title: aae_D7

status: Public on Jan 19 2026

city: Wuhan

first: Han

last: Xia

state: Hubei

department: Key Laboratory of pathogenic Viruses and Biosafety

institute: Wuhan Institute of Virology, CAS

description: Library name: sample1

data_processing:
Raw reads were qualified, demultiplexed, mapped to the reference library of midgut cells of mosquitoes,  barcode counting, gene counting and data aggregation using with celescope
Assembly: AaegL5.0, AalbF5, TS_CPP_V2
Supplementary files format and content: Tab-seperated value files and matrix files

organism: Aedes aegypti

source_name: midgut

extract_protocol:
For each sample, an appropriate number of midguts were dissected from female mosquitoes, then washed and temporarily stored in Schneider’s Drosophila Medium (SDM) within a microcentrifuge tube on ice. After dissection, the medium was discarded, and the midguts were finely minced and then 300 μl of dissociation buffer was added, followed by further mincing. The tissue fragments were resuspended in 700 μl of dissociation buffer and then incubated in a 28 °C water bath for 15-25 min. The suspension was mixed and the cell concentration, viability and aggregation were measured by staining with 0.4% trypan blue every five minutes. Once the quality control  requirements were met, the suspension was loaded into a 50 ml centrifuge tube equipped with a pre-wetted 40 μm filter to remove larger cell debris, and then washed with 1× PBS until the final volume reached 15 ml. The resulting filter was centrifuged at 350× g, 4 °C for 5 min. A viable cell band could be found near or at the bottom of the tube and 100-200 μl of the supernatant was retained to avoid disturbing the pellet. The cell pellet was suspended, followed by a second counting with 0.4% trypan blue. Cell suspension samples with viability ≥ 80% and were used for subsequent scRNA-seq.
According to the manufacturer’s guidelines, the single-cell suspension was adjusted to appropriate concentration prior to loading onto a microfluidic microwell SCOPE-chip. The cDNA synthesis of captured cells and sequencing library construction were performed with GEXSCOPE Single Cell RNA Library Kit.

value: midgut

tag: strain

value: Rockefeller

tag: age

tag: Sex

value: female

tag: developmental stage

value: adult


title: aae_denv_D14

type: SRA

country: China

description: Library name: sample7

library_source: transcriptomic single cell

molecule: total RNA

tag: tissue


title: Patient8_3V

status: Public on Dec 31 2025

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

description:
Library name: Patient8_3V
PolyA RNA

data_processing:
Demultiplexing, genome alignment, and gene quantification were performed with Cell Ranger ARC 50. Specifically, data was processed using the cellranger-arc count v.2.0.2 and aligned against the human genome (GRCh38) to generate count matrices for the RNA pipeline (v.7.0.1). All subsequent analysis was done using Seurat (v5) in R.
Assembly: GRCh38
Supplementary files format and content: rds contains the sparse normalized matrix of the ependymal cells used in the study. The data is organized with genes as rows and cell barcodes as columns.
Supplementary files format and content: csv contains the metadata information, allowing the reader to access the specific details and annotations for each cell/sample in the object.

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary cells

extract_protocol:
The ventricular/subventricular dissected samples were immediately weighed, minced using scalpels, dissociated into single cell suspension using the Adult Brain Dissociation Kit (Mil-tenyi Biotec) according to the manufacturer’s protocol but without the red blood cell removal step. The isolated single cells were then counted using a hemocytometer and assessed via LIVE/DEAD viability testing (Thermo Fisher).
The single cells were processed, and single-cell libraries were generated using the 10x Ge-nomics Chromium Controller and Chromium Next GEM Single Cell 5’ Reagent Kits (10x Ge-nomics), as per the manufacturer’s protocol. The sequencing-ready libraries were quality con-trolled for size distribution and yield (LabChip GX Perkin Elmer) and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms). Libraries were loaded on NovaSeq 6000 and sequenced using the following parameters: 100 bp Read1, 10 bp Index i7, 10 bp Index i5 and 100 bp Read2.

value: Brain

tag: cell type

value: primary CNS cells


title: Patient6_LV2

description:
Library name: Patient6_LV2
PolyA RNA


title: aal_D7

description: Library name: sample2

organism: Aedes albopictus

value: Jiangsu


title: Patient7_3V

description:
Library name: Patient7_3V
PolyA RNA


title: Patient7_LV

description:
Library name: Patient7_LV
PolyA RNA


title: Patient2_LV

description:
Library name: Patient2_LV
PolyA RNA


title: Patient3_LV

description:
Library name: Patient3_LV
PolyA RNA


title: Patient1_3V

description:
Library name: Patient1_3V
PolyA RNA


title: Skin, control, rep3

status: Public on Dec 22 2025

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

country: USA

institute: Morgridge Institute For Research

description: 10x Genomics

data_processing:
CellRanger (v 6.0.1) was used to process raw sequencing data before subsequent analyses with parameter '--include-introns=false' and 'refdata-gex-mm10-2020-A' reference data.
Assembly: mm10
Supplementary files format and content: Tab-separated values file and count matrix

organism: Mus musculus

source_name: Skin

extract_protocol:
The excised skin from MAFIA mice was cut into small pieces and incubated in 5 mL of dissociation buffer (5 mL RPMI 1640 (no calcium or magnesium) with 232U DNAse I, 0.25 mg/mL Liberase stock (2.5 mg/mL), 23.2 mM HEPES, and 2.32mM sodium pyruvate) at 37°C for 60 minutes. The digestion was stopped by adding 10 µL of 0.5 M EDTA and 400 µL FBS, and the samples were transferred to GentleMacs tubes (Miltenyi Biotec, Cat#130-093-237) for dissociation (program: m_impTumor_01.01). The digested samples were filtered through a 70 µm filter, resuspended in 4 mL of FACS buffer (500 mL PBS, 2 mL of 0.5 M EDTA, 25 mL FBS, and 5 mL non-essential amino acids (100x stock)) and stained with viability dye (Propidium iodide). Live cells were sorted by DiVa cell sorter (BD Biosciences). 18K sorted PI- live cells were loaded for scRNA-seq library preparation.
The live cells were sorted and loaded on the 10x Genomics Chromium using the Chromium Single Cell 3’ Reagent V3 Kit and the sequencing libraries were constructed following the user guide.

value: Skin

value: Male

value: 5 months old

tag: genotype

value: MaFIA

tag: treatment

value: Vehicle


title: Patient4_3V

description:
Library name: Patient4_3V
PolyA RNA


title: Patient8_LV

description:
Library name: Patient8_LV
PolyA RNA


title: Skin, depleted, rep2

description: 10x Genomics


title: Patient6_LV1

description:
Library name: Patient6_LV1
PolyA RNA


title: Patient5_LV

description:
Library name: Patient5_LV
PolyA RNA


title: Patient2_3V

description:
Library name: Patient2_3V
PolyA RNA


title: Patient3_3V

description:
Library name: Patient3_3V
PolyA RNA


title: Thymus, LAR, Mouse 3

status: Public on Dec 18 2025

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

country: Germany

institute: Saarland University

description: Library name: Thymus-LAR_2_2-Mouse_3-Pool_3

data_processing:
The obtained reads were mapped to the mm10 reference genome using cellranger (version 5.0.0, 10X Genomics). Ambient cell free mRNA contamination of each sample was removed using SoupX (version 1.5.2). Samples with more than 10% estimated contamination were removed. Raw gene counts were loaded into Seurat (version 4.0.3) for further processing. Cells with less than 200 or more than 2500 features, as well as cells with more than 50% mitochondrial RNA were removed. Samples with less than 50 cells were removed from the dataset. Finally, doublets were removed using DoubletFinder (version 2.0.3).
Assembly: mm10 2020 A
Supplementary files format and content: barcode.tsv:Barcode file containing the valid cell barcodes (output of cellranger pipeline)
Supplementary files format and content: features.tsv:file containing the feature names (output of cellranger pipeline)
Supplementary files format and content: matrix.mtx:Matrix file containing the gene counts for each cell barcode (output of cellranger pipeline)

source_name: unknown

growth_protocol: Rodent Research Reference Mission 1 (RRR-1) / Rodent Research-8 (RR-8) consisted of 40 BALB/cAnNTac females (8 used for this study) termed Flight which were sent on 12/5/2018 to the International Space Station (ISS), and a control group of 40 mice remained on Earth, termed Habitat Ground Control (HC). Furthermore, two age groups were used, younger (∼3 months) and older (∼8 months). Flight mice were housed at double density on launch and again during the return to earth. HC mice were housed to match, as closely as possible, conditions experienced by Flight mice. This included double density housing in identical Mouse Habitat Units and Transporters as used by NASA during launch for Flight mice, and matched temperature, humidity, and carbon dioxide levels (elevated on the ISS compared to Earth) based on actual flight environmental monitoring. HC mice were shipped to Scripps Institute just prior to the return of the Flight mice so that all mice could be dissected together in matching conditions (+/- 1 day). The mice from the Flight group were returned alive to Earth on 1/14/2019 after 39.5 days on the ISS and collected 2-4 days after splashdown following functional assays at Scripps Research Institute. In this study, fresh organ samples were obtained and immediately processed from 8 live mice that arrived at Stanford University from Scripps Research Institute on 1/16/2019. Two mice each from the following groups were included: Flight 3mo, Flight 8mo, HC 3mo, HC 8mo. All four Flight mice were dissected on 1/16/2019 to minimize time spent outside of microgravity, and all four HC mice dissected on 1/17/2019. All mice were adapted to NASA Nutrient Food Bars, four weeks prior to launch, and bars were exchanged weekly. Mice had ad libitum access to both food and water.

extract_protocol:
Peripheral blood samples (0.5 – 1 mL) were collected by cardiac puncture into K2/EDTA-coated syringes and MiniCollect tubes (Greiner Bio-One) immediately after mice were euthanized by CO2 inhalation and cervical dislocation. Red blood cells were depleted with Histopaque-1119 (SigmaAldrich RNBF0417). The cell suspension was then pelleted (300 x g, 4o C, 5 min), filtered through a 70 μm strainer, and resuspended in FACS buffer (2% sterile FBS in PBS) with 100 U/mL DNase I (Worthington LS006344) prior to loading cells on a 10x chromium chip.  Murine eyes were collected carefully using forceps in cold PBS. The whole eyes from each donor were weighed. Subsequently, each of the eyes was dissected under a dissecting microscope to segregate the extraocular muscles, retina, cornea, lens and optic nerve tissue components. Each of these tissues for each donor were digested separately for single cell preparation and pooled together as eye cell suspension. The optic nerves and retina were digested for 15 mins in papain and subsequently resuspended in HBSS solution for mechanical dissociation of single cells by pipetting. The corneal tissue was incubated in Dispase II for an hour with shaking followed by 10 mins of 0.25% trypsin digestion. The corneal cells were then mechanically dissociated using pipetting and resuspended in PBS (with 1% FBS). The lens tissue was processed in 0.02% EDTA for 10 mins and mechanically resuspended into single cells by pipetting. The extraocular muscles were treated with 1mg/ml collagenase for 45mins with pipetting every 15 mins for single cell suspension. All the pooled cells were finally resuspended in 1% FBS containing PBS at a concentration of 106 cells/ml for subsequent processing on 10X.  Femurs, hip bones and vertebral columns were dissected and cleaned of soft tissue. Bones were then processed as previously described (https://doi.org:10.1016/j.cell.2014.12.002, https://doi.org:10.1038/nprot.2018.041). Briefly, bones were crushed using mortar and pestle and subsequently digested in M199 (cat#11150067, Thermo Fisher Scientific) with 2.2 mg ml-1 collagenase II buffer (cat#C6885, Sigma-Aldrich) at 37 °C for 60 min under constant agitation. Dissociated cells were strained through a 100-μm nylon filter, washed in staining medium (10% fetal bovine serum (FBS) in PBS) and pelleted at 200g at 4°C. The cell pellet was resuspended in staining medium and red blood cells were depleted via ACK lysis for 3 min. After an additional wash step cells were pelleted at 200g at 4°C. The single cell suspension was then prepared for fluorescence activated cell sorting (FACS) by staining them with fluorochrome-conjugated antibodies (Thermo Fisher Scientific) against CD45 (cat#15-0451; 1:200), TER119 (cat#15-5921; 1:200), CD51 (cat#12-0512; 1:50), Tie2 (cat#14-5987; 1:20), CD31 (cat#11-0311;1:200), Th1.1 (cat#47-0900; 1:100), Thy1.2 (47-0902; 1:100), 6c3 (cat#17-5891; 1:100), CD105 (cat#13-1051; 1:50) and streptavidin–PE–Cy7 conjugate (cat#25-4317-82; 1:100). Target populations were sorted on a FACS Aria II Instrument (BD BioSciences) using a 70-μm nozzle in the Shared FACS Facility in the Lokey Stem Cell Institute (Stanford). 16 Gating of cell populations was guided by appropriate isotype and fluorescence-minus- one controls. Propidium iodide staining was used to separate dead cells. Cells were sorted into staining medium and directly processed for 10X Genomics scRNA-seq.  All other tissues were processed as previously described (https://doi.org:10.1038/s41586-020-2496-1).
Single cells were captured in droplet emulsions using the GemCode Single-Cell Instrument (10x Genomics) and scRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3’ Gel Bead and Library v3 Kit. Cells were loaded in each channel with a target output of up to 5,000 cells per sample, though fewer cells were captured for small sample types. All reactions were performed in the Biorad C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated on a Fragment Analyzer using a High Sensitivity NGS Analysis Kit (Advanced Analytical). Library preparation was performed one organ type at a time, in sets of 8 samples. Within each organ set, cDNA was normalized and 13-20 PCR cycles run depending on cDNA amount. The average fragment length of 10x cDNA libraries was quantitated on a Fragment Analyzer (AATI), and by qPCR with the Kapa Library Quantification kit for Illumina. Each library was diluted to 4nM, and equal volumes were pooled for each NovaSeq sequencing run. Pools were sequenced with 100 cycle run kits with 28 bases for Read 1, 8 bases for Index 1, and 91 bases for Read 2 (Illumina 20012862). A PhiX control library was spiked in at 0.2 to 1%. Libraries were sequenced on the NovaSeq 6000 Sequencing System (Illumina).

value: BALB/cAnNTac

tag: batch

value: Pool 3

value: unknown


title: Skin, control, rep2

description: 10x Genomics


title: Patient1_LV

description:
Library name: Patient1_LV
PolyA RNA


title: Patient4_LV

description:
Library name: Patient4_LV
PolyA RNA


title: Skin, control, rep1

description: 10x Genomics

value: Female


title: Skin, depleted, rep1

description: 10x Genomics


title: Spleen, HC, Mouse 4

description: Library name: Spleen-HC_1_6-Mouse_4-Pool_1

value: Pool 1


title: Spleen, LAR, Mouse 4

description: Library name: Spleen-LAR_1_5-Mouse_4-Pool_1


title: Thymus, HC, Mouse 4

description: Library name: Thymus-HC_1_5-Mouse_4-Pool_3


title: Thymus, HC, Mouse 2

description: Library name: Thymus-HC_1_5-Mouse_2-Pool_3


title: Thymus, HC, Mouse 3

description: Library name: Thymus-HC_1_5-Mouse_3-Pool_3


title: cxpip_D7

description: Library name: sample3

organism: Culex pipiens pallens

value: midgut

value: Beijing


title: Thymus, LAR, Mouse 2

description: Library name: Thymus-LAR_2_2-Mouse_2-Pool_3

value: female


title: Thymus, HC, Mouse 1

description: Library name: Thymus-HC_1_5-Mouse_1-Pool_3


title: Spleen, LAR, Mouse 3

description: Library name: Spleen-LAR_1_5-Mouse_3-Pool_1


title: Skin, depleted, rep3

description: 10x Genomics


title: Skin, LAR, Mouse 4

description: Library name: Skin-LAR_2_1-Mouse_4-Pool_1


title: Skin, LAR, Mouse 1

description: Library name: Skin-LAR_2_1-Mouse_1-Pool_1


title: Thymus, LAR, Mouse 1

description: Library name: Thymus-LAR_2_2-Mouse_1-Pool_3


title: Spleen, HC, Mouse 1

description: Library name: Spleen-HC_1_6-Mouse_1-Pool_1


title: Spleen, HC, Mouse 2

description: Library name: Spleen-HC_1_6-Mouse_2-Pool_1


title: Spleen, HC, Mouse 3

description: Library name: Spleen-HC_1_6-Mouse_3-Pool_1


title: Skin, LAR, Mouse 3

description: Library name: Skin-LAR_2_1-Mouse_3-Pool_1


title: Thymus, LAR, Mouse 4

description: Library name: Thymus-LAR_2_2-Mouse_4-Pool_3


title: Skin, HC, Mouse 3

description: Library name: Skin-HC_1_3-Mouse_3-Pool_1


title: Spleen, LAR, Mouse 2

description: Library name: Spleen-LAR_1_5-Mouse_2-Pool_1


title: Spleen, LAR, Mouse 1

description: Library name: Spleen-LAR_1_5-Mouse_1-Pool_4

value: Pool 4


title: Skeletal Stem Cells, LAR, Mouse 4

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_4-Pool_3

value: spaceflight


title: Skin, HC, Mouse 1

description: Library name: Skin-HC_1_3-Mouse_1-Pool_1


title: Skin, LAR, Mouse 2

description: Library name: Skin-LAR_2_1-Mouse_2-Pool_1


title: Skeletal Stem Cells, LAR, Mouse 2

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_2-Pool_3


title: Skeletal Stem Cells, LAR, Mouse 3

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_3-Pool_3


title: Skin, HC, Mouse 4

description: Library name: Skin-HC_1_3-Mouse_4-Pool_1


title: Skeletal Stem Cells, HC, Mouse 3

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_3-Pool_3

value: control


title: Skeletal Stem Cells, HC, Mouse 1

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_1-Pool_3


title: Skin, HC, Mouse 2

description: Library name: Skin-HC_1_3-Mouse_2-Pool_1


title: SCAT, HC, Mouse 4

description: Library name: SCAT-HC_2_2-Mouse_4-Pool_1

source_name: SCAT

value: SCAT


title: Skeletal Stem Cells, HC, Mouse 2

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_2-Pool_3


title: Skeletal Stem Cells, HC, Mouse 4

description: Library name: Skeletal_Stem_Cells-HC_3_6-Mouse_4-Pool_3


title: Pancreas, LAR, Mouse 4

description: Library name: Pancreas-LAR_1_3-Mouse_4-Pool_2

source_name: Pancreas

value: Pool 2

value: Pancreas


title: Skeletal Stem Cells, LAR, Mouse 1

description: Library name: Skeletal_Stem_Cells-LAR_2_8-Mouse_1-Pool_3


title: SCAT, HC, Mouse 3

description: Library name: SCAT-HC_2_2-Mouse_3-Pool_1


title: SCAT, LAR, Mouse 2

description: Library name: SCAT-LAR_2_5-Mouse_2-Pool_1


title: SCAT, HC, Mouse 2

description: Library name: SCAT-HC_2_2-Mouse_2-Pool_1


title: SCAT, LAR, Mouse 3

description: Library name: SCAT-LAR_2_5-Mouse_3-Pool_1


title: Pancreas, HC, Mouse 3

description: Library name: Pancreas-HC_1_5-Mouse_3-Pool_2


title: SCAT, LAR, Mouse 4

description: Library name: SCAT-LAR_2_5-Mouse_4-Pool_1


title: SCAT, LAR, Mouse 1

description: Library name: SCAT-LAR_2_5-Mouse_1-Pool_1


title: Pancreas, HC, Mouse 2

description: Library name: Pancreas-HC_1_5-Mouse_2-Pool_2


title: Pancreas, HC, Mouse 1

description: Library name: Pancreas-HC_1_5-Mouse_1-Pool_2


title: Pancreas, LAR, Mouse 3

description: Library name: Pancreas-LAR_1_3-Mouse_3-Pool_2


title: Pancreas, HC, Mouse 4

description: Library name: Pancreas-HC_1_5-Mouse_4-Pool_2


title: SCAT, HC, Mouse 1

description: Library name: SCAT-HC_2_2-Mouse_1-Pool_1


title: Pancreas, LAR, Mouse 1

description: Library name: Pancreas-LAR_1_3-Mouse_1-Pool_2


title: Pancreas, LAR, Mouse 2

description: Library name: Pancreas-LAR_1_3-Mouse_2-Pool_2


title: Non, myeloid Forebrain, LAR, Mouse 3

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_3-Pool_2


title: Non, myeloid Forebrain, LAR, Mouse 2

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_2-Pool_2


title: Non, myeloid Forebrain, LAR, Mouse 4

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_4-Pool_2


title: Non, myeloid Forebrain, LAR, Mouse 1

description: Library name: Non-myeloid_Forebrain-LAR_1_3-Mouse_1-Pool_2


title: Non, myeloid Cerebellum, LAR, Mouse 3

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_3-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 1

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_1-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 4

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_4-Pool_3


title: Non, myeloid Forebrain, HC, Mouse 4

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_4-Pool_2


title: Non, myeloid Cerebellum, LAR, Mouse 4

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_4-Pool_3


title: Non, myeloid Forebrain, HC, Mouse 3

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_3-Pool_2


title: Non, myeloid Cerebellum, LAR, Mouse 1

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_1-Pool_3


title: Non, meyloid Hippocampus, HC, Mouse 4

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_4-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 3

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_3-Pool_3


title: Non, meyloid Hippocampus, LAR, Mouse 3

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_3-Pool_3


title: Non, myeloid Cerebellum, LAR, Mouse 2

description: Library name: Non-myeloid_Cerebellum-LAR_1_1-Mouse_2-Pool_3


title: Myeloid Hippocampus, LAR, Mouse 4

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_4-Pool_2


title: Non, meyloid Hippocampus, LAR, Mouse 4

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_4-Pool_3


title: Non, meyloid Hippocampus, HC, Mouse 2

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_2-Pool_3


title: Non, myeloid Cerebellum, HC, Mouse 2

description: Library name: Non-myeloid_Cerebellum-HC_1_1-Mouse_2-Pool_3


title: Myeloid Hippocampus, LAR, Mouse 3

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_3-Pool_2


title: Non, meyloid Hippocampus, HC, Mouse 3

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_3-Pool_3


title: Non, meyloid Hippocampus, HC, Mouse 1

description: Library name: Non-meyloid_Hippocampus-HC_1_3-Mouse_1-Pool_3


title: Non, meyloid Hippocampus, LAR, Mouse 2

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_2-Pool_3


title: Myeloid Hippocampus, LAR, Mouse 2

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_2-Pool_2


title: Myeloid Hippocampus, LAR, Mouse 1

description: Library name: Myeloid_Hippocampus-LAR_1_7-Mouse_1-Pool_2


title: Non, meyloid Hippocampus, LAR, Mouse 1

description: Library name: Non-meyloid_Hippocampus-LAR_1_1-Mouse_1-Pool_3


title: Non, myeloid Forebrain, HC, Mouse 1

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_1-Pool_2


title: Non, myeloid Forebrain, HC, Mouse 2

description: Library name: Non-myeloid_Forebrain-HC_1_1-Mouse_2-Pool_2


title: Myeloid Hippocampus, HC, Mouse 4

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_4-Pool_2


title: Myeloid Forebrain, LAR, Mouse 1

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_1-Pool_1


title: Myeloid Hippocampus, HC, Mouse 2

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_2-Pool_2


title: Myeloid Hippocampus, HC, Mouse 3

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_3-Pool_2


title: Myeloid Forebrain, HC, Mouse 4

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_4-Pool_1


title: Myeloid Forebrain, LAR, Mouse 3

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_3-Pool_1


title: Myeloid Forebrain, LAR, Mouse 2

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_2-Pool_1


title: Myeloid Forebrain, HC, Mouse 2

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_2-Pool_1


title: Myeloid Forebrain, LAR, Mouse 4

description: Library name: Myeloid_Forebrain-LAR_2_1-Mouse_4-Pool_1


title: Myeloid Forebrain, HC, Mouse 1

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_1-Pool_1


title: Myeloid Cerebellum, LAR, Mouse 4

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_4-Pool_1


title: Myeloid Cerebellum, LAR, Mouse 3

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_3-Pool_1


title: Myeloid Hippocampus, HC, Mouse 1

description: Library name: Myeloid_Hippocampus-HC_1_10-Mouse_1-Pool_2


title: MAT, LAR, Mouse 1

description: Library name: MAT-LAR_2_6-Mouse_1-Pool_3

source_name: MAT

value: MAT


title: MAT, HC, Mouse 1

description: Library name: MAT-HC_2_3-Mouse_1-Pool_3


title: MAT, HC, Mouse 3

description: Library name: MAT-HC_2_3-Mouse_3-Pool_3


title: MAT, HC, Mouse 4

description: Library name: MAT-HC_2_3-Mouse_4-Pool_3


title: Myeloid Cerebellum, HC, Mouse 4

description: Library name: Myeloid_Cerebellum-HC_1_10-Mouse_4-Pool_1


title: MAT, LAR, Mouse 4

description: Library name: MAT-LAR_2_6-Mouse_4-Pool_3


title: Myeloid Cerebellum, LAR, Mouse 2

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_2-Pool_1


title: Myeloid Cerebellum, LAR, Mouse 1

description: Library name: Myeloid_Cerebellum-LAR_1_7-Mouse_1-Pool_1


title: MAT, LAR, Mouse 2

description: Library name: MAT-LAR_2_6-Mouse_2-Pool_3


title: Myeloid Cerebellum, HC, Mouse 2

description: Library name: Myeloid_Cerebellum-HC_1_10-Mouse_2-Pool_1


title: Myeloid Cerebellum, HC, Mouse 3

description: Library name: Myeloid_Cerebellum-HC_1_10-Mouse_3-Pool_1


title: MAT, HC, Mouse 2

description: Library name: MAT-HC_2_3-Mouse_2-Pool_3


title: Marrow, LAR, Mouse 4

description: Library name: Marrow-LAR_2_4-Mouse_4-Pool_3

source_name: Marrow

value: Marrow


title: Myeloid Forebrain, HC, Mouse 3

description: Library name: Myeloid_Forebrain-HC_1_11-Mouse_3-Pool_1


title: MAT, LAR, Mouse 3

description: Library name: MAT-LAR_2_6-Mouse_3-Pool_3


title: Marrow, LAR, Mouse 3

description: Library name: Marrow-LAR_2_4-Mouse_3-Pool_3


title: Marrow, LAR, Mouse 1

description: Library name: Marrow-LAR_2_4-Mouse_1-Pool_3


title: Marrow, HC, Mouse 1

description: Library name: Marrow-HC_1_8-Mouse_1-Pool_3


title: Mammary, LAR, Mouse 2

description: Library name: Mammary-LAR_1_6-Mouse_2-Pool_2


title: Mammary, LAR, Mouse 4

description: Library name: Mammary-LAR_1_6-Mouse_4-Pool_2


title: Marrow, HC, Mouse 3

description: Library name: Marrow-HC_1_8-Mouse_3-Pool_3


title: Mammary, LAR, Mouse 3

description: Library name: Mammary-LAR_1_6-Mouse_3-Pool_2


title: Marrow, HC, Mouse 2

description: Library name: Marrow-HC_1_8-Mouse_2-Pool_3


title: Marrow, LAR, Mouse 2

description: Library name: Marrow-LAR_2_4-Mouse_2-Pool_3


title: Mammary, LAR, Mouse 1

description: Library name: Mammary-LAR_1_6-Mouse_1-Pool_2


title: Liver, LAR, Mouse 3

description: Library name: Liver-LAR_1_4-Mouse_3-Pool_2

source_name: Liver

value: Liver


title: Mammary, HC, Mouse 3

description: Library name: Mammary-HC_1_7-Mouse_3-Pool_2

value: BALB/cAnNTac


title: Liver, LAR, Mouse 2

description: Library name: Liver-LAR_1_4-Mouse_2-Pool_2


title: Mammary, HC, Mouse 1

description: Library name: Mammary-HC_1_7-Mouse_1-Pool_2


title: Lung, LAR, Mouse 2

description: Library name: Lung-LAR_1_4-Mouse_2-Pool_2

source_name: Lung

value: Lung


title: Lung, LAR, Mouse 1

description: Library name: Lung-LAR_1_4-Mouse_1-Pool_2


title: Liver, LAR, Mouse 4

description: Library name: Liver-LAR_1_4-Mouse_4-Pool_2


title: Lung, HC, Mouse 4

description: Library name: Lung-HC_1_4-Mouse_4-Pool_2


title: Mammary, HC, Mouse 2

description: Library name: Mammary-HC_1_7-Mouse_2-Pool_2

value: unknown


title: Lung, HC, Mouse 1

description: Library name: Lung-HC_1_4-Mouse_1-Pool_2


title: Lung, HC, Mouse 3

description: Library name: Lung-HC_1_4-Mouse_3-Pool_2


title: Lung, HC, Mouse 2

description: Library name: Lung-HC_1_4-Mouse_2-Pool_2


title: Liver, HC, Mouse 4

description: Library name: Liver-HC_1_9-Mouse_4-Pool_2


title: Liver, LAR, Mouse 1

description: Library name: Liver-LAR_1_4-Mouse_1-Pool_2


title: Lung, LAR, Mouse 3

description: Library name: Lung-LAR_1_4-Mouse_3-Pool_2


title: Mammary, HC, Mouse 4

description: Library name: Mammary-HC_1_7-Mouse_4-Pool_2


title: Liver, HC, Mouse 1

description: Library name: Liver-HC_1_9-Mouse_1-Pool_2


title: Limb Muscle, HC, Mouse 3

description: Library name: Limb_Muscle-HC_2_1-Mouse_3-Pool_2


title: Liver, HC, Mouse 2

description: Library name: Liver-HC_1_9-Mouse_2-Pool_2


title: Limb Muscle, HC, Mouse 2

description: Library name: Limb_Muscle-HC_2_1-Mouse_2-Pool_2


title: Limb Muscle, LAR, Mouse 1

description: Library name: Limb_Muscle-LAR_2_6-Mouse_1-Pool_2


title: Liver, HC, Mouse 3

description: Library name: Liver-HC_1_9-Mouse_3-Pool_2


title: Limb Muscle, HC, Mouse 1

description: Library name: Limb_Muscle-HC_2_1-Mouse_1-Pool_2


title: Limb Muscle, LAR, Mouse 2

description: Library name: Limb_Muscle-LAR_2_6-Mouse_2-Pool_2


title: Limb Muscle, LAR, Mouse 4

description: Library name: Limb_Muscle-LAR_2_6-Mouse_4-Pool_2


title: Limb Muscle, LAR, Mouse 3

description: Library name: Limb_Muscle-LAR_2_6-Mouse_3-Pool_2


title: LAR, LAR, Mouse 3

description: Library name: Large_Intestine-LAR_2_7-Mouse_3-Pool_1


title: LAR, LAR, Mouse 4

description: Library name: Large_Intestine-LAR_2_7-Mouse_4-Pool_1


title: Limb Muscle, HC, Mouse 4

description: Library name: Limb_Muscle-HC_2_1-Mouse_4-Pool_2


title: LAR, HC, Mouse 4

description: Library name: Large_Intestine-HC_1_7-Mouse_4-Pool_1


title: LAR, HC, Mouse 3

description: Library name: Large_Intestine-HC_1_7-Mouse_3-Pool_1


title: LAR, LAR, Mouse 2

description: Library name: Large_Intestine-LAR_2_7-Mouse_2-Pool_1


title: LAR, HC, Mouse 2

description: Library name: Large_Intestine-HC_1_7-Mouse_2-Pool_1


title: LAR, LAR, Mouse 1

description: Library name: Large_Intestine-LAR_2_7-Mouse_1-Pool_1


title: Kidney, LAR, Mouse 2

description: Library name: Kidney-LAR_1_5-Mouse_2-Pool_4


title: Kidney, LAR, Mouse 3

description: Library name: Kidney-LAR_1_5-Mouse_3-Pool_1


title: LAR, HC, Mouse 1

description: Library name: Large_Intestine-HC_1_7-Mouse_1-Pool_1


title: Heart Ventricles, LAR, Mouse 4

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_4-Pool_3

value: Pool 3


title: Kidney, HC, Mouse 2

description: Library name: Kidney-HC_1_6-Mouse_2-Pool_1

value: Pool 1


title: Kidney, HC, Mouse 3

description: Library name: Kidney-HC_1_6-Mouse_3-Pool_1


title: Kidney, HC, Mouse 1

description: Library name: Kidney-HC_1_6-Mouse_1-Pool_1


title: Heart Ventricles, LAR, Mouse 2

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_2-Pool_3


title: Heart Atria, LAR, Mouse 4

description: Library name: Heart_Atria-LAR_1_2-Mouse_4-Pool_3


title: Heart Ventricles, HC, Mouse 2

description: Library name: Heart_Ventricles-HC_1_2-Mouse_2-Pool_3


title: Heart Ventricles, HC, Mouse 1

description: Library name: Heart_Ventricles-HC_1_2-Mouse_1-Pool_3


title: Kidney, HC, Mouse 4

description: Library name: Kidney-HC_1_6-Mouse_4-Pool_1


title: Heart Ventricles, LAR, Mouse 1

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_1-Pool_3


title: Kidney, LAR, Mouse 1

description: Library name: Kidney-LAR_1_5-Mouse_1-Pool_4


title: Heart Atria, HC, Mouse 4

description: Library name: Heart_Atria-HC_1_2-Mouse_4-Pool_3


title: Heart Atria, LAR, Mouse 3

description: Library name: Heart_Atria-LAR_1_2-Mouse_3-Pool_3


title: Heart Ventricles, HC, Mouse 3

description: Library name: Heart_Ventricles-HC_1_2-Mouse_3-Pool_3


title: Kidney, LAR, Mouse 4

description: Library name: Kidney-LAR_1_5-Mouse_4-Pool_1


title: Heart Atria, LAR, Mouse 2

description: Library name: Heart_Atria-LAR_1_2-Mouse_2-Pool_3


title: Heart Ventricles, HC, Mouse 4

description: Library name: Heart_Ventricles-HC_1_2-Mouse_4-Pool_3


title: Heart Atria, LAR, Mouse 1

description: Library name: Heart_Atria-LAR_1_2-Mouse_1-Pool_3


title: Heart Ventricles, LAR, Mouse 3

description: Library name: Heart_Ventricles-LAR_1_2-Mouse_3-Pool_3


title: Heart Atria, HC, Mouse 3

description: Library name: Heart_Atria-HC_1_2-Mouse_3-Pool_3


title: Heart Atria, HC, Mouse 2

description: Library name: Heart_Atria-HC_1_2-Mouse_2-Pool_3


title: Heart Atria, HC, Mouse 1

description: Library name: Heart_Atria-HC_1_2-Mouse_1-Pool_3


title: GAT, LAR, Mouse 2

description: Library name: GAT-LAR_2_3-Mouse_2-Pool_1

source_name: GAT

value: GAT


title: GAT, LAR, Mouse 1

description: Library name: GAT-LAR_2_3-Mouse_1-Pool_1


title: GAT, LAR, Mouse 3

description: Library name: GAT-LAR_2_3-Mouse_3-Pool_1


title: GAT, HC, Mouse 1

description: Library name: GAT-HC_2_1-Mouse_1-Pool_1


title: GAT, LAR, Mouse 4

description: Library name: GAT-LAR_2_3-Mouse_4-Pool_1


title: Diaphragm, LAR, Mouse 3

description: Library name: Diaphragm-LAR_2_5-Mouse_3-Pool_1

source_name: Diaphragm

value: Diaphragm


title: Eye, LAR, Mouse 4

description: Library name: Eye-LAR_2_7-Mouse_4-Pool_2

source_name: Eye

value: female

value: Eye


title: GAT, HC, Mouse 3

description: Library name: GAT-HC_2_1-Mouse_3-Pool_1


title: Eye, LAR, Mouse 3

description: Library name: Eye-LAR_2_7-Mouse_3-Pool_2

value: spaceflight


title: GAT, HC, Mouse 2

description: Library name: GAT-HC_2_1-Mouse_2-Pool_1

value: control


title: Eye, LAR, Mouse 1

description: Library name: Eye-LAR_2_7-Mouse_1-Pool_2


title: Eye, HC, Mouse 3

description: Library name: Eye-HC_1_9-Mouse_3-Pool_2


title: Eye, HC, Mouse 2

description: Library name: Eye-HC_1_9-Mouse_2-Pool_2


title: Diaphragm, LAR, Mouse 1

description: Library name: Diaphragm-LAR_2_5-Mouse_1-Pool_1


title: Diaphragm, HC, Mouse 4

description: Library name: Diaphragm-HC_2_2_-Mouse_4-Pool_1


title: Diaphragm, LAR, Mouse 2

description: Library name: Diaphragm-LAR_2_5-Mouse_2-Pool_1


title: Eye, HC, Mouse 4

description: Library name: Eye-HC_1_9-Mouse_4-Pool_2


title: GAT, HC, Mouse 4

description: Library name: GAT-HC_2_1-Mouse_4-Pool_1


title: Diaphragm, HC, Mouse 3

description: Library name: Diaphragm-HC_2_2_-Mouse_3-Pool_1


title: Eye, LAR, Mouse 2

description: Library name: Eye-LAR_2_7-Mouse_2-Pool_2


title: Eye, HC, Mouse 1

description: Library name: Eye-HC_1_9-Mouse_1-Pool_2


title: Diaphragm, LAR, Mouse 4

description: Library name: Diaphragm-LAR_2_5-Mouse_4-Pool_1


title: Diaphragm, HC, Mouse 1

description: Library name: Diaphragm-HC_2_2-Mouse_1-Pool_4

value: Pool 4


title: Bone, LAR, Mouse 3

description: Library name: Bone-LAR_2_8-Mouse_3-Pool_3

source_name: Bone

value: Bone


title: Bone, LAR, Mouse 4

description: Library name: Bone-LAR_2_8-Mouse_4-Pool_3


title: Bone, LAR, Mouse 1

description: Library name: Bone-LAR_2_8-Mouse_1-Pool_3


title: Bone, LAR, Mouse 2

description: Library name: Bone-LAR_2_8-Mouse_2-Pool_3


title: Bone, HC, Mouse 1

description: Library name: Bone-HC_3_6-Mouse_1-Pool_3


title: Blood, HC, Mouse 1

description: Library name: Blood-HC_1_8-Mouse_1-Pool_3

source_name: Blood

value: Blood


title: Bone, HC, Mouse 4

description: Library name: Bone-HC_3_6-Mouse_4-Pool_3


title: BAT, HC, Mouse 4

description: Library name: BAT-HC_2_3-Mouse_4-Pool_1

source_name: BAT

value: BAT


title: BAT, HC, Mouse 3

description: Library name: BAT-HC_2_3-Mouse_3-Pool_1


title: BAT, HC, Mouse 2

description: Library name: BAT-HC_2_3-Mouse_2-Pool_1


title: Blood, LAR, Mouse 2

description: Library name: Blood-LAR_2_4-Mouse_2-Pool_3


title: Bone, HC, Mouse 3

description: Library name: Bone-HC_3_6-Mouse_3-Pool_3


title: Blood, LAR, Mouse 1

description: Library name: Blood-LAR_2_4-Mouse_1-Pool_3


title: Blood, LAR, Mouse 4

description: Library name: Blood-LAR_2_4-Mouse_4-Pool_3


title: Blood, HC, Mouse 2

description: Library name: Blood-HC_1_8-Mouse_2-Pool_3


title: BAT, LAR, Mouse 1

description: Library name: BAT-LAR_2_3-Mouse_1-Pool_1


title: Diaphragm, HC, Mouse 2

description: Library name: Diaphragm-HC_2_2_-Mouse_2-Pool_1


title: Blood, HC, Mouse 4

description: Library name: Blood-HC_1_8-Mouse_4-Pool_3


title: Blood, LAR, Mouse 3

description: Library name: Blood-LAR_2_4-Mouse_3-Pool_3


title: BAT, LAR, Mouse 3

description: Library name: BAT-LAR_2_3-Mouse_3-Pool_1


title: Blood, HC, Mouse 3

description: Library name: Blood-HC_1_8-Mouse_3-Pool_3


title: Aorta, LAR, Mouse 4

description: Library name: Aorta-LAR_2_2-Mouse_4-Pool_2

value: Pool 2


title: BAT, HC, Mouse 1

description: Library name: BAT-HC_2_3-Mouse_1-Pool_1


title: Aorta, LAR, Mouse 3

description: Library name: Aorta-LAR_2_2-Mouse_3-Pool_2


title: BAT, LAR, Mouse 2

description: Library name: BAT-LAR_2_3-Mouse_2-Pool_1


title: Bone, HC, Mouse 2

description: Library name: Bone-HC_3_6-Mouse_2-Pool_3


title: BAT, LAR, Mouse 4

description: Library name: BAT-LAR_2_3-Mouse_4-Pool_1


title: Aorta, LAR, Mouse 2

description: Library name: Aorta-LAR_2_2-Mouse_2-Pool_2


title: Aorta, LAR, Mouse 1

description: Library name: Aorta-LAR_2_2-Mouse_1-Pool_2


title: Aorta, HC, Mouse 4

description: Library name: Aorta-HC_1_4-Mouse_4-Pool_2


title: Aorta, HC, Mouse 3

description: Library name: Aorta-HC_1_4-Mouse_3-Pool_2


title: Aorta, HC, Mouse 2

description: Library name: Aorta-HC_1_4-Mouse_2-Pool_2


title: Aorta, HC, Mouse 1

description: Library name: Aorta-HC_1_4-Mouse_1-Pool_4


title: PDAC, Human Tumor, sample106

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

description: Library name: ST5425

library_source: transcriptomic

data_processing:
Space Ranger (v2.1.0) was used, following10X Genomics guidelines, to process the raw data and generate gene count files.
“spaceranger mkfastq” with default settings was used to convert BCL files to FASTQ files.
“spaceranger count” was applied with default settings and required input files, including FASTQ files, brightfield microscope image, CytAssist image, as well as the manual alignment JASON file.
Seurat (v5.1.0) was used for subsequent data processing.
Assembly: Human GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg.gz:  aligned tissue image
Supplementary files format and content: cytassist_image.tiff:  cytassist image
Supplementary files format and content: detected_tissue_image.jpg.gz:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz:  scalefactors in json format
Supplementary files format and content: spatial_enrichments.csv.gz:  spatial enrichments
Supplementary files format and content: tissue_hires_image.png.gz:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz:  low-res image of tissue
Supplementary files format and content: tissue_positions.csv.gz:  list of spatial barcodes and the coordinates specifiying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5:  h5 file of features, barcode, matrix
Library strategy: Spatial Transcriptomics

source_name: Primary PDAC

extract_protocol:
Spatial transcriptomics was done using the 10X Genomics Visium Cytassist platform using 5 µm tissue sections that were mounted onto a glass slide. Tumor areas of interest were aligned with a 6.5 x 6.5 mm capture area on a Cytassist Spatial Gene Expression slide. Following the manufacturer protocol, sections were deparaffinized, H&E stained, imaged, and then decrosslinked to release mRNAs which bind to the spatially barcoded oligos on the 4992 spots of each capture area, at a spatial resolution of 55 µm. Once probe pairs hybridized and ligated to the RNA, the single-stranded ligation product was released from the tissue and captured on the Visium slide.
Probe products were reverse transcribed and extended to incorporate a unique molecular identifier (UMI) and the spatial barcode. Following amplification, libraries were constructed from the cDNA. qPCR of pre-amplification material was used to determine cycle number for the sample index PCR to generate the final library. After a SPRIselect bead cleanup, generated libraries were sequenced on the Illumina NextSeq2000 platform using a P3 100 cycle kit at a depth of ~300M reads per section, resulting in >60,000 reads per spot.

value: Primary PDAC


title: PDAC, Human Tumor, sample118

description: Library name: ST10772

value: FOLFIRINOX


title: EA18.1_RNAseq_NPC_dTAG13_24h_rep6

status: Public on Nov 27 2025

city: San Francisco

first: Elphege

last: Nora

state: California

address: 555 Nelson Rising Lane

department: CVRI

institute: UCSF

description:
Library name: KHRNA97
KHRNA97

data_processing:
Reads were trimmed to 100 base pairs as needed using cutadapt.
Alignment of raw RNA-seq data was produced using STAR version 2.7.7a with default parameters and basic two-pass mapping in mm10. GENCODE VM23 (GRCm38.p6) was used as the reference gene set.
bigWig files were generated using bamCoverage (deepTools) separated by strand with BPM normalization.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Supplementary files format and content: bigWigs separated by forward and reverse strand and normalized using BPM

growth_protocol: Parental WT E14Tg2a (karyotype 19, XY, 129/Ola isogenic background) mouse ESCs and subclones were cultured in 2iSL medium [DMEM + GlutaMAX + sodium pyruvate (ThermoFisher 10569044) supplemented with 15% fetal bovine serum, 550 µM 2-mercaptoethanol (ThermoFisher 21985-023), 1X nonessential amino acids (ThermoFisher 11140-050), 104 U of Leukemia Inhibitory Factor (Millipore ESG1107), 1µM PD0325901 (Apex Bio/Fischer A3013-25), and 3µM CHIR99021 (Apex Bio/Fischer A3011-100)]. Cells were maintained at a density of 0.2-1.5 x 105 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48 hours on 0.1% gelatin-coated dishes (Sigma-Aldrich G1890-100G) at 37 °C and 7% CO2. The medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
Cells were washed with PBS and lysed directly with 1 mL TRIzol (Thermo Fisher 15596-018), transferred to a 1.5 mL tube, vortexed, and incubated at room temperature for 5 minutes. After incubation, mixture was supplemented with 250 µL Chloroform, vortexed again, and centrifuged at 12,000g at 4ºC for 15 minutes. Upper phase was transferred to a new tube, mixed with an equal volume of isopropanol, and spun at 12,000g at 4ºC for 15 minutes. Pellet was washed with 70% ethanol, air dried, and resuspended in 25 µL water.
100-500ng of DNase-treated total RNA was used as input for polyA+ capture and library preparation using the Illumina Stranded mRNA kit (Illumina 20040532)

treatment_protocol: FKBP12 depletion was triggered using 500 nM of PROTAC dTAG-13 (dTAG) (Sigma-Aldrich SML2601) final, diluted in culture medium. AID depletion was triggered using 500 mM of Indole-3-Acetic Acid sodium salt (IAA, auxin analog) (Tocris Bioscience 7932) final, diluted in culture medium.

tag: cell line

value: neural progenitor cells


title: PDAC, Human Tumor, sample20

description: Library name: ST5068


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 48h replicate 2

description: Library name: NIPBL_gast_48_rep2

library_source: genomic

data_processing:
ATAC-seq reads underwent mapping using bwa mem v0.7.17-r1188123 to the mm10 mouse reference genome assembly. Reads that were uniquely mapped and not assigned to mitochondrial DNA, with MAPQ > 10, were retained through selection using SAMtools v1.12.  Duplicate reads were then removed using the Picard v2.25.6 “MarkDuplicates” function.
To decipher the cell type compositions within bulk ATAC-seq samples from both control and NIPBL-depleted gastruloids, a previously published single-cell ATAC-seq atlas of gastruloid development was used (Braccioli et al, 2025). Initially, pseudobulk ATAC-seq profiles for each cell type (cluster) were generated from single-cell data by summing counts in each peak across all cells belonging to the same clusters. Subsequently, read counts of DMSO and dTAG treated bulk samples within the same peak set utilized in the single-cell data were generated. These bulk and pseudobulk counts were then concatenated, normalized using the median of ratios normalization method implemented in DESeq2 v1.30.1147, and transformed using the variance stabilizing transform (VST).
Independent component analysis (ICA) was employed to decipher the contributions of constituent cell types in the bulk samples. ICA was conducted on VST-transformed and zero-centered pseudobulk counts using the FastICA algorithm, implemented in the “icafast” function from the ica R package. The number of components was set to 7 with a maximum of 100 algorithm iterations. The source signal estimates and the unmixing matrix obtained from ICA were then applied to the VST-transformed bulk count matrix to deconvolve the cell type contributions. Finally, cell type proportion estimates were derived by setting the negative contributions to zero and normalizing contributions to the sum of the contributions for each sample.
Assembly: mm10
Supplementary files format and content: BigWig files with ATAC-seq signal - Compressed, indexed, binary files for visualizing continuous genomic data.

molecule: genomic DNA

growth_protocol: Before the aggregation of gastruloids, NIPBL-FKBP ESCs were maintained in 2i-LIF medium, comprising a mixture of 50% DMEM/F12 (Thermo Fisher Scientific 11320-033) and 50% Neurobasal media (Thermo Fisher Scientific 21103-049). This medium was supplemented with 0.5X N2 (Thermo Fisher Scientific 17502-048), 0.5X B27 + retinoic acid (Thermo Fisher Scientific 17504-044), 0.05% BSA (Thermo Fisher Scientific), 3 μM CHIR99021 (BioConnect), 1 μM PD03259010 (BioConnect), 2 mΜ Glutamine (Thermo Fisher Scientific), 1.5 × 10-4 M 1-thioglycerol (Sigma-Aldrich), 100 U/mL LIF (BioConnect, GFM200-5), and 50 U/mL penicillin-streptomycin (Thermo Fisher Scientific). These cells were cultured on gelatin-coated 10 cm petri dishes within a humidified incubator set at 5% CO2 and 37ºC. The protocol for gastruloid culture followed previously established methods (71). Briefly, gastruloids were formed through the aggregation of ESCs in differentiation medium (N2B27). This medium consisted of a mix of DMEM/F12 and Neurobasal medium, supplemented with 2mΜ Glutamine, β-mercaptoethanol, and 50 U/mL penicillin-streptomycin. U-bottom 96-well plates (Thermo Fisher Scientific) were employed for culture, and the process was conducted in a humidified incubator maintained at 5% CO2 and 37ºC. Cell dissociation was carried out in N2B27 medium using a serological pipette in conjunction with a 200 µL pipette tip. Subsequently, 3.75×104 cells were transferred into N2B27 medium, resulting in a final volume of 5 mL. Each well received a 40 µL aliquot of this suspension, containing approximately 300 cells. After 48 hours, 150 µL of N2B27 medium containing 3 μM CHIR99021 was added using the Hamilton Star R&D liquid handling platform.

extract_protocol:
At 120 hours, gastruloids were fixed with 4% formaldehyde for 30 minutes at RT (Sigma-Aldrich), underwent a single wash with PBS, and were subsequently stored at 4ºC. Gastruloids were dissociated into a single-cell suspension through gentle trypsinization and frozen with the addition of 10% DMSO and 10% fetal bovine serum. These samples were then stored at -70ºC until further use.
The Tn5 protein purification was carried out by the NKI protein facility as previously described (Braccioli et al., 2025). Transposon annealing was achieved by combining 10 µL of 10X TE buffer with 45 µL each of 100 µM Tn5MErev oligonucleotides and 100 µM corresponding Tn5ME-A and Tn5ME-B oligonucleotides. The adapter solution was then subjected to incubation at 95ºC for 10 minutes followed by gradual cooling to 4ºC at a rate of 0.1ºC per second. For transposome formation, the annealed adapters were diluted with an equal volume of H2O. This resulting adapter solution was mixed with 0.2 mg/mL Tn5 at a 1:20 ratio and incubated for 1 hour at 37ºC. The transposomes were either utilized immediately for tagmentation or stored at -20ºC for up to 2 weeks. A total of 50,000 cells were collected in cold PBS and lysed using a 2X lysis buffer (1M Tris-HCl pH 7.5, 5M NaCl, 1M MgCl2, 10% IGEPAL). Following centrifugation, the resulting pellet was treated with 2X TD buffer and 2 µL of transposon mix. PCR amplification was performed twice using KAPA HiFi HotStart ReadyMix (Roche) and P5 and P7 indexed primers (please refer to the oligonucleotide list). Fragments ranging from 200 to 700 bp were purified using AMPure XP beads (Beckman Coulter), and the DNA quality was assessed through Bioanalyzer High Sensitivity DNA analysis (Agilent). ATAC-seq oligos available in Supplementary Table S1.

treatment_protocol: Degradation of proteins tagged with the FKBP degron [FKBP12-F36V] was induced by adding dTAG-13 (abbreviated dTAG; Sigma Cat, SML2601) to a final concentration of 500 nM (from a 1000X filter-sterilized stock diluted in DMSO) at the specified time point. Starting from the subsequent day, the culture medium was refreshed with fresh N2B27 medium daily.

value: embryonic stem cell-derived gastruloid

value: dTAG13 at 48h


title: EA18.1_RNAseq_NPC_dTAG13_24h_rep4

description:
Library name: KHRNA95
KHRNA95


title: PDAC, Human Tumor, sample112

description: Library name: ST10708


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 72h replicate 1

description: Library name: NIPBL_gast_72_rep1

value: dTAG13 at 72h


title: EA18.1_RNAseq_NPC_DMSO_24h_rep4

description:
Library name: KHRNA92
KHRNA92


title: NIPBL-FKBP mESC-derived gastruloidsDMSO treated replicate 2

description: Library name: NIPBL_gast_NT_rep2

value: DMSO


title: EA18.1_RNAseq_NPC_DMSO_24h_rep5

description:
Library name: KHRNA93
KHRNA93


title: EN272.2_RAD21-AID_WT-SRR2_IAA_3h30_rep2

description: Library name: KH4C58-62

data_processing:
To generate DpnII/Csp6I fragment maps, the mm10 mouse genome was scanned for restriction enzyme recognition sites using the Biostrings package. Only fragments containing both the primary (DpnII) and secondary (Csp6I) enzyme site were retained. Sequencing reads from different viewpoints were demultiplexed by scanning raw reads for viewpoint-specific primer sequences using the Biostrings package, allowing up to two mismatches, and trimming the reads up to the DpnII restriction site. Trimmed reads were aligned to the mm10 genome using bwa-aln (v0.7.17-r1188) and filtered for uniquely mapped reads using samtools (v1.19.2). Fragment-level read counts were calculated by requiring exact matches between read start or end positions and fragment boundaries. Library size normalization was performed by scaling read counts to counts per million, based on the total number of mapped reads per library. The normalized counts were then smoothed using a rolling mean with a window size of 21 fragments.
Assembly: mm10
Supplementary files format and content: bigWig files for each 4C viewpoint.
Library strategy: 4C-Seq

growth_protocol: Parental WT E14Tg2a (karyotype 19, XY, 129/Ola isogenic background) mouse embryonic stem cells (ESCs) and subclones were cultured in 2iSL medium [DMEM + GlutaMAX + sodium pyruvate (ThermoFisher 10569044) supplemented with 15% fetal bovine serum (Gibco SKU A5256701), 550 µM 2-mercaptoethanol (ThermoFisher 21985-023), 1X nonessential amino acids (ThermoFisher 11140-050), 10^4 U/mL of Leukemia Inhibitory Factor (Millipore ESG1107), 1 µM PD0325901 (Apex Bio/Fischer A3013-25), and 3 µM CHIR99021 (Apex Bio/Fischer A3011-100)]. Cells were maintained at a density of 0.2-1.5 x 10^5 cells/cm^2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48 hours on 0.1% gelatin-coated dishes (Sigma-Aldrich G1890-100G in 1XPBS) at 37 °C and 5% CO2. The medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 6 months and tested negative.

extract_protocol:
4C was performed as previously described (Krijger et al., 2020). MboI was used for the first digestion and Csp6I was used for the second digestion.
4C was performed using a two-step PCR method for indexing.

treatment_protocol: Degradation of proteins tagged with the Auxin-Inducible Degron [44 amino-acid AID* truncation with residues 71–114] was induced by adding Indole-3-acetic acid sodium (IAA, Sigma Cat #I5148-2G) to a final concentration of 500 μM (from a 1000X filter-sterilized stock diluted in water). Degradation of proteins tagged with the FKBP degron [FKBP12-F36V] was induced by adding dTAG-13 (abbreviated dTAG; Sigma Cat, SML2601) to a final concentration of 500 nM (from a 1000X filter-sterilized stock diluted in DMSO).

value: embryonic stem cell

value: RAD21-AID-eGFP; Tir1-2A-PuroR(Tigre)


title: KH150.1_RAD21-AID_del-SRR2_IAA_3h30_rep2

description: Library name: KH4C65-66

value: RAD21-AID-eGFP; Tir1-2A-PuroR(Tigre); SRR2 KO


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 96h replicate 2

description: Library name: NIPBL_gast_96_rep2

value: dTAG13 at 96h


title: EA18.1_RNAseq_NPC_dTAG13_24h_rep5

description:
Library name: KHRNA96
KHRNA96


title: PDAC, Human Tumor, sample28

description: Library name: ST5473


title: EA18.1_RNAseq_NPC_DMSO_24h_rep6

description:
Library name: KHRNA94
KHRNA94


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 72h replicate 2

description: Library name: NIPBL_gast_72_rep2


title: KH150.1_RAD21-AID_del-SRR2_unt_rep2

description: Library name: KH4C63-64

value: untreated


title: PDAC, Human Tumor, sample120

description: Library name: ST11592


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 48h replicate 1

description: Library name: NIPBL_gast_48_rep1


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 96h replicate 1

description: Library name: NIPBL_gast_96_rep1


title: NIPBL-FKBP mESC-derived gastruloids DMSO treated replicate 1

description: Library name: NIPBL_gast_NT_rep1


title: EN272.2_RAD21-AID_WT-SRR2_unt_rep2

description: Library name: KH4C53-57


title: PDAC, Human Tumor, sample53

description: Library name: ST11588


title: KH128.3_NIPBL-FKBP_del-SRR2_dTAG13_24h_rep2

description: Library name: KH4C51-52

value: BlastR-T2A-2xHA-FKBP12-Nipbl; SRR2 KO


title: KH128.3_NIPBL-FKBP_del-SRR2_DMSO_24h_rep2

description: Library name: KH4C49-50


title: EA18.1_NIPBL-FKBP_WT-SRR2_dTAG13_24h_rep2

description: Library name: KH4C44-48


title: EN272.2_RAD21-AID_WT-SRR2_unt_rep1

description: Library name: KH4C20-24


title: EN272.2_RAD21-AID_WT-SRR2_IAA_3h30_rep1

description: Library name: KH4C25-29


title: KH128.3_NIPBL-FKBP_del-SRR2_DMSO_24h_rep1

description: Library name: KH4C16-17


title: KH128.3_NIPBL-FKBP_del-SRR2_dTAG13_24h_rep1

description: Library name: KH4C18-19


title: EA18.1_NIPBL-FKBP_WT-SRR2_DMSO_24h_rep1

description: Library name: KH4C6-10


title: E14_WT_unt_rep1

description: Library name: KH4C1-5

value: WT


title: KH105.2_mutCBS-Car2-prom_ESC_CTCF

data_processing:
Fastq files were aligned to the catenated mm10 reference genome with Bowtie2(Langmead and Salzberg, 2012). Reads with a mapq score ≥ 30 were retained, using Samtools. Scaling factor was calculated based on the number of mouse and human reads from input and human reads from the ChIP sample.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
For crosslinking, ESCs with CTCF site mutation in the Car2 promoter (KH105.1 and KH105.2) were dissociated using TrypLE, resuspended in culture medium and counted. 15e6  ESCs were pelleted at 100g for 5 minutes at RT. Supernatant was discarded and cell pellets were resuspended in 5 mL of 10% FBS prepared in 1X PBS. To this, 5 mL of freshly prepared 2% formaldehyde solution was added to get final formaldehyde concentration of 1%. 2% formaldehyde was diluted from 16% methanol-free formaldehyde in 1X PBS (ThermoFisher 28908). Resuspended cells were incubated on rocker to allow for mixing for 10 minutes at RT. Quenching was performed using 0.125M Glycine prepared in 1X PBS and incubated on rocker for 5 minutes at RT. Tubes were then stored on ice for 15 minutes followed by centrifuging at 100g for 5 minutes at 4° C. Supernatant was discarded and cell pellets were washed twice with 5 mL of ice-cold 1X PBS. Cell pellets were resuspended in 1 mL of ice-cold PBS and transferred to 1.5 ml tubes, centrifuged at 100g for 5 minutes at 4° C. Supernatant was discarded and pellets were snap frozen on dry ice and stored at -70°C. Fixed cells were thawed on ice, resuspended in 1 mL of ice-cold lysis buffer [10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2% NP-40 (IGEPAL), 0.2% TritonX-100, 1 mM EDTA, 0.5 mM EGTA, supplemented with fresh protease inhibitor] and incubated on ice for 10 minutes. 9.75 x 106 ESC nuclei were transferred to a pre-chilled 1.5 mL tube and 0.25 x 106 crosslinked HEK nuclei were added as spike-in. Nuclei were pelleted at 400g for 5 minutes at 4°C, supernatant discarded and nuclear pellets resuspended in 900 μL of shearing buffer (0.5% SDS, 10 mM Tris HCl pH 7.5, supplemented with fresh protease inhibitor). Chromatin was sheared using Covaris with settings PIP 105, Duty factor 5, Cycles per burst 200, total time 15 minutes. After shearing, samples were collected in pre-chilled 1.5 mL tubes and spun at 13,000 rpm for 5 minutes at 4° C. Supernatant was collected in a fresh tube. 5% sample was removed as Input and stored at -20°C. For immunoprecipitation (IP), 40 μl Dynabeads/ChIP were prepared by washing them once in 1 mL of 1X ChIP incubation buffer (diluted from 5X ChIP incubation buffer in 1X PBS; 5% TritonX-100, 0.75 M NaCl, 5 mM EDTA, 2.5 mM EGTA, 50 mM Tris-Cl pH7.5) and resuspended in the 40 μL of same buffer. For IP, tubes were incubated overnight on end-to-end rocker at 10 rpm, 4°C. Following overnight incubation, beads were collected using magnetic rack and washed sequentially with different wash buffers for 5 minutes each on end-to-end rocker at 10 rpm, 4°C. Beads were washed twice with 500 μL of cold wash buffer 1 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8). Beads were then washed once each with 500 μL of cold wash buffer 2 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.5 M NaCl, 1 mM EDTA, 10 mM Tris pH 8) and 500ul of cold wash buffer 3 [0.25 M LiCl, 0.5% Sodium deoxycholate, 0.5% NP-40 (IGEPAL), 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8]. Finally, beads were washed twice with 500 μL of cold wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8). For elution, beads were resuspended in 200 μL of elution buffer (1% SDS, 0.1M NaHCO3) and incubated on end-to-end rocker at 10 rpm for 20 minutes, RT. Beads were then separated using magnetic rack and the eluate (supernatant) was transferred to a fresh tube. 5% input samples were thawed on ice and elution buffer was added to bring the volume to 200 μL. To each sample, 2 μL of 1 mg/ml RNaseA was added and incubated at 37°C for 30 minutes. For reverse crosslinking, 8 μL of 5 M NaCL and 5 μL of 10 mg/ml Proteinase K was added and incubated overnight at 65°C. Following reverse crosslinking, DNA was eluted using MinElute kit from Qiagen (28604).
Eluted DNA was quantified using Qubit and libraries were prepared using NEBNext Ultra II DNA library prep kit as per manufacturer’s protocol (E7645S). All of ChIP samples and 4 ng of Input samples were used for library prep. Final library amplification was done for 17 cycles, followed by 0.9X SPRI bead purification (Bulldog Bio CNGS005). Eluted in 10 μL of 10 mM Tris-Cl pH7.5. Entire eluate was run on a 2% E-gel (Invitrogen G401002) and fragments between 200-600bp were excised and eluted using MinElute gel extraction kit (Qiagen 28604). Quality and quantity of libraries were assessed using Qubit and Bioanalyzer High Sensitivity DNA kit.

value: embryonic stem cells

tag: chip antibody

value: CTCF (Active Motif 61311)


title: KH150.1_RAD21-AID_del-SRR2_IAA_3h30_rep1

description: Library name: KH4C32-33


title: EA18.1_NIPBL-FKBP_WT-SRR2_dTAG13_24h_rep1

description: Library name: KH4C11-15


title: E14_RNAseq_ESC_DMSO_24h_rep4


title: EA18.1_CUTTag_ESC_H3K27me3_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.

data_processing:
Fastq files for CUT&Tag samples were processed using Nextflow and the nf-core CUT&RUN pipeline v3.1. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using Bowtie2 and peaks were called using SEACR with a peak threshold of 0.05 with spike in normalization performed using the E. coli genome K12.
Peaks in ENCODE blacklisted regions (Amemiya et al., 2019) were removed using the intersect function in bedtools2 v2.30.0.
Assembly: mm10
Supplementary files format and content: bigWig files for individual replicates and the average of two replicates, SEACR consensus peak lists
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was conducted using the protocol from Kaya-Okur et al. 2020 with the following modifications: freshly collected cells were bound to Concanavalin A beads at a ratio of 2e5 cells/7 μL beads in CR wash at RT. At least 1e5 cells were used as input per sample. Bead-bound cells were then incubated rotating overnight at 4°C in CT Antibody buffer (CR Wash with 0.05% Digitonin, 2 mM EDTA, 1 mg/mL BSA) containing primary antibody. After primary, samples were washed 3 times for 5 minutes each using CR Dig-wash buffer and resuspended in 1:100 secondary antibody (Guinea pig anti-rabbit, Antibodies Online #ABIN101961) in CR Dig-wash buffer at 4°C for 1 hour rotating at 4°C. Samples were then incubated for 1 hour at 4°C with 50 μL of approximately 25 nM homemade pA-Tn5 in CT Dig300 wash buffer (20 mM HEPES, 300 mM NaCl, 0.01% Digitonin, 0.5 mM Spermidine with Roche cOmplete protease inhibitors added). Recombinant Tn5 was purified and loaded with adapters as previously described (Kaya-Okur et al. 2019). After Tn5 incubation, samples were washed 3 times for 5 minutes each with CT Dig300 wash buffer. Tagmentation was then initiated for 1hr at 37°C in a thermocycler by adding MgCl2 to 10 mM final concentration in 50 μL volume. The tagmentation reaction was quenched immediately afterwards by adding 1.6 μL l of 0.5 M EDTA, 1 μL of 10 mg/mL Proteinase K, and 1 μL of 5% SDS. Samples were then incubated at 55°C for 2 hours in a thermocycler to denature Tn5 and solubilize tagmented chromatin. After incubation, samples were magnetized, and the supernatant was transferred to new wells where SPRI bead purification was performed using homemade beads to select all DNA fragment lengths larger than 100 bp. Samples were eluted in 0.1X TE
Approximately half of each sample was used for library preparation using NEBNext HIFI Polymerase with custom indices synthesized by IDT. An appropriate number of cycles for each target was chosen to prevent overamplification bias. After amplification, libraries were purified with 1.2X homemade SPRI beads to select for fragments >250 bp and eluted in 0.1X TE.

tag: antibody

value: H3K27me3 (Cell Signaling 9733)


title: EA18.1_CUTTag_ESC_H3K27me3_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_Exit_H3K27ac_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.

value: ESC exit from pluripotency differentiation

value: H3K27ac (Abcam ab4729)


title: EA18.1_CUTTag_Exit_H3K27me3_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EN273.7_RNAseq_ESC_IAA_96h_rep3

value: eGFP-AID-Nipbl, Tir1-2A-PuroR (Tigre), Rad21-HaloTag


title: KH105.1_mutCBS-Car2-prom_ESC_CTCF


title: EA18.1_CUTTag_Exit_H3K27me3_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_Exit_H3K27ac_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: E14_RNAseq_ESC_DMSO_24h_rep3


title: EN273.7_RNAseq_ESC_IAA_96h_rep2


title: EA18.1_CUTTag_ESC_H3K27ac_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: E14_RNAseq_ESC_DMSO_24h_rep2


title: EA18.1_CUTTag_ESC_H3K27ac_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_NIPBL-FKBP_WT-SRR2_DMSO_24h_rep2

description: Library name: KH4C39-43


title: EN273.7_RNAseq_ESC_IAA_96h_rep1


title: KH150.1_RAD21-AID_del-SRR2_unt_rep1

description: Library name: KH4C30-31


title: EN273.7_RNAseq_ESC_IAA_48h_rep3


title: EN273.7_RNAseq_ESC_IAA_48h_rep2


title: EA18.1_CUTTag_Exit_H3K27me3_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EN273.7_RNAseq_ESC_IAA_24h_rep2


title: EA18.1_CUTTag_Exit_H3K27ac_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_Exit_H3K27ac_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_Exit_H3K27me3_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EN273.7_RNAseq_ESC_IAA_12h_rep3


title: EN273.7_RNAseq_ESC_IAA_24h_rep1


title: EN273.7_RNAseq_ESC_IAA_24h_rep3


title: EN273.7_RNAseq_ESC_untreated_rep3


title: EA18.1_CUTTag_ASC_H3K27me3_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.

value: NPC-derived astrocyte differentiation


title: EN273.7_RNAseq_ESC_IAA_48h_rep1


title: EA18.1_CUTTag_ESC_H3K27me3_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ESC_H3K27me3_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ESC_H3K27ac_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EN273.7_RNAseq_ESC_IAA_12h_rep2


title: EA18.1_CUTTag_ASC_H3K27me3_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ESC_H3K27ac_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_NPC_H3K27me3_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.

value: neural progenitor cells


title: EA18.1_RNAseq_ASC_dTAG13_48h_rep3


title: EN273.7_RNAseq_ESC_untreated_rep2


title: EN273.7_RNAseq_ESC_untreated_rep1


title: EA18.1_CUTTag_ASC_H3K27ac_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_ASC_dTAG13_48h_rep2


title: EA18.1_RNAseq_ASC_dTAG13_48h_rep1


title: EA18.1_CUTTag_ASC_H3K27ac_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_ASC_DMSO_48h_rep3


title: EA18.1_CUTTag_NPC_H3K27me3_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ASC_H3K27me3_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ASC_H3K27me3_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_NPC_H3K27ac_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_NPC_H3K27me3_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_NPC_dTAG13_48h_rep2


title: EA18.1_CUTTag_NPC_H3K27ac_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_ASC_DMSO_48h_rep1


title: EA18.1_RNAseq_ASC_DMSO_48h_rep2


title: EA18.1_RNAseq_NPC_dTAG13_48h_rep1


title: EA18.1_RNAseq_NPC_DMSO_48h_rep3


title: EA18.1_RNAseq_NPC_dTAG13_48h_rep3


title: EA18.1_CUTTag_NPC_H3K27me3_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_NPC_DMSO_48h_rep2


title: EA18.1_CUTTag_ASC_H3K27ac_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ASC_H3K27ac_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_NPC_H3K27ac_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_NPC_DMSO_48h_rep1


title: E14_RNAseq_NPC_dTAG13_24h_rep3


title: EA18.1_RNAseq_Exit_dTAG13_48h_rep3


title: EA18.1_RNAseq_Exit_dTAG13_48h_rep2


title: E14_RNAseq_NPC_dTAG13_24h_rep4


title: EA18.1_CUTTag_NPC_H3K27ac_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_Exit_dTAG13_48h_rep1


title: E14_RNAseq_NPC_dTAG13_24h_rep1


title: EA18.1_RNAseq_Exit_DMSO_48h_rep3


title: EA18.1_RNAseq_Exit_DMSO_48h_rep1


title: E14_RNAseq_NPC_DMSO_24h_rep4


title: EA18.1_RNAseq_Exit_DMSO_48h_rep2


title: EA18.1_RNAseq_ESC_dTAG13_48h_rep2


title: EA18.1_RNAseq_ESC_dTAG13_48h_rep3


title: EA18.1_RNAseq_ESC_dTAG13_24h_rep1


title: E14_RNAseq_NPC_DMSO_24h_rep3


title: EA18.1_RNAseq_ESC_dTAG13_48h_rep1


title: E14_RNAseq_ESC_dTAG13_24h_rep3


title: EA18.1_RNAseq_ESC_DMSO_24h_rep2


title: ANAPC1P2 KD in OVCAR3 cells Set 3

status: Public on Nov 26 2025

city: Pune

first: Dr. Sharmila

middle: A

last: Bapat

state: Maharashtra

address: NCCS campus, SPPU, Ganeshkhind road.

country: India

institute: National Centre for Cell Science

description:
Library name: Sample 3
Illumina NovaSeq X Plus instrument used to generate ~60 million 150 bp paired-end reads per sample.

data_processing:
Paired-end reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b). Gene-level read counts were estimated using FeatureCounts (v2.0.6). Raw counts were normalized and used for differential expression analysis using DESeq2.
Assembly: human genome (hg38)
Supplementary files format and content: csv files contain normalized read counts for each sample.

source_name: Ovarian

growth_protocol: OVCAR3_KD and OVCAR3 WT cells were grown in RPMI+10% FBS. All cell lines were maintained in a humidified incubator at 37°C under 5% CO2 atmosphere.

extract_protocol:
Libraries for total RNA sequencing were prepared using the KAPA RNA HyperPrep Kit (Roche KAPA) according to the manufacturer's instructions. Briefly, 100 ng of total RNA was used as input, and ribosomal RNA (rRNA) was depleted using KAPA RiboErase HMR.
The rRNA-depleted RNA was fragmented at 94 °C for 6 minutes using divalent cations. Fragmented RNA was reverse transcribed to synthesize first-strand cDNA. Second-strand synthesis with A-tailing generated double-stranded cDNA with dUTP incorporated into the second strand, enabling strand-specific sequencing. Indexed adapters with 3' dTMP overhangs were ligated to the fragments, followed by PCR enrichment (13 cycles). Libraries were purified and fragment size distribution was assessed using a Fragment Analyzer with the HS NGS Fragment Kit (Agilent).

value: Ovarian

value: Ovarian cancer cells

value: OVCAR3 ANAPC1P2 KD


title: E14_RNAseq_NPC_DMSO_24h_rep1


title: EA18.1_RNAseq_ESC_dTAG13_24h_rep4


title: OVCAR3 WT

description:
Library name: Sample 4
Illumina NovaSeq X Plus instrument used to generate ~60 million 150 bp paired-end reads per sample.


title: EA18.1_RNAseq_ESC_DMSO_24h_rep4


title: Dot1l_KO_TT-seq_rep1

status: Public on Nov 13 2025

city: Montrreal

first: Javier

middle: M

last: Di Noia

address: 110 Av des Pins Ouest

institute: Institut de Recherches Cliniques de Montreal

description: Library name: KO1

data_processing:
*library strategy: TT(chem)-seq
Sequencing adapters were trimmed with Trimmomatic  (0.36) with (parameter- PE ILLUMINACLIP:adapters.fa:2:30:10: TRAILING:3 MINLEN:25).
Trimmed means were mapped to custom CH12F3 genome (modified mm10) and  S.cerevisiae R64 genomes with STAR (2.7.9a) following manual instructions for multi-sample 2-pass mapping.
Mapped reads to mouse genome were filtered for mapping quality (MAPQ>=1)  using samtools (1.16.1).
Scaling factors were calculated based on number of reads mapped to S. cerevisiae R64 genome (library size).
Bigwig files were generated using bamCoverage from deepTools (3.5.0) using the calculated scaling factors with a bin size of 10bp.
Assembly: custom reference genome reflecting the recombined V(D)J loci in CH12, produced by modifying mouse (mm10) reference genome based on the IgH and Igκ cDNA sequences from CH12F3 cells using Reform; and S.cerevisiae R64
Supplementary files format and content: bigwig (forward and reverse strands)

molecule: nuclear RNA

growth_protocol: CH12F3-G (a subclone with higher CSR activity derived by limiting dilution from CH12F3) were cultured in RPMI 1640 media (Wisent) supplemented with 10% fetal bovine serum (Wisent), 1% penicillin/streptomycin (Wisent) and 0.1 mM 2-mercaptoethanol (Bioshop).

extract_protocol:
4SU enriched RNA was extracted following TT(chem)-seq protocol (Gregersen et al 2020). Briefly, RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 5 min. Total RNA was extracted following a hot-phenol purification (Collin et al 2019.). For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 30 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries were prepared using the strand-specific TruSeq total RNA kit (Illumina) using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples.

value: unstimulated


title: ANAPC1P2 KD in OVCAR3 cells Set 1

description:
Library name: Sample 1
Illumina NovaSeq X Plus instrument used to generate ~60 million 150 bp paired-end reads per sample.


title: E14_RNAseq_ESC_dTAG13_24h_rep1


title: E14_RNAseq_ESC_dTAG13_24h_rep4


title: Dot1l_KO_TT-seq_rep3

description: Library name: KO3


title: WT_TT-seq_rep2

description: Library name: WT2


title: EA18.1_RNAseq_ESC_dTAG13_24h_rep2


title: Dot1l_KO_TT-seq_rep2

description: Library name: KO2


title: S5P-RNAPII_Dot1l_KO_rep2

description: Library name: S5P_RNAPII_KO_2

data_processing:
Sequencing adapters and first 10bp were trimmed with fastp 0.23.1.
Trimmed reads were aligned with bowtie2 (2.4.4) to the spiked-in Drosophila melanogaster genome (dm6) and custom CH12F3 genome (modified mm10).
Duplicates reads were removed with MarkDuplicatesSpark from Picard tools through gatk (4.2.4.0) and were filtered for mapping quality (MAPQ>=1) using samtools (1.16.1).
Normalization was performed using DiffBind package (3.8.3), specifically by using DESeq2 (1.38.2) to calculate scaling factors based on “background bin” signals estimated by the csaw package (1.32.0).
These scaling factors were then used to generate bigwig files using bamCoverage and bamCompare from deepTools (3.5.0) with a bin size of 20bp.
Assembly: custom reference genome reflecting the recombined V(D)J loci in CH12, produced by modifying mouse (mm10) reference genome based on the IgH and Igκ cDNA sequences from CH12F3 cells using Reform; and dm6
Supplementary files format and content: bigWig

growth_protocol: CH12F3-G (a subclone with higher CSR activity derived by limiting dilution from CH12F3) were cultured in RPMI 1640 media (Wisent) supplemented with 10% fetal bovine serum (Wisent), 1% penicillin/streptomycin (Wisent) and 0.1umM 2-mercaptoethanol (Bioshop).

extract_protocol:
10 million CH12F3 cells cultured in 10mL of media were cross-linked with 1% formaldehyde for 8 minutes at room temperature, washed and resuspended in RIPA buffer and sonicated with Covaris E220 for 10 min with 10% Duty Factor, 140W PIP and 200 CBP and clarified by centrifugation. S2/Kc167 chromatin was prepared by crosslinking cells in 1X PBS containing 1% formaldehyde at RT for 20 min and quenched with 125 mM glycine for 5 min, washed and resuspended in 130 μL of RIPA buffer and fragmented using Covaris E220 for 150s with 140W PIP, 20% DF and 200 CPB and clarified by centrifugation. For spike-in, 1μg of S2/Kc167 chromatin was spiked to 24μg of CH12-F3 chromatin (1:24 ratio) before IP. Samples were pre-cleared with 20μL of Dynabeads Protein G for 1h (4°C). For the IP, 30μL Dynabeads Protein G were coupled with the target Ab (amounts as per manufacturer instructions) and 2μg of a spike-in Ab against Drosophila H2Av for 30 min and blocked 1h (4°C) with BT buffer. IP was performed by overnight incubation of the pre-cleared chromatin with blocked Ab-beads complexes. Beads were then washed and immunocomplexes were eluted and incubated overnight with proteinase K at 65°C. DNA was purified using QIAquick PCR purification kit (Qiagen), and DNA resuspended in 50μl Tris-HCl (pH 8).
Libraries were prepared using the KAPA HyperPrep library kit (Roche Diagnostics) as per manufacturer's instructions. Normalization of the samples quantities was done after quantification of the ligation products by qPCR and library size distribution was assessed on a 2100 bioanalyzer.


title: WT_TT-seq_rep1

description: Library name: WT1


title: S5P-RNAPII_Dot1l_KO_rep1

description: Library name: S5P_RNAPII_KO_1


title: WT_TT-seq_rep3

description: Library name: WT3


title: S5P-RNAPII_WT_rep2

description: Library name: S5P_RNAPII_WT_2


title: EA18.1_RNAseq_ESC_DMSO_24h_rep1


title: S5P-RNAPII_WT_rep1

description: Library name: S5P_RNAPII_WT_1


title: ANAPC1P2 KD in OVCAR3 cells Set 2

description:
Library name: Sample 2
Illumina NovaSeq X Plus instrument used to generate ~60 million 150 bp paired-end reads per sample.


title: Nipbl_Dot1l_KO_rep1

description: Library name: Nipbl_KO_1


title: S2P-RNAPII_WT_rep2

description: Library name: S2P_RNAPII_WT_2


title: RNAPII_WT_rep2

description: Library name: RNAPII_WT_2


title: RNAPII_Dot1l_KO_rep2

description: Library name: RNAPII_KO_2


title: Rad21_WT_rep2

description: Library name: Rad21_WT_2


title: Rad21_Dot1l_KO_rep2

description: Library name: Rad21_KO_2


title: S2P-RNAPII_Dot1l_KO_rep1

description: Library name: S2P_RNAPII_KO_1


title: Nipbl_WT_rep2

description: Library name: Nipbl_WT_2


title: S2P-RNAPII_WT_rep1

description: Library name: S2P_RNAPII_WT_1


title: Nipbl_Dot1l_KO_rep2

description: Library name: Nipbl_KO_2


title: RNAPII_WT_rep1

description: Library name: RNAPII_WT_1


title: Rad21_Dot1l_KO_rep1

description: Library name: Rad21_KO_1


title: RNAPII_Dot1l_KO_rep1

description: Library name: RNAPII_KO_1


title: S2P-RNAPII_Dot1l_KO_rep2

description: Library name: S2P_RNAPII_KO_2


title: H3K79me3_rep2

description: Library name: H3K79me3_2


title: H3K79me3_rep1

description: Library name: H3K79me3_1


title: Dot1l_KO_rep2

data_processing:
Sequencing adapters were trimmed with fastp (0.23.1) with (parameter- --detect_adapter_for_pe).
Trimmed means were mapped to custom CH12F3 genome (modified mm10) and dm6 genomes with STAR (2.7.9a) following manual instructions for multi-sample 2-pass mapping.
Gene expression counts were determined with featureCounts (Rsubread 2.12.2). Drosophila reads were used to scale DESeq2 (1.38.2) for differential gene expression.
Mapped reads to mouse genome were filtered for mapping quality (MAPQ>=1) with using samtools (1.16.1) to generate bigwig files using bamCoverage and bamCompare from deepTools (3.5.0) with a bin size of 1bp.
Assembly: custom reference genome reflecting the recombined V(D)J loci in CH12, produced by modifying mouse (mm10) reference genome based on the IgH and Igκ cDNA sequences from CH12F3 cells using Reform; and dm6
Supplementary files format and content: bigwig (forward and reverse strands)

extract_protocol:
Briefly, 0.5million CH12F3 WT or Dot1l-/- cells and 0.1million Kc167 Drosophila cells (as spike-in) were mixed. RNA was extracted using Qiagen RNeasy Micro kit.
mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and library was prepared using KAPA RNA HyperPrep kit (Roche Diagnostics) as per manufacturer's instructions.


title: Nipbl_WT_rep1

description: Library name: Nipbl_WT_1


title: IgG_WT

data_processing:
Sequencing adapters and first 10bp were trimmed with fastp 0.23.1.
Trimmed means were mapped to before alignment with bowtie2 (2.4.4) to the spiked-in E. coli (k12) and custom CH12F3 genome (modified mm10).
Duplicates reads were removed with MarkDuplicatesSpark from Picard tools through gatk (4.2.4.0) and were filtered for mapping quality (MAPQ>=1) using samtools (1.16.1).
Normalization using spike-in reads was performed using DiffBind package (3.8.3), specifically by using DESeq2 (1.38.2) to calculate scaling factors on “background bin” signals for spike-in reads estimated by the csaw package (1.32.0).
These scaling factors were then used to generate bigwig files using bamCoverage and bamCompare from deepTools (3.5.0) with a bin size of 20bp.
Assembly: custom reference genome reflecting the recombined V(D)J loci in CH12, produced by modifying mouse (mm10) reference genome based on the IgH and Igκ cDNA sequences from CH12F3 cells using Reform; and k12
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed following a protocol described previously (Hogan AK, et al. 2021 EMBO J.), with the following modifications: 5 million CH12-F3 of viable cells were employed per condition. CH12-F3 cells were permeabilized with 0.001% digitonin as determined by optimization. Following incubation with Calcium Incubation Buffer for 30min at 0C, reaction was stopped with STOP buffer containing 1ng of E.coli Spike-in DNA (Epicypher, 15-1016). The released chromatin fragments were purified with Nucleotide Purification Kit (Qiagen) and eluted in 25µL of Tris-HCl (pH 8).
Libraries were prepared using the KAPA HyperPrep library kit (Roche Diagnostics) as per manufacturer's instructions. Normalization of the samples quantities was done after quantification of the ligation products by qPCR and library size distribution was assessed on a 2100 bioanalyzer.

value: IgG


title: Rad21_WT_rep1

description: Library name: Rad21_WT_1


title: Dot1l_KO_rep3


title: H3K79me2_rep1

description: Library name: H3K79me2_1


title: Dot1l_KO_rep1


title: WT_rep3


title: WT_rep1


title: WT_rep2


title: S343_J130_T6 [S343_S85_L004]

status: Public on Nov 07 2025

city: Canyon

first: Matthew

last: Scott

state: TX

address: 3201 Russell Long Blvd

institute: Texas A&M University

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina Universal adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. ComBat-Seq within sva was used to account for lane bias. Differential expression analysis was performed with edgeR v3.36.0 and glmmSeq v0.2.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated via Tempus Spin RNA Isolation Kits (Applied Biosystems), per product instruction.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: All samples were collected into Tempus RNA Blood tubes (Applied Biosystems) and stored per product recommendation the same day of collection.

value: Whole blood

tag: ID

tag: timepoint

tag: vaccinated

value: yes

tag: marketing

value: direct

tag: treated for_brd

tag: sequencing lane


title: CTCF_Dot1l_KO_1

value: CTCF


title: H3K79me2_rep2

description: Library name: H3K79me2_2

value: WT


title: CTCF_WT_1


title: H3K27me3_WT


title: S342_J128_T6 [S342_S84_L004]

value: auction

value: no


title: Rpb1_WT


title: IgG_Dot1l_KO


title: S340_J122_T6 [S340_S82_L004]


title: CTCF_Dot1l_KO_2


title: S337_J115_T6 [S337_S79_L004]


title: CTCF_WT_2


title: Rpb1_Dot1l_KO


title: S335_J112_T6 [S335_S77_L004]


title: S338_J117_T6 [S338_S80_L004]


title: S341_J123_T6 [S341_S83_L004]


title: S339_J121_T6 [S339_S81_L004]


title: S333_J110_T6 [S333_S75_L004]


title: S331_J108_T6 [S331_S73_L004]


title: S332_J109_T6 [S332_S74_L004]


title: S334_J111_T6 [S334_S76_L004]


title: S330_J107_T6 [S330_S72_L004]


title: S317_J081_T6 [S317_S60_L004]


title: S336_J113_T6 [S336_S78_L004]


title: S312_J071_T6 [S312-2_S57_L004]


title: S321_J086_T6 [S321_S64_L004]


title: S327_J097_T6 [S327_S69_L004]


title: S316_J078_T6 [S316_S59_L004]


title: S328_J103_T6 [S328_S70_L004]


title: S329_J104_T6 [S329_S71_L004]


title: S319_J084_T6 [S319_S62_L004]


title: S326_J091_T6 [S326_S68_L004]


title: S324_J089_T6 [S324_S67_L004]


title: S310_J062_T6 [S310_S53_L004]


title: S323_J088_T6 [S323_S66_L004]


title: S309_J061_T6 [S309_S52_L004]


title: S307_J055_T6 [S307_S50_L004]


title: S322_J087_T6 [S322_S65_L004]


title: S306_J053_T6 [S306_S49_L004]


title: S311_J068_T6 [S311-2_S55_L004]


title: S305_J052_T6 [S305_S48_L004]


title: S318_J082_T6 [S318_S61_L004]


title: S320_J085_T6 [S320_S63_L004]


title: S302_J047_T6 [S302_S45_L004]


title: S300_J043_T6 [S300_S43_L004]


title: S293_J032_T6 [S293_S37_L004]


title: S298_J040_T6 [S298_S41_L004]


title: S299_J041_T6 [S299_S42_L004]


title: S292_J031_T6 [S292_S36_L004]


title: S291_J030_T6 [S291_S35_L004]


title: S289_J028_T6 [S289_S33_L004]


title: S304_J051_T6 [S304_S47_L004]


title: S288_J027_T6 [S288_S32_L004]


title: S314_J038_T6 [S314_S58_L004]


title: S308_J059_T6 [S308_S51_L004]


title: S303_J050_T6 [S303_S46_L004]


title: S296_J036_T6 [S296_S39_L004]


title: S294_J033_T6 [S294_S38_L004]


title: S290_J029_T6 [S290_S34_L004]


title: S301_J045_T6 [S301_S44_L004]


title: S297_J037_T6 [S297_S40_L004]


title: S285_J024_T6 [S285_S30_L004]


title: S287_J026_T6 [S287_S31_L004]


title: S284_J023_T6 [S284_S29_L004]


title: S283_J022_T6 [S283_S28_L004]


title: S280_J018_T6 [S280_S25_L004]


title: S281_J019_T6 [S281_S26_L004]


title: S279_J017_T6 [S279_S24_L004]


title: S282_J020_T6 [S282_S27_L004]


title: S277_J015_T6 [S277_S22_L004]


title: S278_J016_T6 [S278_S23_L004]


title: S274_J011_T6 [S274_S19_L004]


title: S271_J128_T5 [S271_S16_L004]


title: S262_J085_T5 [S262_S7_L004]


title: S276_J014_T6 [S276_S21_L004]


title: S267_J107_T5 [S267_S12_L004]


title: S264_J088_T5 [S264_S9_L004]


title: S263_J087_T5 [S263_S8_L004]


title: S272_J132 _T5 [S272_S17_L004]


title: S266_J104_T5 [S266_S11_L004]


title: S265_J089_T5 [S265_S10_L004]


title: S269_J115_T5 [S269_S14_L004]


title: S259_J081_T5 [S259_S4_L004]


title: S261_J084_T5 [S261_S6_L004]


title: S273_J009_T6 [S273_S18_L004]


title: S258_J075_T5 [S258_S3_L004]


title: S268_J110_T5 [S268_S13_L004]


title: S260_J082_T5 [S260_S5_L004]


title: S256_J061_T5 [S256_S1_L004]


title: S257_J068_T5 [S257_S2_L004]


title: S254_J045_T5 [S254-2_S86_L003]


title: S255_J051_T5 [S255_S87_L003]


title: S252_J036_T5 [S252_S82_L003]


title: S250_J030_T5 [S250_S80_L003]


title: S251_J034_T5 [S251_S81_L003]


title: S253_J037_T5 [S253-2_S84_L003]


title: S249_J029_T5 [S249_S79_L003]


title: S245_J018_T5 [S245_S75_L003]


title: S246_J020_T5 [S246_S76_L003]


title: S243_J132 _T4 [S243_S73_L003]


title: S244_J016 _T5 [S244_S74_L003]


title: S242_J130_T4 [S242_S72_L003]


title: S247_J025_T5 [S247_S77_L003]


title: S239_J122_T4 [S239_S69_L003]


title: S238_J121_T4 [S238_S68_L003]


title: S236_J115_T4 [S236_S66_L003]


title: S241_J128_T4 [S241_S71_L003]


title: S235_J112_T4 [S235_S65_L003]


title: S233_J110_T4 [S233_S63_L003]


title: S240_J123_T4 [S240_S70_L003]


title: S270_J117_T5 [S270_S15_L004]


title: S234_J111_T4 [S234_S64_L003]


title: S229_J103_T4 [S229_S59_L003]


title: S275_J013_T6 [S275_S20_L004]


title: S237_J117_T4 [S237_S67_L003]


title: S232_J108_T4 [S232_S62_L003]


title: S228_J097_T4 [S228_S57_L003]


title: S226_J091_T4 [S226_S56_L003]


title: S230_J104_T4 [S230_S60_L003]


title: S248_J028_T5 [S248_S78_L003]


title: S225_J089_T4 [S225_S55_L003]


title: S227_J092_T4 [S227_S58_L003]


title: S221_J085_T4 [S221_S51_L003]


title: S212_J062_T4 [S212_S40_L003]


title: S204_J045_T4 [S204_S32_L003]


title: S215_J075_T4 [S215_S45_L003]


title: S202_J041_T4 [S202_S30_L003]


title: S223_J087_T4 [S223_S53_L003]


title: S218_J081_T4 [S218_S48_L003]


title: S219_J082_T4 [S219_S49_L003]


title: S208_J052_T4 [S208_S36_L003]


title: S222_J086_T4 [S222_S52_L003]


title: S217_J078_T4 [S217_S47_L003]


title: S220_J084_T4 [S220_S50_L003]


title: S214_J071_T4 [S214-2_S44_L003]


title: S211_J061_T4 [S211_S39_L003]


title: S210_J059_T4 [S210_S38_L003]


title: S213_J068_T4 [S213-2_S42_L003]


title: S201_J037_T4 [S201_S29_L003]


title: S207_J051_T4 [S207_S35_L003]


title: S206_J050_T4 [S206_S34_L003]


title: S209_J055_T4 [S209_S37_L003]


title: S205_J047_T4 [S205_S33_L003]


title: S216_J076_T4 [S216_S46_L003]


title: S224_J088_T4 [S224_S54_L003]


title: S200_J036_T4 [S200_S28_L003]


title: S203_J043_T4 [S203_S31_L003]


title: S231_J107_T4 [S231_S61_L003]


title: S199_J034_T4 [S199_S27_L003]


title: S197_J031_T4 [S197_S25_L003]


title: S196_J030_T4 [S196_S24_L003]


title: S195_J029_T4 [S195_S23_L003]


title: S194_J028_T4 [S194_S22_L003]


title: S193_J026_T4 [S193_S21_L003]


title: S192_J025_T4 [S192_S20_L003]


title: S190_J020_T4 [S190_S18_L003]


title: S189_J019_T4 [S189_S17_L003]


title: S191_J024_T4 [S191_S19_L003]


title: S187_J017_T4 [S187_S15_L003]


title: S198_J033_T4 [S198_S26_L003]


title: S185_J014_T4 [S185_S13_L003]


title: S179_J123_T3 [S179_S7_L003]


title: S184_J013_T4 [S184_S12_L003]


title: S178_J122_T3 [S178_S6_L003]


title: S188_J018_T4 [S188_S16_L003]


title: S171_J108_T3 [S171_S87_L002]


title: S175_J115_T3 [S175_S4_L003]


title: S186_J016_T4 [S186_S14_L003]


title: S183_J011_T4 [S183_S11_L003]


title: S172_J110_T3 [S172_S1_L003]


title: S181_J130_T3 [S181_S9_L003]


title: S180_J128_T3 [S180_S8_L003]


title: S182_J132 _T3 [S182_S10_L003]


title: S177_J121_T3 [S177_S5_L003]


title: S174_J112_T3 [S174_S3_L003]


title: S173_J111_T3 [S173_S2_L003]


title: S170_J107_T3 [S170_S86_L002]


title: S168_J103_T3 [S168_S84_L002]


title: S167_J097_T3 [S167_S83_L002]


title: S164_J089_T3 [S164_S80_L002]


title: S344_J132 _T6 [S344_S86_L004]


title: S153_J071_T3 [S153_S67_L002]


title: S158_J082_T3 [S158_S74_L002]


title: S159_J084_T3 [S159_S75_L002]


title: S152_J068_T3 [S152_S66_L002]


title: S166_J092_T3 [S166_S82_L002]


title: S169_J104_T3 [S169_S85_L002]


title: S160_J085_T3 [S160_S76_L002]


title: S165_J091_T3 [S165_S81_L002]


title: S155_J076_T3 [S155_S69_L002]


title: S163_J088_T3 [S163_S79_L002]


title: S157_J081_T3 [S157-2_S73_L002]


title: S161_J086_T3 [S161_S77_L002]


title: S162_J087_T3 [S162_S78_L002]


title: S156_J078_T3 [S156-2_S71_L002]


title: S146_J051_T3 [S146_S61_L002]


title: S150_J061_T3 [S150_S64_L002]


title: S154_J075_T3 [S154_S68_L002]


title: S148_J055_T3 [S148_S63_L002]


title: S151_J062_T3 [S151_S65_L002]


title: S147_J052_T3 [S147_S62_L002]


title: S145_J050_T3 [S145_S60_L002]


title: S143_J045_T3 [S143_S58_L002]


title: S137_J033_T3 [S137_S52_L002]


title: S117_J122_T2 [S117_S35_L002]


title: S118_J123_T2 [S118_S36_L002]


title: S119_J128_T2 [S119_S37_L002]


title: S141_J041_T3 [S141_S56_L002]


title: S132_J026_T3 [S132_S47_L002]


title: S134_J029_T3 [S134_S49_L002]


title: S116_J121_T2 [S116_S34_L002]


title: S138_J034_T3 [S138_S53_L002]


title: S124_J014_T3 [S124_S42_L002]


title: S133_J028_T3 [S133_S48_L002]


title: S121_J132 _T2 [S121_S39_L002]


title: S135_J030_T3 [S135_S50_L002]


title: S129_J020_T3 [S129_S45_L002]


title: S123_J013_T3 [S123_S41_L002]


title: S126_J017_T3 [S126_S44_L002]


title: S122_J011_T3 [S122_S40_L002]


title: S144_J047_T3 [S144_S59_L002]


title: S120_J130_T2 [S120_S38_L002]


title: S115_J117_T2 [S115_S33_L002]


title: S142_J043_T3 [S142_S57_L002]


title: S125_J016_T3 [S125_S43_L002]


title: S130_J024_T3 [S130_S46_L002]


title: S136_J031_T3 [S136_S51_L002]


title: S140_J037_T3 [S140_S55_L002]


title: S114_J115_T2 [S114_S32_L002]


title: S139_J036_T3 [S139_S54_L002]


title: S112_J111_T2 [S112-2_S29_L002]


title: S113_J112_T2 [S113-2_S31_L002]


title: S105_J092_T2 [S105_S21_L002]


title: S111_J110_T2 [S111_S27_L002]


title: S110_J108_T2 [S110_S26_L002]


title: S104_J091_T2 [S104_S20_L002]


title: S103_J089_T2 [S103_S19_L002]


title: S98_J084_T2 [S98_S14_L002]


title: S109_J107_T2 [S109_S25_L002]


title: S107_J103_T2 [S107_S23_L002]


title: S106_J097_T2 [S106_S22_L002]


title: S101_J087_T2 [S101_S17_L002]


title: S99_J085_T2 [S99_S15_L002]


title: S108_J104_T2 [S108_S24_L002]


title: S93_J075_T2 [S93_S9_L002]


title: S96_J081_T2 [S96_S12_L002]


title: S97_J082_T2 [S97_S13_L002]


title: S100_J086_T2 [S100_S16_L002]


title: S95_J078_T2 [S95_S11_L002]


title: S91_J068_T2 [S91_S7_L002]


title: S102_J088_T2 [S102_S18_L002]


title: S92_J071_T2 [S92_S8_L002]


title: S90_J062_T2 [S90_S6_L002]


title: S89_J061_T2 [S89_S5_L002]


title: S94_J076_T2 [S94_S10_L002]


title: S88_J059_T2 [S88_S4_L002]


title: S87_J055_T2 [S87_S3_L002]


title: S86_J052_T2 [S86_S2_L002]


title: S85_J051_T2 [S85_S1_L002]


title: S78_J036_T2 [S78_S81_L001]


title: S72_J028_T2 [S72_S75_L001]


title: S69_J024_T2 [S69_S72_L001]


title: S84_J050_T2 [S84_S87_L001]


title: S80_J041_T2 [S80_S83_L001]


title: S83_J047_T2 [S83_S86_L001]


title: S79_J037_T2 [S79_S82_L001]


title: S81_J043_T2 [S81_S84_L001]


title: S65_J017_T2 [S65_S68_L001]


title: S77_J034_T2 [S77_S80_L001]


title: S76_J033_T2 [S76_S79_L001]


title: S73_J029_T2 [S73_S76_L001]


title: S66_J018_T2 [S66_S69_L001]


title: S67_J019_T2 [S67_S70_L001]


title: S70_J025_T2 [S70_S73_L001]


title: S64_J016_T2 [S64_S67_L001]


title: S63_J014_T2 [S63_S66_L001]


title: S71_J026_T2 [S71_S74_L001]


title: S68_J020_T2 [S68_S71_L001]


title: S75_J031_T2 [S75_S78_L001]


title: S82_J045_T2 [S82_S85_L001]


title: S74_J030_T2 [S74_S77_L001]


title: S62_J011_T2 [S62_S65_L001]


title: S59_J128_T1 [S59_S62_L001]


title: S60_J130_T1 [S60_S63_L001]


title: S61_J132 _T1 [S61_S64_L001]


title: S51_J110_T1 [S51_S53_L001]


title: S55_J117_T1 [S55-2_S58_L001]


title: S50_J108_T1 [S50_S52_L001]


title: S49_J107_T1 [S49_S51_L001]


title: S58_J123_T1 [S58_S61_L001]


title: S56_J121_T1 [S56-2_S60_L001]


title: S48_J104_T1 [S48_S50_L001]


title: S53_J112_T1 [S53_S55_L001]


title: S54_J115_T1 [S54_S56_L001]


title: S47_J103_T1 [S47_S49_L001]


title: S46_J097_T1 [S46_S48_L001]


title: S41_J087_T1 [S41_S43_L001]


title: S43_J089_T1 [S43_S45_L001]


title: S45_J092_T1 [S45_S47_L001]


title: S39_J085_T1 [S39_S41_L001]


title: S38_J084_T1 [S38_S40_L001]


title: S40_J086_T1 [S40_S42_L001]


title: S35_J078_T1 [S35_S37_L001]


title: S37_J082_T1 [S37_S39_L001]


title: S34_J076_T1 [S34_S36_L001]


title: S42_J088_T1 [S42_S44_L001]


title: S33_J075_T1 [S33_S35_L001]


title: S30_J062_T1 [S30_S32_L001]


title: S32_J071_T1 [S32_S34_L001]


title: S44_J091_T1 [S44_S46_L001]


title: S52_J111_T1 [S52_S54_L001]


title: S29_J061_T1 [S29_S31_L001]


title: S26_J052_T1 [S26_S28_L001]


title: S27_J055_T1 [S27_S29_L001]


title: S31_J068_T1 [S31_S33_L001]


title: S23_J047_T1 [S23_S25_L001]


title: S22_J045_T1 [S22_S24_L001]


title: S36_J081_T1 [S36_S38_L001]


title: S25_J051_T1 [S25_S27_L001]


title: S28_J059_T1 [S28_S30_L001]


title: S24_J050_T1 [S24_S26_L001]


title: S20_J041_T1 [S20_S22_L001]


title: S17_J034_T1 [S17_S19_L001]


title: S15_J031_T1 [S15-2_S16_L001]


title: S11_J026_T1 [S11_S11_L001]


title: S18_J036_T1 [S18_S20_L001]


title: S13_J029_T1 [S13_S13_L001]


title: S16_J033_T1 [S16-2_S18_L001]


title: S21_J043_T1 [S21_S23_L001]


title: S14_J030_T1 [S14_S14_L001]


title: S19_J037_T1 [S19_S21_L001]


title: S12_J028_T1 [S12_S12_L001]


title: S8_J020_T1 [S8_S8_L001]


title: S6_J018_T1 [S6_S6_L001]


title: S5_J017_T1 [S5_S5_L001]


title: S10_J025_T1 [S10_S10_L001]


title: S4_J016_T1 [S4_S4_L001]


title: S9_J024_T1 [S9_S9_L001]


title: S3_J014_T1 [S3_S3_L001]


title: S1_J011_T1 [S1_S1_L001]


title: S2_J013_T1 [S2_S2_L001]