title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad002

tag: Sex


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad007

status: Public on Oct 01 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PIR

value: male

tag: age

tag: strain


title: 5571AA_MSCB-097

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

description:
cryopreserved HCA reference
In total, 4 sample pools were analyzed with 192 cells/pool. Each of the groups should be considered identical except for batch correction during the statistical analysis.

library_source: transcriptomic

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the genome reference  for human, mouse and canine cells. Smart-seq2 libraries were equally mapped as paired-end reads.
For MARS-seq samples, gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Human: Gencode release 27, assembly GRCh38;  mouse: Gencode release M15, assembly GRCm38; dog:  Ensembl v90, assembly CanFam3.1
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts (MARS-Seq) for each cell (columns).

molecule: polyA RNA

organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

extract_protocol:
Human cell line HEK293 (human embryonic kidney cells) was acquired from the German Collection of Microorganisms and Cell Cultures (DSMZ). NIH3T3 (mouse embryo fibroblasts) were kindly provided by Dr. Manel Esteller (IDIBELL, Spain). HEK293, NIH3T3 and MDCK were maintained in DMEM (10% Fetal Bovine Serum, FBS; 1% Penicillin/Streptomycin) at 37ºC (5% CO2).    For cryopreservation, cells were trypsinized, pelleted and resuspended in freezing solution I (10% DMSO; 10% heat-inactivated FBS; 80% DMEM) or solution II (10% DMSO; 90% non-inactivated FBS). Subsequently, cells were frozen with gradually decreasing temperatures (1ºC/min) to -80ºC (cryopreserved).For single cell analysis, cryopreserved cells were rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Fresh cells were trypsinized, pelleted and resuspended in 1x HBSS. Before sorting, cells from both conditions were filtered (70 µm nylon mesh) and propidium iodide staining identified dead/damaged cells.    Whole blood was collected from a healthy donor into EDTA tubes (Becton, Dickinson and Co). Separation of peripheral blood mononuclear cells (PBMC) was performed with Ficoll-Paque PREMIUM (GE Healthcare) according to manufacturer's instructions. Briefly, for density gradient separation, 4 ml of blood was added onto 3 ml of Ficoll-Paque PREMIUM. Centrifuged at 400 x g for 30 minutes at 18ºC without brake. PBMC layer was recuperated and washed twice with PBS at 400g for 15 minutes at 18ºC. PBMC were resuspended in freezing solution (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to ‑80ºC (cryopreserved). After storage for one week at -80ºC, the cryopreserved sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. To avoid batch effects, fresh PBMC were sorted in parallel with the cryopreserved material and distributed over the same sequencing pools. Therefore, blood from the same donor was isolated as described above and directly resuspended in DMEM. Dead and damaged cells were identified by propidium iodide staining.    Primary mouse colon was dissected from an athymic nu/nu mouse and placed on ice. The sample was divided and half of the colon was immediately prepared for single cell separation, while the other half was minced on ice, placed into freezing solution II (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to ‑80ºC (cryopreserved). After storage for one week at -80ºC, the sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. For single cell separation the fresh and conserved samples were minced on ice and enzymatically digested in 5 ml 1x HBSS and 83 µl collagenase IV (10,000 U/ml) for 10 min at 37ºC. Single cells were separated by passing the sample through a 0.9 mm needle and filtration (70 µm nylon mesh). Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. Dead and damaged cells were identified by propidium iodide staining.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014).  This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes. Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

tag: cell type

value: human PBMC and mouse colon (80%), HEK293 (10%), NIH3T3 (10%), MDCK (< 1%)

tag: sample pool


title: 5571AA_MSCB-096


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad006


title: 5571AA_MSCB-086


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad004


title: 5571AA_MSCB-095


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad002


title: 5571AA_MSCB-084


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C6_ad001


title: 5571AA_MSCB-083


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad008


title: 5571AA_MSCB-082


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C6_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C6_ad010


title: 5571AA_MSCB-081


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C6_ad004


title: 5571AA_MSCB-080


title: 5571AA_MSCB-079


title: 5571AA_MSCB-088


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C6_ad002


title: 5571AA_MSCB-078


title: 5571AA_MSCB-077


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C6_ad008


title: 5571AA_MSCB-076


title: 5571AA_MSCB-087


title: 5571AA_MSCB-075


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C5_ad001


title: 5571AA_MSCB-074


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C5_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C5_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C5_ad008


title: 5571AA_MSCB-073


title: 5571AA_MSCB-072


title: 5571AA_MSCB-126


title: 5571AA_MSCB-071


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C4_ad001


title: 5571AA_MSCB-069


title: 5571AA_MSCB-070


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C4_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C6_ad006


title: 5571AA_MSCB-067


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C4_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C4_ad002


title: 5571AA_MSCB-068


title: 5571AA_MSCB-065


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C4_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C3_ad012


title: 5571AA_MSCB-066


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C3_ad007


title: 5571AA_MSCB-063


title: 5571AA_MSCB-064


title: 5571AA_MSCB-062


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C5_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C5_ad006


title: 5571AA_MSCB-061


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C3_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C4_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C3_ad004


title: 5571AA_MSCB-060


title: 5571AA_MSCB-059


title: 5571AA_MSCB-058


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C3_ad008


title: 5571AA_MSCB-057


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C4_ad012


title: 5571AA_MSCB-056


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C2_ad001


title: 5571AA_MSCB-055


title: 5571AA_MSCB-053


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C2_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C2_ad004


title: 5571AA_MSCB-052


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C2_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C2_ad002


title: 5571AA_MSCB-049


title: 5571AA_MSCB-051


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C3_ad010


title: 5571AA_MSCB-050


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad010


title: 5571AA_MSCB-048


title: 5571AA_MSCB-047


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad007


title: 5571AA_MSCB-046


title: 5571AA_MSCB-045


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C2_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad004


title: 5571AA_MSCB-044


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C3_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C12_ad012


title: 5571AA_MSCB-042


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad012


title: 5571AA_MSCB-041


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad008


title: 5571AA_MSCB-040


title: 5571AA_MSCB-039


title: 5571AA_MSCB-038


title: 5571AA_MSCB-037


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad004


title: 5571AA_MSCB-054


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad002


title: 5571AA_MSCB-035


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C2_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad001


title: 5571AA_MSCB-099


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad010


title: 5571AA_MSCB-034


title: 5571AA_MSCB-043


title: 5571AA_MSCB-031


title: 5571AA_MSCB-033


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad007


title: 5571AA_MSCB-030


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad004


title: 5571AA_MSCB-028


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C11_ad006


title: 5571AA_MSCB-029


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad002


title: 5571AA_MSCB-027


title: 5571AA_MSCB-026


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B9_ad001


title: 5571AA_MSCB-025


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B9_ad007


title: 5571AA_MSCB-023


title: 5571AA_MSCB-032


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B9_ad010


title: 5571AA_MSCB-085


title: 5571AA_MSCB-022


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B9_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C10_ad008


title: 5571AA_MSCB-020


title: 5571AA_MSCB-021


title: 5571AA_MSCB-019


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B9_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad012


title: 5571AA_MSCB-018


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B9_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad010


title: 5571AA_MSCB-016


title: 5571AA_MSCB-015


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad001


title: 5571AA_MSCB-017


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad006


title: 5571AA_MSCB-014


title: 5571AA_MSCB-013


title: 5571AA_MSCB-036


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad004


title: 5571AA_MSCB-012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B8_ad008


title: 5571AA_MSCB-011


title: 5571AA_MSCB-024


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B9_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad012


title: 5571AA_MSCB-008


title: 5571AA_MSCB-010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad001


title: 5571AA_MSCB-007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad006


title: 5571AA_MSCB-006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad004


title: 5571AA_MSCB-005


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad012


title: 5571AA_MSCB-003


title: 5571AA_MSCB-002


title: 5571AA_MSCB-004


title: 5571AA_MSCB-001


title: 5570AA_MSCB-192


title: 5571AA_MSCB-009


title: 5570AA_MSCB-189


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad010


title: 5570AA_MSCB-191


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad012


title: 5570AA_MSCB-190


title: 5570AA_MSCB-186


title: 5570AA_MSCB-188


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad007


title: 5570AA_MSCB-184


title: 5570AA_MSCB-185


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad010


title: 5570AA_MSCB-183


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad002


title: 5570AA_MSCB-187


title: 5570AA_MSCB-181


title: 5570AA_MSCB-182


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad008


title: 5570AA_MSCB-179


title: 5570AA_MSCB-180


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B4_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B4_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B4_ad001


title: 5570AA_MSCB-175


title: 5570AA_MSCB-177


title: 5570AA_MSCB-178


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B4_ad002


title: 5570AA_MSCB-176


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B3_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B3_ad001


title: 5570AA_MSCB-173


title: 5570AA_MSCB-171


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B7_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B3_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B3_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B3_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B3_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B2_ad001


title: 5570AA_MSCB-167


title: 5570AA_MSCB-174


title: 5570AA_MSCB-168


title: 5570AA_MSCB-169


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B4_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B5_ad001


title: 5570AA_MSCB-170


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B4_ad004


title: 5570AA_MSCB-165


title: 5570AA_MSCB-172


title: 5570AA_MSCB-164


title: 5570AA_MSCB-163


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B2_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B3_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B2_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B2_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B2_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B2_ad012


title: 5570AA_MSCB-159


title: 5570AA_MSCB-160


title: 5570AA_MSCB-158


title: 5570AA_MSCB-166


title: 5570AA_MSCB-157


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B6_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B12_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B11_ad012


title: 5570AA_MSCB-162


title: 5570AA_MSCB-156


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B11_ad010


title: 5570AA_MSCB-153


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B12_ad007


title: 5570AA_MSCB-152


title: 5570AA_MSCB-151


title: 5570AA_MSCB-154


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B11_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B12_ad008


title: 5570AA_MSCB-155


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B2_ad004


title: 5570AA_MSCB-150


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B12_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B11_ad007


title: 5570AA_MSCB-148


title: 5570AA_MSCB-147


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B11_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B11_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B1_ad012


title: 5570AA_MSCB-146


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B12_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_B1_ad001


title: 5570AA_MSCB-144


title: 5570AA_MSCB-143


title: 5570AA_MSCB-149


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title: hRabMab1-3-6959RR

city: Cincinnati

first: Kateryna

last: Matiash

state: Ohio

address: 3125 Eden Ave

department: Hematology/Oncology

institute: University of Cincinnati

description: mouse tumor comprised of human PDAC cells

data_processing:
Illumina bcl2fastq ver. 2.2 was used for base-calling.
A quality control check on the fastq files was performed using FastQC.
The reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic [Version 0.33].
Trimmed reads were then mapped to a reference genome (hg19) using default parameters with strandness (RF for paired-end) option in Hisat2 [Version 2.0.5]
Transcript/gene abundance was determined using kallisto [Version 0.43.1].
A transcriptome index was created in kallisto using Ensembl cDNA sequences for the reference genome, and the index was used to quantify transcript abundance in raw counts and transcripts per million (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: pancreatic ductal adenocarcinoma (PDAC)

growth_protocol: Prior to orthotopic implantation, Pt45.P1 cells were cultured for a week in antibitotic-free DMEM supplemented with 10% FBS.

extract_protocol:
Tumors were extracted during necropsies, flash frozen in liquid nirogen and stored at -80C. Total RNA was extracted, and Illumina’s TruSeq® stranded mRNA library preparation kit was used to construct sequencing libraries (300 ng of total RNA per sample was used).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with equal volume vehicle, 18 mg/kg hIgG1, or 18 mg/kg hRabMab1 (tail-vein injection) for 22 treatment cycles.

tag: tissue

value: pancreas - tumor

tag: cell line

tag: treatment


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C7_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C7_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C7_ad008


title: hRabMab1-2-6957O


title: hRabMab1-1-6957LL


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C6_ad012


title: hIgG1-1-6958O


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C6_ad007


title: hIgG1-3-6961LL


title: Veh-3-6956O

value: Vehicle


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C6_ad010


title: L-Exo 3

type: RNA

city: LOUISVILLE

first: Anil

last: Kumar

state: Kentucky

address: 505 S Hancock ST, 333 CTRB

department: Microbiology & Immunology

institute: University of Louisville

description: Gene expression from liver tissues of mice orally gavaged with L-Exo for 14 days while they fed HFD.

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip™ Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the  GeneChip™   Scanner 3000 7G

data_processing: Transcriptome analysis console 4.0 was used to analyze the data.  RMA algorithm.

label: biotin

source_name: B6 liver tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 90 ng total RNA (IonAmpliseq Trancriptome Mouse gene expression).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 2E+09 exosomes (L-Exo or H-Exo) per dose were orally given to each mice every day for 14 days while they fed HFD. After 14 days mice were sacrificed and organs (liver) tissues were harvested for RNA isolation.

value: Exosomes (L-Exo) treated liver

value: liver


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C6_ad006


title: H-Exo 1

description: Gene expression from liver tissues of mice orally gavaged with H-Exo for 14 days while they fed HFD.

value: Exosomes (H-Exo) treated liver


title: L-Exo 1


title: H-Exo 3


title: L-Exo 2


title: H-Exo 2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C6_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C6_ad004


title: Veh-2-6955RR


title: Veh-1-6955L


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad012


title: MSC-melatonin(1 µM)-Input

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

country: China

institute: Tianjin Medical University

data_processing:
Basecalls performed using HiSeqX
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.7.13 with the following configurations -q 5 -l 32 -k 2
Data were filtered using Picard-tools version 1.126
peaks were called using macs2 version 2.1.0 with the following setting: -pvalue 0.01 --keep-dup all --extsize -1 --shift 0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using macs2; Scores represent an average read coverage
Supplementary_files_format_and_content: narrowpeak files

source_name: MSC

growth_protocol: MSCs was cultured in DMEM medium with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the TruePrep® DNA Library Prep Kit V2 for Illumina (TD503-02). Briefly, TruePrep Tagment Enzyme Mix (TTEMix) contains transposase and two kinds of adapters (Adapter 1 and Adapter 2) with equal molar. Input DNA are fragmented and linked with adapters on both ends just by mixing with TTE Mix, followed by a 10-minute incubation at 55℃. The tagged DNA fragments can be further amplified with two pairs of primers N5 (N5XX) / N7 (N7XX) and P5 / P7 (PCR Primer Mix, PPM).  After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

treatment_protocol: MSCs was 1 µM melatonin treated for 24 hours.

value: human bone marrow

tag: chip antibody

value: treated with 1 microM melatonin for 24 hours


title: MSC-melatonin(1 µM)-H3K36me2-IP


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad007


title: MSC-H3K36me2-IP

value: untreated


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad006


title: MSC-Input


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad004


title: hIgG1-2-6958RR


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad010


title: 5568AA_MSCB-052


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C3_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C3_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C3_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C3_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C3_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C3_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C5_ad010


title: SMARCB1 knockdown organoid 3

first: Frank

last: Furnari

state: California

address: 9500 Gilman Drive

institute: UC San Diego

description: 905 organoid 3

data_processing:
Cell Ranger counting/aggregation
Mitochondrial DNA filtering
Canonical correlation analysis and clustering (resolution value of 0.6)
Generation of aggregated counts file of gene expression in each cluster separated by condition
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts file of expression in each cluster separated by condition

source_name: 20 day iPSC-derived cerebral organoid

growth_protocol: Organoids were generated from iPS12 iPSCs using the Stemcell Technologies STEMdiff Cerebral Organoid kit

extract_protocol:
10X Chromium 3' Reagents kit v2
10X protocol was followed for a desired 10,000 cells per organoid using 10 cycles of cDNA amplification.

treatment_protocol: Organoids were induced with doxycline at Day 0 of organoid generation to induce expression of non-targeting or SMARCB1 knockdown shRNA

tag: condition

value: Knockdown


title: SMARCB1 knockdown organoid 1

description: 905 organoid 1


title: SMARCB1 knockdown organoid 4

description: 905 organoid 4


title: Control organoid 2

description: 116 organoid 2

value: Control


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C4_ad004


title: Control organoid 1

description: 116 organoid 1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad006


title: Im-GCT-6176__M2__parental__G34W-parental__snRNAseq

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

description:
Single Nucleus mRNA Sequencing
RNA Chromium Single Cell 3′ v3

data_processing:
Raw base call files were demultiplexed into FASTQ files using CellRangers mkfastq function (v3.0.2) with default parameters. The FASTQ files were aligned to the reference human genome hg19 using CellRanger’s count function (v3.0.2), in order to create a matrix of gene read counts per cell.
Genome_build: hg19
Supplementary_files_format_and_content: barcodes.tsv: Barcode labels for counts matrix in MatrixMarket format
Supplementary_files_format_and_content: features.tsv: Feature labels for counts matrix in MatrixMarket format.
Supplementary_files_format_and_content: matrix.mtx: Counts matrix in MatrixMarket format.

source_name: Xenograft tumor

extract_protocol:
Fresh tumours collected after surgery were dissociated in Collagenase-Dispase (Sigma-Aldrich). Red blood cells were lysed by ammonium chloride treatment for 5 min on ice. Cell viability was assessed with Trypan Blue. For samples with low viability (<60%), dissociated cells were enriched for live cells using Dead Cell Removal kit (Miltenyi Biotech).
10,000 dissociated cells per sample were loaded on the 10X Genomics Chromium controller. The Chromium Single Cell 3′ (10X Genomics, Version 3) protocol was strictly followed to prepare libraries. The 10X libraries were sequenced on Illumina NovaSeq 6000 S4 platforms.

tag: genotype

value: Xenograft tumor


title: Im-GCT-6176__M1__parental__G34W-parental__snRNAseq


title: Im-GCT-4072__M107__parental__G34W-parental__snRNAseq


title: Im-GCT-4072__M101__2B2__G34W-unedited__snRNAseq


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C12_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C12_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C12_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C12_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C12_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C12_ad004


title: Control organoid 4

description: 116 organoid 4


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C12_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C11_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C11_ad012


title: ZSTK474_Dose4_Rep2

city: Chicago

first: Sonia

last: Brockway

state: IL

address: 303 E Superior St, SQBRC 7-500

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.

source_name: Pool of 5 breast cancer cell lines

growth_protocol: Cell line pools were cultured in RPMI-1640, 10% Tet System Approved FBS, 1% Penicillin/Streptomycin, 100 ng/mL doxycycline for 7 days prior to compound treatment.

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).

treatment_protocol: Cell line pools were treated with compound or DMSO over a four-point concentration range (10-fold dilutions) in duplicate using either a standard dose range (10 nM to 10 μM) or a low dose range (1 nM to 1 μM). Dose1=lowest dose. Dose4=highest dose. Cells were treated for 72 hours.

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: StemRegenin1_Dose4_Rep2


title: Ganetespib_Dose4_Rep2


title: Istradefylline_Dose4_Rep2


title: GSKJ4_Dose4_Rep2


title: CAL101_Dose4_Rep2


title: GSK4112_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C11_ad007


title: OSI027_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C2_ad008


title: Triptolide_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C11_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C11_ad004


title: YM155_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C11_ad002


title: Linifanib_Dose4_Rep2


title: BIX01294_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C11_ad001


title: Palbociclib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad012


title: Semagacestat_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad006


title: Afatinib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad004


title: KW2449_Dose4_Rep2


title: DMSOPlate16WellF10_Dose4_Rep2


title: KU60019_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad002


title: Lomeguatrib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C1_ad007


title: DMSOPlate16WellC10_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C1_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C1_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C10_ad001


title: AZD5363_Dose4_Rep2


title: PF3758309_Dose4_Rep2


title: EX527_Dose4_Rep2


title: Belinostat_Dose4_Rep2


title: Olaparib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad012


title: GSK1059615_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C1_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C1_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C1_ad002


title: GDC0941_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_C1_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad007


title: BetulinicAcid_Dose4_Rep2


title: TubastatinA_Dose4_Rep2


title: AZD4547_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad006


title: NSC74859_Dose4_Rep2


title: PX12_Dose4_Rep2


title: Bortezomib_Dose4_Rep2


title: MK1775_Dose4_Rep2


title: Mdivi1_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad007


title: MLN2238_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad001


title: Teniposide_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad002


title: Entinostat_Dose4_Rep2


title: GSK461364_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad010


title: Masitinib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B9_ad008


title: IBET151_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad001


title: Navitoclax_Dose4_Rep2


title: Spautin1_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad006


title: BMS754807_Dose4_Rep2


title: STF083010_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad007


title: BGJ398_Dose4_Rep2


title: Neratinib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad006


title: FourHydroxytamoxifen_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad002


title: DMSOPlate16WellF6_Dose4_Rep2


title: AZD7545_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B8_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B6_ad012


title: SNS032_Dose4_Rep2


title: Isoliquiritigenin_Dose4_Rep2


title: DMSOPlate16WellC6_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B7_ad008


title: WAY362450_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B6_ad008


title: SN38_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B6_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B5_ad010


title: BMS345541_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B6_ad006


title: MG132_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B5_ad002


title: Erastin_Dose4_Rep2


title: Purmorphamine_Dose4_Rep2


title: Canertinib_Dose4_Rep2


title: KU0063794_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B6_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B5_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B6_ad007


title: Methotrexate_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B5_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B5_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad001


title: SB743921_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B6_ad004


title: Etomoxir_Dose4_Rep2


title: TG101348_Dose4_Rep2


title: Necrostatin1_Dose4_Rep2


title: SU11274_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B5_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad007


title: PifithrinAlpha_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad006


title: SJ172550_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad004


title: GSK2636771_Dose4_Rep2


title: SixMercaptopurine_Dose4_Rep2


title: BMS536924_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B3_ad012


title: PAC1_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B3_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B3_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B3_ad006


title: DMSOPlate16WellF3_Dose4_Rep2


title: Curcumin_Dose4_Rep2


title: JQ1_Dose4_Rep2


title: DMSOPlate16WellC3_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B3_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B3_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B4_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B3_ad008


title: TPCA1_Dose4_Rep2


title: LRRK2IN1_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad007


title: PI103_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad010


title: Ifosfamide_Dose4_Rep2


title: Gossypol_Dose4_Rep2


title: AT7867_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad006


title: ABT737_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad004


title: ETP46464_Dose4_Rep2


title: DBeQ_Dose4_Rep2


title: GDC0879_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad010


title: RO4929097_Dose4_Rep2


title: APY29_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad007


title: AZD8186_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad008


title: IC87114_Dose4_Rep2


title: ABT199_Dose4_Rep2


title: Phloretin_Dose4_Rep2


title: Entrectinib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad002


title: PF573228_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B11_ad012


title: Veliparib_Dose4_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B12_ad001


title: Ganetespib_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B11_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B2_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B11_ad007


title: YM155_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B11_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B11_ad002


title: CAL101_Dose4_Rep1


title: GSK4112_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B11_ad001


title: GSKJ4_Dose4_Rep1


title: Istradefylline_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B10_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B10_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B10_ad002


title: BIX01294_Dose4_Rep1


title: ZSTK474_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B1_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B10_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B10_ad001


title: OSI027_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B1_ad007


title: Triptolide_Dose4_Rep1


title: Semagacestat_Dose4_Rep1


title: Palbociclib_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B1_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B1_ad010


title: Afatinib_Dose4_Rep1


title: PF3758309_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B1_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B1_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A9_ad007


title: Lomeguatrib_Dose4_Rep1


title: DMSOPlate15WellF10_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A9_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_B1_ad008


title: StemRegenin1_Dose4_Rep1


title: KW2449_Dose4_Rep1


title: Linifanib_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A9_ad002


title: Olaparib_Dose4_Rep1


title: NSC74859_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A9_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A9_ad004


title: TubastatinA_Dose4_Rep1


title: AZD5363_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad012


title: EX527_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A9_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A9_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad001


title: KU60019_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad004


title: Belinostat_Dose4_Rep1


title: Teniposide_Dose4_Rep1


title: GSK1059615_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A8_ad008


title: GDC0941_Dose4_Rep1


title: PX12_Dose4_Rep1


title: AZD4547_Dose4_Rep1


title: BetulinicAcid_Dose4_Rep1


title: Bortezomib_Dose4_Rep1


title: DMSOPlate15WellC10_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad001


title: Navitoclax_Dose4_Rep1


title: Mdivi1_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad004


title: MK1775_Dose4_Rep1


title: GSK461364_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad002


title: BGJ398_Dose4_Rep1


title: MLN2238_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A7_ad007


title: Entinostat_Dose4_Rep1


title: FourHydroxytamoxifen_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad001


title: Isoliquiritigenin_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad004


title: Masitinib_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad002


title: Spautin1_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad008


title: Neratinib_Dose4_Rep1


title: BMS754807_Dose4_Rep1


title: STF083010_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A5_ad012


title: SB743921_Dose4_Rep1


title: AZD7545_Dose4_Rep1


title: DMSOPlate15WellF6_Dose4_Rep1


title: DMSOPlate15WellC6_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A5_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A5_ad001


title: SNS032_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A5_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A5_ad007


title: MG132_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A5_ad004


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad012


title: WAY362450_Dose4_Rep1


title: IBET151_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A5_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A6_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad012


title: KU0063794_Dose4_Rep1


title: Purmorphamine_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad010


title: SN38_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad004


title: Erastin_Dose4_Rep1


title: BMS345541_Dose4_Rep1


title: PifithrinAlpha_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad008


title: Canertinib_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A3_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A3_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A3_ad001


title: Etomoxir_Dose4_Rep1


title: Methotrexate_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A3_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A3_ad006


title: SU11274_Dose4_Rep1


title: SixMercaptopurine_Dose4_Rep1


title: SJ172550_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A2_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A3_ad008


title: BMS536924_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A3_ad004


title: PAC1_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A2_ad007


title: GSK2636771_Dose4_Rep1


title: JQ1_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A4_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A2_ad004


title: DMSOPlate15WellF3_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A2_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A2_ad002


title: Curcumin_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A2_ad006


title: TG101348_Dose4_Rep1


title: ETP46464_Dose4_Rep1


title: Necrostatin1_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A12_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A12_ad012


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A12_ad008


title: DMSOPlate15WellC3_Dose4_Rep1


title: PI103_Dose4_Rep1


title: LRRK2IN1_Dose4_Rep1


title: TPCA1_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A12_ad004


title: Ifosfamide_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A12_ad002


title: AT7867_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A11_ad012


title: ABT737_Dose4_Rep1


title: DBeQ_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A11_ad008


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A11_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A11_ad010


title: GDC0879_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A2_ad008


title: RO4929097_Dose4_Rep1


title: IC87114_Dose4_Rep1


title: APY29_Dose4_Rep1


title: Entrectinib_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A11_ad002


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A11_ad006


title: Gossypol_Dose4_Rep1


title: Phloretin_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad010


title: AZD8186_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad008


title: PF573228_Dose4_Rep1


title: ABT199_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad006


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad012


title: Veliparib_Dose4_Rep1


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad004


title: YM155_Dose3_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad002


title: GSK4112_Dose3_Rep2


title: CAL101_Dose3_Rep2


title: StemRegenin1_Dose3_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A12_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A1_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A11_ad004


title: GSKJ4_Dose3_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A1_ad010


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A1_ad004


title: ZSTK474_Dose3_Rep2


title: Istradefylline_Dose3_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A1_ad007


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A10_ad007


title: OSI027_Dose3_Rep2


title: Triptolide_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H9_ad012

value: ACA,PL,ILA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H9_ad001


title: BIX01294_Dose3_Rep2


title: Ganetespib_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H9_ad004


title: Linifanib_Dose3_Rep2


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A1_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H9_ad002


title: PF3758309_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H9_ad008


title: TNFR DKO ChAdOx1 immunization 1

city: Oxford

first: Nicholas

last: Provine

state: Oxfordshire

address: John Radcliffe Hospital

department: NDM - Experimental Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Trimming was performed using Trimmomatic v. 0.39
Pseudoalignment was performed using Kallisto v. 0.46.1
Differential expression analysis was performed using DESeq2 (v. 1.26), with cut-offs of log2 fold-change >1 and p-adjusted <0.05
As appropriate for cross-comparisons, mouse gene symbols were converted to human using biomaRt (v. 2.42.0) and matching on Ensemble gene ID
Genome_build: GRCh38 was used for human data; GRCm38 was used for mouse data
Supplementary_files_format_and_content: Normalized read counts

source_name: mucosal-associated invariant T cells

extract_protocol:
RNA extraction was performed as described in: R. A. Barnitz, S. Imam, K. Yates, W. N. Haining, Isolation of RNA and the synthesis and amplification of cDNA from antigen-specific T cells for genome-wide expression analysis. Methods Mol Biol. 979, 161–173 (2013).
cDNA library preparation was performed as described in: S. Picelli et al., Full-length RNA-seq from single cells usingSmart-seq2. Nat Protoc. 9, 171–181 (2014).

treatment_protocol: Treatment protocols listed on a per-sample basis

value: inguinal lymph nodes

value: Collected 24h after intramuscular immunization with 10^8 IU of ChAdOx1-GFP


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad012

value: male


title: IL18RAP KO ChAdOx1 immunization 3


title: Afatinib_Dose3_Rep2


title: TNFR DKO ChAdOx1 immunization 2


title: TNFR DKO ChAdOx1 immunization 3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H9_ad007


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H9_ad010


title: IL18RAP KO ChAdOx1 immunization 4


title: IFNAR KO ChAdOx1 immunization 4


title: Lomeguatrib_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad001


title: CEMBA190205_6D_1_CEMBA190205_6D_2_A1_ad002

value: PIR


title: Palbociclib_Dose3_Rep2


title: IL18RAP KO ChAdOx1 immunization 1


title: KW2449_Dose3_Rep2


title: IFNAR KO ChAdOx1 immunization 3


title: DMSOPlate14WellF10_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad006


title: IL18RAP KO ChAdOx1 immunization 2


title: TNFR DKO ChAdOx1 immunization 4


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad007


title: B6 mouse naïve 9


title: IFNAR KO ChAdOx1 immunization 2


title: TubastatinA_Dose3_Rep2


title: IFNAR KO ChAdOx1 immunization 1


title: KU60019_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad004


title: B6 mouse naïve 7


title: B6 mouse ChAdOx1 immunization 8


title: B6 mouse ChAdOx1 immunization 7


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad010


title: EX527_Dose3_Rep2


title: B6 mouse naïve 6


title: B6 mouse ChAdOx1 immunization 6


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad012


title: NSC74859_Dose3_Rep2


title: B6 mouse ChAdOx1 immunization 5


title: B6 mouse naïve 4


title: B6 mouse naïve 5


title: B6 mouse naïve 3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad007


title: AZD5363_Dose3_Rep2


title: DMSOPlate14WellC10_Dose3_Rep2


title: GSK1059615_Dose3_Rep2


title: B6 mouse ChAdOx1 immunization 9


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad002


title: B6 mouse naïve 2


title: B6 mouse ChAdOx1 immunization 3


title: Olaparib_Dose3_Rep2


title: Belinostat_Dose3_Rep2


title: B6 mouse ChAdOx1 immunization 2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H8_ad008


title: B6 mouse naïve 1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad006


title: Teniposide_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad004


title: B6 mouse ChAdOx1 immunization 1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad001


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad002


title: BetulinicAcid_Dose3_Rep2


title: B6 mouse ChAdOx1 immunization 4


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad010


title: PX12_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H6_ad001


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H6_ad007


title: Bortezomib_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H6_ad010


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H7_ad008


title: 5_Bmal1Het_DOX_beta_1

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
The reads were mapped on mouse genome mm10 using STAR
Differential expression was analyzed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include rawcount values for each Sample …
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values(cpm = count per millions) for each Sample …

source_name: FACS-sorted pancreatic β-cells

extract_protocol:
RNeasy® Plus Micro Kit (Qiagen)
Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit


title: AZD4547_Dose3_Rep2


title: 6_Bmal1Het_DOX_beta_2


title: Semagacestat_Dose3_Rep2


title: 3_Bmal1KO_DOX_beta_1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H6_ad006


title: Navitoclax_Dose3_Rep2


title: MK1775_Dose3_Rep2


title: 4_Bmal1KO_DOX_beta_2


title: B6 mouse naïve 8


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H6_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H6_ad004


title: GDC0941_Dose3_Rep2


title: Mdivi1_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H6_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H5_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H5_ad001


title: BGJ398_Dose3_Rep2


title: GSK461364_Dose3_Rep2


title: Entinostat_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H5_ad007


title: Masitinib_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H5_ad004


title: IBET151_Dose3_Rep2


title: Tregs_RNAseq_WT1

first: Fotini

last: Gounari

address: 924 E 27th Street, JFK

department: Medicine

institute: University of Chicago

data_processing:
Fastq files were grommed and aligned to the mm10 genome using FastqGroomer Bowtie via Galaxy V1.1.1
Aligned bam files were filtered and indices were generated using the Filter SAM or BAM file tool via Galaxy V1.1.1
Peak_Bed files were generated using Homer (ChIPseq, -style factor -o -F 5 -P .00001 -gsize 1.87e9) and MACS2 (ATACseq, peaks calling parameters: -p .00001 --broad --broad-cutoff .00001 -f BAM  ) from filtered bam files, bedGraphs were generatd using Homer, FPKM tacking and differential gene expression analysis was performed with CufLinks/Cuffdiff2,
Genome_build: mm10
Supplementary_files_format_and_content: Peak_Bed files were generated using Homer (ChIPseq) and MACS2 (ATACseq) and contain chr, start end information of each peak, bedGraphs were generatd using Homer, FPKM tacking and differential  expression analysis was performed with CufLinks/Cuffdiff2 (CAT over WT)

source_name: ex vivo peripheral regulatory T cells

growth_protocol: N/A - primary cells were used

extract_protocol:
ChIPseq: 1×107 CD25+YFP+ Tregs were FACS sorted from LN and SPL isolated CD4+ T cells (CD4+ T Cell Isolation Kit, mouse, 130-104-454, Miltenyi) of 10-12-week-old Foxp3YFP-Cre WT mice. ATACseq/RNAseq: For ATAC–seq, 5-10x104 YFP+CD25+ Tregs were FACS sorted from MACS-pre-purified CD4+ T cells (CD4+ T Cell Isolation Kit, mouse, 130-104-454, Miltenyi) isolated from LNs of Foxp3YFP-Cre Ctnnb1fl(ex3) and Foxp3YFP-Cre WT mice
ChIPseq: Emmanuel, A.O. et al. TCF-1 and HEB cooperate to establish the epigenetic and transcription profiles of CD4(+)CD8(+) thymocytes. Nature immunology 19, 1366-1378 (2018)., ATACseq: Cells were centrifuged at 500g at 4°C for 5 min, washed with 1 x PBS, and centrifuged again. Cells were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and immediately centrifuged at 500 g at 4 °C for 10 min. Pellets were resuspended in transposition reaction buffer (25 μl 2× Tagment Buffer (FC-121-1030, Illumina), 2.5 μl Tagment DNA Enzyme, and 22.5 μl nuclease-free H2O) for 30 min at 37 °C. DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs). Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a HiSeq 4000 sequencer at the University of Chicago Genomics Facility, RNAseq: Total RNA was isolated using the PicoPureTM RNA Isolation Kit (KIT0202, Arcturus) following the manufacturer’s instructions. Libraries were generated and sequenced by the University of Chicago Genomics Facility.

tag: genotype/variation

value: Foxp3Cre-YFP (WT)

value: ex vivo peripheral regulatory T cells


title: Tregs_RNAseq_CAT2

value: Foxp3Cre-YFP Ctnnb1flex3 (CAT)


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H5_ad006


title: Tregs_RNAseq_CAT3


title: Tregs_RNAseq_WT2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H5_ad002


title: FourHydroxytamoxifen_Dose3_Rep2


title: Tregs_RNAseq_CAT1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H4_ad012


title: MLN2238_Dose3_Rep2


title: Tregs_RNAseq_WT3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H5_ad008


title: Tregs_ATACseq_CAT1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H4_ad001


title: Isoliquiritigenin_Dose3_Rep2


title: Tregs_ATACseq_CAT2


title: Tregs_ATACseq_WT3


title: BMS754807_Dose3_Rep2


title: Tregs_ATACseq_WT1


title: STF083010_Dose3_Rep2