title: Dyrk, Hippocampus, HT, male,replicate2

description: Library name: Dyrk_HPC_HvM_2


title: Dyrk, Hippocampus, HT, male,replicate1

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: Dyrk_HPC_HvM_1

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: Hippocampus

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

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: Hippocampus

tag: strain

tag: genotype

value: Heterozygous

tag: Sex

value: male

tag: batch


title: Dyrk, Hippocampus, HT, female,replicate3

description: Library name: Dyrk_HPC_HvF_3

value: female


title: Dyrk, Hippocampus, HT, female,replicate4

description: Library name: Dyrk_HPC_HvF_4


title: Dyrk, Hippocampus, HT, female,replicate2

description: Library name: Dyrk_HPC_HvF_2


title: G2b, Hippocampus, HT, female,replicate4

description: Library name: G2b_HPC_HvF_4


title: Dyrk, Hippocampus, HT, female,replicate1

description: Library name: Dyrk_HPC_HvF_1


title: CHN, Hippocampus, WT, male,replicate4

description: Library name: CHN_HPC_WvM_4

value: Wildtype


title: CHN, Hippocampus, WT, male,replicate3

description: Library name: CHN_HPC_WvM_3


title: Dyrk, Hippocampus, WT, female,replicate3

description: Library name: Dyrk_HPC_WvF_3


title: CHN, Hippocampus, WT, male,replicate2

description: Library name: CHN_HPC_WvM_2


title: CHN, Hippocampus, WT, male,replicate1

description: Library name: CHN_HPC_WvM_1


title: CHN, Hippocampus, WT, female,replicate3

description: Library name: CHN_HPC_WvF_3


title: CHN, Hippocampus, WT, female,replicate4

description: Library name: CHN_HPC_WvF_4


title: CHN, Hippocampus, WT, female,replicate2

description: Library name: CHN_HPC_WvF_2


title: CHN, Hippocampus, WT, female,replicate1

description: Library name: CHN_HPC_WvF_1


title: CHN, Hippocampus, HT, male,replicate4

description: Library name: CHN_HPC_HvM_4


title: CHN, Hippocampus, HT, male,replicate3

description: Library name: CHN_HPC_HvM_3


title: CHN, Hippocampus, HT, male,replicate2

description: Library name: CHN_HPC_HvM_2


title: CHN, Hippocampus, HT, male,replicate1

description: Library name: CHN_HPC_HvM_1


title: CHN, Hippocampus, HT, female,replicate4

description: Library name: CHN_HPC_HvF_4


title: CHN, Hippocampus, HT, female,replicate3

description: Library name: CHN_HPC_HvF_3


title: CHN, Hippocampus, HT, female,replicate1

description: Library name: CHN_HPC_HvF_1


title: ASH, Hippocampus, WT, male,replicate4

description: Library name: ASH_HPC_WvM_4


title: CHN, Hippocampus, HT, female,replicate2

description: Library name: CHN_HPC_HvF_2


title: ASH, Hippocampus, WT, male,replicate3

description: Library name: ASH_HPC_WvM_3


title: ASH, Hippocampus, WT, male,replicate2

description: Library name: ASH_HPC_WvM_2


title: ASH, Hippocampus, WT, female,replicate4

description: Library name: ASH_HPC_WvF_4


title: ASH, Hippocampus, WT, male,replicate1

description: Library name: ASH_HPC_WvM_1


title: ASH, Hippocampus, WT, female,replicate3

description: Library name: ASH_HPC_WvF_3


title: ASH, Hippocampus, WT, female,replicate2

description: Library name: ASH_HPC_WvF_2


title: ASH, Hippocampus, WT, female,replicate1

description: Library name: ASH_HPC_WvF_1


title: ASH, Hippocampus, HT, male,replicate3

description: Library name: ASH_HPC_HvM_3


title: ASH, Hippocampus, HT, male,replicate2

description: Library name: ASH_HPC_HvM_2


title: ASH, Hippocampus, HT, male,replicate1

description: Library name: ASH_HPC_HvM_1


title: ASH, Hippocampus, HT, male,replicate4

description: Library name: ASH_HPC_HvM_4


title: ASH, Hippocampus, HT, female,replicate4

description: Library name: ASH_HPC_HvF_4


title: ASH, Hippocampus, HT, female,replicate3

description: Library name: ASH_HPC_HvF_3


title: ASH, Hippocampus, HT, female,replicate2

description: Library name: ASH_HPC_HvF_2


title: ASH, Hippocampus, HT, female,replicate1

description: Library name: ASH_HPC_HvF_1


title: Arid, Hippocampus, WT, male,replicate3

description: Library name: Arid_HPC_WvM_4


title: Arid, Hippocampus, WT, male,replicate2

description: Library name: Arid_HPC_WvM_3


title: Arid, Hippocampus, WT, male,replicate1

description: Library name: Arid_HPC_WvM_2


title: Arid, Hippocampus, WT, female,replicate4

description: Library name: Arid_HPC_WvF_4


title: Arid, Hippocampus, WT, female,replicate2

description: Library name: Arid_HPC_WvF_2


title: Arid, Hippocampus, WT, female,replicate3

description: Library name: Arid_HPC_WvF_3


title: Arid, Hippocampus, WT, female,replicate1

description: Library name: Arid_HPC_WvF_1


title: Arid, Hippocampus, HT, male,replicate4

description: Library name: Arid_HPC_HvM_4


title: Arid, Hippocampus, HT, male,replicate3

description: Library name: Arid_HPC_HvM_3


title: Arid, Hippocampus, HT, male,replicate2

description: Library name: Arid_HPC_HvM_2


title: Arid, Hippocampus, HT, male,replicate1

description: Library name: Arid_HPC_HvM_1


title: Arid, Hippocampus, HT, female,replicate4

description: Library name: Arid_HPC_HvF_4


title: Arid, Hippocampus, HT, female,replicate3

description: Library name: Arid_HPC_HvF_3


title: ADNP, Hippocampus, WT, male,replicate4

description: Library name: ADNP_HPC_WvM_4


title: Arid, Hippocampus, HT, female,replicate2

description: Library name: Arid_HPC_HvF_2


title: Arid, Hippocampus, HT, female,replicate1

description: Library name: Arid_HPC_HvF_1


title: ADNP, Hippocampus, WT, male,replicate3

description: Library name: ADNP_HPC_WvM_3


title: ADNP, Hippocampus, WT, male,replicate2

description: Library name: ADNP_HPC_WvM_2


title: ADNP, Hippocampus, WT, male,replicate1

description: Library name: ADNP_HPC_WvM_1


title: ADNP, Hippocampus, WT, female,replicate4

description: Library name: ADNP_HPC_WvF_4


title: ADNP, Hippocampus, WT, female,replicate3

description: Library name: ADNP_HPC_WvF_3


title: ADNP, Hippocampus, WT, female,replicate2

description: Library name: ADNP_HPC_WvF_2


title: ADNP, Hippocampus, WT, female,replicate1

description: Library name: ADNP_HPC_WvF_1


title: ADNP, Hippocampus, HT, male,replicate3

description: Library name: ADNP_HPC_HvM_3


title: ADNP, Hippocampus, HT, male,replicate4

description: Library name: ADNP_HPC_HvM_4


title: ADNP, Hippocampus, HT, male,replicate2

description: Library name: ADNP_HPC_HvM_2


title: ADNP, Hippocampus, HT, male,replicate1

description: Library name: ADNP_HPC_HvM_1


title: ADNP, Hippocampus, HT, female,replicate3

description: Library name: ADNP_HPC_HvF_3


title: ADNP, Hippocampus, HT, female,replicate4

description: Library name: ADNP_HPC_HvF_4


title: ADNP, Hippocampus, HT, female,replicate2

description: Library name: ADNP_HPC_HvF_2


title: ADNP, Hippocampus, HT, female,replicate1

description: Library name: ADNP_HPC_HvF_1


title: Pdpn_VhlhKO_01

city: Taichung

first: Hieu-Huy

last: Nguyen-Tran

state: Taichung

address: Xueshi

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

description:
Library name: Sample2
Podoplanin-positive (PDPN⁺) kidney cells isolated from conditional Vhlh knockout mice (Hoxb7-Cre-GFP; Vhlh^loxP/loxP), age 12 weeks, no treatment

data_processing:
Raw BCL files were converted to FASTQ with bcl-convert (or bcl2fastq). Read quality was assessed with FastQC and aggregated using MultiQC. Adapters and low-quality bases were trimmed with Cutadapt. Filtered reads were aligned to Mus musculus reference mm10 (GRCm38) with STAR (two-pass mode) using Ensembl gene annotations (e.g., release 98); alignment metrics (uniquely mapped reads, rRNA content, duplication) were recorded. Gene-level counts were generated with featureCounts (subread) in stranded mode (reverse/forward per library chemistry). Downstream analysis was performed in R: low-count genes were filtered; counts were normalized and differential expression tested with DESeq2 (primary contrast: KO vs WT). Where applicable, sequencing lane or sex was included as a covariate. Significance thresholds were set at FDR < 0.05.
Assembly: mm10
Supplementary files format and content: Full table content count and TPM expresison level

source_name: Kidney

growth_protocol: Mice were maintained under specific pathogen–free (SPF) housing conditions with a 12-h light/12-h dark cycle, 20–24 °C temperature, and 40–60% humidity. Animals had ad libitum access to food and water. Wild-type (Vhlh^loxP/loxP or Hoxb7-Cre-GFP; n=6) and conditional knockout (Hoxb7-Cre-GFP; Vhlh^loxP/loxP; n=6) mice were bred on a C57BL/6 background. All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Kidneys were minced and digested enzymatically (collagenase II, dispase, DNase I) to generate single-cell suspensions. Podoplanin-positive (PDPN⁺) cells were enriched by magnetic cell sorting (MACS) or fluorescence-activated cell sorting (FACS) using anti-PDPN antibody. Enriched cell pellets were lysed in TRIzol reagent (Invitrogen) and total RNA was isolated according to the manufacturer’s instructions. RNA was further purified with the RNeasy Mini Kit (Qiagen), including on-column DNase digestion. RNA quality and integrity were assessed by Agilent Bioanalyzer, and only samples with RIN ≥ 8 were used for library construction.
Total RNA (RIN ≥ 8) from Pdpn⁺ cells was poly(A)-enriched using oligo-dT magnetic beads (e.g., NEBNext Poly(A) mRNA Magnetic Isolation Module or equivalent). Stranded Illumina libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit following the manufacturer’s instructions: RNA fragmentation, first- and second-strand cDNA synthesis (dUTP method for strand specificity), end repair/A-tailing, adaptor ligation, and limited-cycle PCR enrichment with unique dual indexes. Libraries were purified with SPRI beads, quantified by Qubit, and fragment size distributions were verified on an Agilent Bioanalyzer. Equimolar pools were sequenced on an Illumina NovaSeq 6000 (paired-end, 2×150 bp).

treatment_protocol: No pharmacologic or surgical treatments were applied. Kidneys were harvested directly from 8–12 week-old wild-type and Vhlh conditional knockout mice for downstream Pdpn⁺ cell isolation.

value: Kidney

tag: cell type

value: Podoplanin-positive

value: Hoxb7-Cre-GFP; Vhlh^loxP/loxP

value: Male

tag: age

value: 12 weeks


title: Pdpn_WT_01

description:
Library name: Sample1
Podoplanin-positive (PDPN⁺) kidney cells isolated from wild-type C57BL/6J mice (Vhlh^loxP/loxP), age 12 weeks, no treatment.
Control


title: Ank2, WT, Vehicle, male, replicate5

description: Library name: Ank2_WvM_5

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.

value: prefrontal cortex


title: Ank2, WT, Vehicle, male, replicate3

description: Library name: Ank2_WvM_3


title: Ank2, WT, Vehicle, male, replicate4

description: Library name: Ank2_WvM_4


title: Ank2, WT, Vehicle, male, replicate2

description: Library name: Ank2_WvM_2


title: Ank2, WT, Vehicle, male, replicate1

description: Library name: Ank2_WvM_1


title: Ank2, WT, Vehicle, female, replicate5

description: Library name: Ank2_WvF_5


title: Ank2, WT, Vehicle, female, replicate4

description: Library name: Ank2_WvF_4


title: Ank2, WT, Vehicle, female, replicate3

description: Library name: Ank2_WvF_3


title: Ank2, WT, Vehicle, female, replicate2

description: Library name: Ank2_WvF_2


title: Ank2, WT, Vehicle, female, replicate1

description: Library name: Ank2_WvF_1


title: Ank2, WT, Lithium, male, replicate5

description: Library name: Ank2_WLM_5


title: Ank2, WT, Lithium, male, replicate1

description: Library name: Ank2_WLM_1


title: Ank2, WT, Lithium, male, replicate2

description: Library name: Ank2_WLM_2


title: Ank2, WT, Lithium, male, replicate3

description: Library name: Ank2_WLM_3


title: Ank2, WT, Lithium, female, replicate4

description: Library name: Ank2_WLF_4


title: Ank2, WT, Lithium, male, replicate4

description: Library name: Ank2_WLM_4


title: Ank2, WT, Lithium, female, replicate5

description: Library name: Ank2_WLF_5


title: Ank2, WT, Lithium, female, replicate3

description: Library name: Ank2_WLF_3


title: Ank2, WT, Lithium, female, replicate2

description: Library name: Ank2_WLF_2


title: Ank2, WT, Lithium, female, replicate1

description: Library name: Ank2_WLF_1


title: Ank2, WT, Fluoxetine, male, replicate4

description: Library name: Ank2_WfM_4


title: Ank2, WT, Fluoxetine, male, replicate3

description: Library name: Ank2_WfM_3


title: Ank2, WT, Fluoxetine, male, replicate2

description: Library name: Ank2_WfM_2


title: Ank2, WT, Fluoxetine, female, replicate5

description: Library name: Ank2_WfF_5


title: Ank2, WT, Fluoxetine, male, replicate1

description: Library name: Ank2_WfM_1


title: Ank2, WT, Fluoxetine, female, replicate3

description: Library name: Ank2_WfF_3


title: Ank2, WT, Fluoxetine, female, replicate4

description: Library name: Ank2_WfF_4


title: Ank2, WT, Fluoxetine, female, replicate2

description: Library name: Ank2_WfF_2


title: Ank2, WT, Fluoxetine, female, replicate1

description: Library name: Ank2_WfF_1


title: Ank2, HT, Vehicle, male, replicate5

description: Library name: Ank2_HvM_5


title: Ank2, HT, Vehicle, male, replicate4

description: Library name: Ank2_HvM_4


title: Ank2, HT, Vehicle, male, replicate3

description: Library name: Ank2_HvM_3


title: Ank2, HT, Vehicle, male, replicate1

description: Library name: Ank2_HvM_1


title: Ank2, HT, Vehicle, female, replicate5

description: Library name: Ank2_HvF_5


title: Ank2, HT, Vehicle, female, replicate4

description: Library name: Ank2_HvF_4


title: Ank2, HT, Vehicle, female, replicate3

description: Library name: Ank2_HvF_3


title: Ank2, HT, Vehicle, male, replicate2

description: Library name: Ank2_HvM_2


title: Ank2, HT, Vehicle, female, replicate2

description: Library name: Ank2_HvF_2


title: Ank2, HT, Lithium, male, replicate5

description: Library name: Ank2_HLM_5


title: Ank2, HT, Vehicle, female, replicate1

description: Library name: Ank2_HvF_1


title: Ank2, HT, Lithium, male, replicate4

description: Library name: Ank2_HLM_4


title: Ank2, HT, Lithium, male, replicate3

description: Library name: Ank2_HLM_3


title: Ank2, HT, Lithium, male, replicate2

description: Library name: Ank2_HLM_2


title: Ank2, HT, Lithium, male, replicate1

description: Library name: Ank2_HLM_1


title: Ank2, HT, Lithium, female, replicate3

description: Library name: Ank2_HLF_3


title: Ank2, HT, Lithium, female, replicate4

description: Library name: Ank2_HLF_4


title: Ank2, HT, Lithium, female, replicate5

description: Library name: Ank2_HLF_5


title: Ank2, HT, Lithium, female, replicate2

description: Library name: Ank2_HLF_2


title: Ank2, HT, Fluoxetine, male, replicate5

description: Library name: Ank2_HfM_5


title: Ank2, HT, Fluoxetine, male, replicate4

description: Library name: Ank2_HfM_4


title: Ank2, HT, Lithium, female, replicate1

description: Library name: Ank2_HLF_1


title: Ank2, HT, Fluoxetine, male, replicate3

description: Library name: Ank2_HfM_3


title: Ank2, HT, Fluoxetine, male, replicate2

description: Library name: Ank2_HfM_2


title: Ank2, HT, Fluoxetine, male, replicate1

description: Library name: Ank2_HfM_1


title: Ank2, HT, Fluoxetine, female, replicate5

description: Library name: Ank2_HfF_5


title: Ank2, HT, Fluoxetine, female, replicate3

description: Library name: Ank2_HfF_3


title: Ank2, HT, Fluoxetine, female, replicate2

description: Library name: Ank2_HfF_2


title: Chd8-S62X, WT, Vehicle, male, replicate5

description: Library name: Chd8S_WvM_5


title: Ank2, HT, Fluoxetine, female, replicate1

description: Library name: Ank2_HfF_1


title: Chd8-S62X, WT, Vehicle, male, replicate1

description: Library name: Chd8S_WvM_1


title: Chd8-S62X, WT, Vehicle, male, replicate3

description: Library name: Chd8S_WvM_3


title: Chd8-S62X, WT, Vehicle, male, replicate4

description: Library name: Chd8S_WvM_4


title: Chd8-S62X, WT, Vehicle, female, replicate5

description: Library name: Chd8S_WvF_5


title: Chd8-S62X, WT, Vehicle, female, replicate4

description: Library name: Chd8S_WvF_4


title: Chd8-S62X, WT, Vehicle, female, replicate3

description: Library name: Chd8S_WvF_3


title: Chd8-S62X, WT, Vehicle, female, replicate2

description: Library name: Chd8S_WvF_2


title: Chd8-S62X, WT, Lithium, male, replicate5

description: Library name: Chd8S_WLM_5


title: Chd8-S62X, WT, Lithium, male, replicate3

description: Library name: Chd8S_WLM_3


title: Chd8-S62X, WT, Lithium, male, replicate4

description: Library name: Chd8S_WLM_4


title: Chd8-S62X, WT, Lithium, male, replicate2

description: Library name: Chd8S_WLM_2


title: Chd8-S62X, WT, Lithium, female, replicate5

description: Library name: Chd8S_WLF_5


title: Chd8-S62X, WT, Lithium, male, replicate1

description: Library name: Chd8S_WLM_1


title: Chd8-S62X, WT, Lithium, female, replicate4

description: Library name: Chd8S_WLF_4


title: Ank2, HT, Fluoxetine, female, replicate4

description: Library name: Ank2_HfF_4


title: Chd8-S62X, WT, Vehicle, male, replicate2

description: Library name: Chd8S_WvM_2


title: Chd8-S62X, WT, Lithium, female, replicate3

description: Library name: Chd8S_WLF_3


title: Chd8-S62X, WT, Fluoxetine, male, replicate5

description: Library name: Chd8S_WfM_5


title: Chd8-S62X, WT, Lithium, female, replicate2

description: Library name: Chd8S_WLF_2


title: Chd8-S62X, WT, Lithium, female, replicate1

description: Library name: Chd8S_WLF_1


title: Chd8-S62X, WT, Fluoxetine, male, replicate3

description: Library name: Chd8S_WfM_3


title: Chd8-S62X, WT, Fluoxetine, male, replicate4

description: Library name: Chd8S_WfM_4


title: Chd8-S62X, WT, Vehicle, female, replicate1

description: Library name: Chd8S_WvF_1


title: Control (NT) replicate 1

city: New York

first: Morgan

last: Huse

state: NY

address: 417 E 68th St

country: USA

institute: Sloan Kettering Institute

description:
Library name: NT1
Bulk RNA-seq of non-targeting control cells (biological replicate 1)

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

molecule: polyA RNA

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

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

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

tag: cell line

value: Melanoma cells

value: Non-targeting control

value: batch 1


title: Liver, WT, replicate 1

city: Oak Ridge

first: Alice

last: Townsend

state: TN

address: 1 Bethel Valley Rd

institute: ORNL

description:
Library name: Sample 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
STARSolo aligner v2.7.9a was used to generate the mouse reference genome (GRCm38) and to align the fastq file reads for each sample. The EmptyDrops methodology was used within STARSolo to filter low quality cells with minimal total UMI counts.
Assembly: mm10
Supplementary files format and content: Barcode and feature files in .tsv.gz format. Count matrix files in .mtx.gz format.

molecule: nuclear RNA

source_name: Liver

extract_protocol:
Livers were collected from 7-week old mice, 3 Npc1+/+ and 3 Npc1-/- following isoflurane euthanasia and decapitation. Liver tissue was dissected, flash frozen in liquid nitrogen, and homogenized with a glass Dounce tissue grinder 25X with pestle A and 25X with pestle B) in 2 mL of EZ PREP buffer (Sigma NUC-101). Homogenized liver tissue was incubated on ice for 5 minutes, followed by an addition of 2 mL of EZ PREP, then centrifuged at 500 g for 5 minutes at 4 °C to pellet nuclei. Resulting nuclei were washed with 4 mL EZ PREP and incubated for 5 minutes on ice then centrifuged using the same parameters. Samples were washed with 4 mL nuclear suspension buffer (0.01% BSA, RNase inhibitor [Takara 2313 A]) and centrifuged using the same parameters. 1 mL of nuclear suspension buffer was added to the pellet for resuspension, then filtered with a 35 µM cell strainer (Corning 352235) and counted. Nuclei were diluted to 800-1500 cells/µL and libraries were generated with the 10X Chromium Controller system.
Llibraries were generated with the 10X Chromium Controller system. Single-nucleus libraries were sequenced using the Illumina NovaSeq 6000.

value: Liver

value: WT


title: Bioreplicate 3 Cfh KO glutamate

city: Hamburg

first: Christina

last: Mayer

address: Falkenried 94

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Library name: Bio3_KO_Glut

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

source_name: Cortex

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

value: Cortex

value: primary cortical neurons

value: neuronal Cfh conditional knockout

tag: treatment

value: 50 µM glutamate for 6h


title: Bioreplicate 4 Cfh KO control

description: Library name: Bio4_KO_Ctrl

value: no treatment


title: Control (NT) replicate 2

description:
Library name: NT2
Bulk RNA-seq of non-targeting control cells (biological replicate 2)


title: Chd8-S62X, WT, Fluoxetine, male, replicate2

description: Library name: Chd8S_WfM_2

value: Wildtype


title: Chd8-S62X, WT, Fluoxetine, male, replicate1

description: Library name: Chd8S_WfM_1


title: Chd8-S62X, WT, Fluoxetine, female, replicate5

description: Library name: Chd8S_WfF_5


title: Chd8-S62X, WT, Fluoxetine, female, replicate4

description: Library name: Chd8S_WfF_4


title: Chd8-S62X, WT, Fluoxetine, female, replicate3

description: Library name: Chd8S_WfF_3


title: Chd8-S62X, WT, Fluoxetine, female, replicate2

description: Library name: Chd8S_WfF_2


title: Chd8-S62X, WT, Fluoxetine, female, replicate1

description: Library name: Chd8S_WfF_1


title: Chd8-S62X, HT, Vehicle, male, replicate5

description: Library name: Chd8S_HvM_5

value: Heterozygous


title: Chd8-S62X, HT, Vehicle, male, replicate4

description: Library name: Chd8S_HvM_4


title: Chd8-S62X, HT, Vehicle, male, replicate3

description: Library name: Chd8S_HvM_3


title: Chd8-S62X, HT, Vehicle, male, replicate2

description: Library name: Chd8S_HvM_2


title: Chd8-S62X, HT, Vehicle, male, replicate1

description: Library name: Chd8S_HvM_1


title: Chd8-S62X, HT, Vehicle, female, replicate5

description: Library name: Chd8S_HvF_5


title: Chd8-S62X, HT, Vehicle, female, replicate3

description: Library name: Chd8S_HvF_3


title: Chd8-S62X, HT, Vehicle, female, replicate2

description: Library name: Chd8S_HvF_2


title: Chd8-S62X, HT, Vehicle, female, replicate1

description: Library name: Chd8S_HvF_1


title: Chd8-S62X, HT, Lithium, male, replicate5

description: Library name: Chd8S_HLM_5


title: Chd8-S62X, HT, Vehicle, female, replicate4

description: Library name: Chd8S_HvF_4


title: Chd8-S62X, HT, Lithium, male, replicate4

description: Library name: Chd8S_HLM_4


title: Chd8-S62X, HT, Lithium, male, replicate3

description: Library name: Chd8S_HLM_3


title: Chd8-S62X, HT, Lithium, male, replicate2

description: Library name: Chd8S_HLM_2


title: Chd8-S62X, HT, Lithium, male, replicate1

description: Library name: Chd8S_HLM_1


title: Chd8-S62X, HT, Lithium, female, replicate5

description: Library name: Chd8S_HLF_5


title: Chd8-S62X, HT, Lithium, female, replicate4

description: Library name: Chd8S_HLF_4


title: Chd8-S62X, HT, Lithium, female, replicate3

description: Library name: Chd8S_HLF_3


title: Chd8-S62X, HT, Lithium, female, replicate1

description: Library name: Chd8S_HLF_1


title: Chd8-S62X, HT, Lithium, female, replicate2

description: Library name: Chd8S_HLF_2


title: Chd8-S62X, HT, Fluoxetine, male, replicate5

description: Library name: Chd8S_HfM_5


title: Chd8-S62X, HT, Fluoxetine, male, replicate3

description: Library name: Chd8S_HfM_3


title: Chd8-S62X, HT, Fluoxetine, male, replicate1

description: Library name: Chd8S_HfM_1


title: Chd8-S62X, HT, Fluoxetine, female, replicate4

description: Library name: Chd8S_HfF_4


title: Chd8-S62X, HT, Fluoxetine, male, replicate2

description: Library name: Chd8S_HfM_2


title: Hepatocytes co-cultured with Phgdh WT cancer cells and CXCR2i rep1

first: Jason

middle: Rodencal

last: Terrell

address: 530 1st Avenue

institute: NYU Langone Health

description: Library name: Hepato_10

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

source_name: mouse hepatocytes

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

value: mouse hepatocytes

value: cocultured with WT cancer cells and CXCR2 inhibitor


title: Chd8-S62X, HT, Fluoxetine, male, replicate4

description: Library name: Chd8S_HfM_4


title: Chd8-S62X, HT, Fluoxetine, female, replicate3

description: Library name: Chd8S_HfF_3


title: Chd8-S62X, HT, Fluoxetine, female, replicate1

description: Library name: Chd8S_HfF_1


title: Chd8-S62X, HT, Fluoxetine, female, replicate2

description: Library name: Chd8S_HfF_2


title: Shank2, WT, Vehicle, male, replicate4

description: Library name: Sh2_WvM_4


title: Shank2, WT, Vehicle, male, replicate3

description: Library name: Sh2_WvM_3


title: Shank2, WT, Vehicle, female, replicate2

description: Library name: Sh2_WvF_3


title: Shank2, WT, Vehicle, female, replicate3

description: Library name: Sh2_WvF_4


title: Shank2, WT, Vehicle, male, replicate2

description: Library name: Sh2_WvM_2


title: Shank2, WT, Vehicle, female, replicate4

description: Library name: Sh2_WvF_5


title: Shank2, WT, Vehicle, male, replicate1

description: Library name: Sh2_WvM_1


title: Shank2, WT, Lithium, male, replicate5

description: Library name: Sh2_WLM_5


title: Shank2, WT, Lithium, male, replicate4

description: Library name: Sh2_WLM_4


title: Shank2, WT, Lithium, male, replicate2

description: Library name: Sh2_WLM_2


title: Shank2, WT, Lithium, male, replicate1

description: Library name: Sh2_WLM_1


title: Shank2, WT, Lithium, female, replicate4

description: Library name: Sh2_WLF_4


title: Shank2, WT, Lithium, female, replicate2

description: Library name: Sh2_WLF_2


title: Shank2, WT, Fluoxetine, male, replicate5

description: Library name: Sh2_WfM_5


title: Shank2, WT, Vehicle, female, replicate1

description: Library name: Sh2_WvF_1


title: Shank2, WT, Lithium, female, replicate3

description: Library name: Sh2_WLF_3


title: Shank2, WT, Lithium, male, replicate3

description: Library name: Sh2_WLM_3


title: Shank2, WT, Fluoxetine, male, replicate2

description: Library name: Sh2_WfM_2


title: Shank2, WT, Fluoxetine, female, replicate5

description: Library name: Sh2_WfF_5


title: Shank2, WT, Fluoxetine, female, replicate4

description: Library name: Sh2_WfF_4


title: Shank2, WT, Lithium, female, replicate1

description: Library name: Sh2_WLF_1


title: Shank2, WT, Fluoxetine, female, replicate2

description: Library name: Sh2_WfF_2


title: Shank2, HT, Vehicle, male, replicate5

description: Library name: Sh2_HvM_5


title: Shank2, WT, Fluoxetine, female, replicate1

description: Library name: Sh2_WfF_1


title: Shank2, HT, Vehicle, male, replicate4

description: Library name: Sh2_HvM_4


title: Shank2, HT, Vehicle, male, replicate2

description: Library name: Sh2_HvM_2


title: Shank2, WT, Fluoxetine, male, replicate1

description: Library name: Sh2_WfM_1


title: Shank2, WT, Fluoxetine, male, replicate3

description: Library name: Sh2_WfM_3


title: Hepatocytes co-cultured with Phgdh WT cancer cells rep3

description: Library name: Hepato_6

value: cocultured with WT cancer cells


title: Shank2, HT, Vehicle, male, replicate1

description: Library name: Sh2_HvM_1


title: Shank2, HT, Vehicle, female, replicate3

description: Library name: Sh2_HvF_3


title: Shank2, HT, Vehicle, female, replicate2

description: Library name: Sh2_HvF_2


title: Shank2, HT, Vehicle, female, replicate1

description: Library name: Sh2_HvF_1


title: Shank2, HT, Vehicle, female, replicate5

description: Library name: Sh2_HvF_5


title: Shank2, HT, Vehicle, female, replicate4

description: Library name: Sh2_HvF_4


title: Shank2, HT, Vehicle, male, replicate3

description: Library name: Sh2_HvM_3


title: Shank2, HT, Lithium, male, replicate4

description: Library name: Sh2_HLM_4


title: Shank2, HT, Lithium, male, replicate3

description: Library name: Sh2_HLM_3


title: Shank2, HT, Lithium, female, replicate4

description: Library name: Sh2_HLF_4


title: Shank2, HT, Lithium, male, replicate5

description: Library name: Sh2_HLM_5


title: Shank2, HT, Lithium, male, replicate2

description: Library name: Sh2_HLM_2


title: Shank2, HT, Lithium, female, replicate1

description: Library name: Sh2_HLF_1


title: Shank2, HT, Fluoxetine, male, replicate3

description: Library name: Sh2_HfM_3


title: Shank2, HT, Fluoxetine, female, replicate5

description: Library name: Sh2_HfF_5


title: Shank2, HT, Fluoxetine, female, replicate4

description: Library name: Sh2_HfF_4


title: Shank2, HT, Lithium, female, replicate5

description: Library name: Sh2_HLF_5


title: Shank2, HT, Lithium, male, replicate1

description: Library name: Sh2_HLM_1


title: Shank2, HT, Lithium, female, replicate3

description: Library name: Sh2_HLF_3


title: Shank2, HT, Fluoxetine, female, replicate3

description: Library name: Sh2_HfF_3


title: Shank2, HT, Fluoxetine, male, replicate5

description: Library name: Sh2_HfM_5


title: Shank2, HT, Fluoxetine, male, replicate2

description: Library name: Sh2_HfM_2


title: Shank2, HT, Lithium, female, replicate2

description: Library name: Sh2_HLF_2


title: Shank2, HT, Fluoxetine, male, replicate1

description: Library name: Sh2_HfM_1


title: Shank2, HT, Fluoxetine, female, replicate2

description: Library name: Sh2_HfF_2


title: Shank2, HT, Fluoxetine, male, replicate4

description: Library name: Sh2_HfM_4


title: Shank3, WT, Vehicle, male, replicate5

description: Library name: Shank3_WvM_5


title: Shank3, WT, Vehicle, male, replicate4

description: Library name: Shank3_WvM_4


title: Shank3, WT, Vehicle, male, replicate2

description: Library name: Shank3_WvM_2


title: Shank2, HT, Fluoxetine, female, replicate1

description: Library name: Sh2_HfF_1


title: Shank3, WT, Vehicle, male, replicate3

description: Library name: Shank3_WvM_3


title: Shank3, WT, Vehicle, female, replicate5

description: Library name: Shank3_WvF_5


title: Shank3, WT, Vehicle, female, replicate4

description: Library name: Shank3_WvF_4


title: Shank3, WT, Vehicle, female, replicate1

description: Library name: Shank3_WvF_1


title: Shank3, WT, Lithium, male, replicate5

description: Library name: Shank3_WLM_5


title: Shank3, WT, Lithium, male, replicate4

description: Library name: Shank3_WLM_4


title: Shank3, WT, Lithium, male, replicate3

description: Library name: Shank3_WLM_3


title: Shank3, WT, Lithium, male, replicate2

description: Library name: Shank3_WLM_2


title: Shank3, WT, Vehicle, female, replicate3

description: Library name: Shank3_WvF_3


title: Shank3, WT, Lithium, female, replicate3

description: Library name: Shank3_WLF_3


title: Shank3, WT, Lithium, female, replicate2

description: Library name: Shank3_WLF_2


title: Shank3, WT, Lithium, female, replicate1

description: Library name: Shank3_WLF_1


title: Shank3, WT, Fluoxetine, male, replicate5

description: Library name: Shank3_WfM_5


title: Shank3, WT, Fluoxetine, male, replicate4

description: Library name: Shank3_WfM_4


title: Shank3, WT, Fluoxetine, male, replicate3

description: Library name: Shank3_WfM_3


title: Shank3, WT, Fluoxetine, male, replicate2

description: Library name: Shank3_WfM_2


title: Shank3, WT, Fluoxetine, male, replicate1

description: Library name: Shank3_WfM_1


title: Shank2, WT, Fluoxetine, female, replicate3

description: Library name: Sh2_WfF_3


title: Shank3, WT, Lithium, male, replicate1

description: Library name: Shank3_WLM_1


title: Shank3, WT, Vehicle, female, replicate2

description: Library name: Shank3_WvF_2


title: Shank3, WT, Fluoxetine, female, replicate4

description: Library name: Shank3_WfF_4


title: Shank3, WT, Fluoxetine, female, replicate3

description: Library name: Shank3_WfF_3


title: Shank3, WT, Vehicle, male, replicate1

description: Library name: Shank3_WvM_1


title: Shank2, WT, Fluoxetine, male, replicate4

description: Library name: Sh2_WfM_4


title: Shank3, WT, Fluoxetine, female, replicate2

description: Library name: Shank3_WfF_2


title: Shank3, WT, Fluoxetine, female, replicate1

description: Library name: Shank3_WfF_1


title: Shank3, KI HT, Vehicle, male, replicate5

description: Library name: Shank3_HvM_5

value: KI Heterozygous


title: Shank3, WT, Fluoxetine, female, replicate5

description: Library name: Shank3_WfF_5

value: prefrontal cortex


title: Shank3, KI HT, Vehicle, male, replicate4

description: Library name: Shank3_HvM_4


title: Shank3, KI HT, Vehicle, male, replicate2

description: Library name: Shank3_HvM_2


title: Shank3, KI HT, Vehicle, male, replicate3

description: Library name: Shank3_HvM_3


title: Shank3, KI HT, Vehicle, male, replicate1

description: Library name: Shank3_HvM_1


title: Shank3, KI HT, Vehicle, female, replicate5

description: Library name: Shank3_HvF_5


title: Shank3, WT, Lithium, female, replicate4

description: Library name: Shank3_WLF_4


title: Shank3, KI HT, Vehicle, female, replicate4

description: Library name: Shank3_HvF_4


title: Shank3, KI HT, Vehicle, female, replicate2

description: Library name: Shank3_HvF_2


title: Shank3, KI HT, Vehicle, female, replicate1

description: Library name: Shank3_HvF_1


title: Shank3, KI HT, Vehicle, female, replicate3

description: Library name: Shank3_HvF_3


title: Shank3, KI HT, Lithium, male, replicate5

description: Library name: Shank3_HLM_5


title: Shank3, KI HT, Lithium, male, replicate3

description: Library name: Shank3_HLM_3


title: Shank3, KI HT, Lithium, male, replicate2

description: Library name: Shank3_HLM_2


title: Shank3, KI HT, Lithium, male, replicate1

description: Library name: Shank3_HLM_1


title: Shank3, KI HT, Lithium, female, replicate5

description: Library name: Shank3_HLF_5


title: Shank3, KI HT, Lithium, male, replicate4

description: Library name: Shank3_HLM_4


title: Shank3, KI HT, Lithium, female, replicate3

description: Library name: Shank3_HLF_3


title: Shank3, KI HT, Lithium, female, replicate4

description: Library name: Shank3_HLF_4


title: Shank3, KI HT, Lithium, female, replicate1

description: Library name: Shank3_HLF_1


title: Shank3, KI HT, Lithium, female, replicate2

description: Library name: Shank3_HLF_2


title: Shank3, KI HT, Fluoxetine, male, replicate5

description: Library name: Shank3_HfM_5


title: Shank3, KI HT, Fluoxetine, male, replicate4

description: Library name: Shank3_HfM_4


title: Shank3, KI HT, Fluoxetine, male, replicate3

description: Library name: Shank3_HfM_3


title: Shank3, KI HT, Fluoxetine, male, replicate2

description: Library name: Shank3_HfM_2


title: Shank3, KI HT, Fluoxetine, male, replicate1

description: Library name: Shank3_HfM_1


title: Shank3, KI HT, Fluoxetine, female, replicate4

description: Library name: Shank3_HfF_4


title: Shank3, KI HT, Fluoxetine, female, replicate3

description: Library name: Shank3_HfF_3


title: Shank3, KI HT, Fluoxetine, female, replicate5

description: Library name: Shank3_HfF_5


title: Shank3, KI HT, Fluoxetine, female, replicate2

description: Library name: Shank3_HfF_2


title: Shank3, KI HT, Fluoxetine, female, replicate1

description: Library name: Shank3_HfF_1


title: Tbr1, WT, Vehicle, male, replicate5

description: Library name: TBR1_WvM_5


title: Tbr1, WT, Vehicle, male, replicate4

description: Library name: TBR1_WvM_4


title: Tbr1, WT, Vehicle, male, replicate3

description: Library name: TBR1_WvM_3


title: Tbr1, WT, Vehicle, male, replicate1

description: Library name: TBR1_WvM_1


title: Tbr1, WT, Vehicle, male, replicate2

description: Library name: TBR1_WvM_2


title: Tbr1, WT, Vehicle, female, replicate5

description: Library name: TBR1_WvF_5


title: Tbr1, WT, Vehicle, female, replicate4

description: Library name: TBR1_WvF_4


title: Tbr1, WT, Vehicle, female, replicate2

description: Library name: TBR1_WvF_2


title: Tbr1, WT, Vehicle, female, replicate1

description: Library name: TBR1_WvF_1


title: Tbr1, WT, Vehicle, female, replicate3

description: Library name: TBR1_WvF_3


title: Tbr1, WT, Lithium, male, replicate4

description: Library name: TBR1_WLM_4


title: Tbr1, WT, Lithium, male, replicate5

description: Library name: TBR1_WLM_5


title: Tbr1, WT, Lithium, male, replicate3

description: Library name: TBR1_WLM_3


title: Tbr1, WT, Lithium, male, replicate1

description: Library name: TBR1_WLM_1


title: Tbr1, WT, Lithium, male, replicate2

description: Library name: TBR1_WLM_2


title: Tbr1, WT, Lithium, female, replicate3

description: Library name: TBR1_WLF_3


title: Tbr1, WT, Lithium, female, replicate4

description: Library name: TBR1_WLF_4


title: Tbr1, WT, Lithium, female, replicate2

description: Library name: TBR1_WLF_2


title: Tbr1, WT, Fluoxetine, male, replicate5

description: Library name: TBR1_WfM_5


title: Tbr1, WT, Fluoxetine, male, replicate4

description: Library name: TBR1_WfM_4


title: Tbr1, WT, Fluoxetine, male, replicate2

description: Library name: TBR1_WfM_2


title: Tbr1, WT, Fluoxetine, male, replicate3

description: Library name: TBR1_WfM_3


title: Tbr1, WT, Fluoxetine, female, replicate5

description: Library name: TBR1_WfF_5


title: Tbr1, WT, Fluoxetine, female, replicate1

description: Library name: TBR1_WfF_1


title: Tbr1, WT, Fluoxetine, female, replicate3

description: Library name: TBR1_WfF_3


title: Tbr1, WT, Fluoxetine, male, replicate1

description: Library name: TBR1_WfM_1


title: Tbr1+/K228E, Vehicle, male, replicate5

description: Library name: TBR1_HvM_5


title: Tbr1+/K228E, Vehicle, male, replicate2

description: Library name: TBR1_HvM_2


title: Tbr1+/K228E, Vehicle, male, replicate1

description: Library name: TBR1_HvM_1


title: Tbr1+/K228E, Vehicle, female, replicate5

description: Library name: TBR1_HvF_5


title: Tbr1+/K228E, Vehicle, female, replicate4

description: Library name: TBR1_HvF_4


title: Tbr1+/K228E, Vehicle, female, replicate3

description: Library name: TBR1_HvF_3


title: Tbr1+/K228E, Vehicle, female, replicate1

description: Library name: TBR1_HvF_1


title: Tbr1+/K228E, Lithium, male, replicate5

description: Library name: TBR1_HLM_5


title: Tbr1+/K228E, Lithium, male, replicate4

description: Library name: TBR1_HLM_4


title: Tbr1+/K228E, Lithium, male, replicate3

description: Library name: TBR1_HLM_3


title: Tbr1+/K228E, Vehicle, female, replicate2

description: Library name: TBR1_HvF_2


title: Tbr1+/K228E, Lithium, male, replicate2

description: Library name: TBR1_HLM_2


title: Tbr1+/K228E, Lithium, female, replicate5

description: Library name: TBR1_HLF_5


title: Tbr1+/K228E, Lithium, male, replicate1

description: Library name: TBR1_HLM_1


title: Tbr1+/K228E, Lithium, female, replicate4

description: Library name: TBR1_HLF_4


title: Dyrk, P40, Vehicle, WT, male,replicate2

description: Library name: Dyrk_WvM_p40_2

growth_protocol: Mice were maintained under standard laboratory housing conditions with ad libitum access to food. Animals were analyzed at postnatal day 40 (P40)

treatment_protocol: Male and female mice were administered two different drugs (fluoxetine and lithium)


title: Tbr1+/K228E, Lithium, female, replicate3

description: Library name: TBR1_HLF_3


title: Tbr1+/K228E, Lithium, female, replicate2

description: Library name: TBR1_HLF_2


title: Tbr1+/K228E, Lithium, female, replicate1

description: Library name: TBR1_HLF_1


title: Tbr1+/K228E, Fluoxetine, male, replicate5

description: Library name: TBR1_HfM_5


title: Tbr1+/K228E, Fluoxetine, male, replicate4

description: Library name: TBR1_HfM_4


title: Tbr1+/K228E, Fluoxetine, male, replicate3

description: Library name: TBR1_HfM_3


title: Tbr1+/K228E, Fluoxetine, male, replicate2

description: Library name: TBR1_HfM_2


title: Tbr1+/K228E, Fluoxetine, female, replicate5

description: Library name: TBR1_HfF_5


title: Tbr1+/K228E, Fluoxetine, female, replicate4

description: Library name: TBR1_HfF_4


title: Tbr1+/K228E, Fluoxetine, male, replicate1

description: Library name: TBR1_HfM_1


title: Tbr1+/K228E, Fluoxetine, female, replicate3

description: Library name: TBR1_HfF_3


title: Tbr1+/K228E, Fluoxetine, female, replicate1

description: Library name: TBR1_HfF_1


title: Tbr1+/K228E, Fluoxetine, female, replicate2

description: Library name: TBR1_HfF_2


title: Tanc2, WT, Vehicle, male, replicate1

description: Library name: Tanc_WvM_1


title: Tanc2, WT, Vehicle, male, replicate3

description: Library name: Tanc_WvM_4


title: Tanc2, WT, Vehicle, male, replicate2

description: Library name: Tanc_WvM_2


title: Tanc2, WT, Vehicle, female, replicate4

description: Library name: Tanc_WvF_4


title: Tanc2, WT, Vehicle, female, replicate2

description: Library name: Tanc_WvF_2


title: Tanc2, WT, Vehicle, female, replicate3

description: Library name: Tanc_WvF_3


title: Tanc2, WT, Vehicle, female, replicate1

description: Library name: Tanc_WvF_1


title: Tanc2, WT, Lithium, male, replicate3

description: Library name: Tanc_WLM_3


title: Tanc2, WT, Lithium, male, replicate5

description: Library name: Tanc_WLM_5


title: Tanc2, WT, Lithium, male, replicate4

description: Library name: Tanc_WLM_4


title: TBR1, Hippocampus, WT, male,replicate4

description: Library name: TBR1_HPC_WvM_4

value: Hippocampus

value: male


title: ADNP, P40, Vehicle, HT, female,replicate3

description: Library name: ADNP_HvF_p40_3


title: Tanc2, WT, Lithium, male, replicate1

description: Library name: Tanc_WLM_1


title: Tanc2, WT, Lithium, female, replicate5

description: Library name: Tanc_WLF_5


title: ADNP, P40, Fluoxetine, HT, female,replicate3

description: Library name: ADNP_HfF_p40_3


title: ADNP, P40, Fluoxetine, HT, male,replicate3

description: Library name: ADNP_HfM_p40_3


title: Tanc2, WT, Lithium, female, replicate4

description: Library name: Tanc_WLF_4


title: Tanc2, WT, Lithium, female, replicate3

description: Library name: Tanc_WLF_3


title: Tbr1, WT, Lithium, female, replicate5

description: Library name: TBR1_WLF_5


title: Tanc2, WT, Lithium, female, replicate2

description: Library name: Tanc_WLF_2


title: Tanc2, WT, Lithium, male, replicate2

description: Library name: Tanc_WLM_2


title: Tbr1, WT, Lithium, female, replicate1

description: Library name: TBR1_WLF_1


title: Tanc2, WT, Lithium, female, replicate1

description: Library name: Tanc_WLF_1


title: Tanc2, WT, Fluoxetine, male, replicate4

description: Library name: Tanc_WfM_4


title: Tanc2, WT, Fluoxetine, male, replicate3

description: Library name: Tanc_WfM_3


title: Tanc2, WT, Fluoxetine, male, replicate2

description: Library name: Tanc_WfM_2


title: Tanc2, WT, Fluoxetine, male, replicate5

description: Library name: Tanc_WfM_5


title: Tbr1, WT, Fluoxetine, female, replicate4

description: Library name: TBR1_WfF_4


title: Tanc2, WT, Fluoxetine, male, replicate1

description: Library name: Tanc_WfM_1


title: Tanc2, WT, Fluoxetine, female, replicate5

description: Library name: Tanc_WfF_5


title: Tanc2, WT, Fluoxetine, female, replicate4

description: Library name: Tanc_WfF_4


title: Tbr1, WT, Fluoxetine, female, replicate2

description: Library name: TBR1_WfF_2


title: Tanc2, WT, Fluoxetine, female, replicate2

description: Library name: Tanc_WfF_2


title: Tanc2, WT, Fluoxetine, female, replicate1

description: Library name: Tanc_WfF_1


title: Tanc2, WT, Fluoxetine, female, replicate3

description: Library name: Tanc_WfF_3


title: Tanc2, HT, Vehicle, male, replicate5

description: Library name: Tanc_HvM_5


title: Tbr1+/K228E, Vehicle, male, replicate4

description: Library name: TBR1_HvM_4


title: Tanc2, HT, Vehicle, male, replicate4

description: Library name: Tanc_HvM_4


title: Tanc2, HT, Vehicle, male, replicate2

description: Library name: Tanc_HvM_2


title: Tanc2, HT, Vehicle, male, replicate3

description: Library name: Tanc_HvM_3


title: Tbr1+/K228E, Vehicle, male, replicate3

description: Library name: TBR1_HvM_3


title: Tanc2, HT, Vehicle, female, replicate5

description: Library name: Tanc_HvF_5


title: Tanc2, HT, Vehicle, male, replicate1

description: Library name: Tanc_HvM_1


title: Tanc2, HT, Vehicle, female, replicate4

description: Library name: Tanc_HvF_4


title: Tanc2, HT, Vehicle, female, replicate3

description: Library name: Tanc_HvF_3


title: Tanc2, HT, Vehicle, female, replicate2

description: Library name: Tanc_HvF_2


title: Tanc2, HT, Lithium, male, replicate4

description: Library name: Tanc_HLM_4


title: Tanc2, HT, Lithium, male, replicate2

description: Library name: Tanc_HLM_2


title: Tanc2, HT, Lithium, male, replicate3

description: Library name: Tanc_HLM_3


title: Tanc2, HT, Lithium, male, replicate1

description: Library name: Tanc_HLM_1


title: Tanc2, HT, Vehicle, female, replicate1

description: Library name: Tanc_HvF_1


title: Tanc2, HT, Lithium, female, replicate5

description: Library name: Tanc_HLF_5


title: Tanc2, HT, Lithium, female, replicate4

description: Library name: Tanc_HLF_4


title: Tanc2, HT, Lithium, female, replicate3

description: Library name: Tanc_HLF_3


title: Tanc2, HT, Lithium, female, replicate2

description: Library name: Tanc_HLF_2


title: Tanc2, HT, Fluoxetine, male, replicate5

description: Library name: Tanc_HfM_5


title: Tanc2, HT, Lithium, female, replicate1

description: Library name: Tanc_HLF_1


title: Tanc2, HT, Fluoxetine, male, replicate4

description: Library name: Tanc_HfM_4


title: Tanc2, HT, Fluoxetine, male, replicate3

description: Library name: Tanc_HfM_3


title: Tanc2, HT, Fluoxetine, male, replicate1

description: Library name: Tanc_HfM_1


title: Tanc2, HT, Fluoxetine, male, replicate2

description: Library name: Tanc_HfM_2


title: Tbl, Hippocampus, HT, female,replicate3

description: Library name: Tbl_HPC_HvF_3

value: female


title: Tanc2, HT, Fluoxetine, female, replicate5

description: Library name: Tanc_HfF_5


title: Tbl, Hippocampus, WT, male,replicate4

description: Library name: Tbl_HPC_WvM_4


title: Tanc2, HT, Fluoxetine, female, replicate4

description: Library name: Tanc_HfF_4


title: Tanc, Hippocampus, WT, male,replicate1

description: Library name: Tanc_HPC_WvM_1


title: Tanc2, HT, Fluoxetine, female, replicate3

description: Library name: Tanc_HfF_3


title: Tanc2, HT, Fluoxetine, female, replicate1

description: Library name: Tanc_HfF_1


title: Tanc2, HT, Fluoxetine, female, replicate2

description: Library name: Tanc_HfF_2


title: Pten, WT, Vehicle, male, replicate3

description: Library name: Pten_WvM_3


title: Pten, WT, Vehicle, male, replicate4

description: Library name: Pten_WvM_4


title: Pten, WT, Vehicle, male, replicate2

description: Library name: Pten_WvM_2


title: Pten, WT, Vehicle, male, replicate5

description: Library name: Pten_WvM_5


title: Pten, WT, Vehicle, male, replicate1

description: Library name: Pten_WvM_1


title: Pten, WT, Vehicle, female, replicate3

description: Library name: Pten_WvF_3


title: Pten, WT, Vehicle, female, replicate5

description: Library name: Pten_WvF_5


title: Pten, WT, Vehicle, female, replicate4

description: Library name: Pten_WvF_4


title: Pten, WT, Vehicle, female, replicate2

description: Library name: Pten_WvF_2


title: Pten, WT, Vehicle, female, replicate1

description: Library name: Pten_WvF_1


title: Pten, WT, Lithium, male, replicate5

description: Library name: Pten_WLM_5


title: Pten, WT, Lithium, male, replicate4

description: Library name: Pten_WLM_4


title: Pten, WT, Lithium, male, replicate3

description: Library name: Pten_WLM_3


title: Pten, WT, Lithium, female, replicate5

description: Library name: Pten_WLF_5


title: Pten, WT, Lithium, female, replicate3

description: Library name: Pten_WLF_3


title: Pten, WT, Lithium, female, replicate2

description: Library name: Pten_WLF_2


title: Pten, WT, Fluoxetine, male, replicate5

description: Library name: Pten_WfM_5


title: Pten, WT, Fluoxetine, male, replicate4

description: Library name: Pten_WfM_4


title: Pten, WT, Fluoxetine, male, replicate3

description: Library name: Pten_WfM_3


title: Pten, WT, Fluoxetine, male, replicate1

description: Library name: Pten_WfM_1


title: Pten, WT, Fluoxetine, female, replicate5

description: Library name: Pten_WfF_5


title: Pten, WT, Fluoxetine, female, replicate4

description: Library name: Pten_WfF_4


title: Pten, WT, Fluoxetine, female, replicate3

description: Library name: Pten_WfF_3


title: Pten, WT, Fluoxetine, female, replicate1

description: Library name: Pten_WfF_1


title: Pten, WT, Fluoxetine, female, replicate2

description: Library name: Pten_WfF_2


title: Pten, KI HT, Vehicle, male, replicate5

description: Library name: Pten_HvM_5


title: Pten, KI HT, Vehicle, male, replicate2

description: Library name: Pten_HvM_2


title: Pten, KI HT, Vehicle, female, replicate3

description: Library name: Pten_HvF_3


title: Pten, KI HT, Vehicle, female, replicate4

description: Library name: Pten_HvF_4


title: Pten, KI HT, Vehicle, female, replicate2

description: Library name: Pten_HvF_2


title: Pten, KI HT, Vehicle, female, replicate1

description: Library name: Pten_HvF_1


title: Pten, KI HT, Lithium, male, replicate4

description: Library name: Pten_HLM_4


title: Pten, KI HT, Lithium, male, replicate1

description: Library name: Pten_HLM_1


title: Pten, KI HT, Lithium, female, replicate5

description: Library name: Pten_HLF_5


title: Pten, KI HT, Lithium, female, replicate3

description: Library name: Pten_HLF_3


title: Pten, KI HT, Fluoxetine, male, replicate5

description: Library name: Pten_HfM_5


title: Pten, KI HT, Fluoxetine, male, replicate4

description: Library name: Pten_HfM_4


title: Pten, KI HT, Fluoxetine, male, replicate2

description: Library name: Pten_HfM_2


title: Pten, KI HT, Fluoxetine, female, replicate5

description: Library name: Pten_HfF_5


title: Kmt5b, WT, Vehicle, male, replicate5

description: Library name: K5B_WvM_5


title: Kmt5b, WT, Vehicle, male, replicate4

description: Library name: K5B_WvM_4


title: Pten, WT, Lithium, male, replicate2

description: Library name: Pten_WLM_2


title: Pten, WT, Lithium, female, replicate1

description: Library name: Pten_WLF_1


title: Pten, WT, Fluoxetine, male, replicate2

description: Library name: Pten_WfM_2


title: Pten, KI HT, Vehicle, male, replicate4

description: Library name: Pten_HvM_4


title: Pten, KI HT, Vehicle, male, replicate3

description: Library name: Pten_HvM_3


title: Kmt5b, WT, Vehicle, male, replicate1

description: Library name: K5B_WvM_1


title: Pten, KI HT, Vehicle, male, replicate1

description: Library name: Pten_HvM_1


title: Pten, KI HT, Vehicle, female, replicate5

description: Library name: Pten_HvF_5


title: Kmt5b, WT, Vehicle, female, replicate5

description: Library name: K5B_WvF_5


title: Pten, KI HT, Lithium, male, replicate5

description: Library name: Pten_HLM_5


title: Pten, KI HT, Lithium, male, replicate3

description: Library name: Pten_HLM_3


title: Pten, KI HT, Lithium, male, replicate2

description: Library name: Pten_HLM_2


title: Kmt5b, WT, Vehicle, female, replicate4

description: Library name: K5B_WvF_4


title: Pten, KI HT, Lithium, female, replicate2

description: Library name: Pten_HLF_2


title: Pten, KI HT, Lithium, female, replicate4

description: Library name: Pten_HLF_4


title: Kmt5b, WT, Vehicle, female, replicate2

description: Library name: K5B_WvF_2


title: Kmt5b, WT, Vehicle, female, replicate3

description: Library name: K5B_WvF_3


title: Pten, KI HT, Lithium, female, replicate1

description: Library name: Pten_HLF_1


title: Kmt5b, WT, Vehicle, female, replicate1

description: Library name: K5B_WvF_1


title: Kmt5b, WT, Lithium, male, replicate4

description: Library name: K5B_WLM_4


title: Kmt5b, WT, Lithium, male, replicate3

description: Library name: K5B_WLM_3


title: Kmt5b, WT, Lithium, male, replicate1

description: Library name: K5B_WLM_1


title: Pten, KI HT, Fluoxetine, male, replicate1

description: Library name: Pten_HfM_1


title: Kmt5b, WT, Lithium, male, replicate2

description: Library name: K5B_WLM_2


title: Kmt5b, WT, Lithium, female, replicate2

description: Library name: K5B_WLF_2


title: Kmt5b, WT, Lithium, female, replicate4

description: Library name: K5B_WLF_4


title: Kmt5b, WT, Lithium, female, replicate3

description: Library name: K5B_WLF_3


title: Pten, KI HT, Fluoxetine, male, replicate3

description: Library name: Pten_HfM_3


title: Pten, KI HT, Fluoxetine, female, replicate4

description: Library name: Pten_HfF_4


title: Kmt5b, WT, Fluoxetine, male, replicate5

description: Library name: K5B_WfM_5


title: Kmt5b, WT, Fluoxetine, male, replicate4

description: Library name: K5B_WfM_4


title: Pten, KI HT, Fluoxetine, female, replicate3

description: Library name: Pten_HfF_3


title: Kmt5b, WT, Lithium, female, replicate1

description: Library name: K5B_WLF_1


title: Pten, KI HT, Fluoxetine, female, replicate2

description: Library name: Pten_HfF_2


title: Kmt5b, WT, Fluoxetine, male, replicate2

description: Library name: K5B_WfM_2


title: Kmt5b, WT, Fluoxetine, female, replicate5

description: Library name: K5B_WfF_5


title: Kmt5b, WT, Fluoxetine, male, replicate1

description: Library name: K5B_WfM_1


title: Kmt5b, WT, Fluoxetine, male, replicate3

description: Library name: K5B_WfM_3


title: Kmt5b, WT, Fluoxetine, female, replicate4

description: Library name: K5B_WfF_4


title: Pten, KI HT, Fluoxetine, female, replicate1

description: Library name: Pten_HfF_1


title: Kmt5b, WT, Fluoxetine, female, replicate3

description: Library name: K5B_WfF_3


title: Kmt5b, WT, Fluoxetine, female, replicate2

description: Library name: K5B_WfF_2


title: Kmt5b, WT, Fluoxetine, female, replicate1

description: Library name: K5B_WfF_1


title: Kmt5b, HT, Vehicle, male, replicate4

description: Library name: K5B_HvM_4


title: Kmt5b, HT, Vehicle, male, replicate5

description: Library name: K5B_HvM_5


title: Kmt5b, HT, Vehicle, male, replicate2

description: Library name: K5B_HvM_2


title: Kmt5b, HT, Vehicle, male, replicate3

description: Library name: K5B_HvM_3


title: Kmt5b, HT, Vehicle, female, replicate5

description: Library name: K5B_HvF_5


title: Kmt5b, HT, Vehicle, female, replicate2

description: Library name: K5B_HvF_2


title: Kmt5b, HT, Vehicle, male, replicate1

description: Library name: K5B_HvM_1


title: Kmt5b, HT, Vehicle, female, replicate4

description: Library name: K5B_HvF_4


title: Kmt5b, HT, Vehicle, female, replicate1

description: Library name: K5B_HvF_1


title: Kmt5b, HT, Lithium, male, replicate4

description: Library name: K5B_HLM_4


title: Kmt5b, HT, Vehicle, female, replicate3

description: Library name: K5B_HvF_3


title: Kmt5b, HT, Lithium, male, replicate2

description: Library name: K5B_HLM_2


title: Kmt5b, HT, Lithium, male, replicate1

description: Library name: K5B_HLM_1


title: Kmt5b, HT, Lithium, male, replicate5

description: Library name: K5B_HLM_5


title: Kmt5b, HT, Lithium, female, replicate5

description: Library name: K5B_HLF_5


title: Kmt5b, HT, Lithium, male, replicate3

description: Library name: K5B_HLM_3


title: Kmt5b, WT, Vehicle, male, replicate3

description: Library name: K5B_WvM_3


title: Kmt5b, HT, Lithium, female, replicate2

description: Library name: K5B_HLF_2


title: Kmt5b, HT, Lithium, female, replicate4

description: Library name: K5B_HLF_4


title: Kmt5b, HT, Lithium, female, replicate3

description: Library name: K5B_HLF_3


title: Kmt5b, HT, Fluoxetine, male, replicate5

description: Library name: K5B_HfM_5


title: Kmt5b, WT, Vehicle, male, replicate2

description: Library name: K5B_WvM_2


title: Kmt5b, HT, Fluoxetine, male, replicate3

description: Library name: K5B_HfM_3


title: Kmt5b, HT, Fluoxetine, female, replicate4

description: Library name: K5B_HfF_4


title: Kmt5b, HT, Fluoxetine, female, replicate5

description: Library name: K5B_HfF_5


title: Kmt5b, HT, Fluoxetine, male, replicate2

description: Library name: K5B_HfM_2


title: Kmt5b, HT, Fluoxetine, female, replicate2

description: Library name: K5B_HfF_2


title: Kmt5b, HT, Fluoxetine, female, replicate1

description: Library name: K5B_HfF_1


title: Kmt5b, HT, Fluoxetine, female, replicate3

description: Library name: K5B_HfF_3


title: Trip12, WT, Vehicle, male, replicate5

description: Library name: T12_WvM_5


title: Trip12, WT, Vehicle, male, replicate4

description: Library name: T12_WvM_4


title: Trip12, WT, Vehicle, male, replicate3

description: Library name: T12_WvM_3


title: Trip12, WT, Vehicle, male, replicate2

description: Library name: T12_WvM_2


title: Trip12, WT, Vehicle, female, replicate5

description: Library name: T12_WvF_5


title: Trip12, WT, Vehicle, female, replicate4

description: Library name: T12_WvF_4


title: Trip12, WT, Vehicle, female, replicate1

description: Library name: T12_WvF_1


title: Trip12, WT, Lithium, male, replicate5

description: Library name: T12_WLM_5


title: Trip12, WT, Lithium, male, replicate4

description: Library name: T12_WLM_4


title: Trip12, WT, Lithium, male, replicate3

description: Library name: T12_WLM_3


title: Trip12, WT, Lithium, female, replicate5

description: Library name: T12_WLF_5


title: Trip12, WT, Lithium, female, replicate3

description: Library name: T12_WLF_3


title: Trip12, WT, Fluoxetine, male, replicate4

description: Library name: T12_WfM_4


title: Trip12, WT, Fluoxetine, female, replicate5

description: Library name: T12_WfF_5


title: Trip12, WT, Fluoxetine, male, replicate2

description: Library name: T12_WfM_2


title: Trip12, WT, Fluoxetine, male, replicate1

description: Library name: T12_WfM_1


title: Trip12, WT, Fluoxetine, female, replicate4

description: Library name: T12_WfF_4


title: Trip12, WT, Fluoxetine, female, replicate3

description: Library name: T12_WfF_3


title: Trip12, HT, Vehicle, male, replicate5

description: Library name: T12_HvM_5


title: Trip12, HT, Vehicle, male, replicate3

description: Library name: T12_HvM_3


title: Trip12, HT, Vehicle, male, replicate4

description: Library name: T12_HvM_4


title: Trip12, HT, Vehicle, female, replicate5

description: Library name: T12_HvF_5


title: Trip12, HT, Vehicle, female, replicate4

description: Library name: T12_HvF_4


title: Trip12, HT, Vehicle, female, replicate1

description: Library name: T12_HvF_1


title: Trip12, HT, Lithium, male, replicate5

description: Library name: T12_HLM_5


title: Trip12, HT, Lithium, male, replicate4

description: Library name: T12_HLM_4


title: Trip12, WT, Vehicle, female, replicate3

description: Library name: T12_WvF_3


title: Trip12, HT, Lithium, male, replicate3

description: Library name: T12_HLM_3


title: Trip12, WT, Fluoxetine, male, replicate5

description: Library name: T12_WfM_5


title: Trip12, WT, Lithium, male, replicate1

description: Library name: T12_WLM_1


title: Trip12, WT, Lithium, female, replicate4

description: Library name: T12_WLF_4


title: Trip12, HT, Lithium, male, replicate2

description: Library name: T12_HLM_2


title: Trip12, WT, Lithium, female, replicate1

description: Library name: T12_WLF_1


title: Trip12, HT, Lithium, female, replicate5

description: Library name: T12_HLF_5


title: Trip12, HT, Lithium, male, replicate1

description: Library name: T12_HLM_1


title: Trip12, WT, Fluoxetine, male, replicate3

description: Library name: T12_WfM_3


title: Trip12, HT, Lithium, female, replicate4

description: Library name: T12_HLF_4


title: Trip12, WT, Fluoxetine, female, replicate1

description: Library name: T12_WfF_1


title: Trip12, HT, Fluoxetine, male, replicate5

description: Library name: T12_HfM_5


title: Trip12, HT, Lithium, female, replicate1

description: Library name: T12_HLF_1


title: Trip12, HT, Lithium, female, replicate3

description: Library name: T12_HLF_3


title: Trip12, HT, Fluoxetine, male, replicate3

description: Library name: T12_HfM_3


title: Trip12, HT, Fluoxetine, male, replicate4

description: Library name: T12_HfM_4


title: Trip12, HT, Fluoxetine, male, replicate2

description: Library name: T12_HfM_2


title: Trip12, HT, Vehicle, male, replicate2

description: Library name: T12_HvM_2


title: Trip12, HT, Vehicle, male, replicate1

description: Library name: T12_HvM_1


title: Trip12, HT, Fluoxetine, male, replicate1

description: Library name: T12_HfM_1


title: Trip12, HT, Fluoxetine, female, replicate5

description: Library name: T12_HfF_5


title: Trip12, HT, Fluoxetine, female, replicate4

description: Library name: T12_HfF_4


title: Trip12, HT, Fluoxetine, female, replicate3

description: Library name: T12_HfF_3


title: Trip12, HT, Fluoxetine, female, replicate2

description: Library name: T12_HfF_2


title: Trip12, HT, Fluoxetine, female, replicate1

description: Library name: T12_HfF_1


title: Shank3dC, WT, Vehicle, male, replicate5

description: Library name: SdC_WvM_5


title: Trip12, HT, Vehicle, female, replicate3

description: Library name: T12_HvF_3


title: Shank3dC, WT, Vehicle, male, replicate4

description: Library name: SdC_WvM_4


title: Shank3dC, WT, Vehicle, female, replicate5

description: Library name: SdC_WvF_5


title: Shank3dC, WT, Vehicle, female, replicate4

description: Library name: SdC_WvF_4


title: Shank3dC, WT, Vehicle, male, replicate2

description: Library name: SdC_WvM_2


title: Shank3dC, WT, Vehicle, female, replicate2

description: Library name: SdC_WvF_2


title: Shank3dC, WT, Vehicle, female, replicate3

description: Library name: SdC_WvF_3


title: Shank3dC, WT, Vehicle, female, replicate1

description: Library name: SdC_WvF_1


title: Shank3dC, WT, Lithium, male, replicate5

description: Library name: SdC_WLM_5


title: Shank3dC, WT, Lithium, male, replicate3

description: Library name: SdC_WLM_3


title: Shank3dC, WT, Lithium, male, replicate2

description: Library name: SdC_WLM_2


title: Shank3dC, WT, Lithium, female, replicate5

description: Library name: SdC_WLF_5


title: Shank3dC, WT, Lithium, male, replicate1

description: Library name: SdC_WLM_1


title: Shank3dC, WT, Lithium, female, replicate4

description: Library name: SdC_WLF_4


title: Shank3dC, WT, Lithium, female, replicate3

description: Library name: SdC_WLF_3


title: Shank3dC, WT, Lithium, female, replicate1

description: Library name: SdC_WLF_1


title: Shank3dC, WT, Fluoxetine, male, replicate5

description: Library name: SdC_WfM_5


title: Shank3dC, WT, Fluoxetine, male, replicate4

description: Library name: SdC_WfM_4


title: Shank3dC, WT, Fluoxetine, male, replicate3

description: Library name: SdC_WfM_3


title: Shank3dC, WT, Fluoxetine, male, replicate2

description: Library name: SdC_WfM_2


title: Shank3dC, WT, Fluoxetine, male, replicate1

description: Library name: SdC_WfM_1


title: Shank3dC, WT, Fluoxetine, female, replicate5

description: Library name: SdC_WfF_5


title: Shank3dC, WT, Fluoxetine, female, replicate4

description: Library name: SdC_WfF_4


title: Shank3dC, WT, Lithium, female, replicate2

description: Library name: SdC_WLF_2


title: Trip12, HT, Lithium, female, replicate2

description: Library name: T12_HLF_2


title: Shank3dC, WT, Fluoxetine, female, replicate2

description: Library name: SdC_WfF_2


title: Shank3dC, WT, Fluoxetine, female, replicate1

description: Library name: SdC_WfF_1


title: Shank3dC, HT, Vehicle, male, replicate3

description: Library name: SdC_HvM_3


title: Shank3dC, HT, Vehicle, male, replicate2

description: Library name: SdC_HvM_2


title: Shank3dC, HT, Vehicle, male, replicate1

description: Library name: SdC_HvM_1


title: Shank3dC, HT, Vehicle, female, replicate5

description: Library name: SdC_HvF_5


title: Shank3dC, HT, Vehicle, female, replicate4

description: Library name: SdC_HvF_4


title: Shank3dC, HT, Vehicle, female, replicate2

description: Library name: SdC_HvF_2


title: Shank3dC, HT, Vehicle, female, replicate3

description: Library name: SdC_HvF_3


title: Shank3dC, HT, Vehicle, female, replicate1

description: Library name: SdC_HvF_1


title: Shank3dC, HT, Lithium, male, replicate4

description: Library name: SdC_HLM_4


title: Shank3dC, HT, Lithium, male, replicate3

description: Library name: SdC_HLM_3


title: Shank3dC, HT, Lithium, male, replicate2

description: Library name: SdC_HLM_2


title: Shank3dC, HT, Lithium, male, replicate1

description: Library name: SdC_HLM_1


title: Shank3dC, WT, Vehicle, male, replicate3

description: Library name: SdC_WvM_3


title: Shank3dC, HT, Lithium, female, replicate5

description: Library name: SdC_HLF_5


title: Shank3dC, HT, Lithium, female, replicate4

description: Library name: SdC_HLF_4


title: Shank3dC, WT, Vehicle, male, replicate1

description: Library name: SdC_WvM_1


title: Shank3dC, HT, Lithium, female, replicate3

description: Library name: SdC_HLF_3


title: Shank3dC, HT, Lithium, female, replicate1

description: Library name: SdC_HLF_1


title: Kmt5b, HT, Lithium, female, replicate1

description: Library name: K5B_HLF_1


title: Shank3dC, HT, Fluoxetine, male, replicate5

description: Library name: SdC_HfM_5


title: Shank3dC, HT, Lithium, female, replicate2

description: Library name: SdC_HLF_2


title: Shank3dC, HT, Fluoxetine, male, replicate4

description: Library name: SdC_HfM_4


title: Shank3dC, HT, Fluoxetine, male, replicate3

description: Library name: SdC_HfM_3


title: Shank3dC, HT, Fluoxetine, male, replicate2

description: Library name: SdC_HfM_2


title: Shank3dC, HT, Fluoxetine, male, replicate1

description: Library name: SdC_HfM_1


title: Shank3dC, HT, Fluoxetine, female, replicate3

description: Library name: SdC_HfF_3


title: Trip12, WT, Vehicle, male, replicate1

description: Library name: T12_WvM_1


title: Trip12, WT, Vehicle, female, replicate2

description: Library name: T12_WvF_2


title: Shank3dC, WT, Lithium, male, replicate4

description: Library name: SdC_WLM_4


title: Shank3dC, HT, Fluoxetine, female, replicate2

description: Library name: SdC_HfF_2


title: Shank3dC, HT, Fluoxetine, female, replicate5

description: Library name: SdC_HfF_5


title: Shank3dC, HT, Fluoxetine, female, replicate1

description: Library name: SdC_HfF_1


title: Myt1l, WT, Vehicle, male, replicate5

description: Library name: Mt1_WvM_5


title: Shank3dC, HT, Fluoxetine, female, replicate4

description: Library name: SdC_HfF_4


title: Myt1l, WT, Vehicle, male, replicate4

description: Library name: Mt1_WvM_4


title: Kmt5b, HT, Fluoxetine, male, replicate4

description: Library name: K5B_HfM_4


title: Kmt5b, HT, Fluoxetine, male, replicate1

description: Library name: K5B_HfM_1


title: Myt1l, WT, Vehicle, male, replicate3

description: Library name: Mt1_WvM_3


title: Myt1l, WT, Vehicle, female, replicate4

description: Library name: Mt1_WvF_4


title: Trip12, WT, Lithium, female, replicate2

description: Library name: T12_WLF_2


title: Myt1l, WT, Vehicle, male, replicate2

description: Library name: Mt1_WvM_2


title: Trip12, WT, Lithium, male, replicate2

description: Library name: T12_WLM_2


title: Myt1l, WT, Vehicle, male, replicate1

description: Library name: Mt1_WvM_1


title: Myt1l, WT, Lithium, male, replicate3

description: Library name: Mt1_WLM_3


title: Myt1l, WT, Vehicle, female, replicate2

description: Library name: Mt1_WvF_2


title: Myt1l, WT, Lithium, female, replicate5

description: Library name: Mt1_WLF_5


title: Myt1l, WT, Vehicle, female, replicate3

description: Library name: Mt1_WvF_3


title: Myt1l, WT, Lithium, male, replicate4

description: Library name: Mt1_WLM_4


title: Myt1l, WT, Vehicle, female, replicate1

description: Library name: Mt1_WvF_1


title: Myt1l, WT, Lithium, male, replicate2

description: Library name: Mt1_WLM_2


title: Myt1l, WT, Lithium, male, replicate5

description: Library name: Mt1_WLM_5


title: Myt1l, WT, Vehicle, female, replicate5

description: Library name: Mt1_WvF_5


title: Myt1l, WT, Lithium, male, replicate1

description: Library name: Mt1_WLM_1


title: Trip12, WT, Fluoxetine, female, replicate2

description: Library name: T12_WfF_2


title: Myt1l, WT, Lithium, female, replicate4

description: Library name: Mt1_WLF_4


title: Myt1l, WT, Lithium, female, replicate3

description: Library name: Mt1_WLF_3


title: Myt1l, WT, Lithium, female, replicate2

description: Library name: Mt1_WLF_2


title: Myt1l, WT, Fluoxetine, male, replicate4

description: Library name: Mt1_WfM_4


title: Myt1l, WT, Fluoxetine, male, replicate3

description: Library name: Mt1_WfM_3


title: Myt1l, WT, Fluoxetine, male, replicate2

description: Library name: Mt1_WfM_2


title: Myt1l, WT, Fluoxetine, male, replicate5

description: Library name: Mt1_WfM_5


title: Myt1l, WT, Fluoxetine, female, replicate1

description: Library name: Mt1_WfF_1


title: Myt1l, WT, Fluoxetine, female, replicate4

description: Library name: Mt1_WfF_4


title: Myt1l, WT, Fluoxetine, female, replicate2

description: Library name: Mt1_WfF_2


title: Myt1l, HT, Vehicle, male, replicate2

description: Library name: Mt1_HvM_2


title: Myt1l, WT, Fluoxetine, female, replicate3

description: Library name: Mt1_WfF_3


title: Myt1l, HT, Vehicle, male, replicate4

description: Library name: Mt1_HvM_4


title: Myt1l, WT, Fluoxetine, male, replicate1

description: Library name: Mt1_WfM_1


title: Myt1l, WT, Lithium, female, replicate1

description: Library name: Mt1_WLF_1


title: Myt1l, HT, Vehicle, male, replicate5

description: Library name: Mt1_HvM_5


title: Myt1l, HT, Vehicle, male, replicate1

description: Library name: Mt1_HvM_1


title: Myt1l, HT, Vehicle, female, replicate4

description: Library name: Mt1_HvF_4


title: Myt1l, HT, Vehicle, female, replicate5

description: Library name: Mt1_HvF_5


title: Myt1l, HT, Vehicle, female, replicate2

description: Library name: Mt1_HvF_2


title: Myt1l, HT, Lithium, male, replicate4

description: Library name: Mt1_HLM_4


title: Myt1l, HT, Lithium, male, replicate3

description: Library name: Mt1_HLM_3


title: Myt1l, HT, Vehicle, female, replicate1

description: Library name: Mt1_HvF_1


title: Myt1l, HT, Lithium, female, replicate5

description: Library name: Mt1_HLF_5


title: Myt1l, HT, Lithium, female, replicate4

description: Library name: Mt1_HLF_4


title: Myt1l, HT, Lithium, male, replicate1

description: Library name: Mt1_HLM_1


title: Myt1l, HT, Fluoxetine, male, replicate3

description: Library name: Mt1_HfM_3


title: Myt1l, HT, Lithium, female, replicate1

description: Library name: Mt1_HLF_1


title: Myt1l, HT, Lithium, female, replicate2

description: Library name: Mt1_HLF_2


title: Myt1l, HT, Lithium, male, replicate2

description: Library name: Mt1_HLM_2


title: Myt1l, HT, Fluoxetine, male, replicate1

description: Library name: Mt1_HfM_1


title: Myt1l, HT, Fluoxetine, female, replicate5

description: Library name: Mt1_HfF_5


title: Myt1l, HT, Fluoxetine, female, replicate4

description: Library name: Mt1_HfF_4


title: Myt1l, HT, Fluoxetine, female, replicate3

description: Library name: Mt1_HfF_3


title: Myt1l, HT, Fluoxetine, female, replicate2

description: Library name: Mt1_HfF_2


title: Myt1l, HT, Fluoxetine, female, replicate1

description: Library name: Mt1_HfF_1


title: Ash1l, WT, Vehicle, male, replicate5

description: Library name: ASH_WvM_5


title: Ash1l, WT, Vehicle, male, replicate4

description: Library name: ASH_WvM_4


title: Ash1l, WT, Vehicle, male, replicate1

description: Library name: ASH_WvM_1


title: Ash1l, WT, Vehicle, female, replicate5

description: Library name: ASH_WvF_5


title: Ash1l, WT, Vehicle, male, replicate3

description: Library name: ASH_WvM_3


title: Ash1l, WT, Vehicle, female, replicate4

description: Library name: ASH_WvF_4


title: Ash1l, WT, Vehicle, male, replicate2

description: Library name: ASH_WvM_2


title: Ash1l, WT, Vehicle, female, replicate2

description: Library name: ASH_WvF_2


title: Ash1l, WT, Lithium, male, replicate3

description: Library name: ASH_WLM_3


title: Ash1l, WT, Lithium, male, replicate2

description: Library name: ASH_WLM_2


title: Ash1l, WT, Lithium, male, replicate4

description: Library name: ASH_WLM_4


title: Ash1l, WT, Lithium, male, replicate5

description: Library name: ASH_WLM_5


title: Ash1l, WT, Lithium, male, replicate1

description: Library name: ASH_WLM_1


title: Ash1l, WT, Lithium, female, replicate4

description: Library name: ASH_WLF_4


title: Ash1l, WT, Lithium, female, replicate2

description: Library name: ASH_WLF_2


title: Ash1l, WT, Lithium, female, replicate5

description: Library name: ASH_WLF_5


title: Ash1l, WT, Lithium, female, replicate3

description: Library name: ASH_WLF_3


title: Ash1l, WT, Fluoxetine, male, replicate3

description: Library name: ASH_WfM_3


title: Ash1l, WT, Fluoxetine, male, replicate4

description: Library name: ASH_WfM_4


title: Ash1l, WT, Fluoxetine, male, replicate5

description: Library name: ASH_WfM_5


title: Ash1l, WT, Fluoxetine, male, replicate2

description: Library name: ASH_WfM_2


title: Ash1l, WT, Fluoxetine, female, replicate5

description: Library name: ASH_WfF_5


title: Ash1l, WT, Fluoxetine, male, replicate1

description: Library name: ASH_WfM_1


title: Ash1l, WT, Fluoxetine, female, replicate4

description: Library name: ASH_WfF_4


title: Ash1l, WT, Fluoxetine, female, replicate2

description: Library name: ASH_WfF_2


title: Ash1l, WT, Fluoxetine, female, replicate1

description: Library name: ASH_WfF_1


title: Ash1l, HT, Vehicle, male, replicate4

description: Library name: ASH_HvM_4


title: Ash1l, HT, Vehicle, male, replicate5

description: Library name: ASH_HvM_5


title: Ash1l, HT, Vehicle, male, replicate3

description: Library name: ASH_HvM_3


title: Ash1l, HT, Vehicle, male, replicate1

description: Library name: ASH_HvM_1


title: Ash1l, HT, Vehicle, female, replicate5

description: Library name: ASH_HvF_5


title: Ash1l, HT, Vehicle, female, replicate4

description: Library name: ASH_HvF_4


title: K562_PolIIS5p_CnRCHIP_input_rep2_(260717_WW_HsEc_WW1994)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: K562_PolIIS5p_CnRCHIP_input_rep2
PolIIS5p CUT&RUN.CHIP input in K562

library_source: genomic

data_processing:
1. We used cutadapt 4.4 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.5.7 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used bedtools 2.30 "bamtobed -bedpe" to extract properly paired reads from the alignments.
4. We used bedtools 2.30 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
PMID:31036827
CUT&Tag: https://dx.doi.org/10.17504/protocols.io.x54v9mkmzg3e/v5; CUT&Run: https://dx.doi.org/10.17504/protocols.io.zcpf2vn; OTHER CUT&Run.ChIP: For each experiment, 2.5 × 106 K562 cells were bound to 50 µl of ConA-coated magnetic beads.ncubation with the Pol II-Ser5p primary antibody (Cell Signaling Technology, 13523S), washes and pA–MN binding were performed as described above for CUT&RUN, using five times the corresponding buffer volumes in 1.5-ml low-binding flip-cap tubes. MNase digestion was initiated by resuspending the ConA beads in 500 µl of dig-wash buffer containing 2 mM CaCl₂ and incubating for 2 h at 4 °C. The reaction was stopped by directly adding 500 µl of stop buffer supplemented with Pol II CTD repeat YSPTSPS phospho-Ser5 peptide (Abcam, ab18488) to a final concentration of 20 µg/ml. Samples were incubated for 20 min at 37 °C and centrifuged for 5 min at 16,000g and 4 °C. The 1 ml of supernatant containing released Pol II-Ser5p-bound native chromatin fragments was collected on a magnetic stand and divided into five 200-µl aliquots. One aliquot was retained at 4 °C as the Pol II-Ser5p CUT&RUN input, and the remaining aliquots were used for ChIP. Rabbit monoclonal IgG isotype-control (Abcam, ab172730), anti-NPAT (Invitrogen, PA565419) or anti-RPB3 (Bethyl Laboratories, A303-771A) antibody was added to the corresponding ChIP aliquot at a final dilution of 1:100, and samples were incubated overnight at 4 °C. Protein A Dynabeads (Invitrogen, 10002D) were equilibrated in Tween wash buffer consisting of wash buffer supplemented with 0.05% Tween-20 (Sigma, P7949). 20 µl of Dynabeads was added to each ChIP sample, followed by incubation for 30 min at 4 °C. Beads were washed once with 500 µl of Tween wash buffer and resuspended in 5 µl of release solution containing 10 mM TAPS, 0.1% SDS and Thermolabile Proteinase K at a 1:10 dilution (New England Biolabs, P8111S). Samples were incubated in a thermocycler with a heated lid for 1 h at 37 °C and then for 1 h at 58 °C. SDS was quenched by adding 4 µl of 1.5% Triton X-100 and and 24 μl of ddH2O. DNA from the input and ChIP samples was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research, D4014), eluted in 10 µl of elution buffer according to the manufacturer’s instructions and used for library preparation.

tag: antibody

value: Cell Signaling Technology, 13523S


title: Ash1l, HT, Vehicle, female, replicate3

description: Library name: ASH_HvF_3


title: K562_PolIIS5p_CnRCHIP_input_rep1_(260717_WW_HsEc_WW1993)

description:
Library name: K562_PolIIS5p_CnRCHIP_input_rep1
PolIIS5p CUT&RUN.CHIP input in K562


title: K562_PolIIS5p_CnRCHIP_NPAT_rep2_(260717_WW_HsEc_WW1986)

description:
Library name: K562_PolIIS5p_CnRCHIP_NPAT_rep2
PolIIS5p CUT&RUN.CHIP targeting NPAT in K562

value: Cell Signaling Technology, 13523S; Invitrogen, PA565419


title: Ash1l, HT, Vehicle, female, replicate2

description: Library name: ASH_HvF_2


title: K562_PolIIS5p_CnRCHIP_NPAT_rep1_(260717_WW_HsEc_WW1981)

description:
Library name: K562_PolIIS5p_CnRCHIP_NPAT_rep1
PolIIS5p CUT&RUN.CHIP targeting NPAT in K562


title: Ash1l, HT, Lithium, male, replicate4

description: Library name: ASH_HLM_4


title: K562_PolIIS5p_CnRCHIP_RPB3_rep2_(260717_WW_HsEc_WW1985)

description:
Library name: K562_PolIIS5p_CnRCHIP_RPB3_rep2
PolIIS5p CUT&RUN.CHIP targeting RPB3 in K562

value: Cell Signaling Technology, 13523S; Bethyl Laboratories, A303-771A


title: K562_PolIIS5p_CnRCHIP_RPB3_rep1_(260717_WW_HsEc_WW1980)

description:
Library name: K562_PolIIS5p_CnRCHIP_RPB3_rep1
PolIIS5p CUT&RUN.CHIP targeting RPB3 in K562


title: Ash1l, HT, Lithium, male, replicate3

description: Library name: ASH_HLM_3


title: K562_PolIIS5p_CnRCHIP_IgG_rep2_(260717_WW_HsEc_WW1984)

description:
Library name: K562_PolIIS5p_CnRCHIP_IgG_rep2
PolIIS5p CUT&RUN.CHIP targeting IgG in K562

value: Cell Signaling Technology, 13523S; Abcam, ab172730


title: Ash1l, HT, Lithium, male, replicate2

description: Library name: ASH_HLM_2


title: Ash1l, HT, Lithium, male, replicate1

description: Library name: ASH_HLM_1


title: K562_H3K4me3_CnR_rep3_(230712_WW_HsEc_WW503)

description:
Library name: K562_H3K4me3_CnR_rep3
CUT&RUN targeting H3K4me3 in K562

data_processing:
1. We used cutadapt 4.4 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.5.7 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used bedtools 2.30 "bamtobed -bedpe" to extract properly paired reads from the alignments.
4. We used bedtools 2.30 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run

value: Epicypher, 13-0041


title: K562_PolIIS5p_CnRCHIP_IgG_rep1_(260717_WW_HsEc_WW1979)

description:
Library name: K562_PolIIS5p_CnRCHIP_IgG_rep1
PolIIS5p CUT&RUN.CHIP targeting IgG in K562


title: K562_H3K4me3_CnR_rep2_(230712_WW_HsEc_WW449)

description:
Library name: K562_H3K4me3_CnR_rep2
CUT&RUN targeting H3K4me3 in K562


title: Ash1l, HT, Lithium, female, replicate3

description: Library name: ASH_HLF_3


title: K562_H3K4me3_CnR_rep1_(230621_WW_HsEc_WW306)

description:
Library name: K562_H3K4me3_CnR_rep1
CUT&RUN targeting H3K4me3 in K562


title: K562_H3K27me3_CnR_rep3_(230712_WW_HsEc_WW450)

description:
Library name: K562_H3K27me3_CnR_rep3
CUT&RUN targeting H3K27me3 in K562

value: Cell Signaling Technology, 9733 BC


title: Ash1l, HT, Fluoxetine, male, replicate5

description: Library name: ASH_HfM_5


title: K562_H3K27me3_CnR_rep2_(230627_WW_Hs_WW339)

description:
Library name: K562_H3K27me3_CnR_rep2
CUT&RUN targeting H3K27me3 in K562


title: Ash1l, HT, Lithium, female, replicate4

description: Library name: ASH_HLF_5


title: Ash1l, HT, Fluoxetine, male, replicate4

description: Library name: ASH_HfM_4


title: Ash1l, HT, Lithium, female, replicate2

description: Library name: ASH_HLF_2


title: K562_H3K27me3_CnR_rep1_(230621_WW_HsEc_WW307)

description:
Library name: K562_H3K27me3_CnR_rep1
CUT&RUN targeting H3K27me3 in K562


title: Ash1l, HT, Fluoxetine, male, replicate3

description: Library name: ASH_HfM_3


title: Myt1l, HT, Vehicle, male, replicate3

description: Library name: Mt1_HvM_3


title: Myt1l, HT, Vehicle, female, replicate3

description: Library name: Mt1_HvF_3


title: K562_H3K27me3_CnR_rep4_(230712_WW_HsEc_WW504)

description:
Library name: K562_H3K27me3_CnR_rep4
CUT&RUN targeting H3K27me3 in K562


title: Ash1l, HT, Lithium, female, replicate1

description: Library name: ASH_HLF_1


title: K562_PolIIS2p_KASCnT_IP_Rep3_(250411_WW_Hs_WW1614)

description:
Library name: K562_PolIIS2p_KASCnT_IP_Rep3
KAS-CUT&Tag IP targeting PolIIS2p in K562

data_processing:
1. We used cutadapt 4.4 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.5.7 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used bedtools 2.30 "bamtobed -bedpe" to extract properly paired reads from the alignments.
4. We used bedtools 2.30 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

value: Cell Signaling Technology, 13499S


title: Ash1l, HT, Fluoxetine, male, replicate2

description: Library name: ASH_HfM_2


title: K562_PolIIS2p_KASCnT_IP_Rep2_(250411_WW_Hs_WW1546)

description:
Library name: K562_PolIIS2p_KASCnT_IP_Rep2
KAS-CUT&Tag IP targeting PolIIS2p in K562


title: Myt1l, HT, Lithium, male, replicate5

description: Library name: Mt1_HLM_5


title: Myt1l, HT, Fluoxetine, male, replicate5

description: Library name: Mt1_HfM_5


title: Myt1l, HT, Lithium, female, replicate3

description: Library name: Mt1_HLF_3


title: Ash1l, HT, Fluoxetine, male, replicate1

description: Library name: ASH_HfM_1


title: Myt1l, HT, Fluoxetine, male, replicate2

description: Library name: Mt1_HfM_2


title: K562_PolIIS2p_KASCnT_IP_Rep1_(250411_WW_Hs_WW1545)

description:
Library name: K562_PolIIS2p_KASCnT_IP_Rep1
KAS-CUT&Tag IP targeting PolIIS2p in K562


title: Myt1l, HT, Fluoxetine, male, replicate4

description: Library name: Mt1_HfM_4


title: K562_PolIIS2p_KASCnT_total_Rep3_(250411_WW_Hs_WW1638)

description:
Library name: K562_PolIIS2p_KASCnT_total_Rep3
KAS-CUT&Tag total targeting PolIIS2p in K562


title: Ash1l, HT, Fluoxetine, female, replicate5

description: Library name: ASH_HfF_5


title: Ash1l, HT, Fluoxetine, female, replicate4

description: Library name: ASH_HfF_4


title: Ash1l, HT, Fluoxetine, female, replicate3

description: Library name: ASH_HfF_3


title: K562_PolIIS2p_KASCnT_total_Rep2_(250411_WW_Hs_WW1570)

description:
Library name: K562_PolIIS2p_KASCnT_total_Rep2
KAS-CUT&Tag total targeting PolIIS2p in K562


title: K562_PolIIS2p_KASCnT_total_Rep1_(250411_WW_Hs_WW1569)

description:
Library name: K562_PolIIS2p_KASCnT_total_Rep1
KAS-CUT&Tag total targeting PolIIS2p in K562


title: K562_RPB1_KASCnT_IP_Rep3_(250411_WW_Hs_WW1613)

description:
Library name: K562_RPB1_KASCnT_IP_Rep3
KAS-CUT&Tag IP targeting RPB1 in K562


title: Ash1l, HT, Fluoxetine, female, replicate1

description: Library name: ASH_HfF_1


title: Ash1l, HT, Fluoxetine, female, replicate2

description: Library name: ASH_HfF_2


title: K562_RPB1_KASCnT_IP_Rep2_(250411_WW_Hs_WW1548)

description:
Library name: K562_RPB1_KASCnT_IP_Rep2
KAS-CUT&Tag IP targeting RPB1 in K562


title: Scn2a, WT, Vehicle, male, replicate4

description: Library name: Scn_WvM_4

value: Wildtype


title: K562_RPB1_KASCnT_total_Rep3_(250411_WW_Hs_WW1637)

description:
Library name: K562_RPB1_KASCnT_total_Rep3
KAS-CUT&Tag total targeting RPB1 in K562


title: Scn2a, WT, Vehicle, male, replicate3

description: Library name: Scn_WvM_3


title: K562_RPB1_KASCnT_IP_Rep1_(250411_WW_Hs_WW1547)

description:
Library name: K562_RPB1_KASCnT_IP_Rep1
KAS-CUT&Tag IP targeting RPB1 in K562


title: Ash1l, WT, Vehicle, female, replicate3

description: Library name: ASH_WvF_3


title: Scn2a, WT, Vehicle, male, replicate2

description: Library name: Scn_WvM_2


title: Scn2a, WT, Vehicle, male, replicate1

description: Library name: Scn_WvM_1


title: K562_RPB1_KASCnT_total_Rep2_(250411_WW_Hs_WW1572)

description:
Library name: K562_RPB1_KASCnT_total_Rep2
KAS-CUT&Tag total targeting RPB1 in K562


title: Ash1l, WT, Vehicle, female, replicate1

description: Library name: ASH_WvF_1


title: K562_RPB1_KASCnT_total_Rep1_(250411_WW_Hs_WW1571)

description:
Library name: K562_RPB1_KASCnT_total_Rep1
KAS-CUT&Tag total targeting RPB1 in K562


title: Scn2a, WT, Vehicle, female, replicate5

description: Library name: Scn_WvF_5


title: Scn2a, WT, Vehicle, female, replicate4

description: Library name: Scn_WvF_4


title: K562_RPB1_CnT_rep1_(260420_WW_Hs_WW1830)

description:
Library name: K562_RPB1_CnT_rep1
CUT&Tag targeting RPB1 in K562 cells


title: K562_RPB1_CnT_rep2_(260420_WW_Hs_WW1838)

description:
Library name: K562_RPB1_CnT_rep2
CUT&Tag targeting RPB1 in K562 cells


title: Scn2a, WT, Vehicle, female, replicate2

description: Library name: Scn_WvF_2


title: K562_PolIISer5p_CnT_rep2_(240709_DX_HS_P2S5_K562-50k)

description:
Library name: K562_PolIISer5p_CnT_rep2
CUT&Tag targeting Pol II-Ser5P in K562 cells (-kethoxal)


title: Scn2a, WT, Vehicle, female, replicate1

description: Library name: Scn_WvF_1


city: New Haven

first: Ramanaiah

last: Mamillapalli

state: CT

address: 310 Cedar Street

department: OBGYN

institute: Yale University

description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-17182_02-01
Differential gene expression in human endometriosis, Sample S19-17182_02-01

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

source_name: Ectopic Endometrium

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

value: Ectopic Endometrium

tag: severity

value: Mild

tag: asrm stage

value: II

tag: hormones


title: Scn2a, WT, Vehicle, female, replicate3

description: Library name: Scn_WvF_3


title: K562_PolIISer5p_CnT_rep3_(240709_DX_HS_P2S5_K562-40k)

description:
Library name: K562_PolIISer5p_CnT_rep3
CUT&Tag targeting Pol II-Ser5P in K562 cells (-kethoxal)


title: Scn2a, WT, Lithium, male, replicate5

description: Library name: Scn_WLM_5


title: Ash1l, WT, Lithium, female, replicate1

description: Library name: ASH_WLF_1


title: Scn2a, WT, Lithium, male, replicate4

description: Library name: Scn_WLM_4


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-10905_06-01-L003
Differential gene expression in human endometriosis, Sample S19-10905_06-01 (Lane 3)


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-17182_01-01
Differential gene expression in human endometriosis, Sample S19-17182_01-01


title: Scn2a, WT, Lithium, male, replicate3

description: Library name: Scn_WLM_3


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-10905_04-01
Differential gene expression in human endometriosis, Sample S19-10905_04-01

value: III

value: OCPs


title: Scn2a, WT, Lithium, male, replicate1

description: Library name: Scn_WLM_1

value: prefrontal cortex


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-07229_02-01
Differential gene expression in human endometriosis, Sample S19-07229_02-01


title: Scn2a, WT, Lithium, female, replicate4

description: Library name: Scn_WLF_5


title: Scn2a, WT, Lithium, female, replicate3

description: Library name: Scn_WLF_4


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-06548_02-01
Differential gene expression in human endometriosis, Sample S19-06548_02-01


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S18-16816_06-01
Differential gene expression in human endometriosis, Sample S18-16816_06-01

value: Severe


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S19-07229_01-01
Differential gene expression in human endometriosis, Sample S19-07229_01-01


title: Scn2a, WT, Lithium, female, replicate2

description: Library name: Scn_WLF_3


title: Scn2a, WT, Lithium, female, replicate1

description: Library name: Scn_WLF_1


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S18-16816_02-01
Differential gene expression in human endometriosis, Sample S18-16816_02-01


title: Scn2a, WT, Fluoxetine, male, replicate5

description: Library name: Scn_WfM_5


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S18-12619_06-01
Differential gene expression in human endometriosis, Sample S18-12619_06-01

value: OCPs (microgestin)


title: Scn2a, WT, Fluoxetine, male, replicate4

description: Library name: Scn_WfM_4


title: Scn2a, WT, Fluoxetine, male, replicate3

description: Library name: Scn_WfM_3


description:
Library name: Human-Endometriosis-GeneExpression-HowardLi-S18-11536_01-01
Differential gene expression in human endometriosis, Sample S18-11536_01-01

value: I