title: single Cell Cme-Cut&Tag

city: Geneva

first: Nahuel

last: Simonet

address: 9 chemin des Mines

country: Switzerland

institute: EPFL

description:
Library name: 20250827_01_Nsi_scNanoCnT_K562vsiPSC_2xMBD2
nuclei

data_processing:
Basecalls were performed using bases2fastq version 1.8.0. Nextera adapters were trimmed with minimal read length tolerated post-trimming: 35 bp.
CUT&Tag sequencing data was  processed using an adapted DNAmapping pipeline from snakePipes. In brief, the fastq files were aligned to a hybrid genome (hg38 and Escherichia phage Lambda spike-in) with the BWA-MEM2 aligner. The resulting alignment BAM files were converted to bigwig files using bamCoverage from deepTools. and subsequently scaled based on the number of reads mapped to the spike-in regions.
CUT&Tag-BS/EM data  data were processed using an adapted WGBS pipeline from snakePipes. In brief, sequence alignment was performed using BWAMETH2, which relies on the BWA-MEM as the underlying aligner.  The BAM files were converted to BigWig files, and peak calling was performed as described above. CpG dinucleotide methylation profiles in the peaks were extracted from the resulting BAM files using MethylDackel60, with the following parameters: --mergeContext, --maxVariantFrac 0.1, --minDepth 5.
Broad peaks were called from the BAM files of each sequencing run using MACS3 (v3.0.1) with the parameters --broad-cutoff 0.1, --nolambda
Assembly: hg38 (with Escherichia phage Lambda ViralProj14204 spike-in)
Supplementary files format and content: bigWig files

source_name: CAU iPSC : K562

extract_protocol:
Preparation of single-cell suspensions: Human brain organoids were dissociated into single-cell suspensions as previously described using the Neural Tissue Dissociation Kit (P) (Milternyi Neural Dissociation protocol). Organoids were cut into pieces using a scalpel, thoroughly washed in DPBS supplemented with 0.5% BSA, and incubated with papain-containing Enzyme Mix 1 at 37 °C for 15 min, followed by DNase-containing Enzyme Mix 2. Mechanical dissociation was performed by sequential trituration using P1000 and P200 pipette tips with intermittent 37 °C incubations until a homogeneous suspension was obtained. Cells were filtered through a 30 μm strainer, pelleted at 300 × g for 5 min, resuspended in wash buffer, and counted using Trypan Blue. Following dissociation of organoids or tissues, genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, #69504) according to the manufacturer’s instructions. Following dissociation of organoids or tissues, genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, #69504) according to the manufacturer’s instructions.
CUT& Tag and DNA-Methylation CUT&Tag: Starting with 0.1-1 Mio cells after dissociation, cells were transferred into CUT&Tag wash buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 150 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001)). Following 15 µl of BioMag ConcanavalinA beads (Polysciences, #86057-3) in binding buffer (20 mM HEPES (pH 7.5), 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) were added to the sample and incubated on the wheel for 15 min at RT. Subsequently, the cells were collected on a magnet and lysed through the addition of CUT&Tag wash buffer supplemented with 0.01% Digitonin. Lysis was monitored under a microscope with Trypan Blue staining. After lysis was complete, the nuclei were washed again with CUT&Tag wash buffer. If possible, all samples were split, and H3 or another chromatin mark CUT&Tag was performed on the same starting material, to be used as a normalizer. The antibody (1 µg per reaction, against histone modifications or 5mC) was added together with 2 mM EDTA final and the sample was incubated on a rocking platform at 4 °C overnight. For DNA methylation profiling, MBD-Tn5 was added for 2 hours in a buffer containing 300 mM salt. ProteinA coupled Tn5 (pA-Tn5) was used a control and treated in the same way. The next day, the samples were washed once with CUT&Tag wash buffer, and the secondary antibody was added to the reaction, which was then incubated for 1 hour at 20 °C on a rocking platform. For CUT&Tag After two additional washes the Tn5 was added (1:100) in CUT&Tag med buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 300 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001)). Tn5 was allowed to bind for 1 hr at 20 °C on a rocking platform. After two additional washes, the cutting was induced through the addition of 10 mM MgCl2 in CUT&Tag med buffer. For DNA methylation profiling, the MBD-Tn5 cutting was directly induced after the 2-hour binding and two washes with CUT&Tag med buffer. For DNA methylation profiling of purified DNA, 50 ng of starting material was used, and MBD-Tn5 cutting was directly induced after a 2-hour binding period without any additional washes. After 1 hr at 37 °C, the reaction was stopped by adding a final concentration of 20 mM EDTA, 0.5% SDS, and 10 mg Proteinase K. The reaction was then incubated at 55 °C for 30 min and finally inactivated at 70 °C for 20 min. The DNA fragments were purified using the ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205). For elution from the columns, 2 pg of Tn5-digested and purified lambda DNA (New England Biolabs, #N3011S) were added as a spike-in normalizer for later analysis.
Overview of the antibodies used in the study:
5mC Diagenode C1520003
H3K27ac Diagenode C15410196
H3K36me3 Abcam AB9050
H3K4me1 Diagenode C15410194
H3K4me3 Diagenode C15410003
H3K4me9 abcam ab176916

value: CAU iPSC :K562


title: RNA-seq_PTBP3_KO-2

status: Public on Apr 16 2026

type: SRA

city: Beijing

first: Zongchang

last: Du

address: 15 Datun Road, Chaoyang District, Beijing, China

country: China

institute: IBP

library_source: transcriptomic

data_processing:
Illumina bcl2fastq-1.8.4 conversion software was used for base calling.
After sequencing of single-cell RNA-seq libraries, adapters and low-qaulity bases were removed by Trimmomatic (Bolger et al., 2014) program. The retained paired-end reads were aligned to the mouse reference genome (mm9) using HISAT2 (Kim et al., 2015) tool with default parameters. The uniquely mapped reads count matrix were subject to DESeq2 (Michael, et al., 2014)  package to identify differentially expressed genes. Alternative splicing events were detected using rMATS (Shihao Shen, et al., 2014) software with defualt parameters.
2P-seq reads were filtered by trimming adaptors and A’s from the end of reads using the Cutadapt (Martin et al., 2014) program. The remaining reads were mapped to the mouse genome, and only uniquely mapped reads were retained. All samples were combined together and reads adjacent to each other were merged to cluster to identify robust polyadenylation sites. The alternative polyadenylation events were detected using DEXSeq (Anders Simon et al,. 2012) package with defualt parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage.

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: Wild type and PTBP3 knockout mice were bred at six- to eight-weeks-old.

extract_protocol:
Total RNAs were extracted with Trizol regent and chloroform.
RNA-seq libraries were generated with some modifications (Mortazavi et al, 2008), 2P-seq libraries were generated with modification (Spies et al., 2013) .

treatment_protocol: Naive B cells were isolated from spleen using MojoSort™ Mouse Pan-B Cell Isolation Kit (Biolegend, 480052) following the manufacture’s protocol.

tag: method

value: RNA-Seq

tag: genotype

value: PTBP3 knockout

tag: cell type

value: Naive B cells

tag: tissue

value: spleen

tag: strain


title: SP_FD_D3_S78

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

description: Library name: Sample118

data_processing:
RNA-seq raw files were processed in Orion High-Performance Computing Cluster (Norwegian University of Life Sciences) to remove adapter sequences and low-quality reads through BBDuk v.34.56. After, cleaned reads were aligned to Atlantic salmon genome SSAL_v3.1 (GenBank: GCA_905237065.2) by HISAT v2.2.1. Then, mapped fragments were counted with FeatureCounts v1.4.6-p1
Assembly: Atlantic salmon genome SSAL_v3.1 (GenBank: GCA_905237065.2)
Supplementary files format and content: Count files with mapped fragments

organism: Salmo salar

source_name: Spleen

extract_protocol:
Total RNA was isolated from head kidney and spleen from 10 fish per dietary group at each location. Briefly, a 5 mm stainless steel bead and 900 μL QIAzol lysis reagent (Qiagen) were added to 50 mg of each sample. Then, a TissueLyser bead mill (Qiagen) at 20 Hz for 2 min was used (twice) to lyse the samples. The homogenate was recovered and 180 μL chloroform were added before vortexing and centrifugation at 14,000 x g (4 °C for 15 min). Each upper phase was recovered in a new tube and 450 μL isopropanol were added. After gentle manual shaking and incubation at room temperature, the samples were centrifuged again (14,000 x g at 4 °C for 15 min). The supernatants were removed and 200 μL 70% ethanol were added before centrifugation (14,000 x g at 4 °C for 10 min). The pellets were left to dry for 5-10 min at room temperature. Finally, each pellet was resuspended in 40 μL RNAse-free water and incubated for 10 min incubation at 55 °C.
The RNA concentration of the samples was estimated with a NanoDrop™ 8000 spectrophotometer (Thermo Fisher Scientific) according to instructions from the manufacturer. Then, RNA integrity (RIN values) was measured with an Agilent 4150 TapeStation (Agilent) following the supplier's protocols. All samples had RIN values ≥ 7. Novogene (United Kingdom) performed the libraries and RNA-seq through an Illumina NovaSeq 6000 System (150 bp paired-end RNA-seq and 30 million reads depth).

value: Spleen

tag: diet

value: Diet 3

tag: treatment

value: 10% Fermented sunflower meal

tag: farm location

value: Fjord (FD)


title: SP_FD_D3_S77

description: Library name: Sample117


title: H4

city: Bareilly

first: Pushpendra

last: Kumar

state: Uttar pradesh

address: Izatnagar

department: Animal Genetics

country: India

institute: ICAR-IVRI

data_processing:
Illumina HiSeq X10 used for basecalling.
The sequenced raw Illumina reads were subjected to Trim galore to automate the quality and adapter trimming as well as quality control of fastq files.
Kallisto pipeline used to create “transcriptome index”. Tximport was used to import and summarize the transcript-level abundance estimates from kallisto for gene-level analysis with DESeq2.
Genome_build: Mus_musculus.GRCm38.cdna.all.fa
Supplementary_files_format_and_content: gene_counts.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: ovary

extract_protocol:
Total RNA from samples was extracted by AgriGenome Labs Pvt. Ltd., Kochi, as per their standard protocol. Poly “A” selection was undertaken to enhance the concentration of mRNA.
TruSeq RNA sample preparation kit_ Poly A capture method was used for library preparation.

value: F4 inbred Swiss albino

value: estrous-phased ovarian tissue

tag: Sex

value: female

tag: age

value: Adult (135-140 days)

tag: litter size

value: high


title: SP_FD_D3_S72

description: Library name: Sample112


title: H1


title: RNA-seq_PTBP3_WT-1

value: wild type


title: SP_FD_D3_S79

description: Library name: Sample119


title: SP_FD_D3_S76

description: Library name: Sample116


title: WIBJ_iPSC_human_DNAmi_rep_2_2

description:
Library name: 20260118__089_HHNSi_mCnTEMseq_WIBJ_iPSC_human_DNAmi_rep_2_1
genomic DNA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: WIBJ

tag: cell line

value: WIBJ

value: iPSC


title: SP_FD_D3_S71

description: Library name: Sample111


title: WIBJ_iPSC_human_CTL_rep_2_2

description:
Library name: 20260118__087_HHNSi_mCnTEMseq_WIBJ_iPSC_human_CTL_rep_2_1
genomic DNA


title: SP_FD_D2_S68

description: Library name: Sample108

value: Diet 2

value: 5% Fermented sunflower meal


title: Titration gDNA 0.25 rep 1

description:
Library name: 20260118__079_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_0_25ul_rep_2_1
genomic DNA

source_name: CAU

value: CAU


title: Serial dilution 5 K rep 1

description:
Library name: 20260118__078_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_5k_rep_2_2
nuclei


title: SP_FD_D2_S69

description: Library name: Sample109


title: Titration gDNA 0.25 rep 2

description:
Library name: 20260118__080_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_0_25ul_rep_2_2
genomic DNA


title: SP_FD_D2_S67

description: Library name: Sample107


title: SP_FD_D2_S66

description: Library name: Sample106


title: Serial dilution 25 K rep 1

description:
Library name: 20260118__073_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_25k_rep_2_1
nuclei


title: WIBJ_iPSC_human_CTL_rep_2_1

description:
Library name: 20251216_120_HHNSi_mCnTEMseq_WIBJ_iPSC_human_CTL_1
genomic DNA


title: SP_FD_D2_S62

description: Library name: Sample102


title: SP_FD_D2_S64

description: Library name: Sample104


title: SP_FD_D2_S70

description: Library name: Sample110


title: untargeted Tn5  rep 1

description:
Library name: 20251216_087_HHNSi_mCnT_CAU_iPSC_nuc_New_Constructs_untargeted_Tn5_1
nuclei


title: Titration nuc 5 rep 2

description:
Library name: 20251216_072_HHNSi_mCnT_CAU_iPSC_nuc_Titration_5ul_2
nuclei


title: SP_FD_D2_S61

description: Library name: Sample101


title: 2xCXXC-MLL1 rep 2

description:
Library name: 20251216_091_HHNSi_mCnT_CAU_iPSC_nuc_New_Constructs_2xCXXC-MLL1_on
nuclei


title: Titration nuc 2 rep 2

description:
Library name: 20251216_070_HHNSi_mCnT_CAU_iPSC_nuc_Titration_2ul_2
nuclei


title: SP_FD_D2_S65

description: Library name: Sample105


title: SP_FD_D2_S63

description: Library name: Sample103


title: SP_FD_D1_S89

description: Library name: Sample99

value: Diet 1

value: Control diet (5% Sunflower meal)


title: WIBJ_iPSC_human_DNAmi_rep_2_1

description:
Library name: 20251216_119_HHNSi_mCnTEMseq_WIBJ_iPSC_human_DNAmi_1
genomic DNA


title: SP_FD_D1_S90

description: Library name: Sample100

value: Spleen


title: 2xCXXC-MLL1 rep 1

description:
Library name: 20251216_082_HHNSi_mCnT_CAU_iPSC_nuc_New_Constructs_2xCXXC-MLL1
nuclei


title: SP_FD_D1_S88

description: Library name: Sample98


title: Titration nuc 5 rep 1

description:
Library name: 20251216_071_HHNSi_mCnT_CAU_iPSC_nuc_Titration_5ul_1
nuclei


title: Titration nuc 2 rep 1

description:
Library name: 20251216_069_HHNSi_mCnT_CAU_iPSC_nuc_Titration_2ul_1
nuclei


title: SP_FD_D1_S87

description: Library name: Sample97


title: SP_FD_D1_S85

description: Library name: Sample95


title: SP_FD_D1_S86

description: Library name: Sample96


title: Titration nuc 1 rep 2

description:
Library name: 20251216_068_HHNSi_mCnT_CAU_iPSC_nuc_Titration_1ul_2
nuclei


title: Titration nuc 1 rep 1

description:
Library name: 20251216_067_HHNSi_mCnT_CAU_iPSC_nuc_Titration_1ul_1
nuclei


title: Titration nuc 0.5 rep 1

description:
Library name: 20251216_065_HHNSi_mCnT_CAU_iPSC_nuc_Titration_0_5ul_1
nuclei


title: SP_FD_D1_S84

description: Library name: Sample94


title: Titration nuc 0.25 rep 2

description:
Library name: 20251216_064_HHNSi_mCnT_CAU_iPSC_nuc_Titration_0_25ul_2
nuclei


title: SP_FD_D1_S82

description: Library name: Sample92


title: Titration nuc 0.25 rep 1

description:
Library name: 20251216_063_HHNSi_mCnT_CAU_iPSC_nuc_Titration_0_25ul_1
nuclei


title: Titration nuc 0.5 rep 2

description:
Library name: 20251216_066_HHNSi_mCnT_CAU_iPSC_nuc_Titration_0_5ul_2
nuclei


title: SP_CS_D3_S170

description: Library name: Sample90

value: Diet 3

value: Coast (CS)


title: Titration gDNA 5 rep 1

description:
Library name: 20251216_059_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_5ul_1
genomic DNA


title: Titration nuc 0.1 rep 2

description:
Library name: 20251216_062_HHNSi_mCnT_CAU_iPSC_nuc_Titration_0_1ul_2
nuclei


title: SP_CS_D3_S155

description: Library name: Sample85

value: 10% Fermented sunflower meal


title: SP_FD_D1_S83

description: Library name: Sample93

value: Fjord (FD)


title: SP_CS_D3_S168

description: Library name: Sample88


title: SP_CS_D3_S169

description: Library name: Sample89


title: Titration nuc 0.1 rep 1

description:
Library name: 20251216_061_HHNSi_mCnT_CAU_iPSC_nuc_Titration_0_1ul_1
nuclei


title: SP_CS_D3_S154

description: Library name: Sample84


title: Titration gDNA 1 rep 2

description:
Library name: 20251216_056_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_1ul_2
genomic DNA


title: SP_CS_D3_S153

description: Library name: Sample83


title: Titration gDNA 1 rep 1

description:
Library name: 20251216_055_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_1ul_1
genomic DNA


title: SP_CS_D3_S166

description: Library name: Sample86


title: Titration gDNA 2 rep 1

description:
Library name: 20251216_057_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_2ul_1
genomic DNA


title: SP_FD_D1_S81

description: Library name: Sample91


title: Titration gDNA 2 rep 2

description:
Library name: 20251216_058_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_2ul_2
genomic DNA


title: SP_CS_D3_S152

description: Library name: Sample82


title: Titration gDNA 0.5 rep 1

description:
Library name: 20251216_053_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_0_5ul_1
genomic DNA


title: Titration gDNA 0.5 rep 2

description:
Library name: 20251216_054_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_0_5ul_2
genomic DNA


title: SP_CS_D3_S167

description: Library name: Sample87


title: Titration gDNA 5 rep 2

description:
Library name: 20251216_060_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_5ul_2
genomic DNA


title: SP_CS_D2_S175

description: Library name: Sample80


title: Titration gDNA 0.1 rep 2

description:
Library name: 20251216_050_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_0_1ul_2
genomic DNA


title: SP_CS_D2_S174

description: Library name: Sample79


title: Titration gDNA 0.1 rep 1

description:
Library name: 20251216_049_HHNSi_mCnT_CAU_iPSC_gDNA_Titration_0_1ul_1
genomic DNA


title: SP_CS_D2_S173

description: Library name: Sample78


title: SP_CS_D2_S171

description: Library name: Sample76


title: SP_CS_D3_S151

description: Library name: Sample81


title: SP_CS_D2_S172

description: Library name: Sample77


title: Serial dilution 200 K rep 2

description:
Library name: 20251216_048_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_200k_2
nuclei


title: SP_CS_D2_S160

description: Library name: Sample75


title: SP_CS_D2_S159

description: Library name: Sample74


title: Serial dilution 25 K rep 2

description:
Library name: 20251216_042_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_25k_2
nuclei


title: Serial dilution 100 K rep 2

description:
Library name: 20251216_046_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_100k_2
nuclei


title: SP_CS_D2_S156

description: Library name: Sample71


title: SP_CS_D2_S158

description: Library name: Sample73


title: Serial dilution 50 K rep 2

description:
Library name: 20251216_044_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_50k_2
nuclei


title: SP_CS_D1_S179

description: Library name: Sample69


title: Serial dilution 100 K rep 1

description:
Library name: 20251216_045_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_100k_1
nuclei


title: Serial dilution 50 ng rep 2

description:
Library name: 20251216_036_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_50ng_2
genomic DNA


title: Serial dilution 5 K rep 2

description:
Library name: 20251216_040_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_5k_2
nuclei


title: Serial dilution 200 K rep 1

description:
Library name: 20251216_047_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_200k_1
nuclei


title: Serial dilution 50 ng rep 1

description:
Library name: 20251216_035_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_50ng_1
genomic DNA


title: Serial dilution 1 K rep 2

description:
Library name: 20251216_038_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_1k_2
nuclei


title: SP_CS_D2_S157

description: Library name: Sample72


title: Serial dilution 25 ng rep 2

description:
Library name: 20251216_034_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_25ng_2
genomic DNA


title: SP_CS_D1_S180

description: Library name: Sample70


title: SP_CS_D1_S178

description: Library name: Sample68


title: SP_CS_D1_S176

description: Library name: Sample66


title: Serial dilution 50 K rep 1

description:
Library name: 20251216_043_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_50k_1
nuclei


title: Serial dilution 1 K rep 1

description:
Library name: 20251216_037_HHNSi_mCnT_CAU_iPSC_nuc_Serial_dilution_1k_1
nuclei


title: SP_CS_D1_S165

description: Library name: Sample65


title: SP_CS_D1_S164

description: Library name: Sample64


title: SP_CS_D1_S163

description: Library name: Sample63


title: Serial dilution 10 ng rep 2

description:
Library name: 20251216_032_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_10ng_2
genomic DNA


title: SP_CS_D1_S177

description: Library name: Sample67


title: Serial dilution 25 ng rep 1

description:
Library name: 20251216_033_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_25ng_1
genomic DNA


title: Serial dilution 5 ng rep 2

description:
Library name: 20251216_030_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_5ng_2
genomic DNA


title: SP_CS_D1_S161

description: Library name: Sample61


title: HK_FD_D3_S50

description: Library name: Sample60

source_name: Head kidney

value: Head kidney


title: Serial dilution 10 ng rep 1

description:
Library name: 20251216_031_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_10ng_1
genomic DNA


title: Serial dilution 1 ng rep 1

description:
Library name: 20251216_027_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_1ng_1
genomic DNA


title: Serial dilution 5 ng rep 1

description:
Library name: 20251216_029_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_5ng_1
genomic DNA


title: Serial dilution 1 ng rep 2

description:
Library name: 20251216_028_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_1ng_2
genomic DNA


title: HK_FD_D3_S49

description: Library name: Sample59


title: Serial dilution 0.5 ng rep 1

description:
Library name: 20251216_025_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_0_5ng_1
genomic DNA


title: SP_CS_D1_S162

description: Library name: Sample62


title: Serial dilution 0.5 ng rep 2

description:
Library name: 20251216_026_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_0_5ng_2
genomic DNA


title: HK_FD_D3_S48

description: Library name: Sample58


title: HK_FD_D3_S46

description: Library name: Sample56


title: HK_FD_D3_S45

description: Library name: Sample55


title: Serial dilution 0.1 ng rep 2

description:
Library name: 20251216_024_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_0_1ng_2
genomic DNA


title: 2xMBD2 EM-seq gDNA rep2

description:
Library name: 20251007_04_Nsi_mCnT_Emseq_2xMBD2_gDNA_CAU_g2
genomic DNA


title: HK_FD_D3_S47

description: Library name: Sample57


title: HK_FD_D3_S43

description: Library name: Sample53


title: HK_FD_D3_S42

description: Library name: Sample52


title: 2xMBD2 EM-seq nuc rep2

description:
Library name: 20251007_03_Nsi_mCnT_Emseq_2xMBD2_iPSC_CAU_c2
nuclei


title: 2xMBD2 EM-seq gDNA rep1

description:
Library name: 20251007_02_Nsi_mCnT_Emseq_2xMBD2_gDNA_CAU_g1
genomic DNA


title: HK_FD_D3_S41

description: Library name: Sample51


title: 2xMBD2 16d gDNA rep2

description:
Library name: 20250708_024_Nsi_mCnT_16d_org_MBD2_gDNA_2
genomic DNA

source_name: Human brain organoid 16d

value: Human brain organoid 16d


title: HK_FD_D2_S40

description: Library name: Sample50


title: HK_FD_D3_S44

description: Library name: Sample54


title: HK_FD_D2_S38

description: Library name: Sample48


title: 2xMBD2 210d gDNA rep2

description:
Library name: 20250708_022_Nsi_mCnT_7M_org_MBD2_gDNA_2
genomic DNA

source_name: Human brain organoid  210d

value: Human brain organoid  210d


title: Serial dilution 0.1 ng rep 1

description:
Library name: 20251216_023_HHNSi_mCnT_CAU_iPSC_gDNA_Serial_dilution_0_1ng_1
genomic DNA


title: HK_FD_D2_S37

description: Library name: Sample47


title: HK_FD_D2_S36

description: Library name: Sample46


title: HK_FD_D2_S39

description: Library name: Sample49


title: 2xMBD2 210d gDNA rep1

description:
Library name: 20250708_021_Nsi_mCnT_7M_org_MBD2_gDNA_1
genomic DNA


title: HK_FD_D2_S35

description: Library name: Sample45


title: 2xMBD2 EM-seq nuc rep1

description:
Library name: 20251007_01_Nsi_mCnT_Emseq_2xMBD2_iPSC_CAU_c1
nuclei


title: 2xMBD2 16d nuc rep2

description:
Library name: 20250708_020_Nsi_mCnT_16d_org_MBD2_nuc_2
nuclei


title: 2xMBD2 210d nuc rep2

description:
Library name: 20250708_018_Nsi_mCnT_7M_org_MBD2_nuc_2
nuclei


title: 2xMBD2 16d nuc rep1

description:
Library name: 20250708_019_Nsi_mCnT_16d_org_MBD2_nuc_1
nuclei


title: HK_FD_D2_S33

description: Library name: Sample43


title: 2xMBD2 16d gDNA rep1

description:
Library name: 20250708_023_Nsi_mCnT_16d_org_MBD2_gDNA_1
genomic DNA


title: HK_FD_D2_S34

description: Library name: Sample44


title: 2xMBD2 210d nuc rep1

description:
Library name: 20250708_017_Nsi_mCnT_7M_org_MBD2_nuc_1
nuclei


title: HK_FD_D2_S32

description: Library name: Sample42


title: HK_FD_D1_S60

description: Library name: Sample40


title: HK_FD_D2_S31

description: Library name: Sample41


title: HK_FD_D1_S59

description: Library name: Sample39


title: 2xMBD2 BS nuc rep2

description:
Library name: 20250708_014_Nsi_mCnT-BS_CAU_MBD2_nuc_2
nuclei


title: 2xMBD2 BS 210d gDNA rep2

description:
Library name: 20250708_012_HHNSi_mCnTBS_CAU_7MonthOrg_gDNA_2MBD2_2
genomic DNA


title: 2xMBD2 BS nuc rep1

description:
Library name: 20250708_013_Nsi_mCnT-BS_CAU_MBD2_nuc_1
nuclei


title: HK_FD_D1_S57

description: Library name: Sample37


title: 2xMBD2 BS gDNA rep1

description:
Library name: 20250708_015_Nsi_mCnT-BS_CAU_MBD2_gDNA_1
genomic DNA


title: HK_FD_D1_S56

description: Library name: Sample36


title: 2xMBD2 BS gDNA rep2

description:
Library name: 20250708_016_Nsi_mCnT-BS_CAU_MBD2_gDNA_2
genomic DNA


title: 2xMBD2 BS 16d gDNA rep2

description:
Library name: 20250708_010_HHNSi_mCnTBS_CAU_16dOrg_gDNA_2MBD2_2
genomic DNA


title: 2xMBD2 BS 16d gDNA rep1

description:
Library name: 20250708_009_HHNSi_mCnTBS_CAU_16dOrg_gDNA_2MBD2_1
genomic DNA


title: HK_FD_D1_S54

description: Library name: Sample34


title: HK_FD_D1_S53

description: Library name: Sample33


title: 5mC Antibody rep1

description:
Library name: 20250531_005_HHNSi_mCnT_CAU_nuc_5mCAB_1
nuclei

data_processing:
Basecalls were performed using bases2fastq version 1.8.0. Nextera adapters were trimmed with minimal read length tolerated post-trimming: 35 bp.
CUT&Tag sequencing data was  processed using an adapted DNAmapping pipeline from snakePipes. In brief, the fastq files were aligned to a hybrid genome (hg38 and Escherichia phage Lambda spike-in) with the BWA-MEM2 aligner. The resulting alignment BAM files were converted to bigwig files using bamCoverage from deepTools. and subsequently scaled based on the number of reads mapped to the spike-in regions.
CUT&Tag-BS/EM data  data were processed using an adapted WGBS pipeline from snakePipes. In brief, sequence alignment was performed using BWAMETH2, which relies on the BWA-MEM as the underlying aligner.  The BAM files were converted to BigWig files, and peak calling was performed as described above. CpG dinucleotide methylation profiles in the peaks were extracted from the resulting BAM files using MethylDackel60, with the following parameters: --mergeContext, --maxVariantFrac 0.1, --minDepth 5.
Broad peaks were called from the BAM files of each sequencing run using MACS3 (v3.0.1) with the parameters --broad-cutoff 0.1, --nolambda
Assembly: hg38 (with Escherichia phage Lambda ViralProj14204 spike-in)
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag


title: HK_FD_D1_S52

description: Library name: Sample32


title: WT DMSO pA/G-Tn5 rep2

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_pA/G-Tn5_2_gDNA
genomic DNA

value: DMSO


title: 2xMBD2 BS 210d gDNA rep1

description:
Library name: 20250708_011_HHNSi_mCnTBS_CAU_7MonthOrg_gDNA_2MBD2_1
genomic DNA


title: 5mC Antibody rep2

description:
Library name: 20250531_006_HHNSi_mCnT_CAU_nuc_5mCAB_2
nuclei


title: HK_CS_D3_S138

description: Library name: Sample28


title: HK_FD_D1_S55

description: Library name: Sample35


title: WT DMSO H3K27me3 rep 2

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_H3K27me3_2_nuclei
nuclei


title: WT DMSO pA/G-Tn5 rep1

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_pA/G-Tn5_1_gDNA
genomic DNA


title: HK_CS_D3_S140

description: Library name: Sample30


title: HK_FD_D1_S51

description: Library name: Sample31


title: HK_FD_D1_S58

description: Library name: Sample38


title: WT DMSO H3K27me3 rep 1

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_H3K27me3_1_nuclei
nuclei


title: WT DMSO 2xMBD2 gDNA rep 2

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_2xMBD2_2_gDNA
genomic DNA


title: HK_CS_D3_S136

description: Library name: Sample26


title: WT DMSO 2xMBD2 nuc rep 1

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_2xMBD2_1_nuclei
nuclei


title: WT DMSO 2xMBD2 gDNA rep 1

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_2xMBD2_1_gDNA
genomic DNA


title: WT DMSO 2xMBD2 nuc rep 2

description:
Library name: 20250505_HHNSi_mCT_WT_iPSC_human_2xMBD2_2_nuclei
nuclei


title: HK_CS_D3_S125

description: Library name: Sample25


title: HK_CS_D3_S137

description: Library name: Sample27


title: HK_CS_D3_S124

description: Library name: Sample24


title: HK_CS_D3_S123

description: Library name: Sample23


title: NTD-MeCP2-IDR nuc rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_NTD-MeCP2-IDR_1
nuclei


title: NTD-MeCP2-IDR nuc rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_NTD-MeCP2-IDR_2
nuclei


title: HK_CS_D3_S122

description: Library name: Sample22


title: HK_CS_D3_S121

description: Library name: Sample21


title: H3K9me3 rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K9me3_2
nuclei


title: HK_CS_D2_S145

description: Library name: Sample20


title: HK_CS_D2_S144

description: Library name: Sample19


title: H3K4me3 rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K4me3_2
nuclei


title: HK_CS_D2_S143

description: Library name: Sample18


title: HK_CS_D2_S142

description: Library name: Sample17


title: H3K4me1 rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K4me1_1
nuclei


title: HK_CS_D2_S130

description: Library name: Sample15


title: H3K4me1 rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K4me1_2
nuclei


title: HK_CS_D2_S141

description: Library name: Sample16


title: H3K36me3 rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K36me3_2
nuclei


title: H3K36me3 rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K36me3_1
nuclei


title: H3K27me3 rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K27me3_2
nuclei


title: HK_CS_D2_S129

description: Library name: Sample14


title: H3K9me3 rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K9me3_1
nuclei


title: H3K27me3 rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K27me3_1
nuclei


title: HK_CS_D2_S126

description: Library name: Sample11


title: HK_CS_D2_S127

description: Library name: Sample12


title: HK_CS_D1_S150

description: Library name: Sample10


title: H3K27ac rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K27ac_1
nuclei


title: MLEC_WT_IgG

city: Mannheim

first: Fredy

middle: Andres

last: Delgado Lagos

address: Ludolf-Krehl- Straße 13-17

department: Vascular Dysfunction

country: Germany

institute: UMM, Heidelberg University

description: Library name: Sample 9

data_processing:
FastQC and MultiQC were run on the raw paired-end ACT FASTQ files for basic QC (per-sample reports and a combined summary). Adapters/low-quality bases were trimmed with Trim Galore (paired-end mode).
Reads were aligned to mouse mm10 (GRCm38.p6) with STAR (sorted BAM output). MACS2 callpeak was run per ACT sample on sorted BAMs (-f BAM, -g mm, --keep-dup all, -q 0.05) to obtain narrowPeak files.
narrowPeak files were converted to SAF (Chr/Start/End/Strand with unique peak IDs) to define a peak set for counting. featureCounts was run in SAF mode (-F SAF -p -T 16) to quantify paired-end fragments per peak across ACT BAMs (output: act_counts.txt).
Count matrices were imported to R and normalized with DESeq2; normalized matrices were used for downstream PCA/heatmap
Assembly: GRCm38.p6 (mm10); gene annotation: mm10 GTF (same build; STAR genome index built from these).
Supplementary files format and content: Per-sample sorted/indexed BAM; per-sample MACS2 peaks (narrowPeak); SAF peak file (act_peaks.saf); featureCounts output (act_counts.txt, tab-delimited; includes GeneID, annotation columns, and per-sample counts); optional DESeq2-normalized count matrix (tab-delimited/CSV) derived from act_counts.txt.
Library strategy: ACT-seq (Antibody-guided Chromatin Tagmentation sequencing)

source_name: lung endothelial cells

extract_protocol:
For ACT-seq library preparation, permeabilised lung endothelial nuclei were incubated with histone-mark antibodies, followed by addition of pre-assembled Protein A/G–Tn5 adaptor complexes; after tagmentation, DNA was purified (phenol–chloroform/ethanol or column) and quantified with Qubit dsDNA HS..
Tagmented DNA was PCR-amplified with indexed primers to add full Illumina adapters (Phusion High-Fidelity or equivalent), size-selected (~200–700 bp), QC’d, and sequenced as paired-end reads on an Illumina NextSeq 2000.

value: lung endothelial cells


title: 4xMeCP2 nuc rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_4xMeCP2_2
nuclei


title: HK_CS_D2_S128

description: Library name: Sample13


title: 4xMeCP2 nuc rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_4xMeCP2_1
nuclei


title: MLEC_WT_H2AK5ac

description: Library name: Sample 7


title: H3K27ac rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K27ac_2
nuclei


title: MLEC_WT_H3K4me3

description: Library name: Sample 8


title: HK_CS_D1_S148

description: Library name: Sample8


title: MLEC_WT_H3K27ac

description: Library name: Sample 5


title: 2xMeCP2 nuc rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_2xMeCP2_2
nuclei


title: MLEC_WT_H3K23ac

description: Library name: Sample 4


title: MLEC_WT_H3K18ac

description: Library name: Sample 3


title: HK_CS_D1_S147

description: Library name: Sample7


title: HK_CS_D1_S149

description: Library name: Sample9


title: HK_CS_D3_S139

description: Library name: Sample29


title: MLEC_WT_H3K9ac

description: Library name: Sample 1


title: H3K4me3 rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_H3K4me3_1
nuclei


title: HK_CS_D1_S146

description: Library name: Sample6


title: 2xMBD2 nuc  rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_2xMBD2_2
nuclei


title: MLEC_CSE-KO_Cre-pos_H3K4me3_2

description:
Library name: Sample 12
AS-1521871-LR-79929

data_processing:
Paired-end FASTQ files were aligned to the mouse genome GRCm39 (GENCODE release M33) using Rsubread 2.16.1 (Liao et al., The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote). BAM files were sorted and indexed with Rsamtools 2.18.0.
Counts were converted to an edgeR DGEList, normalized, and dispersion was estimated using edgeR 4.0.16 (Robinson et al., edgeR: differential expression analysis of digital gene expression data). Differential binding was tested using a generalized linear model and quasi-likelihood F-test in edgeR for all pairwise group comparisons.
Top variable genomic regions were identified based on variance in log2 CPM and visualized with ComplexHeatmap 2.18.0. PCA was performed on normalized logCPM values using prcomp in R 4.3.3 to assess sample clustering, and plotted with ggplot2 3.5.2.
Peak annotation was performed with ChIPseeker 1.38.0, assigning each region to the nearest gene (TSS ± 3000 bp) using TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0 and org.Mm.eg.db 3.18.0.
Assembly: GRCm39 (mm10), GENCODE release M33
Supplementary files format and content: Tab-delimited matrix of normalized counts, CSV files of differential binding results, PNG figures for heatmap, PCA, and peak annotation, TSV table of annotated peaks
Library strategy: ACT-seq (Antibody-guided Chromatin Tagmentation sequencing)

extract_protocol:
For ACT-seq library preparation, antibody–Protein A–Tn5 complexes were pre-assembled with barcoded adaptors, bound to permeabilized lung endothelial cells, and incubated to allow chromatin tagmentation. DNA was purified by phenol-chloroform extraction and ethanol precipitation, and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).
Indexed sequencing libraries were generated by PCR amplification of tagmented DNA using Phusion High-Fidelity PCR Master Mix (NEB), with 5′ and 3′ index barcodes. Amplified products were gel-purified (QIAquick Gel Extraction Kit, Qiagen), and fragment size distribution was confirmed before paired-end sequencing on an Illumina NextSeq 2000.

value: CSE-KO


title: MLEC_WT_H3K14ac

description: Library name: Sample 2


title: MLEC_WT_H4K8ac

description: Library name: Sample 6


title: HK_CS_D1_S134

description: Library name: Sample4


title: MLEC_CSE-KO_Cre-pos_H3K27ac_2

description:
Library name: Sample 10
AS-1521867-LR-79929


title: MLEC_CSE-KO_Cre-pos_H3K23ac_2

description:
Library name: Sample 8
AS-1521863-LR-79929


title: 2xMeCP2 nuc rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_2xMeCP2_1
nuclei

value: iPSC


title: MLEC_CSE-KO_Cre-pos_H3K4me3_1

description:
Library name: Sample 11
AS-1521869-LR-79929


title: HK_CS_D1_S135

description: Library name: Sample5


title: HK_CS_D1_S133

description: Library name: Sample3


title: 2xMBD2 nuc rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_nuclei_2xMBD2_1
nuclei


title: NTD-MeCP2-IDR gDNA rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_NTD-MeCP2-IDR_1
genomic DNA


title: MLEC_WT_Cre-neg_H3K4me3_2

description:
Library name: Sample 6
AS-1521859-LR-79929

value: WT


title: NTD-MeCP2-IDR gDNA rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_NTD-MeCP2-IDR_2
genomic DNA


title: MLEC_CSE-KO_Cre-pos_H3K27ac_1

description:
Library name: Sample 9
AS-1521865-LR-79929


title: MLEC_WT_Cre-neg_H3K4me3_1

description:
Library name: Sample 5
AS-1521857-LR-79929


title: MLEC_CSE-KO_Cre-pos_H3K23ac_1

description:
Library name: Sample 7
AS-1521861-LR-79929


title: MLEC_WT_Cre-neg_H3K27ac_2

description:
Library name: Sample 4
AS-1521855-LR-79929


title: MLEC_WT_Cre-neg_H3K23ac_2

description:
Library name: Sample 2
AS-1521851-LR-79929


title: HK_CS_D1_S131

description: Library name: Sample1


title: 4xMeCP2gDNA rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_4xMeCP2_2
genomic DNA


title: MLEC_WT_Cre-neg_H3K23ac_1

description:
Library name: Sample 1
AS-1521849-LR-79929


title: submandibular, C57, female, rep3

city: Buffalo

first: Omer

last: Gokcumen

state: NY

address: 135 Founders Promenade

department: Biological Sciences

country: USA

institute: University at Buffalo

description: Library name: Mous-6B-SM-Fem-L

data_processing:
Raw sequencing reads were quality trimmed and adapter filtered using Trim Galore.
Reads were aligned .to the Mus musculus GRCm39 (mm39) reference genome using HISAT2.
Reads were assigned to genes using featureCounts.
Assembly: Mus musculus reference genome GRCm39 (mm39).
Supplementary files format and content: Processed data files are comma-delimited text files containing gene-level read counts for each sample, generated from aligned RNA-seq reads using featureCounts.

source_name: submandibular

extract_protocol:
Total RNA was extracted from mouse tissue using a standard RNA isolation protocol, and RNA quantity and quality were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA using a standard library preparation protocol with poly(A) selection for mRNA enrichment.

value: submandibular

value: female


title: HUVEC_t6h_3

description: Library name: Sample 15

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized count.
Library strategy: Ribo-Seq

molecule: nuclear RNA

source_name: Umbilical vein endothelial cells

extract_protocol:
Ribosomal RNA was isolated with anti-HA-tag magentic beads and afterwards RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 500ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: Umbilical vein endothelial cells


title: HK_CS_D1_S132

description: Library name: Sample2

value: Diet 1

value: Control diet (5% Sunflower meal)


title: sublingual, C57, female, rep3

description: Library name: Mous-6B-SL-Fem-L

source_name: sublingual

value: sublingual


title: 4xMeCP2 gDNArep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_4xMeCP2_1
genomic DNA

value: CAU


title: 2xMeCP2 gDNA rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_2xMeCP2_1
genomic DNA


title: HUVEC_t6h_1

description: Library name: Sample 13


title: parotid, C57, female, rep3

description: Library name: Mous-6B-PAR-Fem-L

source_name: parotid

value: parotid


title: MLEC_WT_Cre-neg_H3K27ac_1

description:
Library name: Sample 3
AS-1521853-LR-79929


title: pancreas, C57, female, rep3

description: Library name: Mous-6B-PANC-Fem

source_name: pancreas

value: pancreas


title: 2xMBD2 gDNA rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_2xMBD2_2
genomic DNA


title: HUVEC_t2h_3

description: Library name: Sample 12


title: 2xMeCP2 gDNA rep2

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_2xMeCP2_2
genomic DNA


title: HUVEC_t2h_2

description: Library name: Sample 11


title: HUVEC_t6h_2

description: Library name: Sample 14


title: HUVEC_t24h_3

description: Library name: Sample 9


title: liver, C57, female, rep3

description: Library name: Mous-6B-LIV-Fem

source_name: liver

value: liver


title: HUVEC_t24h_2

description: Library name: Sample 8


title: HUVEC_t2h_1

description: Library name: Sample 10


title: WT DNAmi pA/G-Tn5 gDNA rep2

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_pA/G-Tn5_2_gDNA
genomic DNA

value: GSK3484862, a selective DNMT1 inhibitor


title: HUVEC_t24h_1

description: Library name: Sample 7


title: 2xMBD2 gDNA rep1

description:
Library name: 20250505_HHNSi_mCT_iPSC_CAU_gDNA_2xMBD2_1
genomic DNA


title: sublingual, C57, female, rep2

description: Library name: Mous-5B-SL-Fem-L


title: HUVEC_t12h_2

description: Library name: Sample 5


title: submandibular, C57, female, rep2

description: Library name: Mous-5B-SM-Fem-L


title: HUVEC_t12h_3

description: Library name: Sample 6


title: WT DNAmi H3K27me3 rep 2

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_H3K27me3_2_nuclei
nuclei


title: HUVEC_t12h_1

description: Library name: Sample 4


title: parotid, C57, female, rep2

description: Library name: Mous-5B-PAR-Fem-L


title: HUVEC_t0h_3

description: Library name: Sample 3


title: WT DNAmi H3K27me3 rep 1

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_H3K27me3_1_nuclei
nuclei


title: WT DNAmi pA/G-Tn5 gDNA rep1

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_pA/G-Tn5_1_gDNA
genomic DNA


title: HUVEC_t0h_2

description: Library name: Sample 2


title: LHX2-203-1F,CUT&TAG

city: shenyang

first: Shouyi

last: Zhang

state: Liaoning

address: No. 44 Xiaoheyan Road, Dadong District

institute: Liaoning Cancer Institute and Hospital

description: Library name: LHX2-203-1F,CUT_TAG

data_processing:
ATAC-seq: Library construction, sequencing, and subsequent analysis were outsourced to Applied Protein Technology (Shanghai, China). CUT&TAG: Library construction, sequencing, and subsequent analysis were performed by Epibiotek Co., Ltd. (Guangzhou, China).
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: prostate cancer

growth_protocol: DMEM, 15% fetal bovine serum, 1x penicillin/streptomycin. Cells werecultured at 37C at 5% CO2

extract_protocol:
ATAC-seq: Briefly, fresh cultured cells were harvested, resuspended in PBS, and washed by centrifugation at 1000g for 5 minutes at 4°C. After removal of the PBS, 200 μL pre-cooled lysis buffer was added to the washed cells. The cells were gently pipetted to resuspend and incubated on ice for 10 minutes. The cells were then centrifuged at 500g for 10 minutes, and 1 mL washing buffer was added. After gentle mixing of the solution, the cells were centrifuged again at 500g for 10 minutes at 4°C to collect the nuclei. Next, 50 μL transposition reaction mix was added to the nuclear pellet, and the nuclei were resuspended. The mixture was gently pipetted to mix, then incubated at 37°C for 30 minutes and held at 4°C. DNA was purified with 2× DNA clean beads. To amplify the DNA, 15 PCR cycles were performed with P5 and P7 adapter primers, to generate the primary library. Finally, the ATAC-seq library was subjected to paired-end sequencing on the HiSeq 2500 platform (Illumina). CUT&TAG: The library preparation for CUT&TAG was performed according to the manufacturer’s instructions for the Epi™ Cut and Tag Kit (Epibiotek Co., Ltd., Guangzhou, China). In brief, magnetic beads were washed twice with binding buffer, and antibody buffer was prepared. Cells were resuspended in binding buffer and mixed with the magnetic beads, then incubated 10 minutes at room temperature under gentle rotation. After addition of antibody buffer, the primary antibodies were incubated at room temperature for 2 hours. The reaction was then centrifuged at 500 rpm, the supernatant was discarded, and the beads were washed with antibody buffer. The secondary antibody (IgG) was added and incubated at room temperature for 1 hour under gentle rotation. After incubation, the beads were washed twice with antibody buffer. Tn5 buffer was prepared and mixed with pAG-Tn5 Mix, then incubated at room temperature for 1 hour under gentle rotation. The reaction was then washed twice with 500 μL Tn5 Buffer, and tagmentation buffer was then added and incubated at 37°C for 1 hour. After incubation, 10% SDS was added and incubated at 55°C for 10 minutes, and DNA was purified with 1.8× DNA Clean Beads. The DNA was then amplified with 25 μL 2× AmpliMix, 2.5 μL N5 primer, and 2.5 μL N7 primer; thoroughly mixed by vortexing; and centrifuged. PCR amplification was performed with the following cycling conditions: stage 0: 72°C for 3 minutes; stage 1: 98°C for 30 seconds; stage 2: 98°C for 15 seconds, 60°C for 20 seconds, 72°C for 8 seconds (14 cycles); and stage 3: 72°C for 2 minutes. After amplification, DNA was purified with 1× DNA Clean Beads, and the library was quality-checked with a Bioptic Qsep100 Analyzer to ensure that the size distribution met the theoretical expectations.
ATAC-seq: Library construction, sequencing, and subsequent analysis were outsourced to Applied Protein Technology (Shanghai, China). CUT&TAG: Library construction, sequencing, and subsequent analysis were performed by Epibiotek Co., Ltd. (Guangzhou, China).

value: prostate cancer

value: Human prostate cancer epithelial cells

value: overexpress LHX2-003


title: pancreas, C57, female, rep2

description: Library name: Mous-5B-PANC-Fem


title: LHX2-203-2,CUT&TAG

description: Library name: LHX2-203-2,CUT_TAG


title: LHX2-201-1F,CUT&TAG

description: Library name: LHX2-201-1F,CUT_TAG

value: overexpress LHX2-001


title: liver, C57, female, rep2

description: Library name: Mous-5B-LIV-Fem


title: LHX2-201-2F,CUT&TAG

description: Library name: LHX2-201-2F,CUT_TAG


title: WT DNAmi 2xMBD2 nuc rep 2

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_2xMBD2_2_nuclei
nuclei

value: iPSC


title: submandibular, C57, female, rep1

description: Library name: Mous-4B-SM-Fem-L


title: sublingual, C57, female, rep1

description: Library name: Mous-4B-SL-Fem-L


title: HUVEC_t0h_1

description: Library name: Sample 1


title: WT DNAmi 2xMBD2 nuc rep 1

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_2xMBD2_1_nuclei
nuclei


title: WT DNAmi 2xMBD2 gDNA rep 1

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_2xMBD2_1_gDNA
genomic DNA


title: SY5Y, 40d, 50 uM Mn Replicate 2

city: West Lafayette

first: Priyanka

last: Baloni

state: IN

address: 207 S. Martin Jischke Dr, DLR 342

department: School of Health Sciences

institute: Purdue University

description: Library name: Group2_Treat5.R2

data_processing:
Reads quality was evaluated with FastQC Version 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (Ewels et al., 2016) showing an overall per sequence quality score (Phred score) between 35 – 36. Trimming was not performed considering the minimal content of adapter sequences (less than 2 %). The reads were aligned to the hg38 human reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/hg38.fa.gz) with STAR v2.7.10a (Dobin et al., 2013) and quality checked with FastQC. Aligned reads were mapped and summarized with featureCounts to generate gene-level count matrices (Liao et al., 2014). Following the alignment and mapping, batch effects were adjusted with the ComBat-seq package and differentially expressed genes (DEGs) were determined by DESeq2 (Love et al., 2014; Zhang et al., 2020).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

growth_protocol: The SH-SY5Y cell line was purchased from American Type Culture Collection (ATCC, CRL-2266) and cultured with Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 with GlutaMax supplement (DMEM/F-12, GlutaMax, Gibco, Cat. #: 10565018) with 10 % fetal bovine serum (FBS, R&D Systems, Cat. #: S11150) and 1 % penicillin-streptomycin (Gibco, Cat. #: 15140122) at 37°C in a humidified atmosphere containing 5 % CO2. The expanded culture was replated into 6-well plates for differentiation and exposure. The replated cells first went through 10 µM all-trans retinoic acid (RA, CAS 302–79–4, Thermo Scientific Chemicals, Cat. #: AC207341000) differentiation for 5 days in DMEM/F-12 with GlutaMax supplied with 2.5 % FBS. On day 5, differentiated SH-SY5Y cells displayed outgrowth of neuronal projections compared to cell morphology before RA treatment and without RA treatment, and were subcultured into 6-well plates and divided into two groups for further maintenance and exposures. In the meantime, the culture medium was switched to human induced pluripotent stem cell (hiPSC)-derived cortical neuron maintenance medium (abbreviated as CNM) composed of 1:1 mixture of B27 neurobasal medium (Neurobasal medium (Gibco, Cat. #: 21103049) supplied with 1X B27 (Gibco, Cat. #: 17504044) and 1X GlutaMax (Gibco, Cat. #: 35050061)) and N-2 DMEM/F-12 medium (DMEM/F-12 with GlutaMax supplied with 1X N-2 (Gibco, Cat. #: 17502048), 1X MEM non-essential amino acid solution (Gibco, Cat. #: 11140050), 2 % penicillin-streptomycin, and 100 µM 2-mercaptoethanol (CAS 60–24–2, Sigma-Aldrich, Cat. #: M3148.

extract_protocol:
By the end of the exposure, cells were collected with lysis buffer from Invitrogen PureLink RNA mini kit (Invitrogen, Cat. #: 12183018 A), processed with QIAshredder mini spin column (QIAGEN, Cat. #: 175028900), and RNA isolated with the PureLink RNA mini kit following manufacturer’s instructions.
mRNA sequencing library was prepared using Tecan Universal Plus mRNA sequencing library preparation kit (Tecan, Cat. #: 5020) following manufacturer’s instructions.

treatment_protocol: Following 3 days of adaptation to the CNM, the 40-day chronic exposure group started to receive Mn treatment by adding 0, 0.01, 0.05, 0.5, 5, and 50 µM MnCl2 to the culture medium. The 6-hour acute exposure group was maintained with CNM till 6 hours before harvest, when the Mn exposure was applied at 0, 0.05, 0.5, 5, 50, and 100 µM. Each treatment group has an N of 5.

value: Differentiated neuroblastoma

value: WT

tag: time


title: SY5Y, 40d, 50 uM Mn Replicate 4

description: Library name: Group2_Treat5.R4


title: WT DNAmi 2xMBD2 gDNA rep 2

description:
Library name: 20250505_HHNSi_mCT_DNAmi_iPSC_human_2xMBD2_2_gDNA
genomic DNA


title: SY5Y, 40d, 50 uM Mn Replicate 5

description: Library name: Group2_Treat5.R5


title: parotid, C57, female, rep1

description: Library name: Mous-4B-PAR-Fem-L

value: female


title: SY5Y, 40d, 50 uM Mn Replicate 1

description: Library name: Group2_Treat5.R1


title: SY5Y, 40d, 5 uM Mn Replicate 5

description: Library name: Group2_Treat4.R5


title: SY5Y, 40d, 5 uM Mn Replicate 4

description: Library name: Group2_Treat4.R4


title: liver, C57, female, rep1

description: Library name: Mous-4B-LIV-Fem


title: pancreas, C57, female, rep1

description: Library name: Mous-4B-PANC-Fem


title: Zebrafish embryo 2xMBD2 nuc rep 2

description:
Library name: 20251216_006_HHNSi_mCnT_Zebrafish_nuc_Zebrafish_embryo_2xMBD2_2
nuclei

organism: Danio rerio

source_name: embryo H 22

value: embryo H 22


title: SY5Y, 40d, 5 uM Mn Replicate 3

description: Library name: Group2_Treat4.R3


title: Zebrafish embryo 2xMBD2 gDNA rep1

description:
Library name: 20251216_017_HHNSi_mCnT_Zebrafish_gDNA_Zebrafish_embryo_2xMBD2_1
genomic DNA


title: SY5Y, 40d, 5 uM Mn Replicate 2

description: Library name: Group2_Treat4.R2


title: SY5Y, 40d, 5 uM Mn Replicate 1

description: Library name: Group2_Treat4.R1


title: SY5Y, 40d, 0.5 uM Mn Replicate 5

description: Library name: Group2_Treat3.R5


title: Zebrafish embryo 2xMBD2 gDNA rep2

description:
Library name: 20251216_018_HHNSi_mCnT_Zebrafish_gDNA_Zebrafish_embryo_2xMBD2_2
genomic DNA


title: Zebrafish embryo 2xMBD2 nuc rep 1

description:
Library name: 20251216_005_HHNSi_mCnT_Zebrafish_nuc_Zebrafish_embryo_2xMBD2_1
nuclei


title: sublingual, C57, male, rep3

description: Library name: Mous-3B-SL-Mal-L

value: male


title: SY5Y, 40d, 0.5 uM Mn Replicate 3

description: Library name: Group2_Treat3.R3


title: SY5Y, 40d, 0.5 uM Mn Replicate 4

description: Library name: Group2_Treat3.R4


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 9

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: University of Texas at Austin

description: Library name: CL-9

data_processing:
Custom perl scripts using the FASTX-toolkit and CUTADAPT v. 2.8 were used to remove reads with a homo-polymer run of “A”≥8 bases, retain reads with minimum 20 bases, removal PCR duplicates – defined as sequences sharing the same degenerate header and 20 bases of sequence – and filtered for quality (Phred quality score > 20 for 90% of the nucleotides).
We aligned preprocessed reads using the Burrows-Wheeler Aligner (bwa-mem) and process reads using samtools.
Assembly: Oreochromis niloticus reference (Orenil1.0 Ensembl cdna) and Labroides dimidiatus genome (Accession: PRJNA937036)
Supplementary files format and content: Processed data .counts are raw counts aligned to the Oreochromis niloticus reference
Supplementary files format and content: Processed data .LdimAlign.counts are raw counts aligned to the Labroides dimidiatus genome

organism: Labroides dimidiatus

source_name: Female, forebrain section

extract_protocol:
Total RNA was extracted using Maxwell 16LEV simplyRNA tissue kit (Promega Corporation, Madison, WI, USA) following manufacturer instructions, including DNase treatment. RNA samples were then eluted into 40uL of nuclease-free water.
Libraries are constructed using the University of Texas Genome Sequencing Analysis Facility protocol for 3'tag-seq. Total RNA was fragmented via Mg+ buffer and cDNA was synthesized with poly-dT oligo. cDNA was amplified using PCR and purified with DNA-binding magnetic beads. Sequencing was perfored on an Illumina HiSeq 2000 instrument.

treatment_protocol: Whole heads were transferred into 30 mL conical tubes with RNAlater (ThermoFischer, Waltham, MA, USA) to preserve the integrity of the RNA. The elapsed time between capture and death ranged from 6 to 28 minutes. After 3 hours (on average) in RNAlater, the samples were transferred into O.C.T. Compound (Sakura, Torrance, CA, USA) and flash frozen in liquid nitrogen and shipped to The University of Texas at Austin for RNA isolation.frozen heads were sectioned on a cryostat microtome into 300µm thick slices. The second most rostral slice of the brain, containing pallial areas Dl and Dm (i.e., the putative teleost homologs of the mammalian hippocampus and basolateral amygdala (areas Dl and Dm, respectively), along with partial portions of septal and striatal territories, was collected and stored in 200ul of ice-cold homogenization buffer with 1-thioglycerol (Promega Corporation, Madison, WI, USA) and stored at -80C until further processing.

value: Female, forebrain section

value: high density; Clam Gardens


title: SY5Y, 40d, 0.5 uM Mn Replicate 1

description: Library name: Group2_Treat3.R1


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 8

description: Library name: CL-8


title: submandibular, C57, male, rep3

description: Library name: Mous-3B-SM-Mal-L

value: submandibular


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 7

description: Library name: CL-7

value: low density; Osprey collection


title: SY5Y, 40d, 0.05 uM Mn Replicate 3

description: Library name: Group2_Treat2.R3


title: liver, C57, male, rep3

description: Library name: Mous-3B-LIV-Mal


title: pancreas, C57, male, rep3

description: Library name: Mous-3B-PANC-Mal

value: pancreas


title: SY5Y, 40d, 0.05 uM Mn Replicate 5

description: Library name: Group2_Treat2.R5


title: SY5Y, 40d, 0.05 uM Mn Replicate 4

description: Library name: Group2_Treat2.R4


title: parotid, C57, male, rep3

description: Library name: Mous-3B-PAR-Mal-L

value: parotid


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 6

description: Library name: CL-6


title: SY5Y, 40d, 0.05 uM Mn Replicate 1

description: Library name: Group2_Treat2.R1


title: submandibular, C57, male, rep2

description: Library name: Mous-2B-SM-Mal-L


title: SY5Y, 40d, 0.01 uM Mn Replicate 5

description: Library name: Group2_Treat1.R5


title: SY5Y, 40d, 0.01 uM Mn Replicate 3

description: Library name: Group2_Treat1.R3


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 5

description: Library name: CL-5


title: sublingual, C57, male, rep2

description: Library name: Mous-2B-SL-Mal-L

value: sublingual


title: SY5Y, 40d, 0.5 uM Mn Replicate 2

description: Library name: Group2_Treat3.R2


title: SY5Y, 40d, 0.05 uM Mn Replicate 2

description: Library name: Group2_Treat2.R2


title: SY5Y, 40d, 0.01 uM Mn Replicate 4

description: Library name: Group2_Treat1.R4


title: SY5Y, 40d, 0.01 uM Mn Replicate 2

description: Library name: Group2_Treat1.R2


title: SY5Y, 40d, 0.01 uM Mn Replicate 1

description: Library name: Group2_Treat1.R1


title: parotid, C57, male, rep2

description: Library name: Mous-2B-PAR-Mal-L


title: SY5Y, 40d, 0 uM Mn Replicate 5

description: Library name: Group2_Control.R5


title: pancreas, C57, male, rep2

description: Library name: Mous-2B-PANC-Mal


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 4

description: Library name: CL-4


title: SY5Y, 40d, 0 uM Mn Replicate 4

description: Library name: Group2_Control.R4


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 3

description: Library name: CL-3


title: PTN rPOSTN DRG Neuron 3

city: Guangzhou

first: Caiwei

last: Zhuang

address: No. 74, Zhongshan Second Road, Nonglin Street, Yuexiu District

department: Zhongshan School of Medicine

institute: Sun Yat-Sen University

description:
Library name: Sample22
POSTN-PO-3

data_processing:
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: dorsal root ganglia neuron

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction. The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

value: dorsal root ganglia neuron

value: primary cells

value: Postn knock out

value: recombinant POSTN


title: liver, C57, male, rep2

description: Library name: Mous-2B-LIV-Mal

value: liver


title: SY5Y, 40d, 0 uM Mn Replicate 3

description: Library name: Group2_Control.R3

value: Differentiated neuroblastoma


title: PTN rPOSTN DRG Neuron 2

description:
Library name: Sample21
POSTN-PO-2


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 2

description: Library name: CL-2


title: SY5Y, 40d, 0 uM Mn Replicate 2

description: Library name: Group2_Control.R2

value: WT


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 20

description: Library name: CL-20

value: low density; Watson's Bay


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 1

description: Library name: CL-1


title: PTN rPOSTN DRG Neuron 1

description:
Library name: Sample20
POSTN-PO-1


title: submandibular, C57, male, rep1

description: Library name: Mous-1B-SM-Mal-L


title: sublingual, C57, male, rep1

description: Library name: Mous-1B-SL-Mal-L


title: SY5Y, 40d, 0 uM Mn Replicate 1

description: Library name: Group2_Control.R1


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 19

description: Library name: CL-19


title: parotid, C57, male, rep1

description: Library name: Mous-1B-PAR-Mal-L


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 17

description: Library name: CL-17


title: PTN Ctrl DRG Neuron 2

description:
Library name: Sample18
POSTN-Ctrl-2

value: Control


title: SY5Y, 6h, 100 uM Mn Replicate 4

description: Library name: Group1_Treat5.R4


title: SY5Y, 6h, 100 uM Mn Replicate 5

description: Library name: Group1_Treat5.R5


title: pancreas, C57, male, rep1

description: Library name: Mous-1B-PANC-Mal

value: male


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 15

description: Library name: CL-15

value: Female, forebrain section

value: high density; The Crest


title: PTN Ctrl DRG Neuron 1

description:
Library name: Sample17
POSTN-Ctrl-1


title: PTN Ctrl DRG Neuron 3

description:
Library name: Sample19
POSTN-Ctrl-3


title: liver, C57, male, rep1

description: Library name: Mous-1B-LIV-Mal


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 14

description: Library name: CL-14


title: submandibular, CD1, female, rep3

description: Library name: Mous-6A-SM-Fem-L

value: submandibular

value: female


title: WT rPOSTN DRG Neuron 2

description:
Library name: Sample15
WT-POSTN-2


title: WT rPOSTN DRG Neuron 3

description:
Library name: Sample16
WT-POSTN-3


title: SY5Y, 6h, 100 uM Mn Replicate 2

description: Library name: Group1_Treat5.R2


title: sublingual, CD1, female, rep3

description: Library name: Mous-6A-SL-Fem-L


title: SY5Y, 6h, 100 uM Mn Replicate 3

description: Library name: Group1_Treat5.R3


title: parotid, CD1, female, rep3

description: Library name: Mous-6A-PAR-Fem-L


title: SY5Y, 6h, 50 uM Mn Replicate 5

description: Library name: Group1_Treat4.R5


title: WT rPOSTN DRG Neuron 1

description:
Library name: Sample14
WT-POSTN-1


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 12

description: Library name: CL-12


title: WT Ctrl DRG Neuron 3

description:
Library name: Sample13
WT-Ctrl-3


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 11

description: Library name: CL-11


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 13

description: Library name: CL-13


title: WT Ctrl DRG Neuron 2

description:
Library name: Sample12
WT-Ctrl-2


title: SY5Y, 6h, 50 uM Mn Replicate 3

description: Library name: Group1_Treat4.R3


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 9

description: Library name: MEL-9

organism: Halichoeres melanurus


title: WT Ctrl DRG Neuron 1

description:
Library name: Sample11
WT-Ctrl-1


title: submandibular, CD1, female, rep2

description: Library name: Mous-5A-SM-Fem-L


title: SY5Y, 6h, 50 uM Mn Replicate 2

description: Library name: Group1_Treat4.R2


title: SY5Y, 6h, 50 uM Mn Replicate 4

description: Library name: Group1_Treat4.R4


title: SY5Y, 6h, 100 uM Mn Replicate 1

description: Library name: Group1_Treat5.R1


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 10

description: Library name: CL-10

value: high density; Clam Gardens


title: pancreas, CD1, female, rep3

description: Library name: Mous-6A-PANC-Fem

value: pancreas


title: sublingual, CD1, female, rep2

description: Library name: Mous-5A-SL-Fem-L

value: sublingual


title: SY5Y, 6h, 50 uM Mn Replicate 1

description: Library name: Group1_Treat4.R1


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 7

description: Library name: MEL-7


title: PTN IMQ DRG 1

description:
Library name: Sample9
PTN_IMQ1

source_name: dorsal root ganglia

value: dorsal root ganglia

value: IMQ


title: parotid, CD1, female, rep2

description: Library name: Mous-5A-PAR-Fem-L

value: parotid


title: PTN IMQ DRG 2

description:
Library name: Sample10
PTN_IMQ2

value: primary cells

value: Postn knock out


title: liver, CD1, female, rep3

description: Library name: Mous-6A-LIV-Fem

value: liver


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 8

description: Library name: MEL-8


title: SY5Y, 6h, 5 uM Mn Replicate 4

description: Library name: Group1_Treat3.R4

value: Differentiated neuroblastoma

value: WT


title: PTN Ctrl DRG 2

description:
Library name: Sample7
PTN_CON2

value: Vehicle


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 5

description: Library name: MEL-5


title: PTN Ctrl DRG 3

description:
Library name: Sample8
PTN_CON3


title: SY5Y, 6h, 5 uM Mn Replicate 5

description: Library name: Group1_Treat3.R5


title: pancreas, CD1, female, rep2

description: Library name: Mous-5A-PANC-Fem


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 6

description: Library name: MEL-6


title: SY5Y, 6h, 5 uM Mn Replicate 3

description: Library name: Group1_Treat3.R3


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 4

description: Library name: MEL-4


title: liver, CD1, female, rep2

description: Library name: Mous-5A-LIV-Fem


title: SY5Y, 6h, 5 uM Mn Replicate 2

description: Library name: Group1_Treat3.R2


title: submandibular, CD1, female, rep1

description: Library name: Mous-4A-SM-Fem-L


title: PTN Ctrl DRG 1

description:
Library name: Sample6
PTN_CON1


title: WT IMQ DRG 2

description:
Library name: Sample5
WT_IMQ2


title: sublingual, CD1, female, rep1

description: Library name: Mous-4A-SL-Fem-L


title: WT IMQ DRG 1

description:
Library name: Sample4
WT_IMQ1


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 2

description: Library name: MEL-2


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 3

description: Library name: MEL-3


title: SY5Y, 6h, 5 uM Mn Replicate 1

description: Library name: Group1_Treat3.R1


title: parotid, CD1, female, rep1

description: Library name: Mous-4A-PAR-Fem-L


title: SY5Y, 6h, 0.5 uM Mn Replicate 5

description: Library name: Group1_Treat2.R5


title: SY5Y, 6h, 0.5 uM Mn Replicate 4

description: Library name: Group1_Treat2.R4


title: WT Ctrl DRG 3

description:
Library name: Sample3
WT_CON3


title: pancreas, CD1, female, rep1

description: Library name: Mous-4A-PANC-Fem


title: SY5Y, 6h, 0.5 uM Mn Replicate 3

description: Library name: Group1_Treat2.R3


title: liver, CD1, female, rep1

description: Library name: Mous-4A-LIV-Fem


title: submandibular, CD1, male, rep3

description: Library name: Mous-3A-SM-Mal-L

value: male


title: WT Ctrl DRG 1

description:
Library name: Sample1
WT_CON1


title: delta HNS rep2

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

description: Library name: gav28

data_processing:
The raw reads were processed with distiller-nf pipeline using NC_000913.3 E.coli reference genome and BWA as an aligner.
Assembly: NC_000913.3
Supplementary files format and content: cooler (.cool, a contact matrix) file for each sample

organism: Escherichia coli

growth_protocol: E. coli K-12 MG1655 strain was grown in Luria-Bertani broth at 37 °C and 200 rpm until reaching an OD600 of ~ 0.6.

extract_protocol:
Cells were resuspended in 250 µL TE (10 mM Tris pH 8.0, 1 mM EDTA) supplemented with 1× protease inhibitors (Bimake) followed by adding lysozyme (Sigma L6876) to 4 µg/mL and incubating for 30 min at 37 °C with shaking at 1000 rpm. The sample was pelleted for 5 min at 16100 g and room temperature and resuspended in an appropriate volume of MNase buffer (10 mM Tris pH 7.5, 1 mM CaCl2) followed by adding MNase (ThermoFisher EN0181, used as 5 U/µL stock solution) to 10 U/mL and incubating for 25 min at 37 °C with shaking at 1000 rpm. The volume of MNase buffer ranged from 475 to 1160 µL for different samples; it was determined individually for each sample to obtain the fragment distribution from ~ 75 to 1000 bp. DNA digestion was terminated by adding EGTA to 5 mM followed by centrifugation for 5 min at 16100 g and room temperature.
The libraries were prepared following a modified Micro-C protocol

treatment_protocol: For heat shock treatment, cells were incubated at 44 °C for 10 min. For transcription inhibition, cells were treated with 25 or 750 µg/mL rifampicin for 40 min. For antibiotic treatment cells were treated with the indicated concentration of the drug for 40 min.

value: bacteria

value: delta HNS


title: delta HNS rep1

description: Library name: gav27


title: WT Ctrl DRG 2

description:
Library name: Sample2
WT_CON2


title: Tissue F, day 14 organotypic slice culture, snRNA-seq

city: Houston

first: JP

last: McGinnis

address: 5306 Creekbend Dr

department: Neurosurgery

institute: Baylor College of Medicine

description:
Library name: TissueF_d14U
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

library_source: transcriptomic single cell

data_processing:
BCL files were demultiplexed to FASTQ with bcl2fastq/bcl-convert by the sequencing provider.
FASTQs were aligned and quantified with Cell Ranger Count v9.0.1 against the 10x Genomics GRCh38.p13 reference.
Processed files provided in this submission are the Cell Ranger filtered_feature_bc_matrix.h5 files (one per library), containing gene-by-cell unique molecular identifier (UMI) count matrices restricted to called cells.
NOTE ON CELLBENDER: Downstream analyses reported in the associated publication (McGinnis et al., Brain Communications 8(2):fcag073, 2026) applied CellBender (trained for 150 complete passes, default parameters otherwise) to the raw Cell Ranger output to remove ambient RNA contamination. The CellBender-corrected matrices were used for cell type annotation, differential expression, and correlation analyses in the paper. The files in this GEO submission are the Cell Ranger outputs prior to CellBender correction; users wishing to reproduce the paper's analyses can apply CellBender with the same parameters.
Assembly: GRCh38.p13
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file in 10x Genomics format containing a sparse gene-by-cell UMI count matrix (matrix/data, matrix/indices, matrix/indptr, matrix/shape), cell barcodes (matrix/barcodes), and gene feature metadata (matrix/features/id, name, feature_type, genome).

source_name: Brain

growth_protocol: Resected tissue was transported in ice-cold, pre-carbogenated NMDG-aCSF, sectioned to 300 um on a Leica VT1200 vibratome, recovered in room-temperature carbogenated aCSF for 15-30 min, then plated onto membrane inserts (CellTreat #230617) overlying 600 uL of organotypic slice culture media (OSCM). Plates were maintained at 37 C, 95% humidity, 5% CO2, with daily media changes. Day 0 tissue was flash-frozen in liquid nitrogen immediately after slicing; day 14 tissue was flash-frozen after 14 days in culture. OSCM was prepared as previously described (Ting et al. 2018 Sci Rep), except heparin was omitted and antibiotic-antimycotic (Gibco 15240-062) was increased to 2%.

extract_protocol:
Frozen tissue was dissociated using the Miltenyi Biotec gentleMACS nuclei isolation protocol ('nuclei isolation' program on a gentleMACS Octo Dissociator), followed by sequential 70 um and 30 um filtration and centrifugation. Nuclei were FACS-sorted on a Sony MA900 (DAPI gating) in the Baylor College of Medicine Cytometry Core, with a sort target of 200,000 nuclei when tissue input permitted.
Single-cell gene expression libraries were prepared according to the Chromium Next GEM Single Cell 3' Gene Expression v3.1 protocol (10x Genomics) by the Baylor College of Medicine Single Cell Genomics Core. Libraries were submitted for Illumina NovaSeq 2x150 bp paired-end sequencing (Azenta/Genewiz), targeting approximately 1 billion reads per library.

value: Brain

value: M

tag: pathology

value: Recurrent SHH medulloblastoma

tag: donor

value: Donor F

tag: time point

value: day 14


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 1

description: Library name: MEL-1

value: Female, forebrain section


title: Whole Embryo, 75 nM axitinib, Rep3

city: Pittsburgh

first: William

middle: Brent

last: Douglas

state: PENNSYLVANIA

address: 6336 Aurelia St., 1

institute: Carnegie Mellon University

description: Library name: Sample9

data_processing:
Sequencing data was analyzed using Illumina Casava v1.8
Low quality reads and reads with adapters were filtered out. Quality of base reads determined by Illumina Casava v1.8 using Phred scoring. Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Filtered sequence reads were mapped to the reference genome using HISAT2. Each sequence read was aligned in the following three steps: The whole sequence was aligned to a single exon. The sequencing sequence was piecewise aligned to two exons of the genome. The sequencing sequence was segmented and aligned to more than three (including three) exons of the genome.
read counts were then normalized using DESeq method via DESeq2 software.
Assembly: Lytechinus variegatus genome build version 3.0
Supplementary files format and content: processed read counts for each gene prior to normalization (gene_count.txt)
Supplementary files format and content: processed read counts for each gene after normalization (gene_fpkm.txt)

organism: Lytechinus variegatus

source_name: whole embryo

growth_protocol: Lytechinus variegatus embryos were cultured in ASW at 21oC in temperature controlled incubators.

extract_protocol:
Embryos were lysed and total RNA was extracted using a Pure Link™ RNA Mini Kit (Invitrogen) following the manufacturer's protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.  For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Lytechinus variegatus embryos were cultured until after the formation of the tri-radiate spicule rudiments (~18-20hpf @ 21oC)at which point embryos were incubated in various treatment conditions (DMSO in ASW, 75 nM axitinib in ASW, or 1 μM K02288 in ASW). Embryos were then cultured until the late pluteus stage (2dpf @ 21oC).

value: whole embryo

value: 75 nM axitinib


title: Whole Embryo, 75 nM axitinib, Rep2

description: Library name: Sample8


title: SY5Y, 6h, 0.5 uM Mn Replicate 1

description: Library name: Group1_Treat2.R1


title: parotid, CD1, male, rep3

description: Library name: Mous-3A-PAR-Mal-L

value: parotid


title: sublingual, CD1, male, rep3

description: Library name: Mous-3A-SL-Mal-L

value: sublingual


title: SY5Y, 6h, 0.05 uM Mn Replicate 5

description: Library name: Group1_Treat1.R5


title: Tissue E, day 14 organotypic slice culture, snRNA-seq

description:
Library name: TissueE_d14U
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

value: Recurrent IDH wild-type glioblastoma

value: Donor E


title: Whole Embryo, 75 nM axitinib, Rep1

description: Library name: Sample7

value: WT


title: Tissue E, day 0 (flash-frozen), snRNA-seq

description:
Library name: TissueE_d0
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

value: day 0


title: pancreas, CD1, male, rep3

description: Library name: Mous-3A-PANC-Mal

value: pancreas

value: male


title: Tissue F, day 0 (flash-frozen), snRNA-seq

description:
Library name: TissueF_d0
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.


title: SY5Y, 6h, 0.05 uM Mn Replicate 4

description: Library name: Group1_Treat1.R4

value: Differentiated neuroblastoma


title: SY5Y, 40d, 50 uM Mn Replicate 3

description: Library name: Group2_Treat5.R3


title: SY5Y, 6h, 0.5 uM Mn Replicate 2

description: Library name: Group1_Treat2.R2


title: liver, CD1, male, rep3

description: Library name: Mous-3A-LIV-Mal

value: liver


title: Tissue D, day 14 organotypic slice culture, snRNA-seq

description:
Library name: TissueD_d14U
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

value: Brain

value: M

value: Newly diagnosed IDH wild-type glioblastoma

value: Donor D


title: SY5Y, 6h, 0.05 uM Mn Replicate 3

description: Library name: Group1_Treat1.R3


title: Tissue D, day 0 (flash-frozen), snRNA-seq

description:
Library name: TissueD_d0
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.


title: submandibular, CD1, male, rep2

description: Library name: Mous-2A-SM-Mal-L

value: submandibular


title: Tissue C, day 14 organotypic slice culture, snRNA-seq

description:
Library name: TissueC_d14U
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

source_name: Frontal opercular cortex

value: Frontal opercular cortex

value: Tissue overlying insular glioma

value: Donor C

value: day 14


title: sublingual, CD1, male, rep2

description: Library name: Mous-2A-SL-Mal-L

value: sublingual


title: SY5Y, 6h, 0.05 uM Mn Replicate 1

description: Library name: Group1_Treat1.R1


title: Whole Embryo, 1 μM K02288, Rep1

description: Library name: Sample4

value: whole embryo


title: Whole Embryo, DMSO, Rep3

description: Library name: Sample3

value: WT

value: DMSO


title: Whole Embryo, 1 μM K02288, Rep3

description: Library name: Sample6


title: parotid, CD1, male, rep2

description: Library name: Mous-2A-PAR-Mal-L

value: parotid


title: SY5Y, 6h, 0 uM Mn Replicate 5

description: Library name: Group1_Control.R5


title: Whole Embryo, DMSO, Rep2

description: Library name: Sample2


title: SY5Y, 6h, 0 uM Mn Replicate 3

description: Library name: Group1_Control.R3


title: Whole Embryo, DMSO, Rep1

description: Library name: Sample1


title: liver, CD1, male, rep2

description: Library name: Mous-2A-LIV-Mal

value: male


title: SY5Y, 6h, 0 uM Mn Replicate 4

description: Library name: Group1_Control.R4

value: Differentiated neuroblastoma


title: pancreas, CD1, male, rep2

description: Library name: Mous-2A-PANC-Mal

value: pancreas


title: Tissue B, day 0 (flash-frozen), snRNA-seq

description:
Library name: TissueB_d0
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

source_name: Temporal lobe cortex

value: Temporal lobe cortex

value: Epilepsy; Sturge-Weber syndrome

value: Donor B

value: day 0


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 8

description: Library name: TUB-8

organism: Labrichthys unilineatus

value: Female, forebrain section


title: submandibular, CD1, male, rep1

description: Library name: Mous-1A-SM-Mal-L

value: submandibular


title: Tissue C, day 0 (flash-frozen), snRNA-seq

description:
Library name: TissueC_d0
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

value: Frontal opercular cortex

value: M

value: Tissue overlying insular glioma


title: SY5Y, 6h, 0 uM Mn Replicate 2

description: Library name: Group1_Control.R2


title: SY5Y, 6h, 0.05 uM Mn Replicate 2

description: Library name: Group1_Treat1.R2


title: Whole Embryo, 1 μM K02288, Rep2

description: Library name: Sample5


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 7

description: Library name: TUB-7


title: Tissue B, day 14 organotypic slice culture, snRNA-seq

description:
Library name: TissueB_d14U
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

value: day 14


title: sublingual, CD1, male, rep1

description: Library name: Mous-1A-SL-Mal-L

value: sublingual


title: SY5Y, 6h, 0 uM Mn Replicate 1

description: Library name: Group1_Control.R1

value: WT


title: Tissue A, day 14 organotypic slice culture, snRNA-seq

description:
Library name: TissueA_d14U
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.

value: F

value: Epilepsy; dysplastic hemisphere with migrational abnormalities

value: Donor A


title: Tissue A, day 0 (flash-frozen), snRNA-seq

description:
Library name: TissueA_d0
Processed file is a Cell Ranger v9.0.1 filtered_feature_bc_matrix.h5 (GRCh38.p13 reference). Downstream analyses in the associated publication (Brain Communications 8(2):fcag073, 2026) applied CellBender (150 complete passes) to the raw Cell Ranger output; CellBender-corrected counts were used for the paper's figures and are not included in this submission.


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 6

description: Library name: TUB-6


title: parotid, CD1, male, rep1

description: Library name: Mous-1A-PAR-Mal-L

value: parotid

value: male


title: pancreas, CD1, male, rep1

description: Library name: Mous-1A-PANC-Mal

value: pancreas


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 5

description: Library name: TUB-5


title: LN229,SREBP1,rep2

first: Thomas

last: O'Loughlin

address: Hess CSM Building, 1470 Madison Avenue

department: Neuroscience

institute: Mount Sinai

description: Library name: Sample_4

data_processing:
By Plasmidsaurus: "Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set."
Assembly: hg38
Supplementary files format and content: .tsv file of raw counts and cpm

growth_protocol: LN229 cells were cultured in DMEM (Gibco # 11965-084) supplemented with 10% FBS (VWR Seradigm # 97068-085), 1 mM sodium pyruvate (Gibco # 11360-070), and 100 U/mL penicillin plus 100 µg/mL streptomycin (Gibco # 15140-122). Cells were cultured at 37°C and 5% CO2 in a humidified atmosphere.

extract_protocol:
By Plasmidsaurus: Total RNA extracted using a bead-based extraction approach from cells preserved in Zymo DNA/RNA Shield. Post-extraction RNA concentration assessed using a fluorescence based plate reader assay.
By Plasmidsaurus: mRNA converted into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification. cDNA generated using a poly(dT)VN primer

treatment_protocol: Cells were transduced with GFP or SREBP1 cDNA, puro selected to purity, and then harvested in DNA/RNA shield for RNA extraction

value: glioblastoma


title: LN229,SREBP1,rep1

description: Library name: Sample_3


title: LN229,CRISPRa,RM6RSL3,rep3

description:
Library name: Sample_31
CRISPRa_counts_raw.txt
i24a

data_processing:
ScreenPro2 package (v0.2.10) used for processing dual-guide (V3) CRISPRa/i screens – https://github.com/ArcInstitute/ScreenPro2. Paired-end deep sequencing FASTQ files are first processed using the `GuideCounter` module to capture guide pairs counts mapped to the reference guide sequences provided in a library table. Then, the output count matrix per sample is then used to calculate drug screen phenotypes using the `PhenoScore` module.
Supplementary files format and content: .txt file of raw counts
Library strategy: CRISPR Screen

source_name: LN229 dCas9-Suntag

extract_protocol:
Genomic DNA was purified from cell pellets using NucleoSpin Blood L gDNA extraction kits (Nacherey-Nagel # 740954) in accordance with the manufacturer’s instructions and yields and purity were confirmed by nanodrop.
Amplicons were generated by PCR to introduce sequencing adaptors and sample-specific indexes using a common forward primer within the U6 promoter and reverse primers which bind the sgRNA constant region downstream of the second sgRNA and contain the sample-specific indexes. PCR reactions comprised 2x NEB Next Ultra II Q5 polymerase (NEB # M0544), 10 µg of purified gDNA and 1 µl of each 100 µM primer per 100 μl reaction. PCR amplification was performed with the following cycling conditions: denaturation at 98ºC for 30 secs, 22 cycles of denaturation at 98ºC for 10 secs then annealing and extension at 67ºC for 75 secs, and a final extension at 72ºC for 5 mins. All gDNA was PCR amplified and all reactions for each sample were mixed post-amplification. 300 µl of amplified PCR was subject to a 0.5-0.65X double-sided SPRI selection to enrich for the amplicon and remove excess primer. Sample purity and concentration were determined using an Agilent Tapestation and used to calculate equimolar sample pooling. Pooled libraries were sequenced on a NextSeq550 or NovaSeq 6000 platform with paired end reads using custom read 1, read 2 and index read 1 primers and 10% PhiX achieving a minimum of 6 million reads per sample (i.e. ≥300 reads/library element).

treatment_protocol: LN229 CRISPRi or CRISPRa cells were transduced with compact genome-scale dual-sgRNA libraries generously donated by Jonathan Weissman. Cells were transduced at an MOI of ~0.3 to achieve representation of each sgRNA in an average of >500 cells (500x coverage). At 48 and 72 hrs post-transduction cells were dosed with 3 µg/ml puromycin to select for sgRNA-positive cells. Following selection, sgRNA-positive cells were subsequently recovered in fresh medium for an additional 3 days. 6 days post-transduction cells pellets of 25 million cells were frozen to determine sgRNA composition at selection initiation (T0). Remaining cells were split into treatment conditions in triplicate. For CRISPRi screens conditions were: DMSO, RM-006 1.56 nM, and RM-006 0.098 nM. For CRISPRa screens conditions were: DMSO, RM-006 1.56 nM, RSL3 46.875 nM, and RM-006 1.56 nM+RSL3 46.875 nM. Cells were maintained under selection pressure at 1000x library coverage with passaging every 1 to 4 days as necessary for a total of 14-15 days for the CRISPRi and 12 days for the CRISPRa screens. At the screen endpoint cells were harvested and frozen in 25 million cell pellets prior to library preparation for sequencing.

value: LN229 dCas9-Suntag


title: LN229,GFP,rep2

description: Library name: Sample_2

value: GFP


title: Spatial transcriptome of vitiligo skin sample

city: Osaka

first: fei

last: yang

state: Osaka

address: Abeno Medix 212, 1-2-7, Asahimachi, Abeno-ku

country: Japan

institute: Department of Pigmentation Research and Therapeutics, Graduate School of Medicine, Osaka Metropolitan University

description:
Library name: viti_H200919884
Spatial transcriptomics of human skin using 10x Genomics Visium platform

data_processing:
Raw sequencing data were processed using Space Ranger (10x Genomics) for alignment, barcode assignment, and gene expression quantification.
Reads were aligned to the human reference genome (GRCh38) using the Space Ranger pipeline. Gene expression matrices were generated and spatial coordinates were assigned to each spot.
Downstream analyses, including normalization, clustering, and visualization, were performed using standard bioinformatics workflows.
Assembly: GRCh38
Supplementary files format and content: Processed data include gene expression matrices in HDF5 format (.h5), filtered feature-barcode matrices, and spatial information including spot coordinates and tissue images.
Library strategy: Spatial Transcriptomics

source_name: skin

growth_protocol: Human skin tissue samples were obtained from vitiligo patients and healthy controls. Samples were handled according to standard clinical procedures and processed immediately for spatial transcriptomic analysis.

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) human skin tissue sections using the 10x Genomics Visium Spatial Gene Expression for FFPE protocol. Tissue sections were processed according to the manufacturer’s instructions, including deparaffinization, permeabilization, and probe hybridization.
Spatial transcriptomic libraries were generated using the 10x Genomics Visium Spatial Gene Expression platform for FFPE samples. Tissue sections were placed on Visium slides, followed by probe hybridization, ligation, and library preparation according to the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: No experimental treatment was applied. Samples represent untreated human skin tissues collected from vitiligo patients and healthy controls.

value: skin

value: skin tissue


title: liver, CD1, male, rep1

description: Library name: Mous-1A-LIV-Mal

value: liver