alias	title	study_alias	sample_alias	design_description	library_name	library_source	library_strategy	library_selection	library_layout	insert_size	library_construction_protocol	platform	instrument_model
89cedb23-7097-4df1-bec4-33e2fca83abb;2528eab1-eef7-428c-82d7-bd9c051b84df	Standard Illumina HiSeq 4000 paired-end Sequencing; RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	74cf43e2-11b1-42af-bf79-171ad7a58105	7c8760a8-1848-4d45-b963-a933d64753db	RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	49_KO_Rep1	TRANSCRIPTOMIC	RNA-Seq	Oligo-dT	PAIRED	100	Mouse brains were dissected and processed to obtain primary neuronal cells. Tissue was enzymatically digested and mechanically dissociated into a single-cell suspension. Cells were filtered, counted, and prepared for downstream culture. ; Primary neurons were cultured for two weeks under controlled conditions. Cells were maintained in specialized medium with regular partial medium changes. Culture conditions supported neuronal maturation and network formation. A targeted knockout of Brpf1 was introduced using CRISPR-Cas9 (KO samples). Neuronal cultures were transfected with sgRNA constructs targeting the gene. Edited cells were maintained for downstream transcriptomic analysis. ; RNA was extracted from ~10 million cells using the RNeasy Mini kit (Qiagen) and DNase digestion was performed using TURBO DNase (Thermo Fisher Scientific), according to the manufacturer’s instructions and an additional clean-up of the RNA was then performed using the RNeasy Mini kit (Qiagen). Quality of the RNA was assessed on Bioanalyzer using the Agilent RNA 6000 Nano Kit and samples with a RNA integrity number (RIN) of 10 were used for library generation. ; Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, in combination with the NEBNext Poly(A) mRNA Magnetic Isolation Module for mRNA enrichment, according to the manufacturer’s instructions.	ILLUMINA	Illumina HiSeq 4000
89cedb23-7097-4df1-bec4-33e2fca83abb;73f4d8f1-a899-4901-b790-6512285c829a	Standard Illumina HiSeq 4000 paired-end Sequencing; RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	74cf43e2-11b1-42af-bf79-171ad7a58105	ef3e12e6-8c5a-48a0-a956-7da24d4ddfc3	RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	49_KO_Rep2	TRANSCRIPTOMIC	RNA-Seq	Oligo-dT	PAIRED	100	Mouse brains were dissected and processed to obtain primary neuronal cells. Tissue was enzymatically digested and mechanically dissociated into a single-cell suspension. Cells were filtered, counted, and prepared for downstream culture. ; Primary neurons were cultured for two weeks under controlled conditions. Cells were maintained in specialized medium with regular partial medium changes. Culture conditions supported neuronal maturation and network formation. A targeted knockout of Brpf1 was introduced using CRISPR-Cas9 (KO samples). Neuronal cultures were transfected with sgRNA constructs targeting the gene. Edited cells were maintained for downstream transcriptomic analysis. ; RNA was extracted from ~10 million cells using the RNeasy Mini kit (Qiagen) and DNase digestion was performed using TURBO DNase (Thermo Fisher Scientific), according to the manufacturer’s instructions and an additional clean-up of the RNA was then performed using the RNeasy Mini kit (Qiagen). Quality of the RNA was assessed on Bioanalyzer using the Agilent RNA 6000 Nano Kit and samples with a RNA integrity number (RIN) of 10 were used for library generation. ; Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, in combination with the NEBNext Poly(A) mRNA Magnetic Isolation Module for mRNA enrichment, according to the manufacturer’s instructions.	ILLUMINA	Illumina HiSeq 4000
89cedb23-7097-4df1-bec4-33e2fca83abb;145cc642-d368-4f9a-9772-67bda7f8ee88	Standard Illumina HiSeq 4000 paired-end Sequencing; RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	74cf43e2-11b1-42af-bf79-171ad7a58105	b1513eb5-f3d3-4e5d-9bd3-400e9c4d50de	RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	49_WT_Rep1	TRANSCRIPTOMIC	RNA-Seq	Oligo-dT	PAIRED	100	Mouse brains were dissected and processed to obtain primary neuronal cells. Tissue was enzymatically digested and mechanically dissociated into a single-cell suspension. Cells were filtered, counted, and prepared for downstream culture. ; Primary neurons were cultured for two weeks under controlled conditions. Cells were maintained in specialized medium with regular partial medium changes. Culture conditions supported neuronal maturation and network formation. A targeted knockout of Brpf1 was introduced using CRISPR-Cas9 (KO samples). Neuronal cultures were transfected with sgRNA constructs targeting the gene. Edited cells were maintained for downstream transcriptomic analysis. ; RNA was extracted from ~10 million cells using the RNeasy Mini kit (Qiagen) and DNase digestion was performed using TURBO DNase (Thermo Fisher Scientific), according to the manufacturer’s instructions and an additional clean-up of the RNA was then performed using the RNeasy Mini kit (Qiagen). Quality of the RNA was assessed on Bioanalyzer using the Agilent RNA 6000 Nano Kit and samples with a RNA integrity number (RIN) of 10 were used for library generation. ; Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, in combination with the NEBNext Poly(A) mRNA Magnetic Isolation Module for mRNA enrichment, according to the manufacturer’s instructions.	ILLUMINA	Illumina HiSeq 4000
89cedb23-7097-4df1-bec4-33e2fca83abb;c922a57d-c224-4c1c-addf-132437073dc1	Standard Illumina HiSeq 4000 paired-end Sequencing; RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	74cf43e2-11b1-42af-bf79-171ad7a58105	19e0df52-c2bd-40bc-a982-811a7f076a10	RNA-seq analysis of Brpf1 knockout versus wild-type neurons derived from BALB/c mouse brain [49]	49_WT_Rep2	TRANSCRIPTOMIC	RNA-Seq	Oligo-dT	PAIRED	100	Mouse brains were dissected and processed to obtain primary neuronal cells. Tissue was enzymatically digested and mechanically dissociated into a single-cell suspension. Cells were filtered, counted, and prepared for downstream culture. ; Primary neurons were cultured for two weeks under controlled conditions. Cells were maintained in specialized medium with regular partial medium changes. Culture conditions supported neuronal maturation and network formation. A targeted knockout of Brpf1 was introduced using CRISPR-Cas9 (KO samples). Neuronal cultures were transfected with sgRNA constructs targeting the gene. Edited cells were maintained for downstream transcriptomic analysis. ; RNA was extracted from ~10 million cells using the RNeasy Mini kit (Qiagen) and DNase digestion was performed using TURBO DNase (Thermo Fisher Scientific), according to the manufacturer’s instructions and an additional clean-up of the RNA was then performed using the RNeasy Mini kit (Qiagen). Quality of the RNA was assessed on Bioanalyzer using the Agilent RNA 6000 Nano Kit and samples with a RNA integrity number (RIN) of 10 were used for library generation. ; Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, in combination with the NEBNext Poly(A) mRNA Magnetic Isolation Module for mRNA enrichment, according to the manufacturer’s instructions.	ILLUMINA	Illumina HiSeq 4000