title: Calu-3Ctrl_20hour_3

description:
Library name: Ctrl-3
Column name in raw count.xlsx: S_3_C6

value: wildtype


title: VT4

status: Public on Nov 30 2025

type: SRA

city: shanghai

first: dan

last: zhou

address: shanghai

department: Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine

country: China

institute: Tongji University

description:
Library name: sample 5
vitrified blastocyst group, replicate biosample 3

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

molecule: total RNA

organism: Mus musculus

source_name: Blastocyst

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

tag: tissue

value: Blastocyst

tag: group

value: non-melatonin treated vitrification


title: VT3

description:
Library name: sample 4
vitrified blastocyst group, replicate biosample 2


title: S. Typhimurium ΔcspE, control, replicate 3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
Rockhopper
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimgalore
Trimmed sequence reads were processed using Rockhopper Pipeline
Read count extraction and normalization were performed using featureCounts
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium
Supplementary files format and content: Read_Count_Data_All_Samples.xLSX

source_name: Bacteria

growth_protocol: Salmonella Typhimurium wild type and ΔcspE strains were grown in Luria Broth (LB) (Miller) with or without 3% bile (Sigma) at 37 °C, 180 rpm.

extract_protocol:
RNA was isolated using Trizol (Ambion)-chloroform (Sigma) extraction method.
As per Illumina recommended protocol

treatment_protocol: Cells were grown to O.D. 0.3 and then treated with 3% bile for 90 minutes.

tag: cell type

value: Bacteria

tag: genotype

value: cspE knockout

tag: treatment

value: Control


title: MVT4

description:
Library name: sample 8
vitrified blastocyst with 10-10 M melatonin added to vitrification and thawing media, replicate biosample 3

value: melatonin treated vitrification


title: HT29 subconfluent (2 days)

type: RNA

city: Hannover

first: Ralf

last: Gerhard

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute of Toxicology

country: Germany

institute: Hannover Medical School

description:
M7100
HT29

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 500ng of each fluorescently labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.
Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.
Averaged gPS values were normalized by Quantile normalization. Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 finally normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

label: Alexa Fluor 555

organism: Homo sapiens

source_name: HT29 cell line

label_protocol: 200ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one-round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. The entirety of generated cDNA was used for aaUTP-cRNA synthesis. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

growth_protocol: Cells were kept in standard medium supplemented with 8% fetal bovine serum and 100 µg/ml penicillin and 100 µM streptomycin.

extract_protocol: Total RNA was isolated with RNeasy mini kit from Qiagen.

treatment_protocol: All samples were untreated controls for comparison of constitutive gene expression and cell specific transcriptome.

tag: cell line

tag: culture condition

value: Subconfluent


title: VT2

description:
Library name: sample 3
vitrified blastocyst group, replicate biosample 1


title: Mouse, scRNA, 6-OHDA+NDST3

city: Seoul

first: Yujung

last: Chang

address: 98 Hannamdaero, Yongsan-gu

country: South Korea

institute: Stand Up Therapeutics Inc.

description: Library name: Mouse_SC_6N_R1

library_source: transcriptomic single cell

data_processing:
RNA-seq : The base calls binary is converted into FASTQ utilizing illumina package bcl2fastq. CUT&RUN : The base calls binary is converted into FASTQ utilizing illumina package bcl2fastq. CUT&RUN reads are trimmed using TrimGalore and CUT&RUN data are aligned using Bowtie. ATAC-seq : Raw sequencing reads were preprocessed using Trim Galore to remove adapter sequences and trim low-quality bases from both ends. The low-quality bases were filtered using a sliding window trimming approach. scRNA-seq : Raw BCL files generated by the Illumina HiSeq X Ten were demultiplexed into FASTAQ files using ‘cellranger mkfastq’ pipeline.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts and reads in peak for each sample

source_name: Brain

extract_protocol:
RNA-seq:Total RNA was isolated using an RNA extraction kit (Qiagen).A total of 1 µg of high-quality total RNA from each sample was utilized for library preparation following the manufacturer's protocol. CUT&RUN : The released DNA fragment were extracted using CUT&RUN Kit following manufacture's protocol. ATAC-seq : 50,000 nuclei were used transposition reaction using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) following manufacture's protocol. scRNA-seq : Tissue samples were enzymatically dissociated into single cell suspension using Multi Tissue Dissociation kit 1 (Miltenyi Biotec) in combination with the gentleMACS Dissociator, following the manufacturer's protocol. Post dissociation, myelin debris was removed via Percoll density gradient centrifugation, and red blood cells were eliminated using Red Blood Cell Lysis Solution (Miltenyi Biotec). Cell viability and concentration were assessed using the LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems).
RNA-seq :TruSeq Stranded mRNA Library Prep Kit following manufacture's protocol. CUT&RUN : TruSeq DNA Sample prep Kit following manufacture's protocol. ATAC-seq : Manual ATAC-Seq library preparation involves separate cell lysis, Tn5 transposase tagmentation, DNA purification, and PCR amplification steps performed individually. scRNA-seq : Single-cell libraries were generated using the Chromium Next GEM Single Cell 3’ v3.1 protocol (10x Genomics).

value: Brain

value: CNS

tag: strain

value: ICR

value: WT

value: 6-OHDA with NDST3 treatment


title: S. Typhimurium ΔcspE, control, replicate 2

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: Calu-3SAMHD1knockout1_20hours_2

city: Iowa City

first: Pak Hin Hinson

last: Cheung

state: Iowa

address: 51 Newton Raod

department: Department of Microbiology and Immunology

country: USA

institute: University of Iowa

description:
Library name: KO1-2
Column name in raw count.xlsx: S_5_KO15

data_processing:
Gene expression profiling using RNA-Seq was performed by the University of Iowa Genomics Division using manufacturer recommended protocols. Briefly, at least 500 ng of DNase I-treated total RNA was used to prepare sequencing libraries using the Illumina stranded mRNA library preparation kit (Cat. #20040534, Illumina, Inc., San Diego, CA). Barcoded libraries were quantified using a Qubit fluorometer (ThermoFisher Scientific) and pooled together to give the same molar concentration per sample. The pooled libraries were sequenced on the Element AVITI24 sequencing platform (Element Biosciences, San Diego, CA) on a Cloudbreak FS 150 cycle (2x75 bp) medium output sequencing flow cell (Cat. #:  860-00014) to generate at least 30M paired-end sequencing reads per sample. The raw base files were converted to fastq files using the Bases2fastq v2.1 tool.
Assembly: GRCh38
Supplementary files format and content: Excel

molecule: polyA RNA

growth_protocol: Calu-3 Ctrl, KO1 and KO2 cells were grown in DMEM/F12 with 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin

extract_protocol:
8 x 105 Calu-3 Ctrl, KO1 and KO2 cells were seeded in 6 well plates in biological triplicate. Cells were cultured in 2mL DMEM/F12 with 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. At 20 hours after seeding, cells were washed once with DPBS and lysed with RLT plus lysis buffer. Cellular RNA was purified with RNeasy Plus kit following manufacturer’s instructions. All RNA samples got RNA integrity Number (RIN) scores equal to or more than 9.9 as determined by Agilent BioAnalyzer by Genomics Division of Iowa Institute of Human Genetics (University of Iowa). RNA samples were processed through Illumina Stranded mRNA Prep (illumina) and sequenced by Element Aviti24 using Cloudbreak FS-High output flow cell at 150 cycle (2x75) by the Genomics Division.
The RNA samples were processed through Illumina Stranded mRNA Prep following manufacturer's protocol.

treatment_protocol: No additional treatment

value: Human bronciolar epithelial cells

value: SAMHD1 knockout by exon 1 frameshifting

value: 20 hours culturing in DMEM/F12 20% FBS, 1xP/S


title: Caco-2 subconfluent (2 days)

description:
M7101
Caco-2

source_name: Caco-2 cell line


title: Calu-3Ctrl_20hour_1

description:
Library name: Ctrl-1
Column name in raw count.xlsx: S_1_C4


title: S. Typhimurium ΔcspE, control, replicate 1


title: HeLa subconfluent (2 days)

description:
M7099
HeLa

source_name: HeLa cell line

value: HeLa


title: IVF2

description:
Library name: sample 1
fresh blastocysts without vitrification, serving as the control group, replicate biosample 1

value: fresh blastocysts


title: Mouse, scRNA, 6-OHDA

description: Library name: Mouse_SC_6_R1


title: Mouse, scRNA, sham

description: Library name: Mouse_SC_CTRL_R1

value: Sham-control


title: Caco-2 differentiated (14 days)

description:
M7102
Caco-2 diff

value: Differentiated


title: Met3-IP

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
H3K27ac in metformin-treated and control groups was compared with DNA-input metformin-treated and control groups, respectively. The distribution of reads to the genome on each chromosome was statistically compared. The number of reads is calculated in the range of 5kb, and the number of Log2 reads is calculated. MACS2 software was used to conduct peak calling analysis; count the number, distribution and width of peaks; and screen out peaks with significant enrichment (p value<0.05) and the genes corresponding to each peak. RepeatMasker software was used to remove repeated sequences, while DREME software was used to identify potential binding sites with related genes.
Assembly: mm9
Supplementary files format and content: bigwig file

molecule: genomic DNA

source_name: mFGSCs

growth_protocol: mFGSCre cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (LIF) (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 20 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Gibco), 2 mM L-glutamine (Sigma), 1 mM sodium pyruvate (Amresco),  100 IU/mL penicillin (Gibco), 100 μg/mL streptomycin (Gibco),  and 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Cells were cross-linked with 1% formaldehyde, terminated with 125 mM glycine solution, and centrifuged (4℃, 550 × g) to collect the cells. The resulting pellet was resuspended in Lysis Buffer (160 μl) and incubated on ice for 10min. Next, fragmentation was carried out using an ultrasonic breaker (Diagenode Bioruptor Pico, Belgium). Subsequently, the pellet was resuspended in RIPA ChIP Buffer (275 μl) and centrifuged (4℃; 12,000 × g), and the supernatant was carefully removed and put on ice. From each sonicated sample, 150 μl was retained as the input. Next, the rest of the sample was reacted in RIPA Buffer at 4°C overnight with H3K27ac antibodies (ab4729, Abcam) pre-bonded to paramagnetic beads (Thermo Fisher Scientific). The beads were washed with RIPA Buffer and the sample tubes were placed in a magnetic rack. DNA was isolated and purified using proteinase K (Merck, Darmstadt, Germany), phenol-chloroform-isoamylalcohol (25:24:1) (Bio-Rad, Hercules, CA USA), chloroform-isoamylalcohol (24:1) (Bio-Rad), 100% ethanol, and 75% ethanol. Chromatin samples were sent for library constructing and high-throughput sequencing.
The reads information was compared to the mouse genome (mm9) using bowtie2. Next, Samtools v2.0.1 was used to remove duplicate information, followed by deepTools2 v3.1 to read and generate normalized genome coverage tracks from mapped reads.

treatment_protocol: 1 μM metformin treatment mFGSCs for 24 hours

value: ovary

tag: antibody

value: anti-H3K27ac (ab4729, Abcam)


title: Igf2bp3-/-, replicate 3, RNC-seq

city: Guangzhou

first: Zhenyi

last: Huang

state: GuangDong

address: ShaTaiNan Street 1023-1063,Baiyun

department: Development

institute: Southern Medical University

description:
KO-RNC-rep3
RNC

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (version 0.6.6) was used to trim the 3' adapter in the raw reads. Low-quality reads with the Phred quality score < 25 were discarded.
The trimmed reads were aligned to the mouse reference genome assembly build GRCm38 (mm10) using Hisat2 (version 2-2.1.0).
Mapped reads were then assembled into transcripts under the guidance of reference annotation with Stringtie (v2.1.7).
To normalize gene expression levels, the fragments per kilobase of transcript per million mapped reads (FPKM) was employed.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

source_name: spermatids

growth_protocol: Mice were housed in a light and temperature-controlled room (light: 12 h dark and 12 h light cycles; temperature: 24 ± 0.5 °C) with ad libitum access to food and water. Then, 8-week-old male mice were treated.

extract_protocol:
Samples were dissolved in 1 ml lysis buffer and incubated on ice for 10 mins. After centrifugation at 12,000 g for 15 mins at 4°C, the supernatant was collected, layered onto a 5% to 50% sucrose gradient. Samples were peak fractionated by A260 absorption using the gradient station. mRNAs associated with 4 or more ribosomes were collected as polysome fractions and subjected to RNA extraction with TRIzol reagent.
RNAs were purified by poly(A) selection and used for library construction using NEBNext ultra II directional RNA library prep kit for Illumina (NEB) according to the manufacturer’s protocols. The libraries were sequenced on a Hi-seq X10 instrument.

treatment_protocol: Cells were treated with cycloheximide to block translational elongation during the whole process of spermatids isolation using FACS.

value: spermatids

value: Flow sorting

tag: age

value: 8 weeks

tag: Sex

value: male


title: S. Typhimurium WT, control, replicate 2

value: Bacteria

value: Wild type

value: Control


title: Degenerative NP cells (33 Y M) 2

city: Salt Lake City

first: Jason

last: Gertz

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description: Library name: 25852X4

data_processing:
Sequencing reads were aligned to the hg38 build of the human genome using HISAT2.
SAMtools was used to convert SAM files to BAM files.
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads mapped to known genes were assigned with featureCounts.
Within each cell line, read counts were normalized and analyzed for differential expression via the DESeq2 package in R.
Assembly: hg38
Supplementary files format and content: rna_seq_asc_hek293_normalized_counts.txt
Supplementary files format and content: rna_seq_patient_data_normalized_counts.txt

source_name: Degenerative human nucleus pulposis

growth_protocol: Primary human nucleus pulposus cells (hNPCs) were cultured in complete growth medium containing DMEM-HG (ThermoFisher Scientific) supplemented with 10% FBS (ThermoFisher Scientific), 50 g/mL gentamicin (Corning), 25 mM HEPES (ThermoFisher Scientific), and 2 ng/mL of recombinant human fibroblast growth factor-basic (rhFGF, Peprotech, Cranbury, NJ, 100-18C).

extract_protocol:
RNA was harvested using Quick-RNA-Kit (Zymo Research, Irvine, CA).
Isolated total RNA (100-1000ng) was prepared using an Illumina TruSeq stranded mRNA Library prep Kit with PolyA Selection.

treatment_protocol: hNPCs (p1-p2) were plated at a density of 20,000 cells/cm2, allowed to attach overnight, and transduced with EF-1a-dCas9-VPR-eGFP (Addgene, #241307) lentivirus, (1:2 dilution) in growth medium containing 4 g/mL polybrene, the following day. 72-hours following transduction, hNPCs were subjected to fluorescence activated cells sorting (FACS) to select for GFP+ expressing cells.

value: Degenerative human nucleus pulposis

value: Male

value: Nucleus pulposus

value: Non-targeting gRNA

tag: replicate


title: Met3-Input


title: ZNF865 upregulated degenerative NP cells (32 Y M) 2

description: Library name: 23965X6

source_name: Degenerative human nucleus pulposis with ZNF865 upregulation

value: CRISPRa ZNF865


title: S. Typhimurium WT, control, replicate 1


title: Igf2bp3-/-, replicate 2, RNC-seq

description:
KO-RNC-rep2
RNC


title: ZNF865 upregulated degenerative NP cells (32 Y M) 1

description: Library name: 23965X5

value: Degenerative human nucleus pulposis with ZNF865 upregulation


title: Met2-IP


title: S. Typhimurium WT, control, replicate 3


title: Calu-3Ctrl_20hour_2

description:
Library name: Ctrl-2
Column name in raw count.xlsx: S_2_C5

value: Human bronciolar epithelial cells

value: wildtype

value: 20 hours culturing in DMEM/F12 20% FBS, 1xP/S


title: IVF5

description:
Library name: sample 2
fresh blastocysts without vitrification, serving as the control group, replicate biosample 2

value: Blastocyst

value: fresh blastocysts


title: Degenerative NP cells (33 Y M) 1

description: Library name: 25852X3


title: Igf2bp3-/-, replicate 1, RNC-seq

description:
KO-RNC-rep1
RNC

value: spermatids

value: Flow sorting


title: Healthy NP cells (32 Y F)

description: Library name: 23965X4

source_name: Healthy human nucleus pulposus

value: Healthy human nucleus pulposus

value: Female


title: Met2-Input

value: ovary


title: Igf2bp3+/-, replicate 3, RNC-seq

description:
WT-RNC-rep3
RNC

value: 8 weeks

value: male


title: Healthy NP cells (69 Y F)

description: Library name: 23965X3


title: duodenum tissue and colon tissue, CD or HfiD feed 5w, HFD feed 8w, rep2

city: Huddinge

first: Zhi

last: Peng

state: Stockholm

address: Blickagången 16

department: MedH

country: Sweden

institute: Karolinska Institutet

description: Library name: CD_HfiD_Group_HFD8w_SI_LI_rep2

data_processing:
The FASTQ files of Stereo-seq data were processed following a previously established workflow (Chen et al., 2022; Chen et al., 2023). In this process, the first reads containing CID (Coordinate Identity) sequences were matched to the pre-defined coordinates of the Stereo-seq chip obtained from the initial round of sequencing, allowing up to one base mismatch. Reads with MID (Molecular Identifiers) that included ambiguous bases (N) or had more than two bases with a quality score below 10 were excluded. The CID and MID information were incorporated into the read headers. The remaining reads were aligned to the reference genome using STAR (mm10). UMIs sharing the same CID and gene locus were consolidated into a single UMI, permitting one base mismatch to correct errors from sequencing or PCR. This processed data was binned into bin 50 to create an expression profile matrix for downstream analysis. The full Stereo-seq pipeline, SAW, is available at https://github.com/STOmics/SAW. The expression matrix containing CID spatial information was processed with the Seurat version 5.1.0 in R version 4.4.1. For Stereo-seq data preprocessing, cells containing a total number of detected genes less than 100 or percentage of mitochondrial genes larger than 10% were filtered out. The resulting cells were further processed by scaling, feature genes selection, bath effects remove (Harmony version 1.2.1), PCA dimension reduction, UMPA dimension reduction and clustering with resolution parameter set at 0.7 (small intestinal tissue) and 0.6 (large intestinal tissue). For CD-HFD4w small intestinal and CD large intestinal sections, clusters that exhibit abnormal spatial aggregation were removed by manual coordinate selection. Cell clusters were manually annotated based on previously published marker genes and GO enrichment functions. Trajectory analysis was performed using Monocle3 version 1.3.7 and scvelo version 0.3.2 to construct predicted pseudotime trajectory between enterocyte progenitors, enterocytes and goblet cells. For monocle analysis, the “cluster_cells” was performed with resolution parameter set at 0.01 (small intestinal) and 0.001 (large intestinal). For scvelo analysis, unspliced and spliced RNA for each cell were extracted from all intestinal samples with SAW. Through filtering, normalizing, computing moments and modeling, the velocity “stream” were visualized in embedded UMAP graphics.
Assembly: mm10
Supplementary files format and content: Expression matrix file and loom file for velocity analysis.
Library strategy: Spatial Transcriptomics

source_name: duodenum tissue and colon tissue

extract_protocol:
Tissue section preparation, library construction and sequencing for stereo-seq The procedures were conducted as previously described (Chen et al., 2022). Briefly, 10-μm thick sections of small and large intestine were placed onto a precooled stereo-seq chip for incubation at 37°C for 5 min, followed by fixation in methanol at -20°C for 40 min. The chip with tissue was stained with the Qubit ssDNA labelling and detection kit (Invitrogen, Q10212) for 5 min and subsequently washed with 0.1x SSC buffer (Thermo Fisher, AM9770) supplemented with 0.05 U/μl RNase inhibitor (Solarbio, R8061), before being imaged with an Eclipse Ti-7 microscope (Nikon).
RNA extraction from the tissue to the chip was achieved by incubation with 0.1% pepsin dissolved in 0.01M HCl with a pH value of 2 at 37°C for 12 min. The released RNA was reverse transcribed overnight at 42°C using the SuperScript II kit (Thermo Fisher, 18064-014). The cDNA-containing chip was further processed with a tissue removal buffer containing 10 mM Tris-HCl, 25 mM EDTA, 100 mM NaCl, 0.5% SDS and Exonuclease I (NEB, M0293L), before being amplified with the KAPA HiFi Hotstart Ready Mix kit (Roche, KK2602). 20 ng DNA was fragmented with Tn5 transposase and amplified with the KAPA HiFi Hotstart Ready Mix kit. The PCR product was purified with the AMPure XP Beads (Beckman Coulter) and sequenced with an MGI DNBSEQ-Tx sequencer (MGI).

value: duodenum tissue and colon tissue


title: Met1-IP

value: anti-H3K27ac (ab4729, Abcam)


title: duodenum tissue and colon tissue, CD or HfiD feed 5w, HFD feed 8w

description: Library name: CD_HfiD_Group_HFD8w_SI_LI

extract_protocol:
Tissue section preparation, library construction and sequencing for stereo-seq: The procedures were conducted as previously described (Chen et al., 2022). Briefly, 10-μm thick sections of small and large intestine were placed onto a precooled stereo-seq chip for incubation at 37°C for 5 min, followed by fixation in methanol at -20°C for 40 min. The chip with tissue was stained with the Qubit ssDNA labelling and detection kit (Invitrogen, Q10212) for 5 min and subsequently washed with 0.1x SSC buffer (Thermo Fisher, AM9770) supplemented with 0.05 U/μl RNase inhibitor (Solarbio, R8061), before being imaged with an Eclipse Ti-7 microscope (Nikon).
RNA extraction from the tissue to the chip was achieved by incubation with 0.1% pepsin dissolved in 0.01M HCl with a pH value of 2 at 37°C for 12 min. The released RNA was reverse transcribed overnight at 42°C using the SuperScript II kit (Thermo Fisher, 18064-014). The cDNA-containing chip was further processed with a tissue removal buffer containing 10 mM Tris-HCl, 25 mM EDTA, 100 mM NaCl, 0.5% SDS and Exonuclease I (NEB, M0293L), before being amplified with the KAPA HiFi Hotstart Ready Mix kit (Roche, KK2602). 20 ng DNA was fragmented with Tn5 transposase and amplified with the KAPA HiFi Hotstart Ready Mix kit. The PCR product was purified with the AMPure XP Beads (Beckman Coulter) and sequenced with an MGI DNBSEQ-Tx sequencer (MGI).

value: CD or HfiD feed 5w, HFD feed 8w


title: Igf2bp3+/-, replicate 2, RNC-seq

description:
WT-RNC-rep2
RNC


title: Degenerative NP cells (32 Y M)

description: Library name: 23965X1

value: Degenerative human nucleus pulposis

value: Male

value: Nucleus pulposus

value: Non-targeting gRNA


title: con3-IP


title: duodenum tissue and colon tissue, CD or HfiD feed 5w, HFD feed 0w

description: Library name: CD_HfiD_Group_HFD0w_SI_LI

value: CD or HfiD feed 5w, HFD feed 0w


title: Met1-Input


title: mBMSCCXCR4@OMV3

city: Zhengzhou

first: Yingying

last: Chen

address: Jianshedong Road

institute: Zhengzhou University

data_processing:
Data quality control: Sequencing fragments are converted into sequence data (reads) by base recognition of the image data measured by high-throughput sequencers, and the files are in fastq format, which mainly contain the sequence information of the sequenced fragments as well as their corresponding sequencing quality information.
Sequence alignment to a reference genome: The index of the reference genome was constructed using HISAT2 v2.0.5, and paired-end clean reads were compared to the reference genome using HISAT2 v2.0.5.
Quantification of gene expression levels: The FPKM of each gene is calculated based on the length of the gene and the number of reads mapped to that gene is calculated.
Differential expression analysis: For samples with biological duplicates, differential expression analyses between the two comparison combinations were performed using the DESeq2software.
Differential gene enrichment analysis: GO enrichment analysis and KEGG pathway enrichment statistics of differentially expressed genes were achieved by clusterProfiler software, and GO terms and KEGG pathways with P < 0.05 were set as significant enrichment results.
Assembly: Mus_musculus.GRCm39.chr
Supplementary files format and content: Matrix table includes FPKM values for each sample.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using VAHTS Universal V6 RNA-seq Library Prep Kit following manufacturer's protocols.


title: Degenerative NP cells (60 Y M) 2

description: Library name: 23835X5

data_processing:
Libraries were sequenced on a NovaSeq X at a depth of ~50 million reads/sample and 100 bases from the 3’ end of each read were trimmed using seqtk with the following parameters: trimfq -e 100. Trimmed reads were then aligned to the hg38 build of the human genome using Bowtie with the following parameters: --chunkmbs 512 -m 1 -t --best -q -S -l 32 -e 80 -n 2.
SAM files were converted into BAM files and sorted using SAMtools.
Peaks representing regions of accessible chromatin were called using MACS2 with an adjusted P-value cutoff of <0.05 and an mfold parameter between 15 and 100.
FeatureCounts was used to quantify reads that aligned to ATAC-seq peaks called across all samples. Reads were normalized and chromatin regions displaying differential accessibility were identified using the DESeq2 package for R.
Assembly: hg38
Supplementary files format and content: Indexed genomic coordinates containing regions of open chromatin in a tab-delimited text file (BEDGraph).
Supplementary files format and content: Genomic coordinates of peak calls from BEDGraph output in a Microsoft Excel file (narrowPeak).

extract_protocol:
Primary patient samples were prepared in technical duplicate, where 50,000 cells per replicate were taken from cryogenically frozen vials and centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was aspirated, and the resulting cell pellet was washed with 250 µL of ice-cold 1X PBS, pH 7.4 (Thermo Scientific; 10010072). The cells were then centrifuged at 500 x g for 5 minutes at 4°C, the supernatant was aspirated, and the resulting cell pellet was resuspended in 50 µL of lysis buffer containing the following: 10 mM Tris-HCl, pH 7.4 (Sigma-Aldrich; T2194), 3 mM MgCl2 (Sigma-Aldrich; M1028), 10 mM NaCl (Sigma-Aldrich; 71386), 0.1% NP-40 (Millipore Sigma; 492016), 0.1% Tween-20 (Bio-Rad; 1610781), and 0.01% digitonin (Invitrogen; BN20061). Samples were then lysed via incubation on ice for 15 minutes and centrifuged at 500 x g for 5 minutes at 4°C.  Following lysis, 1 mL of wash buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, and 0.1% Tween-20) was added to each sample, which was then centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was aspirated, and the resulting cell pellet was resuspended a second time in 1 mL of wash buffer. To pellet nuclei, cells were centrifuged at 500 x g for 10 minutes at 4°C. The supernatant was aspirated, and each resulting nuclei pellet was resuspended in transposition buffer containing the following: 10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 10% Dimethylformamide (Fisher Bioreagents; BP1160), and 1 µL of TDE1 Tagment DNA enzyme per sample (Illumina; 20034197) diluted in PBS, pH 7.4. For the transposition reaction, nuclei were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer C (EP5382000015) set to rotate at 1000 RPM. Following transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 kit (D4014) according to the manufacturer’s instructions with a binding buffer to sample ratio of 5:1.
The purified DNA was then amplified by PCR using a final concentration of 1X Phusion Master Mix (New England Biolabs; M0530), and 200 nM each of forward and reverse barcode primers. Amplified libraries were purified using a 1:1 volume ratio of AMPure XP beads (Beckman Coulter; A63882) and fragment size distribution and quality were assessed using a High-Sensitivity D1000 ScreenTape assay.


title: mBMSCCXCR4@OMV2


title: Igf2bp3-/-, replicate 2, RNA-seq

description:
KO-RNA-rep2
RNA


title: con2-IP


description: Library name: 23835X6

value: Degenerative human nucleus pulposis with ZNF865 upregulation

value: CRISPRa ZNF865


title: mBMSCCXCR4@OMV1


description: Library name: 23835X3


title: Control3


title: Healthy NP cells (69 Y F) 2

description: Library name: 23835X4


title: Igf2bp3-/-, replicate 1, RNA-seq

description:
KO-RNA-rep1
RNA

value: spermatids


title: Degenerative NP cells (60 Y M) 1

description: Library name: 23835X2


title: con3-Input


title: Igf2bp3+/-, replicate 3, RNA-seq

description:
WT-RNA-rep3
RNA

value: Flow sorting


title: con1-IP


title: con1-Input


title: Igf2bp3+/-, replicate 1, RNA-seq

description:
WT-RNA-rep1
RNA


title: Healthy NP cells (69 Y F) 1

description: Library name: 23835X1

value: Healthy human nucleus pulposus


title: Igf2bp3+/-, replicate 1, RNC-seq

description:
WT-RNC-rep1
RNC


title: duodenum tissue and colon tissue, CD or HfiD feed 5w, HFD feed 4w

description: Library name: CD_HfiD_Group_HFD4w_SI_LI

value: CD or HfiD feed 5w, HFD feed 4w


title: Igf2bp3+/-, replicate 2, RNA-seq

description:
WT-RNA-rep2
RNA


title: Igf2bp3-/-, replicate 3, RNA-seq

description:
KO-RNA-rep3
RNA


title: Control1


title: Prefrontal Cortex Female VPA Biological Rep 1

status: Public on Nov 29 2025

city: Guelph

first: Olivia

middle: Olga Fraser

last: Williams

state: ON

address: 50 Stone Road West

department: Biomedical Sciences

country: Canada

institute: Unviersity of Guelph

hyb_protocol: Following fragmentation, cRNA were hydridized on Affymetrix GeneChip Porcine Gene 1.0 ST arrays, according to manufacturer's instructions. GeneChips were washed and stained on the Gene Atlas platform.

scan_protocol: GeneChips were scanned on the GeneAtlas platform.

data_processing: The data were analyzed with GeneSpring GX software v. 14.9 using default Affymetrix settings.

label: biotin

organism: Rattus norvegicus

source_name: Female, VPA Autism

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: Prefrontal cortex tissue was dissected on postnatal day 35 (adolescence) from male or female rodents exposed to either saline (control) or valproic acid (VPA) (autism group) in utero

treatment_protocol: Saline group: administered same volume saline by weight (0.9% saline) on gestation day 12.5 VPA group: concentration: 250mg/mL dose: 500mg/kg valproic acid dissolved in 0.9% saline injected on gestation day 12.5 in utero.

tag: condition

value: Autism

tag: in utero exposure

value: VPA

value: Prefrontal cortex


title: Interferon gamma, rep1

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

description: Library name: IFNG_1

data_processing:
Adapter sequences were removed by matching them to a reference with a maximum mismatch of 2, and the clipping thresholds were set for seed and palindrome to 30 and 10, respectively. Reads were then trimmed using a sliding window of 4 base pairs, where trimming occurred if the average quality score within the window fell below 30. Bases at the leading and trailing ends of the reads were removed if their quality score was below 15.
Reads shorter than 30 bases after trimming were discarded. The trimmed reads were then pseudoaligned to the GRCh38 reference genome with Gencode v29 annotations using Kallisto 0.48.0 to quantify transcript abundances.
Assembly: Human GRCh38 reference genome
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for all FASTQ files.

extract_protocol:
RNA was extracted using a standard Trizol extraction protocol.
RNA libraries were made using the Illumina TruSeq Stranded mRNA kit which utilizes oligo-dT beads to select and amplify mRNA. cDNA was synthesized using nine rounds of PCR and quality and concentrations of the DNA libraries were assayed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay and the DNA high sensitivity Qubit. Raw bulk RNA-seq data was initially assessed for quality using FastQC 0.11.9, and results summarized with MultiQC 1.10.1. Data then underwent quality trimming and adapter removal using Trimmomatic 0.39.

treatment_protocol: Cells were treated with DPSB, INF alpha (50 ng/ml), beta (50 ng/ml) or gamma (100 ng/ml).

value: iPSC-Microglia

value: WT

value: IFNgamma


title: Interferon beta, rep4

description: Library name: IFNB_4

value: IFNbeta


title: Interferon gamma, rep3

description: Library name: IFNG_3


title: Interferon gamma, rep2

description: Library name: IFNG_2


title: Prefrontal Cortex Male VPA Biological Rep 5

source_name: Male, VPA Autism

extract_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

value: Male


title: Prefrontal Cortex Female VPA Biological Rep 4

value: Female


title: Prefrontal Cortex Female VPA Biological Rep 5


title: Interferon gamma, rep4

description: Library name: IFNG_4


title: Prefrontal Cortex Female Saline Control Biological Rep 3

source_name: Female, Saline Control

value: Control

value: SAL


title: con2-Input

value: ovary


title: Control2


title: Prefrontal Cortex Male Saline Control Biological Rep 4

source_name: Male, Saline Control


title: Prefrontal Cortex Male Saline Control Biological Rep 2


title: Prefrontal Cortex Male Saline Control Biological Rep 1


title: Prefrontal Cortex Male Saline Control Biological Rep 5


title: Prefrontal Cortex Male Saline Control Biological Rep 3


title: Interferon beta, rep3

description: Library name: IFNB_3


title: Prefrontal Cortex Male VPA Biological Rep 1


title: Prefrontal Cortex Female VPA Biological Rep 2


title: Prefrontal Cortex Female Saline Control Biological Rep 1


title: Prefrontal Cortex Male VPA Biological Rep 3


title: Prefrontal Cortex Female VPA Biological Rep 3


title: Prefrontal Cortex Female Saline Control Biological Rep 4


title: Prefrontal Cortex Female Saline Control Biological Rep 2


title: Prefrontal Cortex Male VPA Biological Rep 4


title: Interferon beta, rep2

description: Library name: IFNB_2


title: Prefrontal Cortex Male VPA Biological Rep 2


title: Interferon beta, rep1

description: Library name: IFNB_1


title: Interferon alpha, rep4

description: Library name: IFNA_4

value: IFNalpha


title: Interferon alpha, rep2

description: Library name: IFNA_2


title: Interferon alpha, rep1

description: Library name: IFNA_1


title: Interferon alpha, rep3

description: Library name: IFNA_3


title: control, rep4

description: Library name: Control_4

value: DPBS


title: control, rep2

description: Library name: Control_2


title: M2-BMDM treated B16F10-2

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: murine melanoma cell

value: CM from M2-BMDM


title: Recipient WBC from mice treated with control CAR T, ADT/HTO (CD45.1+)

city: New York

first: Omar

last: Abdel-Wahab

state: New York

address: 1275 York Ave

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Control_RecipientWBC_ADT_HTO
antibody-derived oligonucleotide
Control_RecipientWBC.filtered_feature_bc_matrix.barcodes.tsv.gz
Control_RecipientWBC.filtered_feature_bc_matrix.features.tsv.gz
Control_RecipientWBC.filtered_feature_bc_matrix.matrix.mtx.gz
Control_RecipientWBC.raw_feature_bc_matrix.barcodes.tsv.gz
Control_RecipientWBC.raw_feature_bc_matrix.features.tsv.gz
Control_RecipientWBC.raw_feature_bc_matrix.matrix.mtx.gz

library_source: other

data_processing:
5’ single-cell RNA and ADT sequencing FASTQs were processed using the nf-core scRNA-seq pipeline v4.0.0 with 10x Genomics CellRanger Multi v8.0.0 and aligned to GRCm39 modified to include U5 snRNP200- and control-CAR constructs.
TCR-seq FASTQ files were processed using CellRanger V(D)J v8.0.0.
Assembly: GRCm39
Supplementary files format and content: Cellranger multi output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger VDJ: filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: Blood

extract_protocol:
Bone marrow mononuclear cells isolated from recipient mice were incubated with mouse Fc receptor blocker (BioLegend; 101320) and then stained with FITC anti-mouse CD45.1 (BioLegend; 110706), PE anti-mouse CD45.2 (BioLegend; 109808), PE-Cy7 anti-mouse CD3 (BioLegend; 100220), and Brilliant Violet 711 anti-mouse CD11b (BioLegend; 101242) antibodies in PBS supplemented with 0.5% BSA. RN2 cells (CD45.2+ CD11b+), donor-derived T cells (CD45.2+ CD3+), and recipient-derived WBCs (CD45.1+) cells were sorted using an Aria cytometer (BD Biosciences). 500,000 sorted cells were incubated with Fc receptor blocker (BioLegend, 101320), stained with TotalSeq-C Mouse Universal Cocktail (BioLegend, 199903) in cell staining buffer (BioLegend, 420201) for 30 min at 4°C, and subsequently washed with PBS supplemented with 0.04% BSA.
Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification.  Between 20,000 and 60,000 cells were targeted for each sample, and several samples were multiplexed together on one lane of 10X Chromium X, following cell hashing protocol using TotalSeqC (BioLgened). The scRNA-seq and scTCR-seq libraries were prepared using the 10x Single Cell Immune Profiling Solution Kit, according to the manufacturer’s instructions. For gene expression library construction, amplified cDNA was fragmented and end-repaired, double-sided size-selected with SPRIselect beads, PCR-amplified with sample indexing primers (98 °C for 45 s; 14–16 cycles of 98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s; 72 °C for 1 min), and double-sided size-selected with SPRIselect beads. For TCR library construction, TCR transcripts were enriched from 2 μl of amplified cDNA by PCR (primer sets 1 and 2: 98 °C for 45 s; 10 cycles of 98 °C for 20 s, 67 °C for 30 s, 72 °C for 1 min; 72 °C for 1 min). Following TCR enrichment, enriched PCR product was fragmented and end-repaired, size-selected with SPRIselect beads, PCR-amplified with sample-indexing primers (98 °C for 45 s; 9 cycles of 98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s; 72 °C for 1 min), and size-selected with SPRIselect beads. Final libraries (GEX, TCR and HTO) were sequenced on Illumina NovaSeq X platform (R1 – 26 cycles, i7 – 10 cycles, i5 – 10 cycles, R2 – 90 cycles).

value: Blood

value: WBC

value: Control CAR


title: control, rep3

description: Library name: Control_3


city: Cambridge

last: Corradin

state: MA

address: 455 Main Street

department: Biology

institute: Whitehead Institute /MIT

description: Library name: iPSC-derived microglia, Perturb-seq, sample 2

data_processing:
Alignment and countaing of scRNA-seq reads were performed using default parameters in Cellranger-8.0.1.  Supplemental file 5_crispr_guides_MG.csv was used for CRISPR guide alignment.  Perturb-seq analyses were performed in Seurat v5.2.1. Cells were filtered using the following metrics: >250 genes per cell, >500 UMIs per cell, <20% mitochondrial reads, and >0.8 log10 genes per UMI. Cells with 3 or more raw reads of a given sgRNA were considered positive for that sgRNA.  Gene expression data was scaled and centered using Seurat ScaleData.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-separated values and matrix files

source_name: AG07657 iPSC

growth_protocol: See manuscript methods for details on iPSC differentiations

extract_protocol:
iMGLs were dissociated with 0.25% Trypsin/EDTA, and FACS was performed to isolate BFP+ cells among the top 50% mCherry-expressing cells.  Cells were spun, washed and counted in FACS buffer lacking EDTA, and the cell suspension containing ~1700 total cells/uL and ~1400 live cells/uL was then subjected to library preparation
Libraries were prepared according to the 10X 5' GEM-X scRNA-seq library prep kit with Feature Barcode Kit containing the CRISPR RT oligo.  29,000 cells were loaded onto each of 7 chip wells, and cDNA and sgRNA libraries from each sample were combined into separate cDNA and sgRNA pools. cDNA and sgRNA pooled samples were loaded across four NovaSeq S4 lanes at a 9:1 molar ratio, respectively, and sequenced with 150bp paired end reads

treatment_protocol: iPSC-derived microglia (iMGLs) were transduced with Vpx-associated lentivirus containing a Perturb-seq sgRNA library after 7 days in microglia maturation media.  7 days later, transduced cells were isolated by FACS for BFP expression, with gating on the top ~50% mCherry levels, representing dCas9-KRAB ZIM3 transgene expression.  After sorting cells were immediately used to prepare libraries for scRNA-seq

value: AG07657 iPSC

value: iPSC-derived microglia

value: AAVS1 dCas9-KRAB ZIM3 clone

value: Lentiviral transduction of Perturb-seq sgRNA library


description: Library name: iPSC-derived microglia, Perturb-seq, sample 7


title: control, rep1

description: Library name: Control_1

value: iPSC-Microglia

value: WT


title: 8882165, with CTL, WT HIV, env positive

first: Louise

last: Leyre

state: NY

address: 413 E 69th St

department: Infectious Diseases

institute: Weill Cornell Medicine

description: Library name: 8882165-pCTL-WT-envp

data_processing:
Raw reads were quality checked with Fast QC
Reads were aligned to the human reference genome (GRCh38.p12) using STAR v2.6.0c71 with default parameters
Gene abundances were calculated with featureCounts v1.6.2 72 using composite gene models from Gencode release 28
Assembly: hg38
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

source_name: PBMC

growth_protocol: Purified human Naïve CD4+ T cells were activated with human anti-CD3/CD28-coated for 7 days before being infected with HIV JRCSF strain and expanded for additional 7 days in presence of IL2

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (Qiagen). 50-500ng of total RNA depending on donor were used to construct the sequencing libraries
RNA libraries were prepared using Illumuna standard mRNA prep kits

value: PBMC

value: CD4+ T Cells

value: pCTL


title: B027, without CTL, WT HIV, env positive

description: Library name: B027-nCTL-WT-envp-9

value: nCTL


title: 8882165, without CTL, WT HIV, env positive

description: Library name: 8882165-nCTL-WT-envp


title: 8882165, with CTL, TW10esc HIV, env positive

description: Library name: 8882165-pCTL-TW10-envp


title: G092594, with CTL, WT HIV, env positive

description: Library name: G092594-pCTL-WT-envp


title: G092504, with CTL, TW10esc HIV, env positive

description: Library name: G092504-pCTL-TW10-envp


title: RG138, without CTL, WT HIV, env positive

description: Library name: RG138-nCTL-WT-envp-11


title: RG138, with CTL, WT HIV, env positive

description: Library name: RG138-pCTL-WT-envp-9


title: RG138, with CTL, TW10esc HIV, env positive

description: Library name: RG138-pCTL-TW10esc-envp-10


title: B027, with CTL, WT HIV, env positive

description: Library name: B027-pCTL-WT-envp-7


description: Library name: iPSC-derived microglia, Perturb-seq, sample 1


description: Library name: iPSC-derived microglia, Perturb-seq, sample 4


title: RG138, without CTL, TW10esc HIV, env positive

description: Library name: RG138-nCTL-TW10esc-envp-12


title: B027, with CTL, TW10esc HIV, env positive

description: Library name: B027-pCTL-TW10esc-envp-8


title: 8882165, without CTL, TW10esc HIV, env positive

description: Library name: 8882165-nCTL-TW10-envp


description: Library name: iPSC-derived microglia, Perturb-seq, sample 5


description: Library name: iPSC-derived microglia, Perturb-seq, sample 6


title: IP_0h_2

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Library name: IP_0h_2

data_processing:
mRNA samples from human and mouse were aligned to the mm9/hg19 genome using STAR v.2.5.3a with default settings (‘--alignIntronMax 1000000’) (Dobin et al., 2013). For gene expression (TPM) and read counts, rsem-calculate-expression (rsem/1.3.3) was employed (Li and Dewey, 2011). m6A-GI and m6A-SI metrics were derived using the bam2ReadEnds.R script (Garcia-Campos et al., 2019) as per Dierks et al. 2021, calculating m6A IP enrichment against input coverage.
Assembly: mm9 & hg19
Library strategy: m6A-seq

growth_protocol: Mammalian cell lines were grown at 37°C and 5 % CO2 in DMEM (10% FBS, with Antibiotics Penn/Strep)

extract_protocol:
Nucleozol total RNA extraction protocol according to the manufacturers protocol.
All libraries were conducted according to the libraray preparation protocol in Dierks et al. 2021. For RNA-seq, the protocol was performed as in Dierks 2021, excluding the m6A IP step, (performed as if only is the input sample.
m6A-seq2 & RNA-seq (m6A-seq2 protocol exluding the m6A IP section)


title: Input_16h_1

description: Library name: IN_16h_1

data_processing:
mRNA samples from human and mouse were aligned to the mm9/hg19 genome using STAR v.2.5.3a with default settings (‘--alignIntronMax 1000000’) (Dobin et al., 2013). For gene expression (TPM) and read counts, rsem-calculate-expression (rsem/1.3.3) was employed (Li and Dewey, 2011). m6A-GI and m6A-SI metrics were derived using the bam2ReadEnds.R script (Garcia-Campos et al., 2019) as per Dierks et al. 2021, calculating m6A IP enrichment against input coverage.
Assembly: mm9 & hg19


title: Input_8h_1

description: Library name: IN_8h_1


title: UC_SCC

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

description: Library name: UC_SCC_20241126

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 43+50-base paired-end mode.
Raw sequencing data were converted to matrices of expression using Space Ranger (version spaceranger-3.1.1, 10X Genomics).
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz:  tar.gz compressed file of Space Ranger output folder "filtered_feature_bc_matrix"
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format file including counts data for each gene and spot-position (barcode) combination
Supplementary files format and content: spatial.tar.gz:  tar.gz compressed file of Space Ranger output folder "spatial" with only selected files
Library strategy: Spatial Transcriptomics

source_name: bladder cancer

extract_protocol:
Human bladder cancer tissue FFPE slice gene expression were detected by 10x Visium HD Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared using Visium HD Reagent Kit (#PN-1000668, 10x Genomics) following the manufacturer’s protocol.

value: bladder cancer


description: Library name: iPSC-derived microglia, Perturb-seq, sample 3


title: IP_16h_2

description: Library name: IP_16h_2


title: Input_4h_2

description: Library name: IN_4h_2


title: IP_16h_1

description: Library name: IP_16h_1


title: IP_8h_2

description: Library name: IP_8h_2


title: IP_2h_2

description: Library name: IP_2h_2


title: IP_4h_2

description: Library name: IP_4h_2


title: Input_2h_2

description: Library name: IN_2h_2


title: IP_8h_1

description: Library name: IP_8h_1


title: Input_8h_2

description: Library name: IN_8h_2


title: Input_0h_2

description: Library name: IN_0h_2


title: Input_0h_1

description: Library name: IN_0h_1


title: Input_16h_2

description: Library name: IN_16h_2


title: TR11_16184

city: Nashville

first: Maxwell

middle: Stuart

last: Hamilton

state: TN

address: 2215 Garland Ave, Medical Research Building IV

department: Cancer Biology

institute: Vanderbilt University

description: Library name: TR11_16184

data_processing:
Data was processed, aligned and normalized according to the standard Space Ranger pipeline.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mts.gz: gene expression count data
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials
Supplementary files format and content: detected_tissue_image.jpg: image of spots in tissue
Supplementary files format and content: scalefactors_json.json: scale factors of images
Supplementary files format and content: tissue_hires_image.png: high res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and their locations
Library strategy: Spatial Transcriptomics

source_name: primary colorectal cancer

extract_protocol:
5 um sections were cut from FFPE blocks
Slides were processed by the standard Visium v2 spatial transcriptomics protocol according to the manufacturer's instructions.

value: primary colorectal cancer


title: IP_4h_1

description: Library name: IP_4h_1


title: TR11_21723

description: Library name: TR11_21723


title: TR11_206

description: Library name: TR11_206


title: TR11_18105

description: Library name: TR11_18105


title: smc3 input

city: State College

first: Shane

middle: Douglas

last: Stoeber

state: Pennsylvania

address: 406 South Frear Building

department: BMMB

institute: Penn State

description: Library name: smc3 input

data_processing:
For ChIP-seq, ~5 million paired-end reads were generated and aligned to S. cerevisiae genome sacCer3 with Bowtie2 (version 2.5.4) using default parameters. Peak calling was performed with MACS2 (version 2.2.7.1). Bigwig files were generated using deepTools bamcoverage (version 3.5.6). Two biological replica were performed at each time point.
Assembly: sacCer3
Supplementary files format and content: bigwig and bed

organism: Saccharomyces cerevisiae

extract_protocol:
For chip-seq, Yeast cultures (50 mL) were grown in SCD–Met medium to an OD660 of 0.4. Crosslinking was performed by adding 1.39 mL of 37% formaldehyde directly to each culture and incubating at room temperature for 20 min. Crosslinking was quenched with 2.7 mL of 2.5 M glycine for 5 min. Cells were pelleted at 3000 rpm for 3 min at 4 °C, resuspended in 1 mL TBS, and washed twice with 1 mL TBS. Cells were lysed by resuspension in 250 μL FSPP buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% protease inhibitor cocktail, 1 mM PMSF) with 300 μL glass beads. Samples were vortexed at 4 °C twice for 20 min each, separated by a 10 -min break. Lysates were released by piercing the tube ends with a hot needle and centrifuging at 3000 rpm for 5 min at 4 °C into 15 mL tubes. Lysates were recovered, supplemented with 1 mL FSPP buffer, and sonicated (30 s on/off cycles for 7 min). After centrifugation at 14,000 rpm for 20 min at 4 °C, 200 μL supernatant was saved as input control. For immunoprecipitation, 200 μL of lysate was diluted with 800 μL FSPP buffer and incubated with 20 μL pre-blocked magnetic IgG beads and 1–2 μg of antibody (TAP: Thermo CAB1001) overnight at 4 °C with rotation. Beads were sequentially washed with 1) FA Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), 2) FA Lysis + 150 mM NaCl, 3) FA Lysis + 500 mM NaCl, 4) LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and 5) TE buffer (pH 8.0). ChIP sample was then eluted with 400 μL elution buffer (50mM NaCl, 50mM Tris-HCl, pH 8.0, 10mM EDTA, 1% SDS) by rotating at 30°C for 30 min. Eluates were treated with 5 μL of 20 mg/mL proteinase K overnight at 65 °C. Input controls were processed in parallel by adding 160 μL FA Lysis buffer, 40 μL 10% SDS, and 5 μL proteinase K, followed by overnight incubation at 65 °C. DNA was extracted with phenol:chloroform:isoamyl alcohol. ChIP samples were resuspended in 40 μL H20. Input samples were resuspended in 380 μL TE buffer with 10 μL of 10mg/mL RNase A and incubated at 37°C for 30 minutes. DNA was washed with EtOH and resuspended in 40 μL H20. Factor enrichment was verified through qPCR.
MNase and ChIP sequencing libraries were prepared using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina® (Catalog # E7645L) according to the manufacturer’s instructions. The sequencing libraries were sequenced on a NextSeq 2000 machine in 2 x 50 bp paired-end sequencing mode at the Genomics Research Incubator at The Pennsylvania State University.

value: Cbf1-AID, Smc3-AID

value: 0min cbf1 induction


title: TR16_23542

description: Library name: TR16_23542


title: input rep2

description: Library name: input rep2


title: Input_2h_1

description: Library name: IN_2h_1


title: input

description: Library name: input


title: Brain input library sequencing; RNA-seq

city: Durham

first: Yanting

last: Luo

state: NC

address: 289 CARL Building, 213 Research Dr

department: Molecular Genetics and Microbiology

institute: Duke University

description:
Library name: Brain Input
FS DNA Library Prep Kit

data_processing:
Final 10X libraries were sequenced using NextSeq 2000 reagents (Illumina; R1 28, I1 10, I2 10, R2 90). We sequenced reporter-targeted enrichment libraries independently on the Illumina NextSeq 1000 platform. FASTQ files from both output libraries were recovered with BCL Convert (v3.10.4, Illumina). We used the following bases mask: Y28;I10;I10;Y90. Output FASTQ files from both the unenriched and reporter-targeted enrichment libraries across multiple lanes were concatenated together for downstream analysis. For the brain experiment, GFP+ cells were pooled from all embryos in each experiment to control for batch effects associated with anatomical differences in electroporation and dissection.
To score enhancer activity from scSTARR-seq data, we produced count matrices using CellRanger v6.0 (10x Genomics) with a custom reference genome. For the brain experiment, the custom reference genome includes the sequence of the mouse reference mm10 with additional FASTA records containing the sequences of each STARR-seq reporter construct and the pCAG-GFP injection reporter sequence. For the heart experiment, the custom reference genome includes the sequence of the human reference hg38 with additional FASTA records containing the sequences of each STARR-seq reporter construct and the pCAG-GFP injection reporter sequence. For the brain experiment, we performed subsequent analysis for cluster identification in Seurat v4.0. Cells containing 200 or fewer genes or more than 7,500 genes were removed. The library was normalized, and 2,000 highly variable features were identified. Variation in gene expression based on cell-cycle related genes was regressed from cluster analysis in dataset scaling using an annotated set of G2M and S phase related genes provided in Seurat. k-nearest neighbors (k=20) were calculated in the space of significant principal components (in this case, 30 principal components) and clustering was performed with the Louvain-Jaccard method. Visualizations were generated in uniform manifold approximation and projection (UMAP) space. Cell clusters with no GFP reads were removed, and the remaining cells were re-clustered. We manually assigned cell type identities to each cluster based on each cluster’s expression of cell type marker genes. Cell type marker genes were curated from literature. Multiple clusters corresponding to the same cell type were pooled as metaclusters for subsequent analysis. For both the brain experiment and the heart experiment, we implemented gonomics: starrSeqAnalysis to remove unique molecular identifier (UMI) duplicates and normalize the output library read count of each construct by both the input library read count of the same construct and the mean output library read count of the negative control constructs. We quantified the enhancer activity score for each construct as the input and negative control-normalized UMI count. To calculate cell type-specific enhancer activity score for each construct, we grouped input-normalized output library UMI counts by construct and cell type, then conducted negative control normalization for each cell type. To calculate the statistical significance of the enhancer activity scores, we first determined that gamma distribution fit our negative controls better than normal distribution, based on its support for values from 0 to positive infinity, the appearance of the distribution and quantile-quantile plots, and the values of goodness-of-fit and Shapiro-Wilk normality tests. We fit a gamma distribution to the enhancer activity scores of the negative controls and calculated the right-tailed p-values of each construct. We conducted this statistical analysis both overall and by cell type. To examine the read distribution among cells in the in vitro scSTARR-seq experiments, we additionally used gonomics: starrSeqAnalysis to create pseudoreplicates by randomly assorting cells into 1 of 5 bins. The number 5 was chosen because it was the maximum number of bins that still assured that each bin still had >1 read of each negative control construct.
To protect the genomic sequence of the human who contributed the DU11 cell line, we filtered the raw files for the heart experiment to only retain reads that map to the input library construct vectors. Using the CellRanger output BAM files, we filtered for BAM reads that mapped to the constructs with mapping quality >=1 and no heavy clipping, then extracted the FASTQ reads corresponding to the BAM reads in both R2 and R1 (samtools:fastq, gonomics: fastqFilter).
Assembly: For the brain experiment: mm10, For the heart experiment: hg38
Supplementary files format and content: rds, matrix files, and tab-separated values files

molecule: other

organism: Escherichia coli

extract_protocol:
For the brain experiment, electroporated brains were harvested and dissected in ice-cold sterile PBS. Meninges were removed and GFP+ portions of the cortices were incubated at 37◦C for 10 minutes in 0.25% trypsin-EDTA supplemented with 0.1% DNAse I. Following incubation, the trypsin solution was removed and replaced with ice- cold 10% FBS/HBSS/Propidium iodide supplemented with 0.01% DNAse I. A single cell suspension was then generated by trituration with a fire-polished glass pipette and filtered with a 30 μm cell strainer. For the heart experiment, at the end of the incubation period, we detached the cardiomyocytes with Accutase to create a single cell suspension. For both the brain experiment and the heart experiment, cells were then stained with the LIVE/DEAD Near-IR Dead Cell Stain per manufacturer’s instructions. Following staining, viable GFP+ cells were bulk sorted using a FACS Aria II cytometer.
Output libraries were constructed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 protocol, 10x Genomics). Briefly, Gel bead-Cell complexess were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Input plasmid libraries were fragmented and sequenced with the NEBNext Ultra II FS DNA Library Prep Kit per manufacturer's instrutions.

treatment_protocol: For the brain experiment, the input STARR-seq plasmid library were delivered to developing mouse cerebral cortices (E14.5) via in utero electroporation and harvested 48 hours post electroporation. For the heart experiment, we differentiated human induced pluripotent stem cells of the DU11 cell line into cardiomyocytes, delivered the input STARR-seq plasmid library via transfection after at least 30 days of differentiation, then incubated the input library for 2 days.

tag: batch


title: Input_4h_1

description: Library name: IN_4h_1


title: IP_0h_1

description: Library name: IP_0h_1


title: Heart input library sequencing; RNA-seq

description:
Library name: Heart Input
FS DNA Library Prep Kit


title: Output mouse  targetEnrich_1A

description:
Library name: Output mouse  targetEnrich_1A
10x Genomics

source_name: Cerebral cortex

value: Cerebral cortex

value: In utero electroporation


title: Output mouse  targetEnrich_1B

description:
Library name: Output mouse  targetEnrich_1B
10x Genomics


title: Adrb2_cKO_RTX_12H_2

first: Ya-Chieh

last: Hsu

address: 7 Divinity Ave, sherman-fairchild

department: Stem Cell and Regenerative Biology

institute: Harvard University

description:
Library name: Adrb2_cKO_RTX_12H_2
RNA sequencing of treatet samples

data_processing:
Data was processed using Cell Ranger v7.1.0, including demultiplexing, barcode processing, gene counting, and aggregation of single-cell gene expression data.
Assembly: mm10
Supplementary files format and content: H5 files - gene exression matrix

source_name: Skin

extract_protocol:
Cells were isolated from Adrb2 cKO C57BL/6J mice in first anagen after 12 hr injection with RTX. Mouse back skin containing the damaged regions was dissected, and the fat layer was removed by scraping with a surgical scalpel. The dermal fraction was isolated by incubating the skin in a collagenase solution in HBSS on an orbital shaker for 45-60 minutes at 37°C with scraping of the dermis. Following collection of the dermis, the remaining skin was incubated in trypsin-EDTA for 25-30 minutes at 37°C to collect the epidermis. Single cell suspensions of each fraction were obtained by filtering through a 70-mm and 40-mm filter. Cell suspensions were then centrifuged for 8 minutes at 350g at 4°C and resuspended in 5% FBS with a CD16/F32 Fc blocking antibody (BioLegend 101302, 1:100).
Libraries were constructed according to the 10x Genomics Single Cell v3.1 protocol

value: Skin

value: C57BL/6 Adrb2 cKO

value: Adrb2 cKO

value: RTX


title: 90min smc3 rep2 ChIP-seq

description: Library name: 90min smc3 rep2 ChIP-seq

value: 90min cbf1 induction


title: IP_2h_1

description: Library name: IP_2h_1


title: Adrb2_cKO_RTX_12H_1

description:
Library name: Adrb2_cKO_RTX_12H_1
RNA sequencing of treated samples


title: Output mouse allCell_1A

description:
Library name: Output mouse allCell_1A
10x Genomics


title: 60min smc3 rep2 ChIP-seq

description: Library name: 60min smc3 rep2 ChIP-seq

value: 60min cbf1 induction


title: smc3 input rep2

description: Library name: smc3 input rep2


title: Output mouse allCell_1B

description:
Library name: Output mouse allCell_1B
10x Genomics


title: CRFR1-KO-1

city: shanghai

first: zhang

last: yue

address: No. 225 Changhai Road, Yangpu District, Shanghai

institute: fudan university

description:
Library name: LC1
LC represents CRFR1-KO

data_processing:
Then sequence quality was verified using FastQC .
Alignment with Reference Genome .
Quantification of Gene Abundance .
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/
Supplementary files format and content: tab-delimited texts file includes raw counts  for each Sample

source_name: para-pancreatic tumor tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

treatment_protocol: Para-tumor tissues were randomly selected from CRFR1 CKO and WT PDAC mice for RNA sequencing.

value: para-pancreatic tumor tissues


title: CRFR1-KO-2

description:
Library name: LC2
LC represents CRFR1-KO


title: 30min smc3 rep2 ChIP-seq

description: Library name: 30min smc3 rep2 ChIP-seq

value: 30min cbf1 induction


title: WT1

description:
Library name: L1
L represents WT

value: WT


title: WT2

description:
Library name: L3
L represents WT


title: Output human cell line scSTARR-seq; scRNA-seq

description:
Library name: Heart Output
10x Genomics

value: Cardiomyocyte

value: In vitro transfection


title: 90min smc3 ChIP-seq

description: Library name: 90min smc3 ChIP-seq


title: SVCT, vector control, normoxia, repeat 3

city: Nathan

first: Yezhou

last: Yu

state: QLD

address: 170 Kessels Road

department: School of Environment and Science

country: Australia

institute: Griffith University

description: Library name: SVCT-N6

data_processing:
GUDSF were processed using STAR, transcript reads were aligned to the reverse strand of the National Center for Biotechnology Information (NCBI) reference genome GRCh38.p14.
The alignment results were processed using featureCounts to obtain the reverse-strand feature counts
Assembly: GRCh38.p14
Supplementary files format and content: A csv file containing raw counts data for each sample.

source_name: SVCT

growth_protocol: Cells were grown at 37°C with 5% CO2 under atmospheric oxygen conditions (21% O2) for normoxic incubation. For hypoxic conditions cells were cultured at 37°C with 5% CO2 and 0.1% O2 in a C-Chamber hypoxic growth chamber attached to the ProOx C21 model controller (Biospherix, New York, USA). Dulbecco's Modified Eagle Medium (DMEM) (Thermo Fisher, Waltham, USA) with 10% foetal bovine serum (FBS) (Bovogen, Victoria, Australia) was used as the complete growth media.

extract_protocol:
RNA was extracted using the Monarch Total RNA Extraction and Isolation Kit (New England Biolabs, Ipswich, USA).
Library Preparation was done using Illumina Stranded Mrna Library Kit & Illumina RNA UDI Indexes

treatment_protocol: Lipofectamine 3000 Reagent (Thermo Fisher, Waltham, USA) was used for transfec-tion. For RNA sequencing, approximately 0.3-0.4 million cells were seeded into 2 mL of complete growth media in each well of a 6-well plate. Cells were cultured at 37°C over-night to let them attach. Two solutions were prepared on the second day. Solution 1 con-tained 5 µg plasmid DNA, 5 µL P3000 Reagent and 125 µL Opti-MEM medium. Solution 2 contained 5 µL Lipofectamine 3000 Reagent and 125 µL Opti-MEM. The two solutions were mixed and incubated at room temperature for 10 min and slowly added to the cells in triplicate. The plate was gently swirled and incubated at 37°C before further experi-mentation.

value: SVCT

value: vector control, normoxia


title: SVCT, CA3 overexpression, normoxia, repeat 1

description: Library name: SVCT-N1

value: CA3 overexpression, normoxia


title: SVCT, CA3 overexpression, normoxia, repeat 3

description: Library name: SVCT-N3


title: SVCT, vector control, normoxia, repeat 1

description: Library name: SVCT-N4


title: SVCT, vector control, hypoxia, repeat 3

description: Library name: SVCT-H6

value: vector control, hypoxia


title: SVCT, CA3 overexpression, normoxia, repeat 2

description: Library name: SVCT-N2


title: SVCT, vector control, hypoxia, repeat 2

description: Library name: SVCT-H5


title: SVCT, vector control, normoxia, repeat 2

description: Library name: SVCT-N5


title: 0min smc3 rep2 ChIP-seq

description: Library name: 0min smc3 rep2 ChIP-seq

value: Cbf1-AID, Smc3-AID

value: 0min cbf1 induction


title: SW780_OE

city: Tianjin

first: Chi

address: No.94 Weijin Road, Nankai District

department: School of medicine

institute: Nankai University

description: Library name: sample 8

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

tag: transfection

value: Transfect with human p53R213* overexpression plasmid


title: SVCT, CA3 overexpression, hypoxia, repeat 3

description: Library name: SVCT-H3

value: CA3 overexpression, hypoxia


title: 60min smc3 ChIP-seq

description: Library name: 60min smc3 ChIP-seq


title: Intracranial syngeneic TRP GBM tumor

city: Ann Arbor

first: Wajd

middle: N.

last: Al-Holou

state: MI

address: 1500 E Medical Center Dr

department: Neurosurgery

institute: University of Michigan

description: Library name: 11913-SP-3

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files and the Cell Ranger Pipeline (version 8.0.0) was used to align reads and generate count matrices.
Assembly: For patient-derived GBM models (GBM12, GBM38, and HF2303), cells were aligned to a combined human and mouse reference transcriptome GRCh38_and_GRCm39-2024-A with the addition of luciferase sequence and the syngeneic TRP GBM cells were aligned to mouse reference transcriptome GRCm39-2024-A with the addition of luciferase sequence using Cell Ranger (version 8.0.0).
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Brain tumor

extract_protocol:
Intracranial syngeneic TRP GBM tumors and patient-derived GBM tumors (GBM12, GBM38, and HF2303) were harvested and dissociated using Collagenase Type II (Invitrogen, 17101015) with rotation at 37°C. The cell suspension was passed through a 40um strainer (Fisherbrand, 22363547), centrifuged, and resuspended followed by application of RBC lysis buffer (Biolegend).
Single cell suspensions were subjected to counting on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 1000 cells/µL. Single cell 3’ gene expression libraries were generated using the 10x Genomics Chromium instrument following the manufacturer’s protocol. In brief, suspensions were loaded onto the 10x chip along with reverse transcription (RT) master mix and appropriate gel beads. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed, and the resulting Post GEM-RT product was cleaned up and the cDNA amplified. cDNA was subjected to enzymatic fragmentation and size selection to optimize the cDNA size prior to final library construction following the manufacturer’s protocol (10x Genomics; 3’ v4 (mouse)).  Final library quality was assessed using the LabChip GX (PerkinElmer). Pooled libraries were then subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files and the Cell Ranger Pipeline (10x Genomics) was used to align reads and generate count matrices.

value: Brain tumor

value: IDH WT


title: SW780_NC

description: Library name: sample 7

value: Transfect with control PCDH empty vector


title: 30min smc3 ChIP-seq

description: Library name: 30min smc3 ChIP-seq


title: SVCT, CA3 overexpression, hypoxia, repeat 2

description: Library name: SVCT-H2


title: 0min smc3 ChIP-seq

description: Library name: 0min smc3 ChIP-seq


title: SVCT, CA3 overexpression, hypoxia, repeat 1

description: Library name: SVCT-H1


title: MDA-MB-231, vector control, normoxia, repeat 3

description: Library name: MDA-N6


title: 90min rep2 ChIP-seq

description: Library name: 90min rep2 ChIP-seq

value: 90min cbf1 induction


title: mb49_oe2

description: Library name: sample 6

value: Transfect with mouse p53R210* overexpression plasmid


title: MDA-MB-231, vector control, normoxia, repeat 2

description: Library name: MDA-N5


title: mb49_oe1

description: Library name: sample 5

value: Transfect with mouse p53Q189* overexpression plasmid


title: 60min rep2 ChIP-seq

description: Library name: 60min rep2 ChIP-seq

value: 60min cbf1 induction


title: SVCT, vector control, hypoxia, repeat 1

description: Library name: SVCT-H4


title: MDA-MB-231, CA3 overexpression, normoxia, repeat 1

description: Library name: MDA-N1


title: MDA-MB-231, CA3 overexpression, normoxia, repeat 3

description: Library name: MDA-N3


title: 0min rep2 ChIP-seq

description: Library name: 0min rep2 ChIP-seq


title: MDA-MB-231, vector control, hypoxia, repeat 1

description: Library name: MDA-H4


title: DMS114-SH2

description: Library name: sample 3

value: Transfect with shP53#2


title: mb49_nc

description: Library name: sample 4


title: MDA-MB-231, vector control, hypoxia, repeat 2

description: Library name: MDA-H5


title: MDA-MB-231, CA3 overexpression, normoxia, repeat 2

description: Library name: MDA-N2


title: 30min rep2 ChIP-seq

description: Library name: 30min rep2 ChIP-seq

value: 30min cbf1 induction


title: MDA-MB-231, CA3 overexpression, hypoxia, repeat 2

description: Library name: MDA-H2


title: MDA-MB-231, vector control, hypoxia, repeat 3

description: Library name: MDA-H6


title: DMS114-SH1

description: Library name: sample 2

value: Transfect with shP53#1


title: HEK293T, vector control, normoxia, repeat 4

description: Library name: Hek-6

value: vector control, normoxia


title: DMS114-NC

description: Library name: sample 1

value: Transfect with control PLKO empty vector


title: LYZKL

city: Wuhan

first: Zhidong

address: Donghu Road, No. 115, Wuchang District

institute: Wuhan University

description: Library name: Sample 2

data_processing:
The Cell Ranger software pipeline (v6.1.2) provided by 10×Genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix, using the reference genome mm10 (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A).
For each cell, we quantified the numbers of genes and UMIs and kept high-quality cells with the detection threshold of 600-4000 genes and 1000-25000 UMIs.
We used a relatively high threshold to ensure that we have filtered out the most of barcodes associated with empty partitions or doublet cells.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

growth_protocol: T cells were sorted from lung tumors of Tmem173fl/fl→KrasLSL-G12D/+Lkb1fl/fl (WTKL) and Tmem173fl/fl;Lyz2-Cre→KrasLSL-G12D/+Lkb1fl/fl (LYZKL) chimeric mice that were intranasally injected with Ad-Cre (2x106 pfu per mouse).

extract_protocol:
the CD4pos and CD8pos population was isolated as described above. Single-cell RNA-seq libraries were generated using Chromium Single cell 3’ Library & Gel Bead Kit v3.0 Kits (10×Genomics) according to the manufacturer’s protocol. Briefly, about 105 single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. About 15000-25000 cells were added to each channel to generate single-cell gel-beads in emulsion (GEMs) for a targeted cell recovery estimate of 10000 single cells (6609 and 7202 for WTKL and LYZKL mice, respectively)
After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). The cDNAs were then amplified by PCR with 12 cycles. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification via PCR (8 cycles). The purified libraries were sequenced on the Illumina NovaSeq 6000 with 28 cycles of read1, 8 cycles of i7 index, and 91 cycles of read2. And finally, 150 bp paired-end reads were generated.

value: lung

value: T cells

value: 8 weeks after intranasal injection of Ad-Cre


title: MDA-MB-231, CA3 overexpression, hypoxia, repeat 3

description: Library name: MDA-H3


title: 60min ChIP-seq

description: Library name: 60min ChIP-seq


title: HEK293T, vector control, normoxia, repeat 3

description: Library name: Hek-5


title: HEK293T, vector control, normoxia, repeat 1

description: Library name: Hek-49


title: 0min ChIP-seq

description: Library name: 0min ChIP-seq

value: 0min cbf1 induction


title: TSMF6

city: Houston

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

description: pool of 12 female retinas

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR (ver2.5) software.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package (2_1.6.3).  The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, pvalue and adjusted pvalue for each group.

source_name: Retina

extract_protocol:
Retinas were extracted, stored in RNAlater solution(QIAGEN). RNA was harvested using RNAeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: Embryonic E15.5


title: WTKL

description: Library name: Sample 1

value: 8 weeks after intranasal injection of Ad-Cre and tamoxifen treatment


title: MDA-MB-231, vector control, normoxia, repeat 1

description: Library name: MDA-N4


title: HEK293T, CA3 overexpression, normoxia, repeat 4

description: Library name: Hek-3

value: CA3 overexpression, normoxia


title: 90min ChIP-seq

description: Library name: 90min ChIP-seq

value: 90min cbf1 induction


title: 90min smc3 rep2 MNase-seq

description: Library name: 90min smc3 rep2 MNase-seq

data_processing:
20 million reads per sample were generated and aligned to the sacCer3 genome assembly using Bowtie2 with presets “--very-sensitive". Bigwig files were generated using deepTools bamcoverage (version 3.5.6) using a 130-170bp size selection and alignments were trimmed by 15bp on either side using offset 15 -15. Two biological replica were performed at each time point
Assembly: sacCer3
Supplementary files format and content: bigwig and bed

extract_protocol:
For MNase-seq, 1.5 OD660 units of cells were harvested and washed sequentially with 1 mL water and 1 mL 1M sorbitol. The pellet was re-suspended in 0.5mL spheroplasting solution (1 M sorbitol, 0.5 mM 2-mercaptoethanol, 0.18 mg/ml zymolyase) and incubated at room temperature for 7 minutes with gentle inversion. Spheroplasts were collected by centrifugation at 500 x g for 3 min, washed twice with 1 mL of 1 M sorbitol, and resuspended in 200 μL digestion buffer (1 M sorbitol, 50 mM NaCl, 100 mM Tris-Cl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 1 mM 2-mercaptoethanol, 0.5 mM spermidine, 0.075% NP-40). Samples were incubated at 37°C for 8 min with 1U of MNase (Sigma N3755). Reactions were terminated by adding 20 μL quench buffer (250 mM EDTA and 5% SDS). DNA was purified by phenol–chloroform extraction.
MNase and ChIP sequencing libraries were prepared using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina® (Catalog # E7645L) according to the manufacturer’s instructions. The sequencing libraries were sequenced on a NextSeq 2000 machine in 2 x 50 bp paired-end sequencing mode at the Genomics Research Incubator at The Pennsylvania State University.

value: Cbf1-AID, Smc3-AID


title: HEK293T, CA3 overexpression, normoxia, repeat 3

description: Library name: Hek-2


title: MDA-MB-231, CA3 overexpression, hypoxia, repeat 1

description: Library name: MDA-H1

value: CA3 overexpression, hypoxia


title: HEK293T, CA3 overexpression, normoxia, repeat 1

description: Library name: Hek-19


title: 30min smc3 rep2 MNase-seq

description: Library name: 30min smc3 rep2 MNase-seq


title: TSMF4

description: pool of 12 female retinas


title: TSCF5

description: pool of 12 female retinas

value: wild type


title: TSMF5

description: pool of 12 female retinas


title: MEC1 cells, Biotinylated miR-scramble mimics, 48h, rep1

city: Granada

first: Francisco

last: Hernández-Torres

state: Granada

address: Avda. de la Investigación, 11

country: Spain

institute: University of Granada

description: Library name: Sample 6

data_processing:
Libraries were sequenced on a HiSeq 2500 platform (Illumina), and base calling was performed with RTA v1.18.66.3. FastQ files for each sample were generated using bcl2fastq v2.20.0.422 (Illumina). Sequencing reads were aligned to the mouse reference transcriptome (mm10 v92) and quantified with RSEM v1.3.1.
Assembly: mouse reference transcriptome (mm10 v92)
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: Cells were seeded on coated wells with 0.1% gelatin solution  and cultured in DMEM high glucose supplemented with 10% Fetal bovine serum  and 2% penicillin/streptomycin and incubated at 37ºC, 5% CO2

extract_protocol:
Transfected epicardial cellswere harvested 48 h post-transfection and lysed using the miRNeasy Tissue/Cells Advanced kit lysis buffer. Complexes of biotinylated RISC and associated mRNAs were captured using streptavidin-coated magnetic beads with background reduction achieved via Argonaute immunoprecipitation
A total of 2.5 ng of RNA was used to generate cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). From this, 1 ng of amplified cDNA was used to prepare barcoded sequencing libraries with the Nextera XT DNA Library Preparation Kit (Illumina), in which cDNA fragmentation and adapter ligation occur in a single reaction, followed by amplification and cleanup. Library size was assessed using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip, and concentrations were determined with a Qubit® fluorometer (Thermo Fisher Scientific).

treatment_protocol: Cells were trasnfected, either with Biotinylated miR-200b mimics or  Biotinylated scramble control miRNA, by using  Lipofectamine-2000 and optiMEM medium  following the manufacturer’s

value: Mouse embryonic epicardial cell line

value: WT

value: Biotinylated miR-scramble mimics transfection


title: 60min smc3 rep2 MNase-seq

description: Library name: 60min smc3 rep2 MNase-seq

value: 60min cbf1 induction


title: MEC1 cells, Biotinylated miR-scramble mimics, 48h, rep4

description: Library name: Sample 9


title: 30min ChIP-seq

description: Library name: 30min ChIP-seq

value: 30min cbf1 induction


title: 0min smc3 rep2 MNase-seq

description: Library name: 0min smc3 rep2 MNase-seq


title: MEC1 cells, Biotinylated miR-200b mimics, 48h, rep5

description: Library name: Sample 5

value: Biotinylated miR-200b mimics transfection


title: MEC1 cells, Biotinylated miR-scramble mimics, 48h, rep5

description: Library name: Sample 10


title: MEC1 cells, Biotinylated miR-scramble mimics, 48h, rep3

description: Library name: Sample 8


title: TSCF4

description: pool of 12 female retinas


title: TSCF6

description: pool of 12 female retinas


title: Mouse, FLOX_19, HFD 16 weeks

first: Xiaoge

state: Hubei

address: BAYI road

institute: wuhan university

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: Pancreatic islet

growth_protocol: Animals were housed in laboratory cages at 22 ± 3 °C unless specifically indicated, with a humidity of 35 ± 5% under a 12-h dark/light cycle (lights on at 7:00 a.m.).

extract_protocol:
Total RNA from tissue was extracted and purified with TRIzol reagent
The sequencing library was performed on DNBSEQ-T7 platform (PE150) using DNBSEQ-T7RS Reagent Kit

treatment_protocol: Endothelial cell specific IRE1α-knockout mice (Ern1EC-KO) mice were produced after Tamoxifen intraperitoneal injection. Ern1fl/fl; VE-cadherin-Cre-ERT2 mice and Ern1fl/fl mice were injected with 2 mg of tamoxifen for 5 consecutive days at the age of 4 weeks. For diet-induced obesity, male Ern1fl/fl mice and their Ern1EC-KO littermates were fed a high-fat diet (HFD, 60% kcal fat; Research Diets) for 16 weeks, starting at 8 weeks of age.

value: Pancreatic islet

value: Ern1 floxed

value: 60% fat diet for 16 weeks


title: MEC1 cells, Biotinylated miR-scramble mimics, 48h, rep2

description: Library name: Sample 7


title: Mouse, FLOX_18, HFD 16 weeks


title: HEK293T, vector control, normoxia, repeat 2

description: Library name: Hek-4

value: vector control, normoxia


title: 60min smc3 MNase-seq

description: Library name: 60min smc3 MNase-seq


title: 30min smc3 MNase-seq

description: Library name: 30min smc3 MNase-seq


title: TSMM6

description: pool of 12 male retinas

value: retina

value: Embryonic E15.5


title: TSMM5

description: pool of 12 male retinas


title: HEK293T, CA3 overexpression, normoxia, repeat 2

description: Library name: Hek-1

value: CA3 overexpression, normoxia


title: MEC1 cells, Biotinylated miR-200b mimics, 48h, rep3

description: Library name: Sample 3


title: 0min smc3 MNase-seq

description: Library name: 0min smc3 MNase-seq

value: 0min cbf1 induction


title: 90min smc3 MNase-seq

description: Library name: 90min smc3 MNase-seq

value: Cbf1-AID, Smc3-AID

value: 90min cbf1 induction


title: TSMM4

description: pool of 12 male retinas


title: Mouse, ECKO_12, HFD 16 weeks

value: Ern1 endothelial cell specific knock out


title: TSCM6

description: pool of 12 male retinas

value: wild type


title: 90min rep2 MNase-seq

description: Library name: 90min rep2 MNase-seq


title: MEC1 cells, Biotinylated miR-200b mimics, 48h, rep1

description: Library name: Sample 1

value: Mouse embryonic epicardial cell line

value: WT


title: MEC1 cells, Biotinylated miR-200b mimics, 48h, rep2

description: Library name: Sample 2


title: 60min rep2 MNase-seq

description: Library name: 60min rep2 MNase-seq

value: 60min cbf1 induction


title: 30min rep2 MNase-seq

description: Library name: 30min rep2 MNase-seq

value: 30min cbf1 induction


title: siUSP32_3

city: Zhengzhou

first: Zehao

last: Hong

state: Henan

address: No. 1 Jianshe East Road

department: Breast surgery

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: Sample6

data_processing:
Using MGISEQ-2000RS sequencing platform.
The sequencing data was filtered with SOAPnuke (v.1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5 ) is more than 20%; (3) Removing reads whose unknown base ('N base') ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Transcripts per million (TPM) were calculated.
Assembly: GCF_00001405.39_GRCh38.p13
Supplementary files format and content: tpms for each Sample

source_name: triple negetive breast cancer

extract_protocol:
Lysis of cells with Trizol Reagent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using MGISEQ-2000RS protocols.

value: triple negetive breast cancer

value: triple negetive breast cancer cells


title: Patient-derived xenograft, HF2303 Brain

description: Library name: 12002-SP-2

organism:
Homo sapiens
Mus musculus

source_name: Brain cortex

value: Brain cortex

value: IDH WT


title: TSCM4

description: pool of 12 male retinas


title: TSCM5

description: pool of 12 male retinas


title: Mouse, ECKO_13, HFD 16 weeks

value: Pancreatic islet

value: 60% fat diet for 16 weeks


title: MEC1 cells, Biotinylated miR-200b mimics, 48h, rep4

description: Library name: Sample 4

value: Biotinylated miR-200b mimics transfection


title: Mouse, ECKO_11, HFD 16 weeks


title: 0min rep2 MNase-seq

description: Library name: 0min rep2 MNase-seq