title: peanut-XN_SY01_P1_F20_180926A_SPRI_482_200507

description:
XN_SY01_P1_F20_180926A_SPRI_482_200507
47K SNPs


title: H1 ESCs，E7+TGFb+2DG3, 24h.2

status: Public on May 05 2025

type: SRA

city: macau

first: Chengcheng

last: SONG

address: universtiy of macau

department: fhs

country: Macau

institute: university of macau

library_source: transcriptomic

data_processing:
Quality control of RNA-seq raw data was performed using Trimmomatic version 0.36
RNA-seq clean data alignment was conducted using STAR version 020201 with the reference genome hg38.
All genes expression were quantified using FeatureCounts version 1.5.3
Differential expression genes (DEGs) were identified with the criteria of p adjusted value < 0.05 and the absolute value of log2(Fold Change) > 1 after profile normalized using DESeq2 version 1.26.0
DEGs analysis were performed the GO and KEGG enrichment analysis through the R package ClusterProfiler 4.0
Assembly: hg38
Supplementary files format and content: Tab-delimited file reports normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: E7 treatment with TGFb and 2DG 3mM for 24h in H1 ESCs

growth_protocol: H1 ESCs  was maintained in E8 medium supplemented with  antibiotics  with 5% CO2 at 37C. E8 medium contained DMEM/F12, sodium selenite, ascorbic acid trisodium, transferrin, insulin, FGF2 and TGFβ.

extract_protocol:
Cells was harvested in RNAiso Plus reagent (Takara). The poly(A) mRNA isolation was performed using Oligo(dT) beads according to manufacturer’s instructions
1 μg total RNA was used for following library preparation. The RNA Library were sequenced for paired end reads on Illumina NextSeq 500 (Illumina).

treatment_protocol: 2DG 3mM was treated with E7 medium (E8-TGFb) in H1 ESCs. Nodal 100ng/mL, Activin A 100ng/mL and TGFb 1.74ng/mL were used for treatment with or without 2DG treatment.

tag: cell line

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

tag: treatment

value: E7+TGFb+2DG3, 24h


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_20CAG_rep1_1

city: Cambridge

first: Matthew

last: Leventhal

state: MA

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

country: USA

institute: Massachusetts Institute of Technology

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data

library_source: genomic

data_processing:
We processed the ATAC-seq data using the ENCODE-DCC ATAC-seq pipeline v.1.7.1. Using this pipeline, we identified FASTQ read adaptors with the detect_adapter.py script in GGR_code (https://github.com/nboley/GGR_code). We trimmed read adaptors with the trim_adaptors function in cutadapt 1.9.1. Processed FASTQs, were aligned using Bowtie2 version 2.2.6, requiring SAMtools version 1.7 and SAMstats version 0.2.1. Picard tools version 1.126 MarkDuplicates was used to deduplicate the aligned reads. These tools were used with default parameters except for setting the parameters “atac.auto_adect_adapter” and “atac.enable_xcor” to “true”.
The ChIP-seq data was analyzed using the ENCODE-DCC ChIP-seq pipeline v1.3.6. In this pipeline, FASTQ data were cropped with Trimmomatic 0.39, aligned with Bowtie2 version 2.26 and deduplicated with Picard version 1.126 MarkDuplicates. Default parameters were used for all arguments except for setting “chip.pipeline_type” to “histone”.
From the aligned, deduplicated ATAC-seq data, MACS2 version 2.1.0 was used to identify peaks that had significant local enrichments at a p-value threshold of 0.01. For the aligned, deduplicated ChIP-seq data, peak calling was performed using SPP version 1.14, GEM 2.4.1 and PeakSeq version 1.25. IDR 2.0.4 was run to determine a high-quality set of consensus peaks from the results of the multiple peak callers. Upon identifying peaks, DiffBind version 2.10.0 was used to perform differential analysis between ChIP-seq or ATAC-seq peaks for the following comparisons: HTT knock-out vs. control, HTT HD knockdown vs HTT wild-type HD, 56/22 (adult onset) HD vs control, and 72/20 (expanded repeat length) HD vs control. We refer to the union of peaks found in 20/20 and 22/20 cells as “control” in these comparisons. DiffBind in R version 3.5.2 was used to identify differential peaks as those with an FDR-adjusted p-value less than 0.1
To determine similarities and differences across cortical neuron replicates and genotypes in the ATAC-seq or ChIP-seq data, Principal Component Analysis (PCA) was used as implemented in Scikit-Learn version 0.23.2. To preprocess the data, peaks were limited to those that were within 5kb from a protein-coding gene. The signal of the filtered peaks was standardized before performing PCA with 10 principal components. Replicates were removed from the analysis if they failed the ATAC-seq or ChIP-seq ENCODE benchmarks determined from FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with peaks quantified with MACS2

molecule: genomic DNA

source_name: Human pluripotent stem cell line

extract_protocol:
For Atac-seq, We used 50,000 nuclei for the transposase reaction, following the method described previously. Subsequently, samples were purified with the DNA Clean & Concentrator–5 Kit (Zymo Research), and then PCR-amplified using Nextera indexing primers (Illumina). The number of PCR cycles were optimized by qPCR to avoid over amplification of the libraries. The final libraries were purified using 1x PCRClean DX beads (Aline Biosciences). The enrichment of accessible chromatin regions in the libraries were assessed by qPCR using primers mapped to open chromatin region and gene desert regions. For ChIP-seq data 1X106 cells were incubated in lysis buffer (50 mM Tris-HCL pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% Na- deoxycholate, and 5 mM CaCl2 supplemented with protease inhibitors and 10 mM sodium butyrate for K27ac ChIP) for 20 min on ice. The chromatin was digested to 1-5 nucleosomes using Micrococcal Nuclease (NEB # M0247S), at concentration determined by titration experiments, for 10 min at 37oC. To terminate the digestion, 20 mM EDTA was added to the samples. The antibody was added and incubated overnight at 4oC. On the next day, 25 µl of protein G Dynabeads (Thermo Scientific # 10004D,) was added and the samples rotated for 2 hr at 4oC. The beads were washed 6 times: 2 washes with RIPA buffer (10 mM Tris-HCl pH8, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), 2 washes with high salt buffer (10 mM Tris-HCl pH8, 1 mM EDTA, 360 mM NaCl, 1% Triton X- 100, 0.1% Na-deoxycholate, 0.1% SDS), 2X washes with LiCl buffer (10 mM Tris-HCl pH8, 1  mM EDTA, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% Na-deoxycholate) and 1 wash with TE (10 mM Tris-HCl pH8, 1 mM EDTA). The DNA was eluted by incubation of the beads in elution buffer (10 mM Tris-HCl pH8, 5 mM EDTA, 300 mM NaCl, 0.1% SDS, 50 µg Proteinase K) for 1 hr. at 62 and purified with 1X PCRClean DX beads (Aline Biosciences).
For Atac-seq, samples were purified with the DNA Clean & Concentrator–5 Kit (Zymo Research), and then PCR-amplified using Nextera indexing primers (Illumina). The number of PCR cycles were optimized by qPCR to avoid over amplification of the libraries. For ChIP-seq, The sequencing libraries were constructed using the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina (NEB # E7645S), followed by analysis using Fragment Analyzer™ instrument (Advanced Analytical), and quantification by a qPCR-based method (KAPA Library Quantification Kit for Illumina Sequencing Platforms)

tag: tissue

value: Human pluripotent stem cell line

value: 20CAG control


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: HTT KO


title: H1 ESCs，E7+TGFb+2DG3, 24h.1


title: peanut-XN_SY01_P1_F19_180926A_SPRI_348_200507

type: genomic

city: Qingdao

first: jing

last: xu

address: 126 Wannianquan Road

country: China

institute: Shandong Peanut Research Institute

description:
XN_SY01_P1_F19_180926A_SPRI_348_200507
47K SNPs

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics process, and scanned using the Symbol® Cyclone™ M2000 Scanner.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console® (version 2.0). The raw data CEL files were typed using Axiom Analysis Suite 3.1.51, according to each site A set of indicators assigned to a specified type: PolyHighResolution, NoMinorHom,  MonoHighResolution, OTV,  CallRateBelowThreshold, Other.
Genotype Call (SNP call): AA, AB, BB, NC.

label: biotin

organism: Arachis hypogaea

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Peanuts were grown according to standard conditions

extract_protocol: Young healthy leaves from each accession were collected, with extraction of total genomic DNA via a Plant Genomic DNA Kit (Tiangen Biotech (Beijing) Co., Ltd.). The extracted DNA quality and concentration were determined via 0.8% agarose gel electrophoresis using standard lambda DNA and a NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Wilmington, DE, USA)

tag: tag

value: leaf


title: peanut-XN_SY01_P1_F18_180926A_SPRI_481_200507

description:
XN_SY01_P1_F18_180926A_SPRI_481_200507
47K SNPs


title: liver, Field, 207363410094_R05C02

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description:
Liver methylome in rewilded mice
207363410094_R05C02

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings
GEO_processed_matrix_GPL30650.csv (Normalized average Beta)
GEO_signal_intensity_matrix_GPL30650.csv (Unmethylated and methylated signal intensities)

label: Cy5 and Cy3

organism: Mus musculus

source_name: primary liver tissue

label_protocol: Standard Illumina Protocol

extract_protocol: A Phenol/Chloroform/Isoamyl alcohol protocol was employed (Molecular cloning: a laboratory manual. No. Ed. 2. Cold Spring Harbor laboratory press, 1989) to extract genomic DNA from mouse liver tissues. The whole liver tissue was homogenized using a tissue homogenizer (OMNI, TH115) in 500 µl of lysis buffer containing 10 mM Tris pH 8.0 (VWR, 97062-674), 300 mM NaCl (VWR, 10128-484), 0.5% SDS (Invitrogen, 15553027), and 5 mM EDTA (VWR, 10128-442). After adding 15 µl of Proteinase K (NEB, P8107S), the solution was incubated at 55°C overnight. Subsequently, 100 µl of the solution was combined with an additional 400 µl of lysis buffer and incubated at 55°C for 2 hours. The 500 µl of the solution was placed into a 5PRIME Phase Lock Gel tube (Quanta bio, 10847-802) pre-centrifuged for 1 minute. 500 µl of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich 77617) was added to the phase Lock Gel tube. The aqueous phase solution was transferred to a new 1.5 mL centrifuge tube (Eppendorf, 05414203). 500 µl of 100% isopropanol (MilliporeSigma, EM1.09634.1011), GlycoBlue (Invitrogen™, AM9515), and Ammonium acetate solution 7.5M (Sigma-Aldrich, A2706) were added to the tube. The solution was vortexed and incubated at -20°C for 30 min up to O/N. Samples were centrifuged at 16,000g for 30 min at 4°C and washed twice by adding 1 ml 70% EtOH (MilliporeSigma, EM1.00983.1011). After the last wash and removal of 70% EtOH, the samples were air-dried for 10 min and resuspended in 200 µl of the Tris buffer pH8.0 (VWR, 97062-674), and incubated at 55°C for 10 min. DNAs that were not completely dissolved were incubated at 4°C for overnight. If the dissolved DNA did not exhibit a transparent color or the DNA quantity was inadequate, an additional bead purification step was carried out. Briefly, 2x volume of AMpure XP (Beckman Coulter, A63881) was added to the DNAs, mixed thoroughly, briefly spun down, incubated the mixture for 5 min at room temperature, placed on a magnet stand, and washed 2 times with 500 μl of freshly made 80% EtOH, allowed to dry for 3 to 5 mins. The final elution was performed using 100 ~ 200 μl autoclaved ultrapure water. DNA amount was measured using the Qubit 4 Fluorometer (Invitrogen) with the dsDNA HS Assay Kit (Invitrogen, Q33231).

tag: Sex

value: male

value: Liver

tag: strain

tag: environment

value: Field


title: liver, Field, 207363410095_R06C01

description:
Liver methylome in rewilded mice
207363410095_R06C01

value: female


title: liver, Field, 207363410094_R04C02

description:
Liver methylome in rewilded mice
207363410094_R04C02


title: H1 ESCs，E7+TGFb, 24h.2

source_name: E7 treatment with TGFb 1.74 ng/mL for 24h in H1 ESCs

value: E7+TGFb, 24h


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_72CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: H1 ESCs，E7+Activin A, 24h.2

source_name: E7 treatment with Activin A 100 ng/mL for 24h in H1 ESCs

value: E7+Activin A, 24h


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_72CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_F16_180926A_SPRI_480_200507

description:
XN_SY01_P1_F16_180926A_SPRI_480_200507
47K SNPs


title: H1 ESCs，E7+TGFb, 24h.1


title: liver, Field, 207363410094_R04C01

description:
Liver methylome in rewilded mice
207363410094_R04C01


title: H1 ESCs，E7+2DG3, 24h.2

source_name: E7 treatment with 2DG 3mM for 24h in H1 ESCs


title: peanut-XN_SY01_P1_F17_180926A_SPRI_347_200507

description:
XN_SY01_P1_F17_180926A_SPRI_347_200507
47K SNPs


title: liver, Field, 207363410094_R03C02

description:
Liver methylome in rewilded mice
207363410094_R03C02


title: peanut-XN_SY01_P1_F15_180926A_SPRI_346_200507

description:
XN_SY01_P1_F15_180926A_SPRI_346_200507
47K SNPs


title: liver, Field, 207363410094_R03C01

description:
Liver methylome in rewilded mice
207363410094_R03C01


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_72CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_F14_180926A_SPRI_479_200507

description:
XN_SY01_P1_F14_180926A_SPRI_479_200507
47K SNPs


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_56CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Embryonic_stem_cell_H3K4me3_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Embryonic_stem_cell_H3K4me3_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: H1 ESCs，E7, 24h.2

source_name: E7 treatment for 24h in H1 ESCs


title: liver, Field, 207363410094_R02C02

description:
Liver methylome in rewilded mice
207363410094_R02C02


title: peanut-XN_SY01_P1_F13_180926A_SPRI_345_200507

description:
XN_SY01_P1_F13_180926A_SPRI_345_200507
47K SNPs


title: H1 ESCs，E7+2DG3, 24h.1


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_56CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: H1 ESCs，E7, 24h.1


title: liver, Field, 207363410094_R06C02

description:
Liver methylome in rewilded mice
207363410094_R06C02


title: liver, Field, 207363410094_R02C01

description:
Liver methylome in rewilded mice
207363410094_R02C01


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_56CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_F12_180926A_SPRI_478_200507

description:
XN_SY01_P1_F12_180926A_SPRI_478_200507
47K SNPs


title: peanut-XN_SY01_P1_F11_180926A_SPRI_344_200507

description:
XN_SY01_P1_F11_180926A_SPRI_344_200507
47K SNPs


title: retina wt4 (Retina wt4 n2)

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
the clean reads were mapped to the mouse genome (mm10) using Hisat2
the number of reads uniquely mapped to each gene was determined using Htseq count
Genome_build: mm10
Supplementary_files_format_and_content: reads count per gene

source_name: retina

extract_protocol:
Total RNA was purified using RNeasy per manufacturer’s instructions (Qiagen)
PolyA-tailed RNA was purified from total RNA and libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s recommendations.

value: retina

value: wt

tag: age


title: liver, Field, 207363410089_R06C01

description:
Liver methylome in rewilded mice
207363410089_R06C01


title: retina wt3 (Retina wt3 h8)


title: liver, Field, 207363410094_R01C01

description:
Liver methylome in rewilded mice
207363410094_R01C01


title: peanut-XN_SY01_P1_F10_180926A_SPRI_477_200507

description:
XN_SY01_P1_F10_180926A_SPRI_477_200507
47K SNPs


title: liver, Field, 207363410089_R05C01

description:
Liver methylome in rewilded mice
207363410089_R05C01


title: peanut-XN_SY01_P1_F09_180926A_SPRI_343_200507

description:
XN_SY01_P1_F09_180926A_SPRI_343_200507
47K SNPs


title: retina wt2 (Retina wt2 h7b)


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_22CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: liver, Field, 207363410089_R02C02

description:
Liver methylome in rewilded mice
207363410089_R02C02


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_20CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_22CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: retina het5 (Het retina R5)

value: Het


title: peanut-XN_SY01_P1_F07_180926A_SPRI_342_200507

description:
XN_SY01_P1_F07_180926A_SPRI_342_200507
47K SNPs


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_20CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410089_R01C02

description:
Liver methylome in rewilded mice
207363410089_R01C02


title: retina het4 (Het retina R4)


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_20CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_F06_180926A_SPRI_473_200507

description:
XN_SY01_P1_F06_180926A_SPRI_473_200507
47K SNPs


title: retina het3 (Het retina R3)


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410088_R05C01

description:
Liver methylome in rewilded mice
207363410088_R05C01


title: retina het2 (Het retina R2)


title: liver, Field, 207363410088_R04C01

description:
Liver methylome in rewilded mice
207363410088_R04C01


title: retina het1 (Het retina R1)


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_22CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: retina wt1 (Retina wt1 h7)


title: peanut-XN_SY01_P1_F03_180926A_SPRI_340_200507

description:
XN_SY01_P1_F03_180926A_SPRI_340_200507
47K SNPs


title: Embryonic_stem_cell_H3K27Ac_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27Ac_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_F04_180926A_SPRI_472_200507

description:
XN_SY01_P1_F04_180926A_SPRI_472_200507
47K SNPs


title: peanut-XN_SY01_P1_F08_180926A_SPRI_476_200507

description:
XN_SY01_P1_F08_180926A_SPRI_476_200507
47K SNPs


title: retina het6 (Het retina n4)


title: peanut-XN_SY01_P1_F02_180926A_SPRI_471_200507

description:
XN_SY01_P1_F02_180926A_SPRI_471_200507
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_72CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410088_R01C02

description:
Liver methylome in rewilded mice
207363410088_R01C02


title: liver, Field, 207363410088_R06C02

description:
Liver methylome in rewilded mice
207363410088_R06C02


title: Het cor5 (19a-5-9)

source_name: cortex

value: cortex


title: liver, Field, 207363410041_R06C02

description:
Liver methylome in rewilded mice
207363410041_R06C02


title: hom cor4 (19a-5-7)

value: Hom


title: peanut-XN_SY01_P1_F01_180926A_SPRI_338_200507

description:
XN_SY01_P1_F01_180926A_SPRI_338_200507
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_72CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410088_R06C01

description:
Liver methylome in rewilded mice
207363410088_R06C01


title: peanut-XN_SY01_P1_E24_180926A_SPRI_249_200507

description:
XN_SY01_P1_E24_180926A_SPRI_249_200507
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_72CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410041_R05C02

description:
Liver methylome in rewilded mice
207363410041_R05C02


title: peanut-XN_SY01_P1_F05_180926A_SPRI_341_200507

description:
XN_SY01_P1_F05_180926A_SPRI_341_200507
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_56CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Hom cb3 (19a-5-6)

source_name: cerebellum

value: cerebellum


title: peanut-XN_SY01_P1_E23_180926C_SPRI-070_210107

description:
XN_SY01_P1_E23_180926C_SPRI-070_210107
47K SNPs


title: hom cor3 (19a-5-3)

value: hom


title: liver, Field, 207363410088_R02C02

description:
Liver methylome in rewilded mice
207363410088_R02C02


title: peanut-XN_SY01_P1_E23_180926A_SPRI_125_200507

description:
XN_SY01_P1_E23_180926A_SPRI_125_200507
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_56CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: peanut-XN_SY01_P1_E22_180926A_SPRI_248_200507

description:
XN_SY01_P1_E22_180926A_SPRI_248_200507
47K SNPs


title: wt cor4 (19a-4-6)


title: wt cb4 (19a-4-5)


title: peanut-XN_SY01_P1_E21_180926C_SPRI-069_210107

description:
XN_SY01_P1_E21_180926C_SPRI-069_210107
47K SNPs


title: liver, Field, 207363410041_R03C02

description:
Liver methylome in rewilded mice
207363410041_R03C02


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_22CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: het thalum (19a-4-4)

source_name: Thalums

value: Thalums

value: het


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_56CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410041_R02C01

description:
Liver methylome in rewilded mice
207363410041_R02C01


title: peanut-XN_SY01_P1_E21_180926A_SPRI_124_200507

description:
XN_SY01_P1_E21_180926A_SPRI_124_200507
47K SNPs

value: leaf


title: peanut-XN_SY01_P1_E20_180926A_SPRI_246_200507

description:
XN_SY01_P1_E20_180926A_SPRI_246_200507
47K SNPs


title: liver, Field, 207363410041_R01C01

description:
Liver methylome in rewilded mice
207363410041_R01C01

value: Liver


title: liver, Field, 207363410041_R03C01

description:
Liver methylome in rewilded mice
207363410041_R03C01

value: Field


title: het Hip (19a-4-3)

source_name: Hipocampus

value: Hipocampus


title: het cb5 (19a-4-1)


title: liver, Field, 207363410040_R05C01

description:
Liver methylome in rewilded mice
207363410040_R05C01

value: male


title: het cor4 (19a-4-2)


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_20CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 20CAG control


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_20CAG_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_22CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410041_R04C02

description:
Liver methylome in rewilded mice
207363410041_R04C02

value: female


title: hom cb2 (19a-3-9)


title: liver, Field, 207363410040_R02C02

description:
Liver methylome in rewilded mice
207363410040_R02C02


title: liver, Field, 207363410041_R04C01

description:
Liver methylome in rewilded mice
207363410041_R04C01


title: peanut-XN_SY01_P1_E18_180926A_SPRI_245_200507

description:
XN_SY01_P1_E18_180926A_SPRI_245_200507
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_20CAG_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E17_180926C_SPRI-064_210107

description:
XN_SY01_P1_E17_180926C_SPRI-064_210107
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: HTT KO


title: het cb4 (19a-3-11)


title: liver, Field, 207363410020_R06C02

description:
Liver methylome in rewilded mice
207363410020_R06C02


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_22CAG_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: peanut-XN_SY01_P1_E17_180926A_SPRI_121_200507

description:
XN_SY01_P1_E17_180926A_SPRI_121_200507
47K SNPs


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410020_R05C02

description:
Liver methylome in rewilded mice
207363410020_R05C02


title: peanut-XN_SY01_P1_E19_180926C_SPRI-066_210107

description:
XN_SY01_P1_E19_180926C_SPRI-066_210107
47K SNPs


title: peanut-XN_SY01_P1_E16_180926A_SPRI_244_200507

description:
XN_SY01_P1_E16_180926A_SPRI_244_200507
47K SNPs


title: het cb3 (19a-2-9)


title: liver, Field, 207363410020_R04C01

description:
Liver methylome in rewilded mice
207363410020_R04C01


title: Embryonic_stem_cell_H3K27me3_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Embryonic_stem_cell_H3K27me3_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: Cortical_neuron_H3K4me1_ChIP_seq_72CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: hom cor2 (19a-3-10)


title: peanut-XN_SY01_P1_E15_180926C_SPRI-062_210107

description:
XN_SY01_P1_E15_180926C_SPRI-062_210107
47K SNPs


title: het cor2 (19a-2-8)


title: peanut-XN_SY01_P1_E19_180926A_SPRI_122_200507

description:
XN_SY01_P1_E19_180926A_SPRI_122_200507
47K SNPs


title: Cortical_neuron_H3K4me1_ChIP_seq_72CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410020_R03C02

description:
Liver methylome in rewilded mice
207363410020_R03C02


title: peanut-XN_SY01_P1_E15_180926A_SPRI_120_200507

description:
XN_SY01_P1_E15_180926A_SPRI_120_200507
47K SNPs


title: het cb2 (19a-2-7)


title: Cortical_neuron_H3K4me1_ChIP_seq_72CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E14_180926A_SPRI_243_200507

description:
XN_SY01_P1_E14_180926A_SPRI_243_200507
47K SNPs


title: liver, Field, 207363410040_R01C02

description:
Liver methylome in rewilded mice
207363410040_R01C02


title: wt cor2 (19a-2-6)

value: wt


title: het cor4 (19a-3-12)

value: cortex


title: liver, Field, 207363410020_R02C01

description:
Liver methylome in rewilded mice
207363410020_R02C01


title: Cortical_neuron_H3K4me1_ChIP_seq_56CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E13_180926C_SPRI-059_210107

description:
XN_SY01_P1_E13_180926C_SPRI-059_210107
47K SNPs


title: peanut-XN_SY01_P1_E13_180926A_SPRI_119_200507

description:
XN_SY01_P1_E13_180926A_SPRI_119_200507
47K SNPs


title: Cortical_neuron_H3K4me1_ChIP_seq_56CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207097260056_R06C02

description:
Liver methylome in rewilded mice
207097260056_R06C02


title: wt cor3 (19a-2-12)


title: wt cb2 (19a-2-5)


title: Cortical_neuron_H3K4me1_ChIP_seq_56CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E12_180926A_SPRI_242_200507

description:
XN_SY01_P1_E12_180926A_SPRI_242_200507
47K SNPs


title: liver, Field, 207097260056_R06C01

description:
Liver methylome in rewilded mice
207097260056_R06C01


title: wt cb3 (19a-2-11)


title: het cor3 (19a-2-10)


title: Cortical_neuron_H3K4me1_ChIP_seq_22CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207097260056_R05C02

description:
Liver methylome in rewilded mice
207097260056_R05C02


title: peanut-XN_SY01_P1_E11_180926C_SPRI-058_210107

description:
XN_SY01_P1_E11_180926C_SPRI-058_210107
47K SNPs


title: Cortical_neuron_H3K4me1_ChIP_seq_22CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410020_R03C01

description:
Liver methylome in rewilded mice
207363410020_R03C01


title: peanut-XN_SY01_P1_E11_180926A_SPRI_117_200507

description:
XN_SY01_P1_E11_180926A_SPRI_117_200507
47K SNPs


title: peanut-XN_SY01_P1_E10_180926A_SPRI_241_200507

description:
XN_SY01_P1_E10_180926A_SPRI_241_200507
47K SNPs


title: liver, Field, 207097260056_R05C01

description:
Liver methylome in rewilded mice
207097260056_R05C01


title: Cortical_neuron_H3K4me1_ChIP_seq_22CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: hom cor1 (19a-1-6)


title: hom cb1 (19a-1-5)


title: liver, Field, 207097260056_R04C02

description:
Liver methylome in rewilded mice
207097260056_R04C02


title: peanut-XN_SY01_P1_E09_180926C_SPRI-057_210107

description:
XN_SY01_P1_E09_180926C_SPRI-057_210107
47K SNPs


title: Cortical_neuron_H3K4me1_ChIP_seq_20CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: wt cor1 (19a-1-4)


title: peanut-XN_SY01_P1_E09_180926A_SPRI_115_200507

description:
XN_SY01_P1_E09_180926A_SPRI_115_200507
47K SNPs


title: wt cb1 (19a-1-3)


title: Cortical_neuron_H3K4me1_ChIP_seq_20CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E08_180926A_SPRI_240_200507

description:
XN_SY01_P1_E08_180926A_SPRI_240_200507
47K SNPs


title: liver, Field, 207097260056_R03C01

description:
Liver methylome in rewilded mice
207097260056_R03C01


title: Cortical_neuron_H3K4me1_ChIP_seq_20CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207363410020_R01C01

description:
Liver methylome in rewilded mice
207363410020_R01C01


title: peanut-XN_SY01_P1_E07_180926C_SPRI-056_210107

description:
XN_SY01_P1_E07_180926C_SPRI-056_210107
47K SNPs


title: liver, Field, 207097260056_R03C02

description:
Liver methylome in rewilded mice
207097260056_R03C02


title: het cor1 (19a-1-2)


title: het cb1 (19a-1-1)


title: liver, Field, 207097260056_R02C02

description:
Liver methylome in rewilded mice
207097260056_R02C02


title: liver, Field, 207097260056_R04C01

description:
Liver methylome in rewilded mice
207097260056_R04C01


title: peanut-XN_SY01_P1_E07_180926A_SPRI_113_200507

description:
XN_SY01_P1_E07_180926A_SPRI_113_200507
47K SNPs


title: Cortical_neuron_H3K4me1_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207097260056_R02C01

description:
Liver methylome in rewilded mice
207097260056_R02C01


title: peanut-XN_SY01_P1_E06_180926A_SPRI_239_200507

description:
XN_SY01_P1_E06_180926A_SPRI_239_200507
47K SNPs


title: wt 84 CB (18c-1-59)


title: peanut-XN_SY01_P1_E05_180926C_SPRI-055_210107

description:
XN_SY01_P1_E05_180926C_SPRI-055_210107
47K SNPs


title: 85 CB (18c-1-58)


title: liver, Field, 207097260056_R01C01

description:
Liver methylome in rewilded mice
207097260056_R01C01


title: WT CB (18c-1-57)


title: Cortical_neuron_H3K4me3_ChIP_seq_72CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E05_180926A_SPRI_112_200507

description:
XN_SY01_P1_E05_180926A_SPRI_112_200507
47K SNPs


title: 19 CB (18c-1-56)


title: Cortical_neuron_H3K4me3_ChIP_seq_72CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E04_180926A_SPRI_238_200507

description:
XN_SY01_P1_E04_180926A_SPRI_238_200507
47K SNPs


title: liver, Field, 207097260014_R05C02

description:
Liver methylome in rewilded mice
207097260014_R05C02


title: peanut-XN_SY01_P1_E03_180926C_SPRI-053_210107

description:
XN_SY01_P1_E03_180926C_SPRI-053_210107
47K SNPs


title: Cortical_neuron_H3K4me1_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207097260014_R06C02

description:
Liver methylome in rewilded mice
207097260014_R06C02


title: 85 HT (18c-1-54)

source_name: hypothalamus

value: hypothalamus


title: peanut-XN_SY01_P1_E03_180926A_SPRI_111_200507

description:
XN_SY01_P1_E03_180926A_SPRI_111_200507
47K SNPs


title: Cortical_neuron_H3K4me1_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Cortical_neuron_H3K4me1_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: Cortical_neuron_H3K4me3_ChIP_seq_56CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: 19 HT (18c-1-53)


title: peanut-XN_SY01_P1_E02_180926A_SPRI_237_200507

description:
XN_SY01_P1_E02_180926A_SPRI_237_200507
47K SNPs


title: liver, Field, 207097260014_R04C02

description:
Liver methylome in rewilded mice
207097260014_R04C02


title: WT HT (18c-1-52)


title: Cortical_neuron_H3K4me3_ChIP_seq_56CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: Cortical_neuron_H3K4me3_ChIP_seq_22CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_E01_180926A_SPRI_110_200507

description:
XN_SY01_P1_E01_180926A_SPRI_110_200507
47K SNPs


title: liver, Field, 207097260056_R01C02

description:
Liver methylome in rewilded mice
207097260056_R01C02


title: Cortical_neuron_H3K4me3_ChIP_seq_22CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207097260014_R03C02

description:
Liver methylome in rewilded mice
207097260014_R03C02


title: Cortical_neuron_H3K4me3_ChIP_seq_56CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Field, 207097260014_R03C01

description:
Liver methylome in rewilded mice
207097260014_R03C01


title: Cortical_neuron_H3K4me3_ChIP_seq_72CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: mouse CB--8568 (18A-2-9)

value: cerebellum


title: liver, Field, 207097260014_R02C01

description:
Liver methylome in rewilded mice
207097260014_R02C01


title: peanut-XN_SY01_P1_E01_180926C_SPRI-052_210107

description:
XN_SY01_P1_E01_180926C_SPRI-052_210107
47K SNPs


title: liver, Field, 207097260014_R01C01

description:
Liver methylome in rewilded mice
207097260014_R01C01


title: mouse CB--8566 (18A-2-8)


title: wt 84 HT (18c-1-55)


title: liver, Lab, 206402260035_R01C01

description:
Liver methylome in lab mice
206402260035_R01C01

value: Lab


title: peanut-XN_SY01_P1_D24_180926A_SPRI_469_200507

description:
XN_SY01_P1_D24_180926A_SPRI_469_200507
47K SNPs


title: liver, Field, 207097260014_R04C01

description:
Liver methylome in rewilded mice
207097260014_R04C01


title: mouse CB--4723 (18A-2-6)

value: HOM


title: peanut-XN_SY01_P1_D23_180926A_SPRI_337_200507

description:
XN_SY01_P1_D23_180926A_SPRI_337_200507
47K SNPs


title: Cortical_neuron_H3K4me3_ChIP_seq_20CAG_rep2_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: peanut-XN_SY01_P1_D22_180926A_SPRI_468_200507

description:
XN_SY01_P1_D22_180926A_SPRI_468_200507
47K SNPs


title: Cortical_neuron_H3K4me3_ChIP_seq_20CAG_rep3_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D21_180926A_SPRI_336_200507

description:
XN_SY01_P1_D21_180926A_SPRI_336_200507
47K SNPs


title: Cortical_neuron_H3K4me3_ChIP_seq_20CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: mouse CB--4721 (18A-2-4)


title: mouse CB--4722 (18A-2-5)


title: liver, Lab, 206402260027_R01C01

description:
Liver methylome in lab mice
206402260027_R01C01


title: liver, Lab, 206402260031_R03C01

description:
Liver methylome in lab mice
206402260031_R03C01


title: Cortical_neuron_H3K4me3_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D20_180926A_SPRI_467_200507

description:
XN_SY01_P1_D20_180926A_SPRI_467_200507
47K SNPs


title: liver, Lab, 206402260003_R01C02

description:
Liver methylome in lab mice
206402260003_R01C02


title: mouse CB--4720 (18A-2-3)


title: Cortical_neuron_H3K4me3_ChIP_seq_22CAG_rep1_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D19_180926A_SPRI_335_200507

description:
XN_SY01_P1_D19_180926A_SPRI_335_200507
47K SNPs


title: Cortical_neuron_H3K4me3_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Lab, 206250300036_R05C01

description:
Liver methylome in lab mice
206250300036_R05C01


title: mouse CB--4719 (18A-2-2)


title: Diff-3-29 (18A-2-12)

source_name: In vitro differentiated neuron

value: In vitro differentiated neuron


title: liver, Lab, 206250300033_R05C01

description:
Liver methylome in lab mice
206250300033_R05C01


title: peanut-XN_SY01_P1_D18_180926A_SPRI_465_200507

description:
XN_SY01_P1_D18_180926A_SPRI_465_200507
47K SNPs

value: leaf


title: Cortical_neuron_H3K4me3_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Cortical_neuron_H3K4me3_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: Cortical_neuron_H3K27Ac_ChIP_seq_72CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D17_180926A_SPRI_334_200507

description:
XN_SY01_P1_D17_180926A_SPRI_334_200507
47K SNPs


title: peanut-XN_SY01_P1_D16_180926A_SPRI_464_200507

description:
XN_SY01_P1_D16_180926A_SPRI_464_200507
47K SNPs


title: Cortical_neuron_H3K27Ac_ChIP_seq_72CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: Diff-9-29 (18A-2-10)


title: Cortical_neuron_H3K27Ac_ChIP_seq_72CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Lab, 206250300029_R01C02

description:
Liver methylome in lab mice
206250300029_R01C02

value: Liver


title: liver, Lab, 206250300028_R01C01

description:
Liver methylome in lab mice
206250300028_R01C01


title: mouse CB-0076 (18A-2-1)

value: WT


title: Diff-3-J1 (18A-2-11)


title: liver, Lab, 206130600021_R01C01

description:
Liver methylome in lab mice
206130600021_R01C01


title: peanut-XN_SY01_P1_D14_180926A_SPRI_461_200507

description:
XN_SY01_P1_D14_180926A_SPRI_461_200507
47K SNPs


title: Cortical_neuron_H3K27Ac_ChIP_seq_56CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: Diff-12-29 (18A-1-5)


title: Cortical_neuron_H3K27Ac_ChIP_seq_56CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D13_180926A_SPRI_332_200507

description:
XN_SY01_P1_D13_180926A_SPRI_332_200507
47K SNPs


title: Diff-9-J1 (18A-1-3)


title: Diff-12-J1 (18A-1-4)


title: Cortical_neuron_H3K27Ac_ChIP_seq_56CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: liver, Lab, 206102340052_R01C02

description:
Liver methylome in lab mice
206102340052_R01C02


title: peanut-XN_SY01_P1_D12_180926A_SPRI_459_200507

description:
XN_SY01_P1_D12_180926A_SPRI_459_200507
47K SNPs


title: liver, Lab, 206102340052_R01C01

description:
Liver methylome in lab mice
206102340052_R01C01


title: peanut-XN_SY01_P1_D11_180926A_SPRI_331_200507

description:
XN_SY01_P1_D11_180926A_SPRI_331_200507
47K SNPs


title: peanut-XN_SY01_P1_D10_180926A_SPRI_458_200507

description:
XN_SY01_P1_D10_180926A_SPRI_458_200507
47K SNPs


title: Cortical_neuron_H3K27Ac_ChIP_seq_22CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D09_180926A_SPRI_329_200507

description:
XN_SY01_P1_D09_180926A_SPRI_329_200507
47K SNPs


title: BRM_KO 50nM ATAC-seq rep1

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

description: Library name: BEAS2B_KO_50nM_1

data_processing:
The raw reads with sequencing adaptors or low-quality ends from reads were trimmed by trim_galore.
The cleaned reads were aligned to human GRCh38 genome via bowtie2.
The bam files were sorted by samtools. Duplicates were marked and removed by Picard, and then, MACS2 was used to call significant peaks with parameters “-f BAMPE --keep-dup all -g mm -q 0.05 --broad --max-gap 200”.
For IGV visualization of the signals, the read coverage was normalized by reads per kilobase per million (RPKM) via bamCoverage.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: cell line

extract_protocol:
Cells were treated homemade pAG-MNase and antibody, then digested DNA was enriched.
NEBNext Ultra II DNA Library Prep Kit for llumina was used for library contrucation following manufacture’s protocol.

treatment_protocol: Cells were treated with dTAG13 by completely replacing the culture medium.

value: cell line

value: human bronchial epithelial cell

value: Brm Knockout

value: 50nM dTag


title: liver, Lab, 206130600039_R03C01

description:
Liver methylome in lab mice
206130600039_R03C01

value: female


title: peanut-XN_SY01_P1_D15_180926A_SPRI_333_200507

description:
XN_SY01_P1_D15_180926A_SPRI_333_200507
47K SNPs


title: mouse CB-0086 (18A-1-1)


title: BRM_KO 50nM ATAC-seq rep2

description: Library name: BEAS2B_KO_50nM_2


title: NPC-9-J1 (17G-1-9)

source_name: NPC

value: NPC


title: BRM_KO 30nM ATAC-seq rep2

description: Library name: BEAS2B_KO_30nM_2

value: 30nM dTag


title: Cortical_neuron_H3K27Ac_ChIP_seq_20CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: 20CAG control


title: NPC-12-29 (17G-1-8)

value: hom


title: mouse CB--8565 (18A-2-7)

value: cerebellum


title: BRM_KO 30nM ATAC-seq rep1

description: Library name: BEAS2B_KO_30nM_1


title: Cortical_neuron_H3K27Ac_ChIP_seq_20CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D08_180926A_SPRI_456_200507

description:
XN_SY01_P1_D08_180926A_SPRI_456_200507
47K SNPs


title: NPC-12-J1 (17G-1-7)

value: wt


title: Cortical_neuron_H3K27Ac_ChIP_seq_22CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: peanut-XN_SY01_P1_D07_180926A_SPRI_328_200507

description:
XN_SY01_P1_D07_180926A_SPRI_328_200507
47K SNPs


title: mouse CB-0088 (18A-1-2)


title: Cortical_neuron_H3K27Ac_ChIP_seq_20CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: mouse CB-0088 (17G-1-18)


title: peanut-XN_SY01_P1_D06_180926A_SPRI_455_200507

description:
XN_SY01_P1_D06_180926A_SPRI_455_200507
47K SNPs


title: Cortical_neuron_H3K27Ac_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: HTT KO


title: Cortical_neuron_H3K27Ac_ChIP_seq_22CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: BRM_KO 10nM ATAC-seq rep1

description: Library name: BEAS2B_KO_10nM_1

value: 10nM dTag


title: peanut-XN_SY01_P1_D05_180926A_SPRI_326_200507

description:
XN_SY01_P1_D05_180926A_SPRI_326_200507
47K SNPs

value: leaf


title: mouse CB-0087 (17G-1-17)


title: Cortical_neuron_H3K27Ac_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: BRM_KO 100nM ATAC-seq rep2

description: Library name: BEAS2B_KO_100nM_2

value: 100nM dTag


title: mouse CB-0086 (17G-1-16)


title: Cortical_neuron_H3K27Ac_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Cortical_neuron_H3K27Ac_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: BRM_KO 100nM ATAC-seq rep1

description: Library name: BEAS2B_KO_100nM_1

value: cell line


title: peanut-XN_SY01_P1_D03_180926A_SPRI_325_200507

description:
XN_SY01_P1_D03_180926A_SPRI_325_200507
47K SNPs


title: peanut-XN_SY01_P1_D02_180926A_SPRI_453_200507

description:
XN_SY01_P1_D02_180926A_SPRI_453_200507
47K SNPs


title: mouse CB-0082 (17G-1-15)


title: BRM_KO 1000nM ATAC-seq rep2

description: Library name: BEAS2B_KO_1000nM_2

value: human bronchial epithelial cell

value: 1000nM dTag


title: BRM_KO 1000nM ATAC-seq rep1

description: Library name: BEAS2B_KO_1000nM_1

value: Brm Knockout


title: Cortical_neuron_H3K27me3_ChIP_seq_72CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Cortical_neuron_H3K27me3_ChIP_seq_72CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: mouse CB-0076 (17G-1-13)


title: BRM_KO 0nM ATAC-seq rep1

description: Library name: BEAS2B_KO_0nM_1

value: 0nM dTag


title: NPC-3-29 (17G-1-12)

value: NPC


title: Cortical_neuron_H3K27me3_ChIP_seq_72CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_D01_180926A_SPRI_324_200507

description:
XN_SY01_P1_D01_180926A_SPRI_324_200507
47K SNPs


title: peanut-XN_SY01_P1_C24_180926A_SPRI_236_200507

description:
XN_SY01_P1_C24_180926A_SPRI_236_200507
47K SNPs


title: Cortical_neuron_H3K27me3_ChIP_seq_56CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_C23_180926A_SPRI_109_200507

description:
XN_SY01_P1_C23_180926A_SPRI_109_200507
47K SNPs


title: WT 1000nM ATAC-seq rep2

description: Library name: BEAS2B_WT_1000nM_2

value: WT


title: peanut-XN_SY01_P1_D04_180926A_SPRI_454_200507

description:
XN_SY01_P1_D04_180926A_SPRI_454_200507
47K SNPs


title: BRM_KO 0nM ATAC-seq rep2

description: Library name: BEAS2B_KO_0nM_2


title: NPC-9-29 (17G-1-10)


title: NPC-3-J1 (17G-1-11)


title: Cortical_neuron_H3K27me3_ChIP_seq_56CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: WT 1000nM ATAC-seq rep1

description: Library name: BEAS2B_WT_1000nM_1


title: peanut-XN_SY01_P1_C22_180926A_SPRI_235_200507

description:
XN_SY01_P1_C22_180926A_SPRI_235_200507
47K SNPs


title: mouse CB-0077 (17G-1-14)


title: peanut-XN_SY01_P1_C21_180926C_SPRI-047_210107

description:
XN_SY01_P1_C21_180926C_SPRI-047_210107
47K SNPs


title: WT 0nM ATAC-seq rep1

description: Library name: BEAS2B_WT_0nM_1


title: Cortical_neuron_H3K27me3_ChIP_seq_22CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: J1-ES-2 (17F-6-40)

source_name: ESC

value: ESC


title: WT 0nM ATAC-seq rep2

description: Library name: BEAS2B_WT_0nM_2


title: 29-ES-2 (17F-6-41)

value: hom


title: peanut-XN_SY01_P1_C21_180926A_SPRI_107_200507

description:
XN_SY01_P1_C21_180926A_SPRI_107_200507
47K SNPs


title: peanut-XN_SY01_P1_C20_180926A_SPRI_234_200507

description:
XN_SY01_P1_C20_180926A_SPRI_234_200507
47K SNPs


title: BRM_KO MED1 Cut&RUN rep2

description: Library name: KO_MED1_2

data_processing:
The raw reads with sequencing adaptors or low-quality ends from reads were trimmed by trim_galore.
The cleaned reads were aligned to human GRCh38 genome via bowtie2.
The bam files were sorted by samtools. Duplicates were marked and removed by Picard, and then, MACS2 was used to call significant peaks with parameters “-f BAMPE --keep-dup all -g mm -q 0.05 --broad --max-gap 200”.
For IGV visualization of the signals, the read coverage was normalized by reads per kilobase per million (RPKM) via bamCoverage.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

tag: targeted protein


title: Cortical_neuron_H3K27me3_ChIP_seq_22CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: ES-29 (17B-01-09)


title: Cortical_neuron_H3K27me3_ChIP_seq_22CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_C23_180926C_SPRI-048_210107

description:
XN_SY01_P1_C23_180926C_SPRI-048_210107
47K SNPs


title: ES-J1 (17B-01-08)


title: Cortical_neuron_H3K27me3_ChIP_seq_20CAG_rep2_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 20CAG control


title: peanut-XN_SY01_P1_C19_180926C_SPRI-046_210107

description:
XN_SY01_P1_C19_180926C_SPRI-046_210107
47K SNPs


title: BRM_KO H3K4me3 Cut&RUN rep2

description: Library name: KO_H3K4me3_2


title: Cortical_neuron_H3K27me3_ChIP_seq_20CAG_rep3_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: NPC-91-3 (17B-01-07)


title: BRM_KO MED1 Cut&RUN rep1

description: Library name: KO_MED1_1


title: BRM_KO H3K4me3 Cut&RUN rep1

description: Library name: KO_H3K4me3_1


title: NPC-18-5 (17B-01-05)

value: het


title: BRM_KO H3K4me1 Cut&RUN rep2

description: Library name: KO_H3K4me1_2


title: peanut-XN_SY01_P1_C19_180926A_SPRI_106_200507

description:
XN_SY01_P1_C19_180926A_SPRI_106_200507
47K SNPs


title: peanut-XN_SY01_P1_C18_180926A_SPRI_233_200507

description:
XN_SY01_P1_C18_180926A_SPRI_233_200507
47K SNPs


title: Cortical_neuron_H3K27me3_ChIP_seq_56CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_C17_180926A_SPRI_105_200507

description:
XN_SY01_P1_C17_180926A_SPRI_105_200507
47K SNPs


title: Cortical_neuron_H3K27me3_ChIP_seq_20CAG_rep1_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: NPC-29-5 (17B-01-06)


title: Cortical_neuron_H3K27me3_ChIP_seq_HTT_KO_rep2_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: peanut-XN_SY01_P1_C17_180926C_SPRI-045_210107

description:
XN_SY01_P1_C17_180926C_SPRI-045_210107
47K SNPs


title: NPC-J1-5 (17B-01-04)

value: wt


title: Cortical_neuron_H3K27me3_ChIP_seq_HTT_KO_rep3_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: BRM_KO H3K4me1 Cut&RUN rep1

description: Library name: KO_H3K4me1_1


title: NPC-29-4 (17B-01-03)


title: BRM_KO H3K27Ac Cut&RUN rep2

description: Library name: KO_H3K27Ac_2


title: NPC-18-4 (17B-01-02)


title: BRM_KO 10nM ATAC-seq rep2

description: Library name: BEAS2B_KO_10nM_2


title: BRM_KO H3K27Ac Cut&RUN rep1

description: Library name: KO_H3K27Ac_1


title: peanut-XN_SY01_P1_C16_180926A_SPRI_232_200507

description:
XN_SY01_P1_C16_180926A_SPRI_232_200507
47K SNPs


title: Input DNA of WT MCF-7

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Input DNA of WT MCF-7

data_processing:
Quality control of the ChIP-Seq reads was performed using FastQC in default settings
ChIP-Seq read alignment as performed using Bowtie2 v2.2.7 (Langmead et al., 2012) with options --local and alignment files sorted and converted to .bam using samtools v1.3 (Li et al., 2009).
Peak calling was performed using the function findPeaks of HOMER v4.11 with option style parameter equal to histone (Heinz et al., 2010).
A reference cistrome for GPS2 and HDAC3 proteins for the wild-type condition was defined using the function mergePeaks of HOMER with parameter -d equal to given. Peaks obtained on the chromosome Y and noncanonical chromosomes were removed.
For each peak, the enrichment of GPS2 IP with respect to the input experiments was computed using the function getDifferentialPeaks of HOMER. The same function was used to compute the differential change of ChIP enrichment between the GPS2 KO experiments and those obtained in the WT condition. A peak was defined as differential enriched if associated with a p-value lower than 0.05. Between the two biological replicates of the GPS2 ChIP-Seq, the signal log2FC was averaged while the p-values were combined using Fisher's method implemented in the sumlog function of the metap R package.
Assembly: hg38
Supplementary files format and content: GPS2 and HDAC3 ChIP-Seq peaks in WT MCF-7

growth_protocol: MCF-7 cell lines were cultured in high glucose Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum.

extract_protocol:
MCF-7 cells were cross-linked with formaldehyde 1% for 10 minutes at room temperature. Cells were lysated and sonicated for 2 cycles of 10 minutes (max power 30 s on 30 s off) to reduce DNA length to between 200 and 500 bp. Cross-linked material was immunoprecipitated with 1-5 μg of the specific antibody overnight at 4°C and followed by incubation with protein A-sepharose beads for 1 h to collect the immunoprecipitated complexes. Collected immunocomplexes were washed with 500 μL of respectively Low Salt Wash Buffer (150 mM NaCl, Tris-HCl pH 8 20 mM, EDTA 2mM, Triton-X 1% and SDS 0.1%) High Salt Wash Buffer (500 mM NaCl, Tris-HCl pH 8 20 mM, EDTA 2mM, Triton-X 1% and SDS 0.1%), LiCl Wash (0.25 M LiCl, Tris-HCl pH 8 10 mM, EDTA 1mM, Igepal 1% and Deoxicholate 1%), 1X TE (Tris-HCl pH 8 10 mM, EDTA). After washes, elution and reversion of crosslinking was performed by heating at 65°C overnight. DNA was recovered with Phenol/Chloroform.
Deep sequencing on the Illumina’s HiSeq 2000 according to the manufacturer’s instructions.

treatment_protocol: GPS2 KO MCF-7 cells were previously made in laboratory using CRISPR/Cas9-mediated genomic recombination using gRNAs against GPS2. Specifically, CRISPR-Cas9 genome editing was performed using two different sets of sgRNAs. In each case, sgRNAs targeted exons 2 and 6 of the human GPS2 sequence. The two sets of sgRNAs each targeting were cloned separately into the LentiCRISPRv2 lentiviral vector (Kindly shared by Dr. Feng Zhang, Addgene plasmid #52961). 3.5 mg of each viral plasmid was co-transfected along with packaging plasmids pCMV-VSV-G and ps.PAX2 (Addgene plasmids #8454 and #12260) into HEK293T cells using Lipofectamine 3000. Media was changed after 24 hours and viral supernatant collected at 60 h. The virus was filtered through a 0.46 μm low protein binding filter membrane and either used immediately or stored at -80°C for later use. Transduction of target cell lines was performed in a six-well plate with 1–1.5 ml of viral supernatant and 8μg/ml polybrene in DMEM with 10% FBS. Media was changed after 24 h and cells split into selection media (puromycin 2.5 μg/ml) at 48 h. The KO lines were maintained as heterogeneous pools without selection of individual clones.


title: GPS2 ChIP-Seq in WT MCF-7 - Replicate 2

description: GPS2 ChIP-Seq in WT MCF-7 - Replicate 2


title: BRM_KO BRM Cut&RUN rep1

description: Library name: KO_BRM_1

value: Brm


title: NPC-J1-4 (17B-01-01)


title: HDAC3 ChIP-Seq in WT MCF-7 - Replicate 2


title: peanut-XN_SY01_P1_C15_180926C_SPRI-044_210107

description:
XN_SY01_P1_C15_180926C_SPRI-044_210107
47K SNPs


title: BRM_KO BRM Cut&RUN rep2

description: Library name: KO_BRM_2


title: High light, 5 mM nitrate, rep 7

city: Urbana

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

data_processing:
Raw reads were filtered for low quality reads using BBDuk (BBtools, Joint Genome Institute)
Reads were aligned to the Arabidopsis thaliana (TAIR10) reference genome using STAR aligner (v2.5.3a)(Dobin et al., 2013)
Gene-level counts were obtained using featureCounts (Liao et al. 2014)
Assembly: Arabidopsis thaliana (thale cress) TAIR10
Supplementary files format and content: tab delimited file contains raw counts for each sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Surface-sterilized Arabidopsis thaliana (Col-0) seeds were vernalized for 72 h at 4°C and plated on 0.5x Murashige and Skoog (MS) media with 1% sucrose. The seedlings were transferred to 3” pots containing a 1:1 mixture of coarse calcined clay (Turface MVP, PROFILE) and fine clay, 10 days after germination.

extract_protocol:
On the 30th day after transplanting, two leaf punches were taken from each individual plant and immediately flash-frozen for RNA-sequencing. Frozen samples were powdered in 2ml tubes with 8-12 beads of Matrix D (cat #116540434 MP biomedicals) with the FastPrep-24 cryo rotor using the following program (2x 5.5m/s2 x 60 sec).
Kapa Hyper Stranded mRNA library kit (Roche)

treatment_protocol: After transfer, the plants were treated with 30 mL ½ Hoagland’s solution with nitrate concentrations of 2 mM, 5 mM, 10 mM and 20 mM. The plants were grown under three light levels with photon flux densities of 100, 250 and 500 𝜇mol m-2 s-1 under 8/16 h day/night cycle and 23/21 °C day/night temperature regime.

value: Leaf

value: High light

value: 5 mM nitrate


title: GPS2 ChIP-Seq in WT MCF-7 - Replicate 1

description: GPS2 ChIP-Seq in WT MCF-7 - Replicate 1

value: cell line


title: peanut-XN_SY01_P1_C14_180926D_SPRI-036_210107

description:
XN_SY01_P1_C14_180926D_SPRI-036_210107
47K SNPs

value: leaf


title: peanut-XN_SY01_P1_C14_180926A_SPRI_231_200507

description:
XN_SY01_P1_C14_180926A_SPRI_231_200507
47K SNPs


title: Mid light, 5 mM nitrate, rep 8

value: Mid light


title: BRM_KO BRG1 Cut&RUN rep1

description: Library name: KO_BRG1_1

value: human bronchial epithelial cell

value: Brm Knockout


title: WT BRM Cut&RUN rep2

description: Library name: WT_BRM_2


title: Cortical_neuron_H3K27me3_ChIP_seq_HTT_KO_rep1_1

description:
Library name: Cortical_neuron_H3K27me3_ChIP_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data

source_name: Human pluripotent stem cell line

value: HTT KO


title: peanut-XN_SY01_P1_C13_180926C_SPRI-043_210107

description:
XN_SY01_P1_C13_180926C_SPRI-043_210107
47K SNPs


title: peanut-XN_SY01_P1_C16_180926D_SPRI-038_210107

description:
XN_SY01_P1_C16_180926D_SPRI-038_210107
47K SNPs


title: HDAC3 ChIP-Seq in GPS2-KO MCF-7 - Replicate 2

value: GPS2 KO


title: peanut-XN_SY01_P1_C13_180926A_SPRI_103_200507

description:
XN_SY01_P1_C13_180926A_SPRI_103_200507
47K SNPs


title: GPS2 ChIP-Seq in GPS2-KO MCF-7 - Replicate 2


title: WT BRM Cut&RUN rep1

description: Library name: WT_BRM_1

value: WT


title: Low light, 5 mM nitrate, rep 8

value: Low light


title: High light, 5 mM nitrate, rep 8


title: peanut-XN_SY01_P1_C15_180926A_SPRI_104_200507

description:
XN_SY01_P1_C15_180926A_SPRI_104_200507
47K SNPs


title: peanut-XN_SY01_P1_C12_180926C_SPRI-500_210107

description:
XN_SY01_P1_C12_180926C_SPRI-500_210107
47K SNPs


title: WT BRG1 Cut&RUN rep1

description: Library name: WT_BRG1_1


title: BRM_KO BRG1 Cut&RUN rep2

description: Library name: KO_BRG1_2


title: WT BRG1 Cut&RUN rep2

description: Library name: WT_BRG1_2


title: Low light, 5 mM nitrate, rep 7


title: GPS2 ChIP-Seq in GPS2-KO MCF-7 - Replicate 1


title: peanut-XN_SY01_P1_C11_180926C_SPRI-040_210107

description:
XN_SY01_P1_C11_180926C_SPRI-040_210107
47K SNPs


title: X6170

city: Houston

first: Michael

last: Jochum

state: TX

address: 1 Baylor Plaza

department: Obstetrics and Gynecology

institute: Baylor College of Medicine

data_processing:
trimmed_PE.fastq.gz, adapter trimmed and paired-end combined sequence files for each sample.
Reads were pre-processed, and quality filtered using FastqQC (v0.11.9) and barcodes and adapters were trimmed using Trimmomatic (v0.33)25. Reads were aligned to the human transcriptome (GRCh38.p13) using STAR (v2.7.8)26. PCR duplicate reads were removed using Picard (v2.24.0)27. Unique reads were counted using HTseq (v0.11.1)28. Counts were used for differential expression analysis in R (v4.0.2) using DEseq2 (v3.12)29 relative to the healthy control placenta samples. GO Biological Processes functional enrichment analysis was done utilizing clusterProfiler (v4)30 to identify significantly enriched terms. The custom scripts used for bulk transcriptomics analyses are available at https://github.com/Aagaardlab/GDMA-Subtype-Transcriptomics.
Assembly: GRCh38.p13
Supplementary files format and content: count_matrix.tsv, a pre-processed htseq raw counts matrix used as input for DESeq2 analysis.

source_name: Placenta

extract_protocol:
RNA was extracted from placental tissue as previously described.24 The Machery Nagel Nucleospin II kit was used to extract RNA from each sample and samples were stored at -80°C. Each sample was analyzed for quality control on the Agilent Bioanalyzer, with a minimum RNA Integrity Number (RIN) of 4.0 accepted for transcriptomic analysis. For each library, mRNA was purified from 10µg of total RNA using the DynaBeads mRNA Purification Kit (Invitrogen) and fragmented using the RNA Fragmentation Reagents (Ambion). Double-stranded cDNA was synthesized from fragmented mRNA using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and Random Hexamer primers (50ng/ul, Invitrogen). cDNA libraries were prepared according to the manufacturer’s protocol (TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina Hiseq 2000.
For each library, mRNA was purified from 10µg of total RNA using the DynaBeads mRNA Purification Kit (Invitrogen) and fragmented using the RNA Fragmentation Reagents (Ambion). Double-stranded cDNA was synthesized from fragmented mRNA using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and Random Hexamer primers (50ng/ul, Invitrogen). cDNA libraries were prepared according to the manufacturer’s protocol (TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina Hiseq 2000.

value: Placenta

value: Heterogeneous

tag: disease state

value: UNK

tag: diabetes subtype


title: High light, 20 mM nitrate, rep 8

value: 20 mM nitrate


title: X6171


title: X6162


title: peanut-XN_SY01_P1_C10_180926C_SPRI-496_210107

description:
XN_SY01_P1_C10_180926C_SPRI-496_210107
47K SNPs


title: High light, 20 mM nitrate, rep 7


title: X6157


title: X6153


title: scRNA-seq, spleen

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: spleen
10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment was done using the Cell Ranger software (https://www.10xgenomics.com/support/jp/software/cell-ranger/8.0/getting-started/cr-what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv-gz, matrix.mtx.gz

source_name: Spleen

extract_protocol:
Kidneys were dissected into small fragments and incubated at 37 °C for 40 min in RPMI 1640 Medium (Thermo Fisher) containing 10% heat inactivated FBS, 1% P/S, 0.4 µg/ml Collagenase D (Roche, Basel, Switzerland) and 0.2 µg/ml DNAse (Roche). Following this, tissue was dissociated using the GentleMACS Dissociator and C-Tubes (both Miltenyi Biotec) and leukocytes were isolated using a gradient centrifugation with 37 % Percoll (GE Healthcare). After the centrifugation, cells were washed with DPBS (Gibco). T cells were sorted by Fluorescence-activated cell sorting (FACS) for CD3+ T cells. From the spleen and blood of nephritic mice, erythocytes were removed by a lysis buffer containing 155 mM NH4Cl, 10 mM KHCO3, and 10 µM EDTA at a pH of 7.2. After washing, CD45+ cells were sorted by FACS for CD3+ and CD3- cells. Twenty thousands of CD45+CD3+ and CD45+CD3- cells were used for scRNA-seq analysis.
Cells were loaded on a 10x Chromium single cell instrument. All steps were performed according to standard protocol of the Chromium single cell 5’ v2 kit to generate high-quality cDNA libraries.

value: Spleen


title: scRNA-seq, T-cells, kidney

description:
Library name: kidney
10x Genomics

source_name: Kidney

value: Kidney

value: T-cell


title: Mid light, 5 mM nitrate, rep 7

value: Leaf

value: 5 mM nitrate


title: Mid light, 20 mM nitrate, rep 8


title: Input DNA of GPS2-KO MCF-7

description: Input DNA of GPS2-KO MCF-7

value: cell line


title: X6151


title: peanut-XN_SY01_P1_C11_180926A_SPRI_101_200507

description:
XN_SY01_P1_C11_180926A_SPRI_101_200507
47K SNPs

value: leaf


title: scRNA-seq, blood

description:
Library name: blood
10x Genomics

source_name: Blood

value: Blood


title: X6105


title: Multiome, 5xFAD mice, ENT, 2 months, ATAC

city: Irvine

first: Kevin

middle: T

last: Beier

state: CA

address: 825 Health Sciences Road Med Sci D320

department: Physiology and Biophysics

institute: UCI

description: Library name: mouse_5xFAD_2mo_ATAC

data_processing:
Gene expression libraries were demultiplexed and aligned to the mouse reference genome (mm10, v2020A) using CellRanger ARC (v2.0.1, 10X Genomics).
Assembly: Mouse mm10
GEX Cellranger output files:  barcode.tsv.gz,  features.tsv.gz, matrix.mtx.gz
ATAC Cellranger output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, per_barcode_metrics.csv

source_name: entorhinal cortex

extract_protocol:
From 5xFAD or wild-type mice, both on the C57BL/6 background, from 2 months or 8 months of age, animals were anesthetized under isoflurane induction and underwent cardiac perfusion with cold 1xPBS to remove blood from the brain. Brain tissue was immediately extracted, and the entorhinal cortex was freshly dissected out of each sample.
Single-nucleus ATAC-seq and RNA-seq were conducted using the 10x Multiome kit. To isolate the nuclei, tissue was homogenized using Lysis Buffer and manually disrupted using pestles, followed by a 4-minute incubation period. Samples were centrifuged at 500g for 5 minutes at 4°C, and the supernatant was discarded. Subsequently, 1 ml of Nuclei Wash and Resuspension buffer (NWR) was added and incubated for 5 minutes. The pellet was carefully resuspended using a P1000 pipette and centrifuged again at 500g for 5 minutes at 4°C. This wash-resuspension-centrifugation process was repeated twice more. After the third centrifugation, the supernatant was discarded, and 200μL of NWR buffer + 20μL 7AAD (1:100) was added and passed through a 40μm filter directly into a tube used for flow cytometry sorting. Cells were sorted at the UC Irvine Institute for Immunology Flow Cytometry Facility to remove debris and distinguish viable nuclei. Following sorting, the samples underwent a permeabilization process, which began with centrifugation at 500g for 5 minutes at 4°C. Subsequently, 100μL of 0.1X Lysis buffer was added, followed by resuspension and a 2-minute incubation. Next, 1mL of Washing Buffer was added, and the sample was centrifuged again for 5 minutes under the same conditions. Then, 500μL of Diluted Nuclei Buffer was added and carefully mixed with a pipette. Finally, the resulting sample was spun down and submitted to the UC Irvine’s Genomics Research and Technology Hub for further processing.

value: entorhinal cortex


title: peanut-XN_SY01_P1_C08_180926C_SPRI-490_210107

description:
XN_SY01_P1_C08_180926C_SPRI-490_210107
47K SNPs


title: Multiome, WT mice, ENT, 2 months, ATAC

description: Library name: mouse_WT_2mo_ATAC

value: WT, C57BL/6J


title: Mid light, 2 mM nitrate, rep 8

value: Mid light

value: 2 mM nitrate


title: Mid light, 20 mM nitrate, rep 7


title: Low light, 20 mM nitrate, rep 8

value: Low light


title: Multiome, 5xFAD mice, ENT, 8 months, GEX

description: Library name: mouse_5xFAD_8mo_GEX

molecule: nuclear RNA


title: peanut-XN_SY01_P1_C10_180926A_SPRI_229_200507

description:
XN_SY01_P1_C10_180926A_SPRI_229_200507
47K SNPs


title: peanut-XN_SY01_P1_C08_180926A_SPRI_228_200507

description:
XN_SY01_P1_C08_180926A_SPRI_228_200507
47K SNPs


title: Multiome, WT mice, ENT, 8 months, ATAC

description: Library name: mouse_WT_8mo_ATAC


title: Low light, 20 mM nitrate, rep 6


title: peanut-XN_SY01_P1_C09_180926C_SPRI-039_210107

description:
XN_SY01_P1_C09_180926C_SPRI-039_210107
47K SNPs


title: X6073

value: Placenta


title: Low light, 2 mM nitrate, rep 7


title: Multiome, 5xFAD mice, ENT, 2 months, GEX

description: Library name: mouse_5xFAD_2mo_GEX


title: Mid light, 2 mM nitrate, rep 7


title: peanut-XN_SY01_P1_C09_180926A_SPRI_098_200507

description:
XN_SY01_P1_C09_180926A_SPRI_098_200507
47K SNPs


title: X6090

value: Heterogeneous


title: High light, 2 mM nitrate, rep 7

value: High light


title: X6076

value: UNK


title: peanut-XN_SY01_P1_C12_180926A_SPRI_230_200507

description:
XN_SY01_P1_C12_180926A_SPRI_230_200507
47K SNPs


title: Multiome, 5xFAD mice, ENT, 8 months, ATAC

description: Library name: mouse_5xFAD_8mo_ATAC


title: X6070


title: X6077


title: High light, 10 mM nitrate, rep 7

value: 10 mM nitrate


title: shCdkn2a #2 shSlc39a9 #2_2

city: Pittsburgh

first: Katherine

last: Aird

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

description:
Library name: I2
Sample name match column name

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data. Quantification: FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Supplementary files format and content: .txt

source_name: Melanoma

growth_protocol: Yumm5.2 murine melanoma cells (ATCC, catalog no. CRL-3367, RRID: CVCL_JK43) were cultured in DMEM and Ham's F-12 (50/50) media (Corning, catalog no. 10-092-CV), supplemented with nonessential amino acids (Corning, catalog no. 25-025-Cl), 10% fetal bovine serum (FBS; BioWest, catalog no. S1620), and 1% Penicillin/Streptomycin (Gibco, catalog no. 15-140-122). Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using Trizol reagent (Ambion, catalog no. 15596018) and treated with DNase to eliminate genomic DNA contamination. RNA was purified and concentrated using Zymo Research columns (Zymo Research, catalog no. R1013) following the manufacturer’s protocol.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA. Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: For gene knockdown, cells were infected with shRNAs targeting Cdkn2a (shCdkn2a: hairpin #1, TRCN0000077816 and hairpin #2, TRCN0000362595), either alone or in combination with shRNAs targeting Slc39a9 (shSlc39a9: hairpin #1, TRCN0000346746 and hairpin #2, TRCN0000346750). Control cells were infected with shRNA targeting GFP (Addgene, catalog no. 110419, RRID: Addgene_110419).

value: Melanoma

value: Murine melanoma

value: shCdkn2a #2 + shSlc39a9 #2

value: shCdkn2a #2 shSlc39a9 #2


title: Multiome, WT mice, ENT, 8 months, GEX

description: Library name: mouse_WT_8mo_GEX


title: peanut-XN_SY01_P1_C07_180926C_SPRI-037_210107

description:
XN_SY01_P1_C07_180926C_SPRI-037_210107
47K SNPs


title: High light, 2 mM nitrate, rep 8

value: Leaf


title: peanut-XN_SY01_P1_C07_180926A_SPRI_097_200507

description:
XN_SY01_P1_C07_180926A_SPRI_097_200507
47K SNPs

value: leaf


title: Low light, 2 mM nitrate, rep 8


title: peanut-XN_SY01_P1_C05_180926A_SPRI_084_200507

description:
XN_SY01_P1_C05_180926A_SPRI_084_200507
47K SNPs


title: peanut-XN_SY01_P1_C04_180926C_SPRI-486_210107

description:
XN_SY01_P1_C04_180926C_SPRI-486_210107
47K SNPs


title: shCdkn2a #2 shSlc39a9 #1_3

description:
Library name: H3
Sample name match column name

value: shCdkn2a #2 + shSlc39a9 #1

value: shCdkn2a #2 shSlc39a9 #1


title: X6035


title: shCdkn2a #2 shSlc39a9 #1_2

description:
Library name: H2
Sample name match column name


title: Low light, 10 mM nitrate, rep 8


title: peanut-XN_SY01_P1_C06_180926A_SPRI_227_200507

description:
XN_SY01_P1_C06_180926A_SPRI_227_200507
47K SNPs


title: Multiome, WT mice, ENT, 2 months, GEX

description: Library name: mouse_WT_2mo_GEX

value: entorhinal cortex

value: WT, C57BL/6J


title: peanut-XN_SY01_P1_C06_180926C_SPRI-489_210107

description:
XN_SY01_P1_C06_180926C_SPRI-489_210107
47K SNPs


title: Low light, 10 mM nitrate, rep 7


title: shCdkn2a #2 shSlc39a9 #2_3

description:
Library name: I3
Sample name match column name


title: shCdkn2a #2 shSlc39a9 #1_1

description:
Library name: H1
Sample name match column name


title: X6041


title: X6033


title: X6064


title: Mid light, 10 mM nitrate, rep 8

value: Mid light


title: peanut-XN_SY01_P1_C05_180926C_SPRI-034_210107

description:
XN_SY01_P1_C05_180926C_SPRI-034_210107
47K SNPs


title: peanut-XN_SY01_P1_C03_180926C_SPRI-030_210107

description:
XN_SY01_P1_C03_180926C_SPRI-030_210107
47K SNPs


title: shCdkn2a #2 shSlc39a9 #2_1

description:
Library name: I1
Sample name match column name


title: X6040


title: High light, 20 mM nitrate, rep 6

value: 20 mM nitrate


title: peanut-XN_SY01_P1_C04_180926A_SPRI_226_200507

description:
XN_SY01_P1_C04_180926A_SPRI_226_200507
47K SNPs


title: X6039

value: Placenta


title: Mid light, 10 mM nitrate, rep 7


title: High light, 10 mM nitrate, rep 8


title: X6030

value: Heterogeneous


title: shCdkn2a #2_shControl_2

description:
Library name: G2
Sample name match column name

value: shCdkn2a #2

value: shCdkn2a #2_shControl


title: X6026

value: UNK


title: peanut-XN_SY01_P1_C02_180926C_SPRI-485_210107

description:
XN_SY01_P1_C02_180926C_SPRI-485_210107
47K SNPs


title: peanut-XN_SY01_P1_C03_180926A_SPRI_060_200507

description:
XN_SY01_P1_C03_180926A_SPRI_060_200507
47K SNPs


title: Mid light, 20 mM nitrate, rep 6


title: peanut-XN_SY01_P1_C02_180926A_SPRI_225_200507

description:
XN_SY01_P1_C02_180926A_SPRI_225_200507
47K SNPs


title: Mid light, 20 mM nitrate, rep 5


title: shCdkn2a #1 shSlc39a9 #2_3

description:
Library name: F3
Sample name match column name

value: Melanoma

value: shCdkn2a #1 + shSlc39a9 #2

value: shCdkn2a #1 shSlc39a9 #2


title: Low light, 20 mM nitrate, rep 7

value: Low light


title: High light, 20 mM nitrate, rep 5

value: Leaf

value: High light


title: X6025


title: X6022


title: peanut-XN_SY01_P1_C01_180926C_SPRI-027_210107

description:
XN_SY01_P1_C01_180926C_SPRI-027_210107
47K SNPs

value: leaf


title: shCdkn2a #2_shControl_1

description:
Library name: G1
Sample name match column name

value: Murine melanoma


title: peanut-XN_SY01_P1_B24_180926A_SPRI_452_200507

description:
XN_SY01_P1_B24_180926A_SPRI_452_200507
47K SNPs


title: shCdkn2a #1 shSlc39a9 #2_1

description:
Library name: F1
Sample name match column name


title: X6002


title: X6003


title: High light, 2 mM nitrate, rep 5

value: 2 mM nitrate


title: peanut-XN_SY01_P1_B22_180926A_SPRI_451_200507

description:
XN_SY01_P1_B22_180926A_SPRI_451_200507
47K SNPs


title: Mid light, 2 mM nitrate, rep 6


title: peanut-XN_SY01_P1_C01_180926A_SPRI_049_200507

description:
XN_SY01_P1_C01_180926A_SPRI_049_200507
47K SNPs


title: Low light, 20 mM nitrate, rep 5


title: peanut-XN_SY01_P1_B21_180926A_SPRI_322_200507

description:
XN_SY01_P1_B21_180926A_SPRI_322_200507
47K SNPs


title: High light, 2 mM nitrate, rep 6


title: shCdkn2a #2_shControl_3

description:
Library name: G3
Sample name match column name


title: shCdkn2a #1 shSlc39a9 #1_3

description:
Library name: E3
Sample name match column name

value: shCdkn2a #1 + shSlc39a9 #1

value: shCdkn2a #1 shSlc39a9 #1


title: shCdkn2a #1 shSlc39a9 #2_2

description:
Library name: F2
Sample name match column name


title: NCS82

value: diabetes


title: Mid light, 2 mM nitrate, rep 5

value: Mid light


title: peanut-XN_SY01_P1_B23_180926A_SPRI_323_200507

description:
XN_SY01_P1_B23_180926A_SPRI_323_200507
47K SNPs


title: peanut-XN_SY01_P1_B20_180926A_SPRI_450_200507

description:
XN_SY01_P1_B20_180926A_SPRI_450_200507
47K SNPs


title: peanut-XN_SY01_P1_B19_180926A_SPRI_321_200507

description:
XN_SY01_P1_B19_180926A_SPRI_321_200507
47K SNPs


title: shCdkn2a #1_shControl_1

description:
Library name: D1
Sample name match column name

value: shCdkn2a #1

value: shCdkn2a #1_shControl


title: shCdkn2a #1 shSlc39a9 #1_2

description:
Library name: E2
Sample name match column name


title: NCS36

value: Placenta

value: Heterogeneous


title: shCdkn2a #1 shSlc39a9 #1_1

description:
Library name: E1
Sample name match column name

value: Melanoma


title: NCS20


title: High light, 10 mM nitrate, rep 5

value: 10 mM nitrate


title: shCdkn2a #1_shControl_3

description:
Library name: D3
Sample name match column name


title: NCS70

value: Control


title: peanut-XN_SY01_P1_B16_180926A_SPRI_447_200507

description:
XN_SY01_P1_B16_180926A_SPRI_447_200507
47K SNPs


title: DM11


title: shCdkn2a #1_shControl_2

description:
Library name: D2
Sample name match column name


title: Low light, 2 mM nitrate, rep 6

value: Low light


title: shControl_shControl_1

description:
Library name: A1
Sample name match column name

value: Wild type


title: NCS69


title: DM10


title: peanut-XN_SY01_P1_B18_180926A_SPRI_448_200507

description:
XN_SY01_P1_B18_180926A_SPRI_448_200507
47K SNPs


title: Low light, 2 mM nitrate, rep 5

value: Leaf


title: High light, 10 mM nitrate, rep 6

value: High light


title: NCS64


title: shControl_shControl_3

description:
Library name: A3
Sample name match column name

value: Murine melanoma


title: peanut-XN_SY01_P1_B13_180926A_SPRI_317_200507

description:
XN_SY01_P1_B13_180926A_SPRI_317_200507
47K SNPs

value: leaf


title: NCS72


title: shControl_shControl_2

description:
Library name: A2
Sample name match column name


title: peanut-XN_SY01_P1_B15_180926A_SPRI_318_200507

description:
XN_SY01_P1_B15_180926A_SPRI_318_200507
47K SNPs


title: Mid light, 5 mM nitrate, rep 5

value: 5 mM nitrate


title: Mid light, 5 mM nitrate, rep 6


title: NCS65


title: peanut-XN_SY01_P1_B14_180926A_SPRI_446_200507

description:
XN_SY01_P1_B14_180926A_SPRI_446_200507
47K SNPs


title: High light, 5 mM nitrate, rep 6


title: NCS73


title: Low light, 5 mM nitrate, rep 6


title: NCS61


title: High light, 5 mM nitrate, rep 5


title: MPOA, mothers, sated

city: Bethesda

first: Ivan

middle: Cedric

last: Alcantara

state: Maryland

address: 10 Center Dr, Room 5-5832

institute: NIDDK

description: Library name: MPOA_MS

data_processing:
All libraries were demultiplexed using cellranger mkfastq
Demultiplexed data was processed using cellranger count
Assembly: mm10
Supplementary files format and content: cellranger count output files

source_name: brain tissue

extract_protocol:
Mice were anesthetized with isoflurane and then rapidly sacrificed by decapitation. Brains were extracted and sliced at 225-μm thickness using a vibratome. Slices were taken in an ice-cold high-sucrose slicing solution consisting of the following components (in mM): 87 NaCl, 75 sucrose, 25 glucose, 25 NaHCO3, 1.25 NaH2PO4, 2.5 KCl, 7.5 MgCl2, 0.5 CaCl2 and 5 ascorbic acid saturated with 95% O2/5% CO2. Slices were then enzyme-treated for ~15 min at 34°C with protease XXIII (2.5 mg/mL; Sigma) in a high-sucrose dissociation solution containing the following (in mM): 185 sucrose, 10 glucose, 30 Na2SO4, 2 K2SO4, 10 HEPES buffer, 0.5 CaCl2, 6 MgCl2, 5 ascorbic acid (pH 7.4) and 319 mOsm. Slices were washed three times with cold dissociation solution then transferred to a trypsin inhibitor/bovine serum albumin (TI/BSA) solution (10 mg/mL; Sigma) in cold dissociation solution. 7-8 slices containing the MPOA and 9-10 slices containing the ARC were obtained per group. MPOA and ARC were microdissected using ultra fine forceps and prepared for sequencing. Microdissected tissue was kept in cold TI/BSA dissociation solution until trituration. Immediately before dissociation, tissue was incubated for ~10 min at 37°C, then triturated with a series of small bore fire-polished Pasteur pipettes. Cell-suspension was kept on ice until single-cell capture. Cell viability was measured for each sample preparation using a Countess II automated cell counter (ThermoFisher) and was between the range of 67.5% to 82.3% before processing with the 10x Genomics platform61. 12,000 cells were loaded for capture onto an individual lane of a Chromium Controller (10x Genomics) for each sample. Single-cell capture, barcoding, and library preparation were performed using the 10x Chromium platform according to the manufacturer’s protocol (#CG00052) using version 3 (V3) chemistry.
The single cell suspension was obtained. The cells were counted and examined for viability with trypan blue staining using a TC-20 cell counter (Bio-Rad). About 12500 cells at average of 5×105 cells/ml live cell concentration with about 70% viability were loaded into the Single Cell Chip G to generate single cell emulsion in Chromium Controller with Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics, Cat. 1000268). Reverse transcription of mRNA and cDNA amplification were carried out following the manufacture’s instruction (10x Genomics, Cat. 1000268). The amplified cDNA was further fragmented to construct NGS libraries. The libraries were then sequenced on NovaSeq 6000 sequencer (Illumina) by the NIEHS Epigenomics and DNA Sequencing Core Laboratory with the parameters recommended in the manufacture’s instruction. Total 40,000 reads/cell were achieved for each sample.

value: brain tissue

value: neurons and glia

value: wild-type


title: peanut-XN_SY01_P1_B17_180926A_SPRI_320_200507

description:
XN_SY01_P1_B17_180926A_SPRI_320_200507
47K SNPs


title: Mid light, 10 mM nitrate, rep 5

value: Mid light


title: Low light, 5 mM nitrate, rep 5


title: peanut-XN_SY01_P1_B12_180926A_SPRI_445_200507

description:
XN_SY01_P1_B12_180926A_SPRI_445_200507
47K SNPs


title: MPOA, virgins, fasted

description: Library name: MPOA_VF


title: NCS62


title: Low light, 10 mM nitrate, rep 6


title: NCS7

value: diabetes


title: NCS63

value: Placenta


title: peanut-XN_SY01_P1_B11_180926A_SPRI_316_200507

description:
XN_SY01_P1_B11_180926A_SPRI_316_200507
47K SNPs


title: MPOA, mothers, fasted

description: Library name: MPOA_MF


title: MPOA, virgins, sated

description: Library name: MPOA_VS


title: NCS60

value: Heterogeneous


title: peanut-XN_SY01_P1_B10_180926A_SPRI_442_200507

description:
XN_SY01_P1_B10_180926A_SPRI_442_200507
47K SNPs


title: ARC, mothers, fasted

description: Library name: ARC_MF


title: Mid light, 10 mM nitrate, rep 6


title: peanut-XN_SY01_P1_B09_180926A_SPRI_315_200507

description:
XN_SY01_P1_B09_180926A_SPRI_315_200507
47K SNPs


title: ARC, mothers, sated

description: Library name: ARC_MS


title: DM2


title: ARC, virgins, fasted

description: Library name: ARC_VF


title: NCS38


title: 2-month Nmnat2 V98M/R232Q;SARM1 KO bulk sciatic nerves rep 1

city: St. Louis

first: Julie

last: Choi

state: MO

address: 4370 Duncan Avenue

department: Genetics

institute: Washington University in St. Louis

description: Library name: Nmnat2 V98M/R232Q;SARM1 KO Bulk Sciatic 1

data_processing:
Basecalling and demultiplexing with bcl2fastq, RNA-seq mapped to reference genome using STAR v2.5.1a Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5 Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2 All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size. Assembly: mm10 Supplementary files format and content: Raw expression count matrix
Assembly: Mouse mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: Raw Nmnat2 V98M/R232Q;SARM1 KO RNA count in Excel

source_name: Sciatic nerve

extract_protocol:
RNA extracted using Trizol/Chloroform extraction and RNeasy MinElute Cleanup Kit (Qiagen 74204)
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000

value: Sciatic nerve

value: Nerve cells

value: Nmnat2 V98M+/-;R232Q+/-;SARM1 KO


title: peanut-XN_SY01_P1_B08_180926A_SPRI_440_200507

description:
XN_SY01_P1_B08_180926A_SPRI_440_200507
47K SNPs


title: ARC, virgins, sated

description: Library name: ARC_VS


title: DM9


title: KO_HFD_rep2

city: Shanghai

first: Zixuan

last: Wang

state: Shanghai

address: 1665 Kongjiang Road, Shanghai, China

institute: Xin Hua Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: KO_HFD_rep2

data_processing:
Read counts mapped to exons of RefSeq-annotated genes were quantified and normalized to FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Differential gene expression analyses were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: text file of raw counts for each sample

source_name: Liver

extract_protocol:
RNA was harvested using Trizol reagent. 1 μg total RNA  was used for the construction of sequencing libraries.
Polyadenylated RNA was isolated from 1 μg of total RNA using two rounds of purification with Dynabeads™ Oligo(dT)25 magnetic beads (Thermo Fisher, Catalog #61005, USA). The enriched poly(A) RNA was subsequently fragmented into small pieces using  the NEBNext® Magnesium RNA Fragmentation Module (NEB, Catalog #E6150, USA) at 94°C for 5–7 minutes. Fragmented RNA was reverse-transcribed into first-strand cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, Catalog #1896649, USA). Second-strand cDNA synthesis was performed with E. coli DNA Polymerase I (NEB, Catalog #M0209, USA), RNase H (NEB, Catalog #M0297, USA), and dUTP Solution (Thermo Fisher, Catalog #R0133, USA) to incorporate deoxyuridine triphosphate (dUTP) into the second strand. An A-base was then added to the blunt ends of each strandpreparing them for ligation to the indexed adapters. Each adapter contains a T-base overhana for ligaling the adapter to the A-tailedfragmented DNA. Single- or dual-index adapters were ligated to the fragments, followed by size selection using AMPure XP beads. After treatment of the U-labeled second-strand DNAs with heat-labile UDG enzyme (NEB, Cat. #M0280, USA), the ligated products were amplified by PCR under the following conditions: initial denaturation at 95°C for 3 min; 8 cycles of denaturation at 98°C for 15 s, annealing at 60°C for 15 s, and extension at 72°C for 30 s; with a final extension at 72°C for 5 min. The average insert size of the final cDNA library was 300 ± 50 bp.

treatment_protocol: ATP7B-knockout mice were subjected to a high-fat diet for 24 weeks.

value: Liver

value: ATP7B knockout

value: High-fat diet for 24 weeks


title: peanut-XN_SY01_P1_B07_180926A_SPRI_314_200507

description:
XN_SY01_P1_B07_180926A_SPRI_314_200507
47K SNPs


title: Low light, 10 mM nitrate, rep 5

value: Leaf

value: Low light

value: 10 mM nitrate


title: 2-month Nmnat2 V98M/R232Q;SARM1 KO bulk sciatic nerves rep 3

description: Library name: Nmnat2 V98M/R232Q;SARM1 KO Bulk Sciatic 3


title: peanut-XN_SY01_P1_B02_180926A_SPRI_437_200507

description:
XN_SY01_P1_B02_180926A_SPRI_437_200507
47K SNPs

value: leaf


title: peanut-XN_SY01_P1_B06_180926A_SPRI_439_200507

description:
XN_SY01_P1_B06_180926A_SPRI_439_200507
47K SNPs


title: NCS5


title: Low light, 2 mM nitrate, rep 4

value: 2 mM nitrate


title: High light, 2 mM nitrate, rep 4

value: High light


title: 2-month Nmnat2 V98M/R232Q;SARM1 KO bulk sciatic nerves rep 2

description: Library name: Nmnat2 V98M/R232Q;SARM1 KO Bulk Sciatic 2


title: DM5


title: peanut-XN_SY01_P1_B05_180926A_SPRI_313_200507

description:
XN_SY01_P1_B05_180926A_SPRI_313_200507
47K SNPs


title: NCS45


title: High light, 2 mM nitrate, rep 3


title: WT_HFD_rep2

description: Library name: WT_HFD_rep2

value: Wild type


title: Mid light, 2 mM nitrate, rep 4

value: Mid light


title: peanut-XN_SY01_P1_B04_180926A_SPRI_438_200507

description:
XN_SY01_P1_B04_180926A_SPRI_438_200507
47K SNPs


title: peanut-XN_SY01_P1_B03_180926A_SPRI_312_200507

description:
XN_SY01_P1_B03_180926A_SPRI_312_200507
47K SNPs


title: KO_HFD_rep3

description: Library name: KO_HFD_rep3


title: NCS10

value: diabetes


title: High light, 5 mM nitrate, rep 3

value: 5 mM nitrate


title: DM4

value: Placenta

value: Heterogeneous


title: WT_HFD_rep1

description: Library name: WT_HFD_rep1


title: NCS74


title: peanut-XN_SY01_P1_A23_180926A_SPRI_022_200507

description:
XN_SY01_P1_A23_180926A_SPRI_022_200507
47K SNPs


title: NCS44


title: Mid light, 2 mM nitrate, rep 3


title: Mid light, 5 mM nitrate, rep 3