-NBW85_plate1
DHMT_2hr_d

value: iPSC-derived excitatory neuron, astrocyte

value: WT


title: ASD mouse PFC snRNA-seq [P131_HvF_1 + P131_HfF_1 + P131_HLF_1 + P131_HvF_2] (4-plex OCM)

description:
Library name: 1031-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: vehicle; fluoxetine; lithium; vehicle

value: Pten; Pten; Pten; Pten


title: 10E_ap2hsKO_plusCHO_rep2_in

description:
Library name: 10E_ap2hsKO_plusCHO_rep2_in
10E_ap2hsKO_plusCHO_rep2_in

value: ap2-hs knockout

value: control choline

tag: biological replicate

tag: chip antibody

tag: time


title: 4_HKM7VBGXT.4.GCGTAGTA_TATGCAGT

description:
Library name: 4_SM-NBW84_plate1
DHMT_2hr_c

tag: cell line

value: no guide


title: ASD mouse PFC snRNA-seq [SdC_HLM_2 + Na_HvM_2 + Na_HfM_2 + Na_HLM_2] (4-plex OCM)

description:
Library name: 1020-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

tag: tissue

tag: cell type

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: male; male; male; male

value: lithium; vehicle; fluoxetine; lithium

value: Shank3-deltaC; Naa15; Naa15; Naa15

value: SdC_HLM_2; Na_HvM_2; Na_HfM_2; Na_HLM_2

tag: sequencing batch


title: ASD mouse PFC snRNA-seq [TBR1_HLM_1 + TBR1_HLM_2 + SdC_HvM_2 + SdC_HfM_2] (4-plex OCM)

description:
Library name: 1020-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: lithium; lithium; vehicle; fluoxetine

value: Tbr1; Tbr1; Shank3-deltaC; Shank3-deltaC

value: TBR1_HLM_1; TBR1_HLM_2; SdC_HvM_2; SdC_HfM_2