title: Astrocyte,WT,P30,HiCAR,rep1

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

data_processing:
reads were aligned to hg38 reference genome using bwa mem with flags -SP. Alignments were parsed and paired end tags (PET) were generated using the pairtools. PET with low mapping quality (MAPQ < 10) were filtered out. PET with the same coordinate on the genome or mapped to the same digestion fragment were removed. Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate.
Assembly: mm10

source_name: cortex

extract_protocol:
For crosslinking, cells were washed once by PBS, then treated by accutase (biolegend, #423201) for 10mins at 37°C. After removing the accutase, cells were resuspended by DMEM. Formaldehyde was added to the final concentration of 1%, incubated at room temperature for 10mins. Glycine was added to the final concentration of 0.2M, incubated at room temperature for 10 mins to quench formaldehyde.
HiCAR libraries were constructed following the method in the HiCAR manuscript.

value: cortex

value: astrocyte

value: WT

tag: timepoint


title: GES1_RG7388_24h

status: Public on Aug 13 2025

type: SRA

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with HISAT2.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Normal human gastric epithelium cell line GES1

growth_protocol: SNU-719, SNU-1, AGS, MKN45, MKN7, MKN74, TMK1, KATO-III and GES1 were grown in RPMI 1640 with 10% FBS,  penicillin-streptomycin. IM95 was grown in DMEM with 10% FBS,  penicillin-streptomycin and 10 mg/L human recombinant insulin. YCCEL1, WI-38 and IMR-90 were grown in MEM with 10% FBS,  penicillin-streptomycin and Non-Essential Amino Acids .

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

tag: stimulation

tag: time

tag: cell line


title: Astrocyte,WT,P17,HiCAR,rep1

country: South Korea

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: ChIP_Ogg1_K27_N1

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

description: Pull-down sample

data_processing:
Quality was assessed using FastQC v0.11.9 & Fastq-Screen v0.15.2
Files were mapped to GRCm38 using Bowtie2 v.2.3.5.1
Duplicates were marked using samtools markduplicates v1.10
Peak calling was performed using Epic2 (FDR cutoff of 0.05. Window and gap sizes were 100 bp, 3 gaps for H3K4me3, 200 bp and 3 gaps for H3K27me3 and 50 bp, 2 gaps for Suz12)
Reads were counted in R using the Bioconductor package DiffBind (v.3.10.1) and differential enrichment was done using edgeR (v.3.42.4)
Regions were assigned to nearest genomic feature using ChIPseeker (v1.36) in R
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-deliminted text files with counts for all replicates and genotypes within each ChIP target across consensus peaks.

source_name: Hippocampus

growth_protocol: C57BL/6N background mice in standard home-cage housing (12h light/dark, ad libitum food and water, 19-22°C, 50-50% air humidity).

extract_protocol:
Tissue was homogenized and nuclei were isolated.
Nuclei were stained with anti-NeuN mouse antibody (Millipore, #mab377), an Alexa 488 secondary antibody (Life Technologies # A11001) and Vybrant DyeCycle Ruby (Life Technologies, #V102673) and nuclei were sorted using flow cytometry.
Sorted nuclei were pelleted by centrifugation at 3.200 g for 15 minutes, transferred to Bioruptor Microtubes (Diagenode, C30010016) shearing tubes and carefully re-suspended in RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS and 1x Complete EDTA free protease inhibitor cocktail (Roche, 11873580001). Samples were incubated 10 minutes at 4°C and then sheared using a Bioruptor (Diagenode) for 4 times at 5 cycles and followed by 2 cycles at 30″ ON/OFF high power. Samples were spun down in between every 5 cycles. Sheared chromatin was cleared by centrifugation at 10.000 rpm for 10 minutes and the supernatant was stored in DNA low-binding tubes (Eppendorf, 022431021).
Sheared chromatin was pre-cleared with BSA-blocked protein G magnetic beads (Dynabeads, Invitrogen, 10004D) for 1 hour at 4°C. For every ChIP-reaction the appropriate amount of chromatin, depending on the different antibodies, was used (Supplementary Table 1). ChIP-reactions were performed by overnight incubation on a rotating wheel at 4°C in ChIP buffer (50 mM Tris-HCl at pH 8.0, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 20 mM EDTA, 1x Complete EDTA free protease inhibitor cocktail). As input control a 10% aliquot of each sheared chromatin sample was saved and stored at -80°C. Subsequently, 30 μl of BSA-blocked protein G magnetic beads were added to each ChIP-reaction and the mixture was incubated on a rotator at 4°C for 4 hours. The chromatin-bead complexes were washed twice at 4°C for 5 minutes at slow rotation (15 rpm) with ChIP buffer containing 0.1% SDS, twice with wash buffer (100 mM Tris-HCl pH 8.0, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 20 mM EDTA) and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). For reverse crosslinking, chromatin-bead complexes and 10% input controls were resuspended in 300 μl elution buffer (100 mM NaHCO3, 1% SDS) with 200 mM NaCl and incubated at 65°C overnight. On the next day, the samples were treated with 1 μl of RNAse A (Thermo Scientific, EN0531) for 1 hour at 37°C. Subsequently, 6 μl 0.5M EDTA and 1 μl Proteinase K (Roche, 3115828001) were added and the samples were incubated at 45°C for 1 hour. DNA was then purified by phenol-chloroform extraction and samples were eluted in 16 μl Tris buffer (10 mM Tris-HCl pH 8.0) in a DNA low-binding tube and stored at −80°C.
Library construction was performed by using QIAseq™ Ultralow Input Library Kits (Qiagen, 180492) according to manufacturer’s protocol and purified using AMPure XP beads (Beckman Coulter, A63880).

treatment_protocol: Animals were sacrificed by cervical dislocation at 6 months of age and hippocampi were dissected, isolated, snap-frozen in liquid nitrogen and stored at −80°C until further use.

value: NeuN + sorted nuclei

value: Hippocampus

tag: chip antibody

value: H3K27trime Ms (Abcam #ab6002)


title: GES1_Nutlin-3_24h


title: ChIP_Ogg1_K4_N3

description: Pull-down sample

value: H3K4trime Rb (Abcam #ab8580)


title: Et-OH_2

city: Beijing

first: Ye-Guang

last: Chen

state: China

address: Haidian  District

country: China

institute: Tsinghua University

description: WT small intestinal organoids

data_processing:
Reads were aligned to the GCRm38/mm10 genome using Bowtie 2 (v2.2.5) and sorted with samtools (v1.5).
mRNA expression analysis was performed using Hisat (version 2.1.0) and Ballgown (version 2.20.0).
Assembly: mm10
Supplementary files format and content: gene_fpkm_matrix_OHRNAseq.csv and gene_fpkm_matrix_RNAseq.csv: Comma-delimited text file includes FPKM values for each sample.

source_name: Small intestinal epithelium

extract_protocol:
Total RNA was extracted and purified by using TRIZOL reagent (Thermo Fisher Scientific). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.

treatment_protocol: For small intestinal organoids RNA-seq, Vill-creERT2;HBO1 fl/fl mice small intestianl crypts were isolated for organoids culture, the organoids were treated with 4-OH-tamoxifen(4-OHT) for HBO1 knock out. Et-OH treatment as the control. For colonic epithelial cells RNA-seq, the control and HBO1 KO mice were all fed with 3% DSS (MW; 36–50 kDa; MP Biomedicals) dissolved in drinking water, and both the control and HBO1 KO crypts were isolated at day 3.

value: Small intestinal epithelium

value: Small intestinal organoids

tag: treatment

value: Et-OH


title: ChIP_Ogg1_K4_N2

description: Pull-down sample


title: Astrocyte,WT,P3,HiCAR,rep1


title: GES1_DMSO_24h

value: DMSO


title: ChIP_Ogg1_K4_N1

description: Pull-down sample


title: ChIP_Ogg1_K27_N3

description: Pull-down sample


title: KATO-III_RG7388_24h

source_name: Human gastric epithelial cancer cell line KATO-III

value: KATO-III


title: Astrocyte,WT,P1,HiCAR,rep1


title: KATO-III_Nutlin-3_24h


title: ChIP_Mutyh_Input_N3

description: 10% aliquot sheared chromatin

value: Mutyh-/-


title: Skingraft, POD6, Non-Treatment, biological replicate 2, technical replicate 3

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

library_source: transcriptomic single cell

data_processing:
Sequencing outputs were demultiplexed using cellranger (6.1.2) mkfastq
Fastq files were aligned to Mus musculus mm10 reference using cellranger (6.1.2) count or multi
Assembly: Mouse reference, mm10
Supplementary files format and content: Processed data files are gzipped cellranger count output directory (sample_feature_bc_matrix or filtered_feature_bc_matrix).

source_name: skin

extract_protocol:
Freshly collected skins were minced using scissors, and suspended  in digestion buffer (RPMI with 5%v/v  fetal bovine serum, 0.3mg/mL Liberase TM (Merck) and 5U/mL DNase1) and incubated 37°C for 30minutes twice. The samples were resuspended in another digestion buffer (TrypLE Select Enzyme(Thermo Fisher Scientific) with 5U/mL DNase1) and incubated 37°C for 15minutes. The obtained cell suspensions were filtered through a 70µm cell strainer, washed in Minimum Essential Medium alpha (Thermo Fisher Scientific) with 2%v/v FBS.
Isolated skin cells were individually labeled using the 3' CellPlex Kit Set A (10x Genomics). SYTOX negative cells from each individual were sorted using the BD FACS Aria III system (BD Biosciences).Library preparation was performed according to the 10x Genomics protocol "Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing".

value: skin

tag: strain


title: Et-OH_1

description: WT small intestinal organoids


title: TMK1_RG7388_24h

source_name: Human gastric epithelial cancer cell line TMK1


title: Skingraft, POD6, Non-Treatment, biological replicate 1, technical replicate 3


title: Astrocyte,WT,E18,HiCAR,rep1


title: Astrocyte,WT,P30,HiCAR,rep2


title: KATO-III_DMSO_24h


title: ChIP_Mutyh_Input_N2

description: 10% aliquot sheared chromatin


title: Skingraft, POD6, Non-Treatment, biological replicate 2, technical replicate 2


title: Astrocyte,WT,P17,HiCAR,rep2


title: 4OH_1

description: HBO1 KO small intestinal organoids


title: Skingraft, POD6, Non-Treatment, biological replicate 1, technical replicate 2


title: Astrocyte,WT,P7,HiCAR,rep2


title: ChIP_Mutyh_Suz12_N3

description: Pull-down sample

value: Suz12 Rb (Cell Signaling #3737S)


title: ChIP_Mutyh_Suz12_N2

description: Pull-down sample


title: Astrocyte,WT,P7,HiCAR,rep1


title: Et-OH_3

description: WT small intestinal organoids


title: MKN74_RG7388_24h

source_name: Human gastric epithelial cancer cell line MKN74


title: Astrocyte,WT,P1,HiCAR,rep2


title: ChIP_Mutyh_Suz12_N1

description: Pull-down sample


title: Astrocyte,WT,E18,HiCAR,rep2


title: Skingraft, POD6, Non-Treatment, biological replicate 1, technical replicate 1


title: MKN74_Nutlin-3_24h


title: ChIP_Mutyh_K27_N3

description: Pull-down sample


title: Astrocyte,WT,E16,HiCAR,rep2


title: Skingraft, POD9, Non-Treatment, biological replicate 2, technical replicate 3


title: MKN74_DMSO_24h


title: ChIP_Mutyh_Input_N1

description: 10% aliquot sheared chromatin


title: ChIP_Mutyh_K27_N1

description: Pull-down sample


title: Skingraft, POD9, Non-Treatment, biological replicate 1, technical replicate 3


title: ChIP_Mutyh_K27_N2

description: Pull-down sample


title: Skingraft, POD6, Non-Treatment, biological replicate 2, technical replicate 1


title: TMK1_Nutlin-3_24h


title: TMK1_DMSO_24h


title: MKN7_RG7388_24h

source_name: Human gastric epithelial cancer cell line MKN7


title: ChIP_Mutyh_K4_N3

description: Pull-down sample


title: MKN7_DMSO_24h


title: Astrocyte,WT,P3,HiCAR,rep2


title: ChIP_Mutyh_K4_N2

description: Pull-down sample


title: Skingraft, POD9, Non-Treatment, biological replicate 1, technical replicate 2


title: Skingraft, POD9, Non-Treatment, biological replicate 1, technical replicate 1


title: cJUN ChIP rep2

description: Library name: cJUN ChIP rep2

data_processing:
Fastq files were aligned using bwa mem with -M -t option. Then, duplicates were removed using picard tools. Using macs2, the peaks which were enriched ChIP-seq signal was estimated by comparing with input DNA enrichment (q<0.01).
Assembly: mm10
Supplementary files format and content: bed, peak calling

source_name: Cortex

extract_protocol:
Primary astrocytes were isolated from postnatal day 0 (P0) mouse brain. Briefly, the cerebral cortices were dissected from P0 mice and enzymatically digested in trypsin-EDTA (Gibco) for 5 minutes at 37°C. Then, the cortices were mechanically dissociated through trituration in DMEM (Welgene) supplemented with 10% FBS (Welgene) and 1% penicillin/streptomycin (Gibco). After dissociation, the cell suspension was filtered through a 70μm cell strainer (SPL). The single-cell suspension was plated in T175 culture flask (SPL). After maintaining for 1 week, the flasks were shaken at 240 rpm for 10 hours to detach microglia and OPCs. The supernatant was removed, and the adherent astrocytes were detached using trypsin, and replated in culture plates for recovery. After one additional week of astrocyte culture, the glucocorticoid receptor was stimulated with 5 μM corticosterone (Sigma-Aldrich, 27840) for 24 hours and collected for further sequencing analysis. The astrocyte culture media consisted of 45% neurobasal medium (Gibco), 45% DMEM (Welgene), 10% FBS (Welgene), 1% penicillin/streptomycin (Gibco), 1 mM sodium pyruvate (Gibco), 292 μg/ml L-glutamine (Gibco), 1X SATO, and 5 ng/ml HBEGF (Sigma-Aldrich).
We collected 3 millions of astrocytes to perform ChIP-seq experiment for each TF. The collected cells were crosslinked twice: first with 2mM disuccinimidyl glutarate for 35 min, followed by 1% formaldehyde for 10 minutes, both at room temperature. The crosslinking was quenched using 1.25M glycine, and then cells were washed twice with PBS. The cells were then lysed in nucleus buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, and protease inhibitors), followed by sonication using a Covaris M220 (70 amplitude, 30-minute process time, alternating 30 seconds ON and 30 seconds OFF). Debris was removed by centrifugation, and DNA fragments were extracted and diluted ten times with dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM pH 8.1 Tris-HCl, and protease inhibitor). To conjugate TF-targeting antibody and protein A Sepharose (ThermoFisher), we added 2ug of TF antibody into 10ul beads (for NR3C1, Thermo Fisher, PA1-511A; for c-JUN, Cell Signaling Technology, #9165). The antibody-conjugated protein A Sepharose was added to the diluted sample for overnight immunoprecipitations at 4 °C. Then, the beads were washed with TSE I buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 150 mM NaCl), TSE II buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl), buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 10 mM Tris-HCl (pH 8.1) and 1 mM EDTA), three times with TE buffer (10 mM pH 8.0 Tris-HCl and 1 mM EDTA), and the eluted in elution buffer (1% SDS and 0.1 M NaHCO3). DNA was reverse-crosslinked by incubation at 65°C overnight. After RNase and Proteinase K treatment, DNA was purified and prepared for next-generation sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB). The ChIP-seq library were sequenced using DNBSEQ-G400 platform.For the data processing, sequencing reads were aligned to the mouse reference genome (GRCm38.p6) using BWA-mem. Low-quality alignments (MAPQ < 10) were removed, and PCR duplicates were eliminated using Picard (v2.6.0). The binding signal on cCREs was quantified using bedtools, counting sequencing reads that overlapped with cCREs by more than 20%.

value: Cortex

value: Astrocyte

value: GC


title: Skingraft, POD12, Non-Treatment, biological replicate 2, technical replicate 3


title: NR3C1 ChIP rep2

description: Library name: NR3C1 ChIP rep2


title: cJUN ChIP rep1

description: Library name: cJUN ChIP rep1


title: ChIP_WT_Input_N2

description: 10% aliquot sheared chromatin


title: Skingraft, POD9, Non-Treatment, biological replicate 2, technical replicate 2


title: Skingraft, POD12, Non-Treatment, biological replicate 1, technical replicate 3


title: NR3C1 ChIP rep1

description: Library name: NR3C1 ChIP rep1


title: MKN7_Nutlin-3_24h


title: Astrocyte,WT,E16,HiCAR,rep1

value: cortex

value: astrocyte


title: input_control

description: Library name: input_control


title: Skingraft, POD12, Non-Treatment, biological replicate 2, technical replicate 2


title: P30 WT ATAC rep2

description: Library name: P30 WT ATAC-seq rep2

data_processing:
ATAC-seq reads were aligned to the mm10 using bowtie2. PCR duplicates were removed and then peaks were called using macs2. Reads in peaks were counted using featurCounts.
Assembly: mm10
Supplementary files format and content: peak count matrix

extract_protocol:
Nuclei was isolated using lysis buffer including Triton-X100, NP40, Digitonin for ATAC-seq.
Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) was used for tagmentation reaction. After cleaning up using MinElute PCR Purification Kit (Qiagen), PCR amplication was done. Finally, size selection was done with AMPure XP (Beckman Coulter).

value: Cre- control


title: Skingraft, POD9, Non-Treatment, biological replicate 2, technical replicate 1


title: ChIP_WT_Suz12_N3

description: Pull-down sample

value: NeuN + sorted nuclei

value: Hippocampus

value: WT


title: P30 WT ATAC rep1

description: Library name: P30 WT ATAC-seq rep1


title: Skingraft, POD12, Non-Treatment, biological replicate 1, technical replicate 2


title: PBMCs_healthy control_sample 8

type: RNA

first: Xiuxiu

last: Ji

address: No. 1, Beiguang Street, Tongzhou District

institute: Department of Molecular Biology, Beijing Chest Hospital, Capital Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: peripheral blood mononuclear cells, healthy control, sample 8

label_protocol: Total RNA was labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from PBMCs using the miRNeasy® Mini kit (QIAGEN, Germany) according to the protocols recommended by the manufacturer.

tag: cell

value: peripheral blood mononuclear cells

tag: age

tag: gender

value: Female


title: P30 KO ATAC rep2

description: Library name: P30 KO ATAC-seq rep2

value: NR3C1 cKO


title: Skingraft, POD12, Non-Treatment, biological replicate 2, technical replicate 1


title: ChIP_WT_Suz12_N2

description: Pull-down sample


title: ChIP_WT_Input_N3

description: 10% aliquot sheared chromatin


title: ChIP_Mutyh_K4_N1

description: Pull-down sample

value: H3K4trime Rb (Abcam #ab8580)


title: PBMCs_healthy control_sample 7

source_name: peripheral blood mononuclear cells, healthy control, sample 7


title: P30 KO ATAC rep1

description: Library name: P30 KO ATAC-seq rep1


title: ChIP_WT_Suz12_N1

description: Pull-down sample


title: Skingraft, POD12, Non-Treatment, biological replicate 1, technical replicate 1


title: P0 WT ATAC rep2

description: Library name: P0 WT ATAC-seq rep2


title: PBMCs_healthy control_sample 5

source_name: peripheral blood mononuclear cells, healthy control, sample 5

value: Male


title: Skingraft, POD3, Non-Treatment, biological replicate 2, technical replicate 3


title: PBMCs_healthy control_sample 6

source_name: peripheral blood mononuclear cells, healthy control, sample 6


title: ChIP_WT_K27_N3

description: Pull-down sample

value: H3K27trime Ms (Abcam #ab6002)


title: ChIP_WT_Input_N1

description: 10% aliquot sheared chromatin


title: P0 WT ATAC rep1

description: Library name: P0 WT ATAC-seq rep1


title: Skingraft, POD3, Non-Treatment, biological replicate 1, technical replicate 3

value: skin


title: ChIP_WT_K27_N2

description: Pull-down sample


title: ChIP_WT_K27_N1

description: Pull-down sample


title: P0 KO ATAC rep2

description: Library name: P0 KO ATAC-seq rep2


title: Skingraft, POD3, Non-Treatment, biological replicate 2, technical replicate 2


title: PBMCs_healthy control_sample 3

source_name: peripheral blood mononuclear cells, healthy control, sample 3


title: ChIP_WT_K4_N3

description: Pull-down sample


title: P0 KO ATAC rep1

description: Library name: P0 KO ATAC-seq rep1


title: P30 WT RNA rep2

description: Library name: P30 WT RNA-seq rep2

data_processing:
RNA-seq reads were aligned to the mm10 using tuxedo. RNA-seq, expected count, TPM, and FPKM were calculated using a Stringtie.
Assembly: mm10
Supplementary files format and content: gene count matrix

extract_protocol:
RNA was extraced for each astrocyte sample using NucleoSpin RNA XS (Macherey-Nagel).
Amplified cDNA from total RNA was obtained using Ovation RNA-Seq System V2 (NuGEN).


title: Skingraft, POD3, Non-Treatment, biological replicate 1, technical replicate 2


title: Skingraft, POD3, Non-Treatment, biological replicate 2, technical replicate 1


title: ChIP_WT_K4_N2

description: Pull-down sample


title: PBMCs_healthy control_sample 4

source_name: peripheral blood mononuclear cells, healthy control, sample 4


title: Skingraft, POD3, Non-Treatment, biological replicate 1, technical replicate 1


title: P30 WT RNA rep1

description: Library name: P30 WT RNA-seq rep1


title: ChIP_WT_K4_N1

description: Pull-down sample


title: ChIP_DKO_Input_G2

description: 10% aliquot sheared chromatin

value: NeuN - sorted nuclei


title: P30 KO RNA rep2

description: Library name: P30 KO RNA-seq rep2

value: Cortex


title: ChIP_DKO_Input_G3

description: 10% aliquot sheared chromatin


title: PBMCs_healthy control_sample 2

source_name: peripheral blood mononuclear cells, healthy control, sample 2


title: P30 KO RNA rep1

description: Library name: P30 KO RNA-seq rep1

value: Astrocyte


title: Skingraft, POD15, Non-Treatment, biological replicate 2, technical replicate 3


title: ChIP_DKO_Input_G1

description: 10% aliquot sheared chromatin


title: P0 WT RNA rep2

description: Library name: P0 WT RNA-seq rep2


title: Skingraft, POD15, Non-Treatment, biological replicate 2, technical replicate 2


title: ChIP_DKO_Suz12_G2

description: Pull-down sample

value: Suz12 Rb (Cell Signaling #3737S)


title: Skingraft, POD15, Non-Treatment, biological replicate 1, technical replicate 3


title: PBMCs_LTBI individual_sample 4

source_name: peripheral blood mononuclear cells, LTBI individual, sample 4


title: PBMCs_healthy control_sample 1

source_name: peripheral blood mononuclear cells, healthy control, sample 1


title: Skingraft, POD15, Non-Treatment, biological replicate 1, technical replicate 2


title: P0 WT RNArep1

description: Library name: P0 WT RNA-seq rep1


title: PBMCs_LTBI individual_sample 7

source_name: peripheral blood mononuclear cells, LTBI individual, sample 7


title: ChIP_DKO_Suz12_G3

description: Pull-down sample

source_name: Hippocampus


title: PBMCs_LTBI individual_sample 6

source_name: peripheral blood mononuclear cells, LTBI individual, sample 6


title: P0 KO RNA rep2

description: Library name: P0 KO RNA-seq rep2


title: Skingraft, POD15, Non-Treatment, biological replicate 2, technical replicate 1

source_name: skin


title: PBMCs_LTBI individual_sample 5

source_name: peripheral blood mononuclear cells, LTBI individual, sample 5


title: ChIP_DKO_K27_G2

description: Pull-down sample


title: Skingraft, POD15, Non-Treatment, biological replicate 1, technical replicate 1


title: PBMCs_LTBI individual_sample 2

source_name: peripheral blood mononuclear cells, LTBI individual, sample 2


title: Trim21_KO_2_UV

city: Los Angeles

first: Lihong

last: Huo

state: CA

address: 8700 Beverly Blvd, Los Angeles, CA 90048

country: USA

institute: Cedars-Sinai

data_processing:
Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0) /RSEM (version 1.2.25) with default parameters, using a custom mouse GRCm38 transcriptome reference downloaded from https://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation.
Aligned reads were sorted and indexed using samtools v 1.18
Assembly: GRCm38
Supplementary files format and content: Comma separated value file containing raw read counts per sample per gene

source_name: splenocytes

extract_protocol:
spleens  were harvested following final UVB exposure. To generate a single cell suspension, spleens were passed through a 70-μM filter. RNA was isolated using TRI Reagent (Millipore Sigma). Total RNA samples were analyzed for RNA integrity on the 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA) and quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA).
Three hundred ng of total RNA Total was ribodepleted using the RiboCop Depletion Kit Human/Mouse/Rat v2 (Lexogen Inc., Greenland, NH).  Stranded RNA-Seq library construction was performed using the xGen Broad-Range RNA Library Prep Kit (Integrated DNA Technologies, Coralville, IA).  Library concentration was measured with a Qubit fluorometer (ThermoFisher Scientific), and library size was evaluated on a 4200 TapeStation (Agilent Technologies). Multiplexed libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75bp single-end sequencing. On average, approximately 50 million reads were generated from each sample.

treatment_protocol: Eight-week-old wild-type (WT) and Trim21-/- were shaved dorsally prior to UVB exposure. Mice were allowed to move freely in their cage during UVB exposure and mice were treated with/without UVB 100 mJ/cm2 for one or three weeks.

value: splenocytes

value: Trim21 KO


title: RNA_DKO_Glia_R3

description: NeuN+ : Lanes 2 & 4, NeuN- : Lanes 1 & 3

data_processing:
Quality was assessed using FastQC v0.11.9 & Fastq-Screen v0.15.2
Files were mapped to GRCm38 using Hisat2 (v.2.1.0) and processed to BAMs using samtools (v.1.10)
Reads were counted using featureCounts from Rsubread in R (v.4.3.2) and the Ensembl GRCm38 relase 102 annotation.
Counts were analyzed for differential expression analysis in R using edgeR (v.3.42.4)
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-deliminted text files with counts for all replicates and genotypes with gene symbols.

molecule: nuclear RNA

extract_protocol:
Tissue was homogenized and nuclei were isolated.
Nuclei were stained with anti-NeuN mouse antibody (Millipore, #mab377), an Alexa 488 secondary antibody (Life Technologies # A11001) and Vybrant DyeCycle Ruby (Life Technologies, #V102673) and nuclei were sorted using flow cytometry.
RNA was extracted using the RNeasy® FFPE Kit (Qiagen, 73504), according to manufacturer’s protocol.
Library was constructed using the SMARTer® Stranded Total RNA-Seq Kit (Takara, 634485) according to the manufacturer's instructions.


title: ChIP_DKO_K27_G3

description: Pull-down sample


title: RNA_DKO_Glia_R2


title: PBMCs_LTBI individual_sample 1

source_name: peripheral blood mononuclear cells, LTBI individual, sample 1


title: WT_2_UV


title: RNA_DKO_Glia_R1


title: Trim21_KO_1_UV


title: PBMCs_LTBI individual_sample 3

source_name: peripheral blood mononuclear cells, LTBI individual, sample 3


title: ChIP_DKO_K4_G2

description: Pull-down sample


title: PBMCs_LTBI individual_sample 8

source_name: peripheral blood mononuclear cells, LTBI individual, sample 8


title: RNA_Ogg1_Glia_R3


title: RNA_Ogg1_Glia_R2


title: Homo3_plt

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Blood

extract_protocol:
Total RNA was extracted from cells with TRIzol reagent and a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: Blood

value: thrombocyte

value: Beta3(R734C) homozygous KI


title: PBMCs_TB patient_sample 7

source_name: peripheral blood mononuclear cells, TB patient, sample 7


title: ChIP_DKO_K4_G1

description: Pull-down sample

value: Hippocampus


title: jazD, ctrl, 24hr, rep3

city: Los Alamos

first: Leah

last: Johnson

state: NM

address: 3917 W Road

institute: Los Alamos National Laboratory

data_processing:
Sequencing and data preprocessing was performed by BGI Genomics to provide adaptor-trimmed, high-quality reads.
Raw sequencing reads were mapped to TAIR10 gene models by RSEM (version 1.3.3) (Li and Dewey 2011).
mRNA abundances for all Arabidopsis genes were expressed as transcripts per million (TPM). DESeq2 (version 3.12) was used to normalize expected counts from RSEM and to determine differential gene expression by comparing normalized counts in mock-treated samples to the coronatine-treated samples at each time point (Love et al. 2014).
Assembly: TAIR10
Supplementary files format and content: TPM_Matrix.csv contains counts data in comma-delimited matrix table for read counts for all samples, as determined by RSEM
Supplementary files format and content: Compiled_jazD_RNAseqTimeCourse_DifferentialExpression.xlsx contains the compiled differential expression data determined by DESeq2. Each tab contains one time point.

organism: Arabidopsis thaliana

source_name: Whole leaf

growth_protocol: Trays of soil-grown plants were covered with a transparent plastic dome for 7 days after seed sowing. Plants were maintained under a 16-h light (100 μE m-2 s-1) and 8-h dark photoperiod at 20 ºC. Plants were 26 days old at time of treatment.

extract_protocol:
Total RNA was isolated using a Macherey-Nagel NucleoSpin RNA plant kit with Macherey-Nagel on-column DNase treatment to remove genomic DNA. RNA integrity was assessed with a 2100 Bioanalyzer (Agilent Bioanalyzer) and all samples had an integrity score of at least 6.5.
Barcoded sequencing libraries were prepared using the BGI transcriptome kit. Normalized libraries were sequenced on the BGI DNBseq platform.

treatment_protocol: Coronatine-treated samples were sprayed with a 5 µM solution of coronatine suspended in water. Mock treated samples were sprayed with water. Samples were harvested and flash-frozen in liquid nitrogen, then stored at -80 C until RNA extraction.

value: Whole leaf

tag: ecotype

value: jazD

value: Water


title: RNA_Ogg1_Glia_R1


title: Homo2_plt


title: jazD, ctrl, 24hr, rep2


title: ChIP_DKO_Suz12_G1

description: Pull-down sample


title: PBMCs_TB patient_sample 6

source_name: peripheral blood mononuclear cells, TB patient, sample 6

value: peripheral blood mononuclear cells


title: P0 KO RNA rep1

description: Library name: P0 KO RNA-seq rep1

source_name: Cortex

value: NR3C1 cKO


title: PBMCs_TB patient_sample 4

source_name: peripheral blood mononuclear cells, TB patient, sample 4

value: Female


title: PBMCs_TB patient_sample 8

source_name: peripheral blood mononuclear cells, TB patient, sample 8

value: Male


title: PBMCs_TB patient_sample 5

source_name: peripheral blood mononuclear cells, TB patient, sample 5


title: ChIP_Ogg1_Input_G2

description: 10% aliquot sheared chromatin

source_name: Hippocampus

value: NeuN - sorted nuclei


title: RNA_Mutyh_Glia_R3

value: Mutyh-/-


title: jazD, ctrl, 24hr, rep1


title: PBMCs_TB patient_sample 2

source_name: peripheral blood mononuclear cells, TB patient, sample 2


title: jazD, ctrl, 12hr, rep3


title: WT2_plt

value: wild type


title: ChIP_Ogg1_Input_G1

description: 10% aliquot sheared chromatin


title: WT_1_UV

value: WT


title: jazD, ctrl, 12hr, rep2


title: PBMCs_TB patient_sample 1

source_name: peripheral blood mononuclear cells, TB patient, sample 1


title: RNA_Mutyh_Glia_R1


title: RNA_WT_Glia_R3


title: WT1_plt


title: ChIP_Ogg1_Suz12_G2

description: Pull-down sample

value: Suz12 Rb (Cell Signaling #3737S)


title: D19_r2 Stage-based media-v2 mKPA, Replicate 2

first: Zhongwei

last: Li

address: 1425 San Pablo St

department: Keck medicine

institute: University of Southern California

description:
library name: D19_r2 mKPA 2
D19_r2 SK 2
Bulk RNA-Seq conducted by Novogene Co

data_processing:
Partek Flow Genomic Analysis Software
FASTQ files were trimmed from both ends based on a minimum read length of 25 bps and an end mininum quality score (Phred) of 20 or higher
For mouse samples, reads were aligned to mm39 - GENCODE Genes - release M28 GENCODE mm10 (release M24) using STAR 2.7.8a.
Aligned reads were quantified to the Partek E/M annotation model. Gene counts were normalized using TMM.
Assembly: mm39
Supplementary files format and content: Tab-delimited excel file include TMM for each Sample

source_name: Mouse kidney progenitor assembloid (mKPA)

growth_protocol: Synthetic kidneys or kidney expalnts were cultured with 10% FBS medium, Stage-based media-v0, v1 or v2, 37C, 5% CO2

extract_protocol:
Total RNA was extracted using Direct-zol RNA MicroPrep Kit/Quick-RNA Microprep Kit (Zymo Research) following manufacturer's protocols.
RNA-Seq library were constructed by NovoGene with total RNA we provided.

value: Kidney cells

value: Cultured with Stage-based media-v2


title: RNA_WT_Glia_R2


title: jazD, ctrl, 3hr, rep3


title: ChIP_Ogg1_Suz12_G1

description: Pull-down sample


title: D19_r2 Stage-based media-v2 mKPA, Replicate 1

description:
library name: D19_r2 mKPA 1
D19_r2 SK 1
Bulk RNA-Seq conducted by Novogene Co

value: Mouse kidney progenitor assembloid (mKPA)


title: RNA_WT_Glia_R1


title: jazD, ctrl, 3hr, rep2


title: ChIP_Ogg1_K27_G2

description: Pull-down sample

value: H3K27trime Ms (Abcam #ab6002)


title: D19_r1 Stage-based media-v2 mKPA, Replicate 2

description:
library name: D19_r1 mKPA 2
D19_r1 SK 2
Bulk RNA-Seq conducted by Novogene Co


title: RNA_DKO_Neuron_R3

value: NeuN + sorted nuclei

value: Hippocampus


title: jazD, ctrl, 3hr, rep1

value: Whole leaf

value: jazD


title: ChIP_Ogg1_K27_G3

description: Pull-down sample


title: D19_r1 Stage-based media-v2 mKPA, Replicate 1

description:
library name: D19_r1 mKPA 1
D19_r1 SK 1
Bulk RNA-Seq conducted by Novogene Co


title: RNA_DKO_Neuron_R2


title: jazD, ctrl, 1hr, rep3

value: Water


title: ChIP_Ogg1_K27_G1

description: Pull-down sample


title: RNA_Mutyh_Glia_R2


title: D13 Stage-based media-v2 mKPA, Replicate 2

description:
library name: D13 mKPA 2
D13 SK 2
Bulk RNA-Seq conducted by Novogene Co


title: jazD, ctrl, 12hr, rep1


title: ChIP_Ogg1_Suz12_G3

description: Pull-down sample


title: jazD, ctrl, 1hr, rep2


title: D13 Stage-based media-v2 mKPA, Replicate 1

description:
library name: D13 mKPA 1
D13 SK 1
Bulk RNA-Seq conducted by Novogene Co


title: Homo1_plt

value: Blood

value: thrombocyte

value: Beta3(R734C) homozygous KI


title: ChIP_Ogg1_K4_G3

description: Pull-down sample

value: NeuN - sorted nuclei

value: H3K4trime Rb (Abcam #ab8580)


title: RNA_Ogg1_Neuron_R3


title: jazD, ctrl, 1hr, rep1


title: D7 Stage-based media-v2 mKPA, Replicate 2

description:
library name: D7 mKPA 2
D7 SK 2
Bulk RNA-Seq conducted by Novogene Co


title: ChIP_Ogg1_Input_G3

description: 10% aliquot sheared chromatin


title: WT3_plt

value: wild type


title: RNA_Ogg1_Neuron_R2


title: jazD, ctrl, 0hr, rep3


title: ChIP_Ogg1_K4_G1

description: Pull-down sample


title: D7 Stage-based media-v2 mKPA, Replicate 1

description:
library name: D7 mKPA 1
D7 SK 1
Bulk RNA-Seq conducted by Novogene Co


title: RNA_Ogg1_Neuron_R1


title: RNA_Mutyh_Neuron_R3

value: Mutyh-/-


title: D3 Stage-based media-v2 mKPA, Replicate 2

description:
library name: D3 mKPA 2
D3 SK 2
Bulk RNA-Seq conducted by Novogene Co


title: ChIP_Mutyh_Input_G2

description: 10% aliquot sheared chromatin


title: jazD, ctrl, 0hr, rep2


title: jazD, ctrl, 0hr, rep1


title: RNA_DKO_Neuron_R1


title: ChIP_Mutyh_Input_G3

description: 10% aliquot sheared chromatin


title: RNA_Mutyh_Neuron_R2


title: ChIP_Ogg1_K4_G2

description: Pull-down sample


title: RNA_Mutyh_Neuron_R1


title: jazD, trt, 24hr, rep3

value: 5 µM coronatine


title: ChIP_Mutyh_Input_G1

description: 10% aliquot sheared chromatin


title: D19 Stage-based media-v2 explant, Replicate 2

description:
library name: D19 v2 explant 2
D19 v2 explant 2
Bulk RNA-Seq conducted by Novogene Co

source_name: Mouse kidneys

value: Mouse kidneys

value: Kidney cells


title: ChIP_Mutyh_Suz12_G2

description: Pull-down sample

value: Suz12 Rb (Cell Signaling #3737S)


title: jazD, trt, 24hr, rep2


title: D19 Stage-based media-v2 explant, Replicate 1

description:
library name: D19 v2 explant 1
D19 v2 explant 1
Bulk RNA-Seq conducted by Novogene Co

value: Cultured with Stage-based media-v2


title: RNA_WT_Neuron_R3

value: NeuN + sorted nuclei

value: WT


title: ChIP_Mutyh_Suz12_G3

description: Pull-down sample

value: Hippocampus


title: jazD, trt, 24hr, rep1

value: Whole leaf

value: jazD


title: RNA_WT_Neuron_R2


title: D19 Stage-based media-v1 explant, Replicate 2

description:
library name: D19 v1 explant 2
D19 v1 explant 2
Bulk RNA-Seq conducted by Novogene Co

value: Cultured with Stage-based media-v1


title: jazD, trt, 12hr, rep3


title: ChIP_Mutyh_Suz12_G1

description: Pull-down sample


title: D19 Stage-based media-v1 explant, Replicate 1

description:
library name: D19 v1 explant 1
D19 v1 explant 1
Bulk RNA-Seq conducted by Novogene Co


title: jazD, trt, 12hr, rep2


title: RNA_WT_Neuron_R1


title: ChIP_Mutyh_K27_G2

description: Pull-down sample

value: H3K27trime Ms (Abcam #ab6002)


title: Astrocyte,AGRcKO,P17,RNA,rep2

data_processing:
RNA-seq reads were aligned to the mm10 using tuxedo. RNA-seq, expected count, TPM, and FPKM were calculated using a Stringtie.
Assembly: mm10

source_name: cortex

value: cortex

value: astrocyte

value: AGR cKO


title: D3 Stage-based media-v2 mKPA, Replicate 1

description:
library name: D3 mKPA 1
D3 SK 1
Bulk RNA-Seq conducted by Novogene Co

value: Mouse kidney progenitor assembloid (mKPA)


title: D13 Stage-based media-v1 explant, Replicate 1

description:
library name: D13 v1 explant 1
D13 v1 explant 1
Bulk RNA-Seq conducted by Novogene Co


title: D13 Stage-based media-v1 explant, Replicate 2

description:
library name: D13 v1 explant 2
D13 v1 explant 2
Bulk RNA-Seq conducted by Novogene Co


title: jazD, trt, 12hr, rep1


title: ChIP_Mutyh_K27_G3

description: Pull-down sample

value: NeuN - sorted nuclei

value: Mutyh-/-


title: ChIP_Mutyh_K27_G1

description: Pull-down sample


title: jazD, trt, 3hr, rep3

value: 5 µM coronatine


title: ChIP_DKO_K27_G1

description: Pull-down sample


title: Astrocyte,AGRcKO,P17,RNA,rep1


title: jazD, trt, 3hr, rep2


title: D7 Stage-based media-v1 explant, Replicate 1

description:
library name: D7 v1 explant 1
D7 v1 explant 1
Bulk RNA-Seq conducted by Novogene Co

value: Mouse kidneys

value: Kidney cells


title: Astrocyte,WT,P17,RNA,rep1


title: jazD, trt, 3hr, rep1


title: ChIP_Mutyh_K4_G2

description: Pull-down sample

value: H3K4trime Rb (Abcam #ab8580)


title: ChIP_Mutyh_K4_G3

description: Pull-down sample


title: D7 Stage-based media-v1 explant, Replicate 2

description:
library name: D7 v1 explant 2
D7 v1 explant 2
Bulk RNA-Seq conducted by Novogene Co


title: D3 Stage-based media-v1 explant, Replicate 1

description:
library name: D3 v1 explant 1
D3 v1 explant 1
Bulk RNA-Seq conducted by Novogene Co


title: Astrocyte,WT,P17,RNA,rep2


title: ChIP_Mutyh_K4_G1

description: Pull-down sample


title: jazD, trt, 1hr, rep2


title: jazD, trt, 1hr, rep3


title: Astrocyte,WT,P17,ATAC,rep2

data_processing:
ATAC-seq reads were aligned to the mm10 using bowtie2. PCR duplicates were removed and then peaks were called using macs2. Reads in peaks were counted using featurCounts.
Assembly: mm10


title: ChIP_WT_Input_G3

description: 10% aliquot sheared chromatin


title: Astrocyte,AGRcKO,P17,ATAC,rep1


title: D17 Stage-based media-v0 explant, Replicate 1

description:
library name: D17 v0 explant 1
D17 v0 explant 1
Bulk RNA-Seq conducted by Novogene Co

value: Cultured with Stage-based media-v0


title: jazD, trt, 1hr, rep1


title: jazD, trt, 0hr, rep3


title: Astrocyte,WT,P17,ATAC,rep1

value: WT


title: ChIP_WT_Input_G1

description: 10% aliquot sheared chromatin

value: Hippocampus


title: jazD, trt, 0hr, rep2

value: Whole leaf


title: ChIP_WT_Suz12_G2

description: Pull-down sample

value: Suz12 Rb (Cell Signaling #3737S)


title: D7 10% FBS explant, Replicate 2

description:
library name: D7 10% FBS explant 2
D7 10% FBS explant 2
Bulk RNA-Seq conducted by Novogene Co

value: Cultured with 10% FBS


title: ChIP_WT_Suz12_G3

description: Pull-down sample


title: D3 Stage-based media-v1 explant, Replicate 2

description:
library name: D3 v1 explant 2
D3 v1 explant 2
Bulk RNA-Seq conducted by Novogene Co

value: Cultured with Stage-based media-v1


title: jazD, trt, 0hr, rep1

value: jazD


title: Astrocyte,AGRcKO,P17,ATAC,rep2

value: cortex

value: astrocyte


title: D7 10% FBS explant, Replicate 1

description:
library name: D7 10% FBS explant 1
D7 10% FBS explant 1
Bulk RNA-Seq conducted by Novogene Co


title: P45 mKidney, Replicate 2

description:
library name: P45 mKid 2
P45 mKid 2
Bulk RNA-Seq conducted by Novogene Co

value: Wild type


title: Astrocyte,AGRcKO,EAE,snRNA,rep1

data_processing:
The feature-barcode matrix was generated using cellranger count (10x Genomics, v3.0.2), aligning the sequenced reads to the human reference genome (mm10; 10x Cell Ranger reference v2.1.0). Then the count matrices were aggregated by cellranger aggr function across the samples with default parameters.
Assembly: mm10
Supplementary files format and content: h5

molecule: polyA RNA

extract_protocol:
The cells were resuspended in sorting buffer of lysis buffer of 0.2% Triton X-100, protease inhibitor (Roche, 04-693-159-001), 1 mM DTT (Sigma-Aldrich, D9779), 0.2 U/µL RNAsin (Promega, N211B), and 2% BSA (Sigma-Aldrich, SRE0036) in PBS. After incubating 5min on ice, the cells were passed through a 40 µm strainer to remove excessive debris.
We generated snRNA-seq libraries using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics).

value: AGR cKO

value: EAE

value: peak


title: Sample_90_Healthy Polish women

type: genomic

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from peripheral blood of Healthy Polish women

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data were processed in R, normalized using BMIQ normalization.
The data_table.csv contains normalized beta-value (BMIQ)

label: Cy5 and Cy3

source_name: Peripheral Blood

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.

tag: subject status

value: Healthy Polish women

tag: as

tag: Sex

value: F

value: Peripheral Blood


title: Astrocyte,AGRcKO,EAE,snRNA,rep2

tag: timepoint


title: ChIP_WT_Suz12_G1

description: Pull-down sample

value: NeuN - sorted nuclei


title: D17 Stage-based media-v0 explant, Replicate 2

description:
library name: D17 v0 explant 2
D17 v0 explant 2
Bulk RNA-Seq conducted by Novogene Co

value: Mouse kidneys

value: Kidney cells

value: Cultured with Stage-based media-v0


title: P45 mKidney, Replicate 1

description:
library name: P45 mKid 1
P45 mKid 1
Bulk RNA-Seq conducted by Novogene Co


title: Sample_89_Healthy Polish women


title: Astrocyte,WT,EAE,snRNA,rep1

value: WT


title: ChIP_WT_K27_G2

description: Pull-down sample

value: Hippocampus

value: H3K27trime Ms (Abcam #ab6002)


title: Sample_88_Healthy Polish women


title: P9 mKidney, Replicate 2

description:
library name: D9 mKid 2
D9 mKid 2
Bulk RNA-Seq conducted by Novogene Co


title: P9 mKidney, Replicate 1

description:
library name: D9 mKid 1
D9 mKid 1
Bulk RNA-Seq conducted by Novogene Co


title: Astrocyte,WT,EAE,snRNA,rep2


title: Sample_87_Healthy Polish women


title: FC, VEH-VEH, Male, Input

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: V-V Male FC

data_processing:
Illumina NovaSeq X  with paired-end 150-nt read was used to sequence each library, generating an average of 19 million reads per sample and input. However, only the forward (R1) strand was used for data analysis.
Read trimming was performed using default settings by Trim Galore!
Reads were subsampled to 95% to generate two artificial replicates using seqtk package.
Raw ChIP-seq reads and input data were then mapped to mouse mm10 genome (GRCm38) using Bowtie2 (2.2.5).
Peaks called using MACS2 (2.2.7.1) using a q-value cutoff of 0.05.
MM10 blacklisted regions (ENCODE) were removed using SAMtools
Mapped reads were extended by 100bp on either side (350 bp total) using BEDtools
Each library was randomly sub-sampled twice to 95% of its original raw reads to generate two artificial replicates using the seqtk package. The artificial replicates were used as input into diffbind (3.12.0) R package for generating a consensus peakset. Consensus peaksets were created independently for each brain region (PFC and NAc) using dba.peakset in diffbind (DBA_BLACKLIST_MM10, consensus = DBA_TREATMENT, minOverlap = 2). The raw read counts were extracted using the diffbind function dba.count (data_blacklist_remove, summits = FALSE, peaks = ConsensusPeaks, filter=1, bScaleControl = TRUE, minCount=1, score=DBA_SCORE_TMM_MINUS_FULL). This count file was then used as the input to DESeq2 (1.42.1) package in R. Uniform Manifold Approximation and Projection (UMAP) was used to identify principal components with outsized impact. The following covariates were regressed out: demographic covariates (sex, condition) and technical covariates (align rate, unique rate, FRiP, NSC, the number of identified peaks, and sequencing batch) by correlating the top 6 principal components (Pearson correlation > 0.7) with these covariates. Differential peak analysis was then performed to identify differential peaks between the conditions (VEH-VEH, VEH-PSI, OXY-VEH, OXY-PSI), and sexes for each brain region (FDR <0.05). The p-values were adjusted by performing a standard Bonferroni correction. For more accurate annotation, enhancers (defined as identified H3K27ac peaks that do not fall within ±2000bp of TSS) were first checked for regional overlap with published Hi-C data on neurons in mice (Bonev et al., Cell, 171, 557-572, e524 (2017)). Overlapped peak regions were annotated based on these existing Hi-C gene links, and the rest of the enhancers were associated with their nearest-neighbor genes. K-means clustering and unsupervised hierarchical clustering (UHC) were performed on differential enhancers for each sex and region. Count files were filtered based on differential peak callouts to form a new consensus peakset comprising the count files of all differential peaks between any two of the three groups (VEH-VEH, OXY-VEH, and OXY-PSI). To normalize the counts based on the number of samples, each row of the count file was divided by √(sum〖(X)〗^2 ). The optimal number of clusters for k-means was determined using Silhouette method. UHC was performed using the default settings of the pheatmap library in R, with cluster position on the x-axis rotated about their dendrogram tentacle for continuity. Gene ontology (GO) biological enrichment analysis was performed on annotated peaks using the bioconducter clusterProfiler package. KEGG pathway analysis was performed using shinyGO version 0.838.  Both GO and KEGG analysis were performed using FDR adjusted P values < 0.05 to ensure generation of high-confidence terms.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: Frontal Cortex

extract_protocol:
Neuronal neclei extracted performed following previously published protocol (Ma et al., Sci Adv., Vol 4, Issue 4, ( 2018); de la Fuente Revenga et al., Cell Rep., Volume 37, Issue 3, (2021)). Each step was performed on ice unless otherwise noted. A small slice (20-30mg) of frozen FC or NAc tissue was plunged into a tissue grinder (D9063, Sigma-Aldrich) filled with 3 ml of ice-cold nuclei extraction buffer (NEB) [0.32M sucrose, 5mM CaCl2, 3mM Mg(Ac)2, 0.1mM EDTA, 10 mM tris-HCl, and 0.1%(v/v) Triton X-100] along with 30 μl of freshly prepared protease inhibitor cocktail (PIC, Sigma-Aldrich), 3 μl of 1 M dithiothreitol (DTT, Sigma-Aldrich), 3 μl of 100mM phenylmethylsulfonyl fluoride (PMSF, Sigma-Aldrich) in isopropyl alcohol, and 4.5 μl of recombinant ribonuclease (RNase) inhibitor (2313A,Takara Bio). The tissue was then homogenized by douncing 25 times with pestle A and 15 times with pestle B. A 40-μm cell strainer (22-363-547, ThermoFisher Scientific) was then used to filter the homogenate, which was then collected into a 15 ml centrifuge tube. Next, the cell suspension was centrifuged at 1000 RCF for 10 min. The supernatant was then discarded, and the collected pellet was resuspended in 0.5 ml of ice-cold NEB with freshly added 5 μl of PIC, 0.5 μl of PMSF, 0.5 μl of DTT, and 0.75 μl of RNase inhibitor. 500 μl of the sample was mixed with 750 μl of 50%(w/v) iodixanol (created by mixing 4 ml of OptiPrepTM gradient (Sigma-Aldrich)) and 0.8 ml of diluent [150 mM KCl, 30 mM MgCl2, and 120 mM Tris-HCl]), along with 7.5 μl of PIC, 0.75 μl of PMSF, 0.75 μl of DTT, and 1.125 μl of RNase inhibitor. The mixture was centrifuged at 10,000 RCF at 4°C for 20 min. The supernatant was then removed and 300 μl of 2% (w/v) normal goat serum (50062Z, Life technologies) in Dulbecco’s PBS (DPBS, Life technologies), and 0.3 μl of RNase inhibitor was gently added to the sample and incubated on ice for 10 min, before resuspending the nuclei pellet by pipetting. In order to label and separate neuronal and glial fractions by FACS, 10 μl of 2 ng/ml anti-NeuN antibody conjugated with Alexa 488 (MAB377X, Millipore) in DPBS was added into the nuclei suspension. This suspension was mixed well by pipetting before being placed on a roto-mixer (Labnet) without light at 4°C for 1 h. Next, NeuN+ and NeuN- fractions were sorted using a BD FACSAriaTM cell sorter (BD Biosciences). Around 192 μl of the sorted solution containing ~24,000 NeuN+ nuclei was then added into 192 μl of 2x lysis buffer [4% (vol/vol) Triton X-100, 100 mM Tris-HCl (pH 8.0), 100 mM NaCl and 30 mM MgCl2 in Milli-Q water], along with 1.92 μl of PIC and 1.92 μl PMSF. This solution was mixed well and incubated at room temperature for 10 min, before addition of 38.4 μl of 100 mM CaCl2 and 4.8 μl of 100U/ul MNase (88216, ThermoFIsher). The solution was mixed by vortex and incubated at room temperature for 10 min. 42.24 μl of 0.5 M UltraPure EDTA (15575-038, Life Technologies) was added and allowed to incubate on ice for 10 min to halt the digestion. The resulting mixture was centrifuged at 16,100g for 10 min at 4°C and all of the supernatant was collected as chromatin sample.
ChIP-seq was performed using previously reported MOWChIP microfluidic platform (Zhu et al., Nat Protocols, 14, 3366–3394, (2019)) from chromatin extracted from 10,000 nuclei per sample, and 2000 nuclei per input. Libraries prepared using Accel-NGS 2 S Plus DNA Library kit (IDT, 1000987). Libraries amplified 10-12 cycles. Enrichment valideated by qPCR and size selected using Agilent tapestation.

treatment_protocol: Mice received three separate administrations of OXY (3 mg/kg) or vehicle on consecutive days (days 1-3), with 24-hour intervals between doses, followed by a single dose of PSI (1 mg/kg) or vehicle (day 4), resulting in four distinct experimental groups: VEH-VEH, VEH-PSI, OXY-VEH, and OXY-PSI. On day 5, tissue samples were collected for H3K27ac profiling

value: Frontal Cortex

value: Neuron

value: Vehicle-Vehicle


title: ChIP_WT_K27_G3

description: Pull-down sample

data_processing:
Quality was assessed using FastQC v0.11.9 & Fastq-Screen v0.15.2
Files were mapped to GRCm38 using Bowtie2 v.2.3.5.1
Duplicates were marked using samtools markduplicates v1.10
Peak calling was performed using Epic2 (FDR cutoff of 0.05. Window and gap sizes were 100 bp, 3 gaps for H3K4me3, 200 bp and 3 gaps for H3K27me3 and 50 bp, 2 gaps for Suz12)
Reads were counted in R using the Bioconductor package DiffBind (v.3.10.1) and differential enrichment was done using edgeR (v.3.42.4)
Regions were assigned to nearest genomic feature using ChIPseeker (v1.36) in R
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-deliminted text files with counts for all replicates and genotypes within each ChIP target across consensus peaks.


title: ChIP_WT_K27_G1

description: Pull-down sample


title: FC, VEH-PSI, Male, Input

description: V-P Male FC

value: Vehicle-Psilocybin


title: Sample_86_Healthy Polish women


title: P0 mKidney, Replicate 2

description:
library name: P0 mKid 2
P0 mKid 2
Bulk RNA-Seq conducted by Novogene Co

value: Wild type


title: FC, OXY-VEH, Male, Input

description: O-V Male FC

value: Oxycodone-Vehicle


title: P0 mKidney, Replicate 1

description:
library name: P0 mKid 1
P0 mKid 1
Bulk RNA-Seq conducted by Novogene Co


title: Sample_85_Healthy Polish women


title: ChIP_WT_K4_G2

description: Pull-down sample

value: H3K4trime Rb (Abcam #ab8580)


title: FC, OXY-PSI, Male, Input

description: O-P Male FC

value: Oxycodone-Psilocybin


title: Sample_84_Healthy Polish women

value: Healthy Polish women

value: F


title: ChIP_WT_K4_G3

description: Pull-down sample

value: NeuN - sorted nuclei


title: FC, VEH-VEH, Female, Input

description: V-V Female FC


title: ChIP_WT_K4_G1

description: Pull-down sample


title: E15.5 mKidney, Replicate 2

description:
library name: E15.5 mKid 2
E15.5 mKid 2
Bulk RNA-Seq conducted by Novogene Co

value: Mouse kidneys


title: E15.5 mKidney, Replicate 1

description:
library name: E15.5 mKid 1
E15.5 mKid 1
Bulk RNA-Seq conducted by Novogene Co

value: Kidney cells


title: Sample_83_Healthy Polish women

value: Peripheral Blood


title: E12.5 mKidney, Replicate 2

description:
library name: E12.5 mKid 2
E12.5 mKid 2
Bulk RNA-Seq conducted by Novogene Co


title: FC, VEH-PSI, Female, Input

description: V-P Female FC


title: Sample12

city: Frederick

middle: M

last: Cook

state: MD

address: 1050 Boyles St, Room 21-89

institute: National Cancer Institute-Frederick

data_processing:
The original FASTQ format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
For quality control (QC), the low quality 3’ regions were trimmed and only high quality reads with Phred score >=30 were retained.
The QC passed trimmed fastq files were mapped to hg38 reference genome using STAR 2.7.0f aligner and
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts, FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for all samples

source_name: Intratibial tumor/bone marrow

extract_protocol:
Cxcl1 shRNA knockdown murine MSCs were generated using stable lentiviral infection of plasmids containg Cxcl1 targeted or non-targeted scrambled control shRNA. RNA from cell lines was collected from cells were cultured in low-glucose DMEM with 10% fetal bovine serum, 1% penicillin/streptomycin, and 10 ng/mL PDGF.RNA was isolated using the RNeasy RNA isolation kit according to manufacturer protocol (Qiagen). Samples were analyzed with respect to purity and potential degradation using a Nanodrop (Thermo Scientific, Nanodrop Products, Wilmington, DE) instrument to measure absorbance, and potential degradation of the sample was assessed by analysis of the RNA using an Advanced Analytical Technical Instrument Fragment Analyzer (AATI, Ames, IA). Samples with A260/280 of 1.8 or above and with RQN scores > 8.0 were utilized to prepare sequencing libraries. Cxcl1 CRISPR-Cas9 murine MSCs were generated using stable lentiviral infection of plasmids containg S.pyogenes Cas9 and Cxcl1 exon 1 targeted or non-targeted scrambled control sgRNAs. RNA from cell lines was collected from cells were cultured in low-glucose DMEM with 10% fetal bovine serum, 1% penicillin/streptomycin, and 10 ng/mL PDGF. Tumor samples were obtained intratibially injected RM1 PCa tumors with Cxcl1 KO or scrambled control MSCs co-injected at a 1:1 ratio to tumor cells (1 x 10^4 of each). RNA was collected from bone marrow flushes obtained by cutting epiphyses from tibia and breifly centrifuging to pellet tumor and bone marrow cells into microcentrifuge tubes. n=3 biological replicates per cell line; 3 tibia per tumor condition. Total RNA was extracted using Trizol following manufacturer’s instructions (ThermoFisher Scientific, Waltham, MA, USA).
Sequencing libraries (Cxcl1 KD MSCs) were generated by the UNMC NGS Core beginning with 1ug of total RNA from each sample using the Universal mRNA library kit from Tecan (previously NuGen) following the manufacturers recommended procedure (TECAN, USA Redwood City, CA 94063). Resultant libraries were assessed for size of insert by analysis of an aliquot of each library on a Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA). Each library had a unique indexing identifier barcode allowing the individual libraries to be multiplexed together for efficient sequencing.RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). Library Preparation (Cxcl1 KO MSC cell line samples). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Library Preparation with rRNA depletion (tumor/bone marrow stromal cell samples). Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Germantown, MD, USA ), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Intratibial tumor/bone marrow

value: prostate cancer and stroma


title: FC, OXY-VEH, Female, Input

description: O-V Female FC


title: Sample_82_Healthy Polish women


title: Sample11


title: FC, OXY-PSI, Female, Input

description: O-P Female FC


title: Sample_81_Healthy Polish women


title: Sample10


title: NAc, VEH-VEH, Male, Input

description: V-V Male NAc

source_name: Nucleus Accumbens

value: Nucleus Accumbens


title: PBMCs_TB patient_sample 3

source_name: peripheral blood mononuclear cells, TB patient, sample 3

value: peripheral blood mononuclear cells

value: Male


title: intestinal mac gp91phox-/- 3_rep 3 [ZM15_3YG]

city: Freiburg

first: Zohreh

last: Mansoori Moghadam

address: Breisacher Str. 115

country: Germany

institute: UNIVERSITÄTSKLINIKUM FREIBURG Center for Chronic Immunodeficiency

data_processing:
paired-end sequencing of the quality-controlled library was conducted using NovaSeq6000.
Demultiplexing of sequenced reads was achieved through Illumina bcl2fastq (version 2.19), and Cutadapt was employed for adapter trimming.
The raw reads were then mapped to the mm10 murine reference genome using STAR (Version 2.5.2b) and counted using feature counts.
The resulting count data underwent processing with the DESeq2 package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file in CSV, and xlsx format

source_name: Colon

extract_protocol:
The extraction of RNA was carried out using the RNeasy MicroKit following the guidelines provided by the manufacturer (Qiagen).
paired-end sequencing of the quality-controlled library was conducted using NovaSeq6000. Demultiplexing of sequenced reads was achieved through Illumina bcl2fastq (version 2.19), and Cutadapt was employed for adapter trimming. The raw reads were then mapped to the mm10 murine reference genome using STAR (Version 2.5.2b) and counted using feature counts.

value: Colon

value: intetinal macrophages


title: Sample_79_Healthy Polish women


title: intestinal mac gp91phox-/- 2_rep 2 [ZM14_2YG]


title: NAc, OXY-VEH, Male, Input

description: O-V Male NAc

value: Neuron


title: ChIP_DKO_K4_G3

description: Pull-down sample

extract_protocol:
Tissue was homogenized and nuclei were isolated.
Nuclei were stained with anti-NeuN mouse antibody (Millipore, #mab377), an Alexa 488 secondary antibody (Life Technologies # A11001) and Vybrant DyeCycle Ruby (Life Technologies, #V102673) and nuclei were sorted using flow cytometry.
Sorted nuclei were pelleted by centrifugation at 3.200 g for 15 minutes, transferred to Bioruptor Microtubes (Diagenode, C30010016) shearing tubes and carefully re-suspended in RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS and 1x Complete EDTA free protease inhibitor cocktail (Roche, 11873580001). Samples were incubated 10 minutes at 4°C and then sheared using a Bioruptor (Diagenode) for 4 times at 5 cycles and followed by 2 cycles at 30″ ON/OFF high power. Samples were spun down in between every 5 cycles. Sheared chromatin was cleared by centrifugation at 10.000 rpm for 10 minutes and the supernatant was stored in DNA low-binding tubes (Eppendorf, 022431021).
Sheared chromatin was pre-cleared with BSA-blocked protein G magnetic beads (Dynabeads, Invitrogen, 10004D) for 1 hour at 4°C. For every ChIP-reaction the appropriate amount of chromatin, depending on the different antibodies, was used (Supplementary Table 1). ChIP-reactions were performed by overnight incubation on a rotating wheel at 4°C in ChIP buffer (50 mM Tris-HCl at pH 8.0, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 20 mM EDTA, 1x Complete EDTA free protease inhibitor cocktail). As input control a 10% aliquot of each sheared chromatin sample was saved and stored at -80°C. Subsequently, 30 μl of BSA-blocked protein G magnetic beads were added to each ChIP-reaction and the mixture was incubated on a rotator at 4°C for 4 hours. The chromatin-bead complexes were washed twice at 4°C for 5 minutes at slow rotation (15 rpm) with ChIP buffer containing 0.1% SDS, twice with wash buffer (100 mM Tris-HCl pH 8.0, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 20 mM EDTA) and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). For reverse crosslinking, chromatin-bead complexes and 10% input controls were resuspended in 300 μl elution buffer (100 mM NaHCO3, 1% SDS) with 200 mM NaCl and incubated at 65°C overnight. On the next day, the samples were treated with 1 μl of RNAse A (Thermo Scientific, EN0531) for 1 hour at 37°C. Subsequently, 6 μl 0.5M EDTA and 1 μl Proteinase K (Roche, 3115828001) were added and the samples were incubated at 45°C for 1 hour. DNA was then purified by phenol-chloroform extraction and samples were eluted in 16 μl Tris buffer (10 mM Tris-HCl pH 8.0) in a DNA low-binding tube and stored at −80°C.
Library construction was performed by using QIAseq™ Ultralow Input Library Kits (Qiagen, 180492) according to manufacturer’s protocol and purified using AMPure XP beads (Beckman Coulter, A63880).

value: Hippocampus


title: Sample7


title: Sample8


title: NAc, VEH-PSI, Male, Input

description: V-P Male NAc

value: Vehicle-Psilocybin


title: Sample9


title: Sample6

source_name: cell line

value: cell line

value: Mesenchymal stem cell


title: NAc, OXY-PSI, Male, Input

description: O-P Male NAc

value: Oxycodone-Psilocybin


title: Sample_76_Healthy Polish women

value: Healthy Polish women

value: F


title: NAc, VEH-VEH, Female, Input

description: V-V Female NAc

value: Vehicle-Vehicle


title: intestinal mac p47phox-/- 2_rep 2 [ZM8_2YP]


title: Sample_77_Healthy Polish women

value: Peripheral Blood


title: Sample_78_Healthy Polish women


title: E12.5 mKidney, Replicate 1

description:
library name: E12.5 mKid 1
E12.5 mKid 1
Bulk RNA-Seq conducted by Novogene Co

value: Mouse kidneys

value: Kidney cells

value: Wild type


title: Sample5


title: intestinal mac p47phox-/- 1_rep 1 [ZM7_1YP]


title: Sample_80_Healthy Polish women


title: Sample_75_Healthy Polish women


title: intestinal mac gp91phox-/-1_rep 1 [ZM13_1YG]


title: NAc, OXY-VEH, Female, Input

description: O-V Female NAc

value: Nucleus Accumbens

value: Oxycodone-Vehicle


title: Sample_74_Healthy Polish women


title: Sample4


title: Sample3


title: intestinal mac p47phox-/- 3_rep 3 [ZM9_3YP]

value: Colon


title: Intestinal mac_WT_rep 2 [ZM2_2YW]

value: intetinal macrophages

value: WT


title: NAc, OXY-PSI, Female, Input

description: O-P Female NAc

value: Neuron


title: NAc, OXY-PSI, Female, 5

description: O-P Female NAc


title: Sample_73_Healthy Polish women


title: Sample_72_Healthy Polish women


title: Sample1


title: Batch2 mKPA, Replicate 2 d24, GEX Library

description:
library name: GEX_batch2_mKPA2
10X Chromium multiome ATAC + gene expression kit
batch2_SK2_filtered_feature_bc_matrix.h5

data_processing:
Sequencing reads were aligned to the mouse genome (GRCm39) with the Cell Ranger ARC software (version 2.0.2) using STAR aligner on the University of Southern California High Performance Cluster.
Assembly: arc-GRCm39-2024-A-v7.2.0
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression and peak by cell matrices

growth_protocol: Synthetic kidneys were cultured with Stage V medium, 37C, 5% CO2

extract_protocol:
Synthetic kidneys were miccrodissected and digested in CAP digestion solution (10mg/ml Cold Active Protease+ 2.5 mg/ml Collagenase type 4 + 0.125U/ul Dnase1)  at 12°C for 30 mins. Cells were then spun down at 350G for 5 mins and resuspended in cold autoMACS Running Buffer. Cell viablity was accessed (99% Live) and cells spun down again. 10X genomics Demonstarated Proocol CG000365 (REV C) was then used to isolate nuclei with 5 min lysis time. The single nuclei suspension was than transposed and run through a microfuidic chip (Chip J) for barcoding.
10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E)

value: Mouse kidney progenitor assembloid (mKPA)

value: SIX2-tdT; Hoxb7-Venus

value: KPAs were cultured with Stage V medium


title: Intestinal mac_WT_rep1 [ZM1_1YW]


title: C3

value: cell line

value: Mesenchymal stem cell


title: Batch2 mKPA, Replicate 2 d24, ATAC Library

description:
library name: ATAC_batch2_mKPA2
10X Chromium multiome ATAC + gene expression kit
batch2_SK2_filtered_feature_bc_matrix.h5

treatment_protocol: Synthetic kidneys were cultured with Stage V medium, 37C, 5% CO2


title: Sample_70_Healthy Polish women

value: Healthy Polish women

value: F


title: NAc, OXY-PSI, Female, 3

description: O-P Female NAc

value: Oxycodone-Psilocybin


title: Sample_69_Healthy Polish women

value: Peripheral Blood


title: NAc, OXY-PSI, Female, 2

description: O-P Female NAc


title: Batch2 mKPA, Replicate 1 d24, GEX Library

description:
library name: GEX_batch2_mKPA1
10X Chromium multiome ATAC + gene expression kit
batch2_SK1_filtered_feature_bc_matrix.h5

value: Kidney cells


title: Intestinal mac_WT_rep 3 [ZM3_3YW]


title: C1


title: Batch2 mKPA, Replicate 1 d24, ATAC Library

description:
library name: ATAC_batch2_mKPA1
10X Chromium multiome ATAC + gene expression kit
batch2_SK1_filtered_feature_bc_matrix.h5


title: NAc, VEH-PSI, Female, Input

description: V-P Female NAc

value: Vehicle-Psilocybin


title: NAc, OXY-PSI, Female, 1

description: O-P Female NAc

value: Nucleus Accumbens


title: Batch1 mKPA, Replicate 2 d24, GEX Library

description:
library name: GEX_batch1_mKPA2
10X Chromium multiome ATAC + gene expression kit
batch1_SK2_filtered_feature_bc_matrix.h5


title: Sample2


title: Sample_68_Healthy Polish women


title: Sample_67_Healthy Polish women


title: B2


title: Sample_71_Healthy Polish women


title: Batch1 mKPA, Replicate 2 d24, ATAC Library

description:
library name: ATAC_batch1_mKPA2
10X Chromium multiome ATAC + gene expression kit
batch1_SK2_filtered_feature_bc_matrix.h5


title: Sample_66_Healthy Polish women

description: DNA extracted from peripheral blood of Healthy Polish women


title: NAc, OXY-PSI, Female, 4

description: O-P Female NAc


title: FC, OXY-PSI, Female, 2

description: O-P Female FC

value: Frontal Cortex


title: Sample_65_Healthy Polish women


title: C2


title: FC, OXY-PSI, Female, 3

description: O-P Female FC


title: B1


title: Batch1 mKPA, Replicate 1 d24, GEX Library

description:
library name: GEX_batch1_mKPA1
10X Chromium multiome ATAC + gene expression kit
batch1_SK1_filtered_feature_bc_matrix.h5


title: A3


title: Batch1 mKPA, Replicate 1 d24, ATAC Library

description:
10X Chromium multiome ATAC + gene expression kit
batch1_SK1_filtered_feature_bc_matrix.h5
library name: ATAC_batch1_mKPA1


title: NAc, OXY-PSI, Male, 4

description: O-P Male NAc


title: FC, OXY-PSI, Female, 1

description: O-P Female FC


title: Sample_64_Healthy Polish women


title: NAc, OXY-PSI, Male, 3

description: O-P Male NAc


title: DKO

city: Chicago

first: Peng

state: Illinois

address: Ward Building Room 3-230/45, 303 E Chicago Avenue

department: Pathology

institute: Northwestern University

data_processing:
Fastq files were processed with Cellranger
Assembly: mm10
Supplementary files format and content: tab separated value file and matrix file

source_name: Bone marrow

extract_protocol:
Mouse bone marrow cells were flushed with PBS
Single cell libraries were generated using a Chromium Single Cell 3’ v3 kit (10x Genomics). RNA Quality and quantity were assessed using an Agilent Bio-analyzer

value: Bone marrow

value: VavCre:Ddx41 fl/fl, cGAS-/- (DKO)


title: A1


title: WT

value: WT


title: B3


title: NAc, OXY-PSI, Male, 2

description: O-P Male NAc

value: Neuron


title: Sample_63_Healthy Polish women


title: Sample_62_Healthy Polish women


title: ScrCtl3


title: Sample_61_Healthy Polish women


title: NAc, OXY-PSI, Male, 1

description: O-P Male NAc


title: WT EAE Day17-3

city: shanghai

first: Yongshun

last: Guo

institute: ION

data_processing:
Data quality check was done by CASAVA.
De-multiplexing was performed with HISAT2 v2.0.5 program. DESeq2 (1.16.1) was used to identify the differentially expressed genes.
Benjamini and Hochberg programs were used to control false discovery rate.
The GO enrichment and KEGG pathway enrichment were performed using ClusterProfiler R program. GSEA was analyzed by GSEA analyses program (http://www.broadinstitute.org/gsea/index.jsp).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the RPKM for each samples

source_name: spinal cord

growth_protocol: Selective ablation of Pts in OPCs or oligodendrocytes was achieved by crossing Ptsflox/flox mice with platelet-derived growth factor receptor, alpha polypeptide (Pdgfra)-CreERT2 transgenic mouse line , to generate Ptsflox/flox; Pdgfra-CreERT2

extract_protocol:
The spinal cord of PtsPdgfra-CreER cKO mice and littermate control were homogenized in TRIzol reagent on day 17 after EAE induction. Total RNA was purified, and cDNA was sequenced.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Mice were subcutaneously injected with myelin oligodendrocyte glycoprotein (MOG35-55, 200 μg/animal) emulsified in CFA containing 5 mg/ml killed Mycobacterium tuberculosis (DIFCO), and i.p. injected with pertussis toxin (350 ng/animal; Calbiochem) on day 0 and day 2.

value: spinal cord

value: Day 17

value: EAE


title: ScrCtl2

value: cell line


title: WT EAE Day17-2


title: FC, OXY-PSI, Male, 6

description: O-P Male FC


title: Sample_60_Healthy Polish women


title: FC, OXY-PSI, Male, 5

description: O-P Male FC


title: WT EAE Day17-1


title: cko EAE Day17-3

value: cko


title: Sample_58_Healthy Polish women

value: Healthy Polish women


title: Sample_59_Healthy Polish women

value: F


title: A2

value: Mesenchymal stem cell


title: ScrCtl1


title: ChIP_WT_Input_G2

description: 10% aliquot sheared chromatin

value: NeuN - sorted nuclei

value: Hippocampus


title: ERY-G4-1

data_processing:
Homer tools are used for the analysis,  findPeaks and annotatePeaks.pl used to generate peak files
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

extract_protocol:
We initiated the experiment by harvesting mouse bone marrow cells through a PBS flushing procedure. Following this, we performed the isolation of erythroid cells utilizing Ter119 antibodies, and concurrently, we purified hematopoietic stem and progenitor cells (HSPCs) by selectively collecting lineage-negative cells.
CUT&RUN libraries were prepared using the True-Seq Chip-Seq Library Preparation Kit following manufacturer’s instructions.

tag: antibody

tag: group

value: ERY


title: FC, OXY-PSI, Male, 4

description: O-P Male FC

value: Oxycodone-Psilocybin


title: cko EAE Day17-1

tag: time


title: HSPC-G4-2

tag: tissue

value: HSPC


title: Sample_56_Healthy Polish women

value: Peripheral Blood


title: FC, OXY-PSI, Male, 2

description: O-P Male FC

value: Frontal Cortex

tag: cell type


title: cko EAE Day17_2

tag: genotype


title: cko EAE Day17-2


title: HSPC-G4-1

value: Bone marrow


title: FC, OXY-PSI, Male, 1

description: O-P Male FC

value: Neuron


title: FC, OXY-PSI, Male, 3

description: O-P Male FC


title: Sample_55_Healthy Polish women


title: cko EAE Day17_1

value: spinal cord


title: NAc, OXY-VEH, Female, 3

description: O-V Female NAc

value: Nucleus Accumbens

value: Oxycodone-Vehicle


title: ERY-DDX41-2


title: Sample_54_Healthy Polish women


title: ERY-DDX41-1


title: Sample_53_Healthy Polish women


title: WT EAE Day17_2

value: Day 17

value: WT

value: EAE


title: NAc, OXY-VEH, Female, 2

description: O-V Female NAc


title: ERY-G4-2


title: Sample_51_Healthy Polish women

value: Healthy Polish women

value: F


title: HSPC-DDX41-1


title: Sample_52_Healthy Polish women


title: WT EAE Day17_1


title: Sample_50_Healthy Polish women


title: Sample_48_Healthy Polish women


title: NAc, OXY-VEH, Female, 1

description: O-V Female NAc


title: FC, OXY-VEH, Female, 1

description: O-V Female FC


title: HO CSA, Male Rep5

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Original RNAseq analysis was provided by Novogene.
Original image data file from Illumina was transformed to sequenced reads (raw data) by CASAVA base recognition (base calling). Datasets are being uploaded to GEO.
Raw data was subjected to data QC including error rate distribution, GC content distribution, and data filtering.
Mapping was performed using Hisat (v2.0.5) and reads were mapped to the mouse reference genome mm10. Quantification was conducted by FeatureCounts (v1.5.0-p3) .
Normalization and differential gene expression used DESeq2 (v1.20). Gene Set Enrichment Analysis (GSEA) was performed with GSEA 4.2.3 software (BROAD Institute). Differentially Expressed Gene (DEG) lists from RNA sequencing are analyzed with default parameters using Mouse_Ensembl_Gene_ID_MSigDB.v2023.1.Mm.chip platform.
Assembly: mm10
Supplementary files format and content: Text files containing raw counts

source_name: Kidney

growth_protocol: Mice were fed standard NIA chow and had access to food and water ad libitum. Each strain (CSA homozygous knockout (HO) and CSBm/m) had their respective WT littermate controls.

extract_protocol:
Mice were deeply anesthetized with isoflurane and then perfused with 1 × phosphate buffered saline (PBS) through the heart. Kidneys were removed and then washed with PBS solution. Kidney was cut in the middle and flash frozen with liquid nitrogen and stored at -80°C.  RNA from the kidney was isolated using RNeasy (Macherey-Nagel, UK) per manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, follwed by the second strand cDNA sythesis using either dUTP for directional or dTTP for non-directional library.

tag: animal id

value: Kidney

value: Male

value: 11.7 months


title: FC, OXY-VEH, Female, 4

description: O-V Female FC

tag: treatment


title: HSPC-DDX41-2


title: HO CSA, Male Rep3

tag: strain

value: 13.1 months


title: FC, OXY-VEH, Female, 2

description: O-V Female FC


title: Sample_49_Healthy Polish women


title: AlHV-1-infected Lymphoblastoid Cell Line (Calf n°911)

city: Namur

first: Damien

last: Coupeau

address: Rue de Bruxelles, 61

department: Namur Research Institute for Life Sciences

country: Belgium

institute: University of Namur

data_processing:
Viral reads recovery (alignment using BWA mem -a -T15) (BWA v0.7.11)
Adapter trimming (Trimmomatic v0.39. Included the trimming of the adapters, quality trimming (Sliding Window 4:15), and a minimal length filter of 70 nucleotides
PCR duplicates removal (dedupe.sh (BBMap v1.0))
vCircTrappist v1.0 pipeline for circRNA-originating reads identification (including Samtools v1.10 and BWA v0.7.11)
Assembly: KX905135.1 ; KT122858.1 ; AC_000008.1 ; NC_001436.1 ; EF523390.1
Supplementary files format and content: tab-delimited text file including raw circRNA-derived reads count, circularization sites sequences, splicing pattern, strandness of the reads, 5' and 3' positions of the circularization sites, max size of the circRNAs, colocalized genes, common k-mers between circularization sites, viral segment, read identifiers

organism: Bos taurus

source_name: Lymphoblastoid Cell Line derived from an infected calf

extract_protocol:
RNA was extracted using TRI-reagent (Thermofisher) and 4ug were sent to sequencing (Novogene).
1µg of total RNA was sent to Novogene for the library preparation and sequencing. Library preparation include : ribosomal depletion, linear RNA degradation, RNA fragmentation, reverse transcription, second strand synthesis (using dUTPs), end-repair, A-tailing, adapter ligation, enzyme digestion to remove dUTPs-containing second strand cDNAs, size selection, PCR amplification


title: HO CSA, Male Rep2

value: 15.6 months


title: AlHV-1-infected Lymphoblastoid Cell Line (Calf n°617)

value: Lymphoblastoid Cell Line derived from an infected calf


title: HO CSA, Male Rep1


title: NAc, OXY-VEH, Male, 3

description: O-V Male NAc


title: NAc, OXY-VEH, Male, 4

description: O-V Male NAc


title: Sample_46_Healthy Polish women

value: Peripheral Blood


title: Sample_57_Healthy Polish women


title: PMK, replicate 2

city: Barcelona

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

country: Spain

institute: CRG

description: Library name: PMK2

data_processing:
Nanopore sequencing basecalling and demultiplexing of raw fast5 files was done using Guppy (version 3.6.1) through the “MasterOfPores” pipeline. Fastq files were then mapped to the GRCm38 mouse genome and the GRCh38 human genome, using minimap2 (version 2.14). Isoquant version 3.0 was used to quantify CSDE1 isoforms. Initial bam files were filtered so that only non-ambiguous CSDE1 reads were kept. The results were manually curated to correct for isoform mis-assignments.
Assembly: GRCh38, GRCm38
Supplementary files format and content: Tab-delimited text file with transcript per million (TPM) values for each detected CSDE1 isoform

source_name: PMK

growth_protocol: SK-Mel-147 cells were cultured in DMEM (high glucose, pyruvate and GlutaMax; Gibco #31966021), supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco #10270106) and 1% penicillin-streptomycin (Gibco #15070063).  PMK were isolated from the skin of newborn C57BL/6J mice and growth in EMEM complete media (Lonza, Cat 06-174G) supplemented with 8% of chelated FBS (Fetal Bovine Serum, see below), 0.05 mM CaCl2, 10 ng/ml EGF (Sigma-Aldrich) and 1% penicillin/streptomycin (Life technologies). Cell lines were maintained at 37 ºC with 5% CO2 .

extract_protocol:
Maxwell kit (Promega #AS1280) was used to extract total RNA. 100 μg of total RNA were incubated with Turbo DNA-free kit components (Invitrogen # AM1907) for DNase digestion in the presence of 40U/20μL reaction of RNaseOUT (Invitrogen # 10777019). Total RNA was then cleaned-up with AMPure XP beads (Agencourt #082A63881) according to the manufacturer's specifications. Poly(A) selection was performed using 100 µl of Oligo (dT)25 Dynabeads (Invitrogen #61002) previously washed with binding buffer (20 mM Tris–HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8) and then resuspended in 100 µl of the same buffer. Poly(A)-containing RNA was eluted twice from beads with 10 mM Tris–HCl pH 7.5 by heating the mixture at 75ºC for 2 minutes.
One hundred ng of poly(A)-selected RNA was mixed with 2.5 µL of VNP (ONT cDNA sequencing kit), 1 µL of 10 mM dNTPs and filled to a total of 7.5 µL with RNase-free water. The mixture was incubated at 65 °C for 5 minutes and then snap cooled on ice. In a separate tube 4 µL of 5x RT buffer, 1 µL RNaseOUT, 1 µL of RNase-free water and 2 µL of Strand-Switching Primer (SSP, ONT cDNA sequencing kit) were mixed. The tubes were gently mixed and incubated at 65 °C for 2 minutes. One µL of Maxima H Minus Reverse Transcriptase (Life Technologies #EP0751) was added to the reaction mixture, and incubated for 90 minutes at 42 °C, followed by heat inactivation at 85 °C for 5 minutes. RNA was degraded by adding 1 µL of RNase Cocktail Enzyme Mix (ThermoFisher #AM2286) followed by incubation for 10 minutes at 37 °C. DNA was cleaned-up using AMPure XP beads and quantity and quality were assessed using Qubit and Tapestation. The second cDNA strand was synthesized by mixing 25 µL of 2X LongAmp Taq Master Mix (NEB #174M0287S), 2 µL PR2 primer (ONT cDNA sequencing kit), 20 µL reverse-transcribed sample and 3 µL RNase-free water. The reaction mixture was incubated at 94 °C for 1 minute, at 50 °C for 1 minute, at 65 °C for 15 minutes and then kept 4 °C. Another AMPure XP beads clean-up step was performed, proceeding to the end-prep step by mixing the following reagents: 20 µL cDNA sample, 30 µL RNase-free water, 7 µL Ultra II End-prep reaction buffer (NEB #E7647A), 3 µL Ultra II End-prep enzyme mix (NEB #E76468). The mixture was incubated at 20 °C for 5 minutes and 65 °C for 5 minutes. After another AMPure XP beads clean-up step, the samples were barcoded by mixing the following reagents: 22.5 µL End-prepped cDNA, 2.5 µL native barcode (NB01-NB12, ONT barcode extension kit #EXP-NBD104), 25 µL Blunt/TA ligase master mix. The reaction mixture was incubated for 10 minutes at room temperature, and the barcoded samples were cleaned up using AMPure XP beads. cDNA amount was measured using Qubit, and samples were pooled in equal ratios, not exceeding 120 ng (200 fmol) as the maximum total amount of barcoded cDNA. The adapter ligation was performed by mixing 65 µL of the pooled barcoded sample, 5 µL Adapter Mix II (AMII, ONT cDNA sequencing kit), 20 µL NEBNext Quick Ligation Reaction Buffer 5X (NEB #B6058S) and 10 µL Quick T4 DNA Ligase (NEB #M2200L). The reaction mixture was incubated for 10 minutes at room temperature, after which the cDNA was cleaned up using AMPure XP beads and eluted in 13 μL of Elution Buffer (EB, ONT cDNA sequencing kit). The final amount was ~50 ng of cDNA, which was mixed with 37.5 µL Sequencing Buffer (SQB) and 2.5 µL Loading Beads (LB, ONT cDNA sequencing kit) and loaded onto a previously primed MinION R9.4.1 flow cell.

tag: cell line

value: PMK

value: Primary Mouse Keratinocyte


title: HO CSA, Male Rep4

tag: age


title: FC, OXY-VEH, Female, 3

description: O-V Female FC

value: Frontal Cortex

value: Neuron


title: PMK, replicate 1

description: Library name: PMK1


title: WT CSA, Male Rep2


title: Sample_45_Healthy Polish women


title: NAc, OXY-VEH, Male, 2

description: O-V Male NAc

value: Nucleus Accumbens

value: Oxycodone-Vehicle


title: NAc, OXY-VEH, Male, 1

description: O-V Male NAc


title: WT CSA, Male Rep1


title: Sample_44_Healthy Polish women


title: HO CSA, Fem Rep4

value: Female

value: 12.6 months


title: Sample_43_Healthy Polish women

value: Healthy Polish women


title: FC, OXY-VEH, Male, 4

description: O-V Male FC


title: FC, OXY-VEH, Male, 3

description: O-V Male FC


title: Sample_42_Healthy Polish women

value: F


title: WT CSA, Male Rep3

value: Kidney

value: 10.8 months


title: Sample_47_Healthy Polish women


title: HO CSA, Fem Rep3


title: HO CSA, Fem Rep2


title: Sample_41_Healthy Polish women


title: FC, OXY-VEH, Male, 2

description: O-V Male FC


title: HO CSA, Fem Rep1


title: FC, OXY-VEH, Male, 1

description: O-V Male FC


title: Sample_40_Healthy Polish women


title: WT CSA, Fem Rep4

value: 12.9 months


title: NAc, VEH-PSI, Female, 5

description: V-P Female NAc

value: Vehicle-Psilocybin


title: Sample_39_Healthy Polish women


title: WT CSA, Fem Rep3

value: 13.1 months


title: Sample_38_Healthy Polish women


title: NAc, VEH-PSI, Female, 4

description: V-P Female NAc


title: Sample_37_Healthy Polish women


title: WT CSA, Fem Rep1

value: 11.7 months


title: 15_2ETD7 repeat Heifer N°15 at the day (7) of the second embryo transfer (repeat)

city: Jouy-en-Josas

first: Mariam

last: Raliou

address: Allée de Vilvert

department: PHASE

country: France

institute: INRAE

description:
Heifer N°15 at the day (7) of the second embryo transfer (repeat)
253680910019_2_4

hyb_protocol: Labelled cRNA were hybridized on the custom bovine gene expression 8x60K array for 17 hours, centrifuge at 10 rpm for 65°C. Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 μm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.

scan_protocol: The slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 μm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.

data_processing: Raw.tiff images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE1_1010_Sep10” protocol. Median raw expression values were further normalized by quantile method

source_name: Peripheral White Blood Cells

label_protocol: RNA labeling was performed according to Agilent protocol “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labelling” version 6.5, May 2010 (Cat # G4140-90050). Complementary RNA (cRNA) samples were linearly amplified and labelled with cyanine 3 starting from 100 ng of total RNA.

extract_protocol: Total RNA of circulating white blood cells was isolated from PAXgene blood samples using the PAXgene Blood RNA system (PreAnalytiX, Qiagen/BD Company, France).

tag: breed

value: heifer

value: Peripheral White Blood Cells

tag: stage of postpartum period

value: Day (7) of the second embryo transfer


title: WT CSA, Fem Rep2


title: Sample_36_Healthy Polish women

tag: subject status

value: Peripheral Blood


title: NAc, VEH-PSI, Female, 2

description: V-P Female NAc

value: Neuron


title: NAc, VEH-PSI, Female, 3

description: V-P Female NAc

value: Nucleus Accumbens


title: 28_PCD14 Heifer N°28 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°28 at day 14 post-estrus of Preconceptional cycle
253680910015_2_4

value: Preconceptional cycle (estrus cycle)


title: 29_PCD14 Heifer N°29 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°29 at day 14 post-estrus of Preconceptional cycle
253680910018_2_2


title: 32_PCD14 Heifer N°32 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°32 at day 14 post-estrus of Preconceptional cycle
253680910016_2_2


title: Sample_35_Healthy Polish women

tag: as


title: CSBm/m, Male Rep3

tag: Sex

value: Male

value: CSBm/m


title: NAc, VEH-PSI, Female, 1

description: V-P Female NAc


title: FC, VEH-PSI, Female, 6

description: V-P Female FC

value: Frontal Cortex


title: Sample_34_Polish women with BC

description: DNA extracted from peripheral blood of Polish women with BC

value: Polish women with BC

value: F


title: 32_2ETD6 Heifer N°32 at the day (6) of the second embryo transfer

description:
Heifer N°32 at the day (6) of the second embryo transfer
253680910013_2_1

value: Day (6) of the second embryo transfer


title: 29_PCD7 Heifer N°29 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°29 at day 7 post-estrus of Preconceptional cycle
253680910016_1_2


title: 32_PCD7 Heifer N°32 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°32 at day 7 post-estrus of Preconceptional cycle
253680910014_1_2


title: 28_PCD7 Heifer N°28 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°28 at day 7 post-estrus of Preconceptional cycle
253680910019_1_1


title: 27_PCD7 Heifer N°27 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°27 at day 7 post-estrus of Preconceptional cycle
253680910017_2_3


title: 27_PCD14 Heifer N°27 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°27 at day 14 post-estrus of Preconceptional cycle
253680910013_1_3


title: 25_PCD7 Heifer N°25 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°25 at day 7 post-estrus of Preconceptional cycle
253680910012_2_2


title: 24_2ETD6 Heifer N°24 at the day (6) of the second embryo transfer

description:
Heifer N°24 at the day (6) of the second embryo transfer
253680910016_1_1


title: Sample_33_Polish women with BC


title: 23_2ETD6 Heifer N°23 at the day (6) of the second embryo transfer

description:
Heifer N°23 at the day (6) of the second embryo transfer
253680910016_1_3


title: FC, VEH-PSI, Female, 5

description: V-P Female FC


title: WT CSB, Male Rep3

value: Kidney

value: 13.3 months


title: Sample_32_Polish women with BC


title: FC, VEH-PSI, Female, 4

description: V-P Female FC

value: Vehicle-Psilocybin


title: WT CSB, Male Rep2


title: Sample_31_Polish women with BC


title: WT CSB, Male Rep1


title: FC, VEH-PSI, Female, 3

description: V-P Female FC


title: CSBm/m, Fem Rep3

value: Female

value: 10.3 months


title: 25_PCD14 Heifer N°25 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°25 at day 14 post-estrus of Preconceptional cycle
253680910016_1_4

value: heifer

value: Peripheral White Blood Cells


title: FC, VEH-PSI, Female, 1

description: V-P Female FC


title: Sample_29_Polish women with BC

value: Peripheral Blood


title: CSBm/m, Fem Rep2

value: 11.7 months


title: CSBm/m, Male Rep1

value: 15.6 months


title: 22_2ETD6 Heifer N°22 at the day (6) of the second embryo transfer

description:
Heifer N°22 at the day (6) of the second embryo transfer
253680910019_2_1


title: CSBm/m, Fem Rep1

value: 12.9 months


title: Sample_28_Polish women with BC


title: CSBm/m, Male Rep2

value: Male


title: 22_PCD14 Heifer N°22 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°22 at day 14 post-estrus of Preconceptional cycle
253680910012_1_1

value: Preconceptional cycle (estrus cycle)


title: WT CSB, Fem Rep3


title: 23_PCD14 Heifer N°23 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°23 at day 14 post-estrus of Preconceptional cycle
253680910015_1_2


title: NAc, VEH-PSI, Male, 4

description: V-P Male NAc

value: Nucleus Accumbens

value: Neuron


title: NAc, VEH-PSI, Male, 2

description: V-P Male NAc


title: 22_PCD7 Heifer N°22 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°22 at day 7 post-estrus of Preconceptional cycle
253680910016_2_3


title: 23_PCD7 Heifer N°23 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°23 at day 7 post-estrus of Preconceptional cycle
253680910019_2_3


title: Sample_30_Polish women with BC

value: Polish women with BC

value: F


title: FC, VEH-PSI, Female, 2

description: V-P Female FC

value: Frontal Cortex


title: Sample_26_Polish women with BC


title: Sample_27_Polish women with BC


title: NAc, VEH-PSI, Male, 1

description: V-P Male NAc


title: WT CSB, Fem Rep2

value: Kidney

value: 13.1 months


title: NAc, VEH-PSI, Male, 3

description: V-P Male NAc

value: Vehicle-Psilocybin


title: 21_PCD14 Heifer N°21 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°21 at day 14 post-estrus of Preconceptional cycle
253680910012_2_1


title: WT CSB, Fem Rep1

value: Female

value: 14.5 months


title: FC, VEH-PSI, Male, 5

description: V-P Male FC


title: Sample_24_Polish women with BC

description: DNA extracted from peripheral blood of Polish women with BC


title: Sample_23_Polish women with BC


title: FC, VEH-PSI, Male, 4

description: V-P Male FC


title: Sample_22_Polish women with BC


title: FC, VEH-PSI, Male, 3

description: V-P Male FC


title: 19_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910015_2_1

value: heifer

value: Peripheral White Blood Cells

value: Day (7) of the first embryo transfer


title: 19_PCD14 Heifer N°19 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°19 at day 14 post-estrus of Preconceptional cycle
253680910014_2_4


title: FC, VEH-PSI, Male, 2

description: V-P Male FC


title: Sample_20_Polish women with BC

value: Peripheral Blood


title: FC, VEH-PSI, Male, 1

description: V-P Male FC


title: Sample_25_Polish women with BC


title: Sample_19_Polish women with BC


title: 19_PCD7 Heifer N°19 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°19 at day 7 post-estrus of Preconceptional cycle
253680910017_2_4


title: Sample_18_Polish women with BC


title: NAc, VEH-VEH, Female, 4

description: V-V Female NAc

value: Vehicle-Vehicle


title: Sample_17_Polish women with BC


title: NAc, VEH-VEH, Female, 3

description: V-V Female NAc


title: 21_2ETD6 Heifer N°21 at the day (6) of the second embryo transfer

description:
Heifer N°21 at the day (6) of the second embryo transfer
253680910019_2_2

value: Day (6) of the second embryo transfer


title: Sample_21_Polish women with BC


title: NAc, VEH-VEH, Female, 5

description: V-V Female NAc


title: Sample_16_Polish women with BC


title: NAc, VEH-VEH, Female, 1

description: V-V Female NAc


title: 17_2ETD7 Heifer N°17 at the day (7) of the second embryo transfer

description:
Heifer N°17 at the day (7) of the second embryo transfer
253680910013_1_2

value: Day (7) of the second embryo transfer