title: PO_M_15410_thalamus

value: thalamus


title: BW_F_15504_septum

status: Public on Oct 20 2023

type: SRA

city: Cambridge

first: Andreas

middle: F

last: Kautt

state: MA

address: 16 Divinity Ave

country: USA

institute: Harvard University

library_source: transcriptomic

data_processing:
Using cutadapt v.2.3, we trimmed very low quality bases (quality score <10) and applied a minimum length cutoff of 25 bp.
We then mapped trimmed reads of P. maniculatus and P. polionotus individuals to their respective reference genome, Pman_2.1 (GCA_003704035.1) or Ppol_1.3.3 (GCA_003704135.2), and in-house annotations generated with Comparative Annotation Toolkit using the GENCODE v15 primary-assembly annotation of Mus musculus (GRCm38 mm10) as reference. We competitively mapped reads from F1 hybrids to a diploid reference genome created by concatenating the two species assemblies and annotations. We performed read mapping with STAR v.2.7.0e (Dobin et al. 2013) in a transcriptome-aware manner.
We estimated gene expression with RSEM v1.3.1 and retained only genes present in both species’ annotations. For F1 samples, allele counts (reads mapped to a diploid reference) were summed up.
Assembly: GCA_003704035.1; GCA_003704135.2
Supplementary files format and content: tab-delimited text file of expected gene counts (rows) for each sample (columns)

molecule: total RNA

organism: Peromyscus maniculatus

source_name: brain

extract_protocol:
For the whole brain dataset, a cohort of 59–137-day-old virgin male P. maniculatus (n=5) and P. polionotus (n=6) animals were euthanized by CO2 inhalation 7–10 h before the start of the dark period. Whole brain samples were then rapidly dissected, flash-frozen, and stored at -70°C. We homogenized the samples in TRIzol Reagent (Invitrogen, 15596026) using a Bio-Gen PRO200 homogenizer (PRO Scientific, Oxford, USA), and extracted RNA using a Direct-zol™ RNA MiniPrep Plus kit (Zymo Research, R2070), including a DNase I treatment; For the brain subregion dataset, a cohort of 82–85-day-old virgin male and female P. maniculatus, P. polionotus, and their F1 hybrids were euthanized by CO2 inhalation followed by cervical dislocation 3–10 h before the onset of the dark period. One cohort was used for dissection of the cerebellum, hippocampus, and hindbrain samples. In these samples, after the brain was removed, a dorsal-to-ventral incision was made posterior to the cerebrum to release the hindbrain and cerebellum. The cerebellar peduncles were cut, and the hindbrain and cerebellum were placed in tubes and flash frozen in liquid nitrogen. The petri dish with the remaining brain was then placed on ice, and the two cerebral hemispheres were cut apart. For each hemisphere separately, the hippocampus was severed from the dorsal fornix and gently scooped out of the hemisphere with a brush in ventral-to-dorsal direction (Lu, Airey, and Williams 2001), and then flash frozen. For a second cohort of animals, we dissected the brains and then immediately submerged them into embedding compound for cryosectioning (Tissue-Tek O.C.T.) and froze them on dry ice. We sectioned brains on a coronal plane at 150 μm using a cryostat at -20°C (Leica CM3050 S, Leica Biosystems Inc., Buffalo Grove, IL) and stored the sections at -70°C until we dissected the medial prefrontal cortex, septum, striatum, hypothalamus, amygdala, thalamus, and midbrain with sample corers according to anatomical landmarks. The sample cores were immediately transferred into homogenization buffer. After subregion dissection, we homogenized samples for 10 seconds in Maxwell RSC Homogenization Buffer (Promega, Madison, USA) with 2% 1-thioglycerol using a Bio-Gen PRO200 homogenizer (PRO Scientific, Oxford, USA) and then extracted RNA using the Maxwell RSC simplyRNA Tissue Kit (Promega).
We prepared each whole brain sequencing library from 1 μg of total RNA using a PrepX PolyA mRNA Isolation Kit (Wafergen, 40047) on the Apollo 324 NGS Library Prep System (Takara Bio USA Holdings, Mountain View, CA). We added Illumina indices and amplified libraries with 12 cycles of PCR and cleaned them using PCRClean DX beads (Aline Biosciences, Woburn, MA); We prepared brain subregion RNA-Seq libraries using an mRNA HyperPrep kit (Kapa Biosystems, Wilmington, USA) automated on a BioMek FXp (Beckman Coulter, Brea, USA). Post-capture, we fragmented mRNA for 6 min at 94°C for a target insert size of 200-300 base pairs. We amplified dual-indexed adapter-ligated libraries in 11 PCR cycles.

tag: tissue

value: brain

tag: brain subregion

value: septum

tag: strain

value: BW

tag: Sex

value: F


title: G45KO_0Gy_1d_rep4

type: RNA

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia 24 h post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

value: male

tag: protocol

tag: genotype


title: G45KO_0Gy_1d_rep3


title: PO_M_15819_cerebellum

organism: Peromyscus polionotus

value: cerebellum

value: PO

value: M


title: ATAC.14_MRTK.78_CTRL_rep2

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description:
ATAC-seq in MRT organoids P78, after 4 days lentiviral transduction with the Luciferase gene
MRTK_ATACseq_peak_coordinates_2022-11-10.txt; MRTK_ATACseq_readcounts_unnormalized_2022-11-10.txt; MRTK_ATACseq_readcounts_normalized_2022-11-10.txt

library_source: genomic

data_processing:
ATAC-seq data were were mapped against the hg38 reference genome using BWA-MEM. The mapped reads with mapping quality score <15, as well as optical PCR duplicates, were discarded using SAMtools. The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools.
Assembly: hg38
Supplementary files format and content: bigWig files, read counts

molecule: genomic DNA

organism: Homo sapiens

source_name: MRT organoids P78

growth_protocol: The cell pellets were seeded in growth factor-reduced BME (Trevigen, 3533-010-02) and cultured in kidney organoid medium (AdDF+++ supplemented with 1.5% B27 supplement (Gibco), 10% R-spondin-conditioned medium, EGF (50 ng ml−1, Peprotech), FGF-10 (100 ng ml−1, Peprotech), N-acetylcysteine (1.25 mM, Sigma), Rho-kinase inhibitor Y-27632 (10 µM, Abmole) and A83-01 (5 µM, Tocris Bioscience). Medium was changed every 3–4 days, and organoids were passaged every 1–3 weeks. Depending on organoid morphology, organoids were either passaged using mechanical dissociation (Wilms tumour organoids, MRTK organoids), or TrypLE Express (Invitrogen, 12605036) containing 10 µM Y-27632 (Wilms tumour organoids, RCCs). Following the addition of 5–10 ml AdDF+++ and centrifugation at 250×g, cells were reseeded in BME and topped with kidney organoid medium. All organoid cultures are stored in the biobank of the Princess Máxima Center and made available to the scientific community according to the rules and regulations under which the patients and parents gave informed consent for donating the tissue.

extract_protocol:
ATAC-seq libraries were prepared following a published protocol (Liu et al. 2017). 100 k organoid cells are harvested. Nuclei were isolated, permeabilized, and tagmented using in-house produced Tn5 transposase.
The resulted DNA fragments underwent two sequential 9-cycle PCR amplification and the fragments < 700 bp were purified using SPRI beads (Liu et al., 2017).

treatment_protocol: For SMARCB1 re-expression, MRT organoids were lentivirally transduced with pLKO.1-UbC-luciferase-blast40 or pLKO.1-UbC-hSMARCB1-blast lentiviruses. After 2 days, 10 µg/ml blasticidin was added to the culture medium.

tag: cell line

value: MRT organoids P78

tag: cell type

value: Malignant rhabdoid tumor cells

tag: treatment

value: Luciferase plasmid


title: BW_F_15504_mPFC

value: mPFC


title: BW_F_15504_midbrain

value: midbrain


title: G45KO_0Gy_1d_rep2


title: PO_M_15410_septum


title: PO_M_15410_mPFC


title: ATAC.13_MRTK.78_CTRL_rep1


title: ATAC.12_MRTK.60_SMARCB1_rep3

description:
ATAC-seq in MRT organoids P60, after 4 days lentiviral transduction with the SMARCB1 gene
MRTK_ATACseq_peak_coordinates_2022-11-10.txt; MRTK_ATACseq_readcounts_unnormalized_2022-11-10.txt; MRTK_ATACseq_readcounts_normalized_2022-11-10.txt

source_name: MRT organoids P60

value: MRT organoids P60

value: a wild-type full-length SMARCB1 gene plasmid


title: D05 MSCs B: Baseline blood MNCs

city: Amman

first: Hind

middle: Moh'd

last: Khwaireh

address: Amman,Jordan

department: Cell Therapy Center

country: Jordan

institute: The University of Jordan

description: Gene expression data from human MNCs blood samples at baseline timepoint prior UC-MSCs treatment

hyb_protocol: Labeled double stranded cDNAwas hybridized according to genechip Human Transcriptome Array 2

scan_protocol: GeneChip were scanned using the GeneArray scanner G3000 7G

data_processing: Affymetrix Expression Console software version 4.0

label: biotin

label_protocol: Biotinylated cRNAwere prepared according to the standard Affymetrix protocol from100ng total RNA GeneChip Human Transcriptome Array 2.

growth_protocol: Fresh mononuclear cells (MNCs) were isolated from the buffy coat of blood samples collected from 6 patients at two timepoints,baseline and at three months post UC-MSCs as the baseline timepoint considered the refrence point to the three months timepoint.

extract_protocol: Total RNA isolation was performed using TRIZOL reagent and consequent enzymes and buffers according to the QIAamp RNA blood Mini kit- QIAGEN recommendation

treatment_protocol: No treatment was performed prior to extraction

tag: disease state

value: Multiple sclerosis (MS)

tag: gender

value: Male

value: blood MNCs

tag: condition


title: D05 MSCs 3M: Three months blood MNCs

description: ene expression data from human MNCs blood samples at three months timepoint post UC-MCSs treatment

source_name: MNCs blood samples at three months timepoint post UC-MSCs treatment


title: BW_F_15504_amygdala

value: brain

value: amygdala


title: D04 MSCs 3M: Three months blood MNCs

value: Female

value: three months timepoint post UC-MCSs treatment


title: PO_M_15410_midbrain


title: BW_F_15504_hypothalamus

value: hypothalamus

value: BW

value: F


title: G45KO_0Gy_1d_rep1

value: male


title: ATAC.10_MRTK.60_SMARCB1_rep1

value: Malignant rhabdoid tumor cells


title: PO_M_15410_hypothalamus

value: PO

value: M


title: ATAC.11_MRTK.60_SMARCB1_rep2


title: BW_F_15504_thalamus

value: thalamus


title: PO_M_15410_striatum

value: striatum


title: PO_M_15410_amygdala


title: D02 MSCs 3M: Three months blood MNCs


title: D02 MSCs B: Baseline blood MNCs

source_name: MNCs blood samples at baseline timepoint prior UC-MSCs treatment


title: ATAC.08_MRTK.60_CTRL_rep2

description:
ATAC-seq in MRT organoids P60, after 4 days lentiviral transduction with the Luciferase gene
MRTK_ATACseq_peak_coordinates_2022-11-10.txt; MRTK_ATACseq_readcounts_unnormalized_2022-11-10.txt; MRTK_ATACseq_readcounts_normalized_2022-11-10.txt

value: MRT organoids P60

value: Luciferase plasmid


title: PO_M_15409_thalamus


title: D04 MSCs B: Baseline blood MNCs

value: Multiple sclerosis (MS)

value: baseline timepoint prior UC-MSCs treatment


title: HeLa cells, DMS CR4/5 amplicon hTR G270C C277G A218T transfection, rep 2

city: Santa Cruz

first: Michael

last: Stone

state: CA

address: 1156 High Street

institute: University of California Santa Cruz

data_processing:
Reads were quality filtered and size selected with TrimGalore. Command: --paired --nextera R1.fastq.gz R2.fastq.gz --length 120
Reads were mapped to the hTR sequence (451 nt) with bowtie2. Command: bowtie2 --local --no-unal --no-discordant --no-mixed --phred33
The Devonvolution of RNA Ensembles with Expectation Maximization (DREEM) program was run on BAM files of Pseudoknot and CR4/5 ampliconsusing start and end nucleotides 22-204 and 213-368, respectively.
Assembly: Human Telomerase RNA (hTR)
Supplementary files format and content: Tab delimited text file containing normalized DMS reactivities for each nucleotide of hTR from the corresponding DREEM cluster. -999 corresponds to NaN.
Supplementary files format and content: Text file containing dot bracket secondary structures for the top predictions of DMS guided structure prediction from the corresponding DREEM cluster.

source_name: HeLa cell culture

growth_protocol: HeLa and HEK293T/17 cells (ATCC CRL-11268, lot:70040949) were cultured in DMEM containing 10% fetal bovine serum, 100 units/mL of penicillin, 100 mg/m of streptomycin, and 1X Gibco GlutaMAX at 37°C, 5% CO2. Cells were seeded into 6-well plates at 0.3 x 106 cells per well and allowed to grow to 90% confluency prior to use.

extract_protocol:
Total RNA was extracted using Trizol following the manufacturer's protocol.
10 μg of HeLa cell derived total RNA was DNAse treated in 1X TURBO DNAse buffer with 1 μL TURBO DNAse enzyme (Thermo Fisher Scientific), followed by column-purification with DNA Clean and Concentrator-5 columns (Zymo Research) following the manufacturer protocol. 5 μg of DNAse-treated RNA was mixed with 5 pmol hTR targeting primer containing a 4-nucleotide unique molecular identifier (UMI) in a volume of 11 μL, heated to 75°C for 3 min and annealed at 35°C for 15 min. Next, 4 μL of 5X M-MLV buffer (Promega), 1 μL 0.1M DTT, 1 μL RNAsin Plus (Promega), and 1 μL TGIRT III (Ingex) were added and the mixture was incubated at room temperature for 30 min. Then, 2 μL of 10mM dNTPs were added, and the reaction was mixed and incubated at 60 °C for 2.5 h. After RT, 1 μL of 5M NaOH was added directly to the cDNA and incubated at 95°C, followed by 2.5 μL of 2M HCl and purification by DNA Clean and Concentrator-5 columns (Zymo Research) using an 8:1 ratio of DNA Binding Buffer to cDNA volume. The cDNA was mixed into a 50 μL second strand synthesis reaction containing 10 μL 5X GC Phusion Buffer (Thermo Fisher Scientific), 1 μL 10 mM dNTP, 25 pmol of a second hTR targeting primer containing a 4 nucleotide UMI, and 1 μL Phusion polymerase. The second strand synthesis reaction was incubated in a thermocycler with the following program: 98°C 2 min, 60°C 2 min, 72°C 10 min. Second strand product was cleaned up with Ampure XP beads (Beckman Coulter) at a 0.8:1 bead to sample volume ratio and eluted in 20 μL nuclease-free H2O. Illumina sequencing libraries of two partially overlapping hTR regions (Pseudoknot: nucleotides 1-286 and CR4/5: nucleotides 193-451) were generated by two successive 50 μL PCR reactions. For the first PCR, 4 μL second strand product was added to a 50 μL PCR reaction containing primers for either the pseudoknot or CR4/5 amplicon and run with the following program: 10 cycles at 66°C annealing temperature, followed by 10 cycles at a 60°C annealing temperature. Amplicons were bead cleaned with a 0.8:1 ratio and went into a second PCR of 10 cycles at an annealing temperature of 65°C to complete the sequencing adapters and multiplexing barcodes. Libraries were bead cleaned with a 0.8:1 ratio and quantified by Qubit (Thermo Fisher Scientific) and Tapestation (Agilent) for quality metrics before sequencing by 150 bp paired end reads on the iSeq100 (Illumina).

treatment_protocol: For DMS modification, plates of HeLa cells were divided into DMS and control groups (3 wells each). Media from the DMS group was aspirated and replaced with 2 mL of a 2% DMS (Sigma) solution in cell media (prepared by brief vortexing to incorporate DMS). Cells were incubated at 37°C for 4 min, media was aspirated from each well and replaced with 10 mL of ice cold DMS quench solution (30% beta-mercaptoethanol in phosphate-buffered saline). Plates were placed on ice and the cells were collected by scraping and brief trituration, then pelleted by centrifugation at 200 x g for 5 min. Cells were washed once with cold PBS.

value: HeLa cell culture

value: HeLa

value: Cervical cancer

value: hTR G270C C277G A281T

value: DMS


title: HeLa cells, DMS CR4/5 amplicon hTR G270C C277G A218T transfection, rep 1


title: A50 MSCs 3M: Three months blood MNCs

value: Female

value: blood MNCs

value: three months timepoint post UC-MCSs treatment


title: ATAC.07_MRTK.60_CTRL_rep1

value: Malignant rhabdoid tumor cells


title: PO_M_15409_septum

value: brain

value: septum

value: PO


title: HeLa cells, DMS CR4/5 amplicon hTR C277G A218T transfection, rep 2

value: hTR C277G A281T


title: A50 MSCs B: Baseline blood MNCs

value: Male


title: PO_M_15409_striatum

value: striatum

value: M


title: HeLa cells, DMS CR4/5 amplicon hTR C277G A218T transfection, rep 1


title: PO_M_15409_midbrain

value: midbrain


title: ATAC.05_MRTK.103_SMARCB1_rep2

description:
ATAC-seq in MRT organoids P103, after 4 days lentiviral transduction with the SMARCB1 gene
MRTK_ATACseq_peak_coordinates_2022-11-10.txt; MRTK_ATACseq_readcounts_unnormalized_2022-11-10.txt; MRTK_ATACseq_readcounts_normalized_2022-11-10.txt

source_name: MRT organoids P103

value: MRT organoids P103

value: a wild-type full-length SMARCB1 gene plasmid


title: PO_M_15409_mPFC

value: mPFC


title: ATAC.04_MRTK.103_SMARCB1_rep1


title: HeLa cells, DMS CR4/5 amplicon hTR G270C transfection, rep 2

value: HeLa cell culture

value: HeLa

value: Cervical cancer

value: hTR G270C


title: ATAC.03_MRTK.103_CTRL_rep3

description:
ATAC-seq in MRT organoids P103, after 4 days lentiviral transduction with the Luciferase gene
MRTK_ATACseq_peak_coordinates_2022-11-10.txt; MRTK_ATACseq_readcounts_unnormalized_2022-11-10.txt; MRTK_ATACseq_readcounts_normalized_2022-11-10.txt

value: Luciferase plasmid


title: A45 MSCs B: Baseline blood MNCs

value: Multiple sclerosis (MS)

value: blood MNCs

value: baseline timepoint prior UC-MSCs treatment


title: PO_M_15409_hypothalamus

value: brain

value: hypothalamus

value: PO


title: A26 MSCs B: Baseline blood MNCs

value: Male


title: HeLa cells, DMS CR4/5 amplicon hTR G270C transfection, rep 1

value: DMS


title: A26 MSCs 3M: Three months blood MNCs

description: Gene expression data from human MNCs blood samples at three months timepoint post UC-MCSs treatment


title: HeLa cells, DMS CR4/5 amplicon hTR WT transfection, rep 1

description: HeLaTWJpTERTphTR

value: WT


title: PO_M_15409_amygdala

value: amygdala

value: M


title: ATAC.02_MRTK.103_CTRL_rep2

value: MRT organoids P103

value: Malignant rhabdoid tumor cells


title: ATAC.01_MRTK.103_CTRL_rep1


title: HeLa cells, DMS CR4/5 amplicon hTR WT transfection, rep 2

value: HeLa cell culture

value: HeLa


title: 159, TME (GM)

city: Adelaide

first: Cedric

last: Bardy

state: SA

address: North Terrace

country: Australia

institute: South Australian Health and Medical Research Institute (SAHMRI)

data_processing:
Cell Ranger v6.1.1 with default settings was used for demultiplexing pooled samples, read alignment to the GRCh38-2020-A genome and generating gene counts.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files for each sample

molecule: polyA RNA

source_name: Glioblastoma

growth_protocol: GBM patient-derived cell lines were cultured in glioma medium (GM also termed TME; DMEM/F12 with GlutaMax supplemented with SM1 with vitamin A, N2A and 5 ng/mL EGF and 5 ng/mL bFGF) or CSF until sub-confluent.

extract_protocol:
Single-cell suspensions of sub-confluent GBM cells, cultured in parallel in either GM or CSF were added to weels of an 8-channel microfluidic chip and transferred to a Chromium Controller. Six cell lines (468, 469, 497, BAH1, HW1 and MN1) were labelled with lipid-conjugated Cell Multiplexing Oligonucleotides (10X Genomics) according to manufacturer’s recommendations for cell pooling prior to loading onto a 10X Genomics chip.
Single-cell pooled suspensions were loaded on a GemCode Single Cell Instrument (10X Genomics) to generate single-cell gel beads in emulsion (GEM). scRNA-seq libraries were prepared from GEMs using a 3’ CellPlex Kit Set A (10X Genomics) and a Chromium i7 Multiplex kit (10X Genomics) according to the manufacturer’s instructions.

value: in vitro patient-derived glioblastoma cell line

value: Glioblastoma

value: TME (GM)

tag: tumor type

value: Primary

tag: library type

value: Gene Expression


title: ATAC.06_MRTK.103_SMARCB1_rep3

value: a wild-type full-length SMARCB1 gene plasmid


title: PO_F_15823_hindbrain

value: brain

value: hindbrain

value: F


title: 159, CSF

value: CSF


title: PO_F_15823_cerebellum

value: cerebellum

value: PO


title: G45KO_7Gy_1d_rep4

value: male

value: 7 Gy of x-rays


title: 134, TME (GM)


title: HeLa cells, Untreated CR4/5 amplicon hTR G270C transfection

value: Cervical cancer

value: hTR G270C


title: S2-Grh-DBD_aGrh_80uM_rep2

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

data_processing:
Bowtie2 version 2.4.4 was used to align ChIP-seq reads to the Drosophila melanogaster genome (version dm6) with the following non-default parameters: -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Aligned reads were filtered to include only reads with a mapping quality score > 30. Reads mapping to unplaced scaffolds or the mitochondrial genome were discarded.
. Peak calling was performed using MACS2 version 2.2 with parameters -g dm --call-summits. Only peaks that were detected in all replicates were considered in downstream analysis.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigwig file: contains z-score normalized read depth for each sample. Reads from two biological replicates were combined prior to generation of bigWig.
Supplementary files format and content: narrowPeak files: contain MACS2 peaks for ChIP samples.

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured at 27°C in Schneider's medium supplemented with 10% fetal bovine serum  and antibiotic/antimycotic.

extract_protocol:
For each ChIP experiment, ~50 million cells were crosslinked by adding methanol-free formaldehyde directly to the cell culture medium to a final concentration of 0.8%. Cells were rotated on a nutator for 7 minutes at room temperature (RT) before quenching of crosslinking by adding glycine to 125 mM. Crosslinked cells were pelleted by centrifugation at 600 × g for 3 minutes. Cells were washed twice with 1X PBS. Cells were lysed by resuspending in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X 100) with protease inhibitors (Pierce) and incubating on ice for 10 minutes. The resulting chromatin was pelleted for 5 minutes at 1500 × g and resuspended in RIPA buffer. Chromatin was sonicated in a Covaris S220 Ultrasonicator (5 cycles of 120 seconds with 60 second delay, 170 peak power, 10% duty factor, 200 cycles/burst). Sonicated chromatin was centrifuged for 10 minutes at 10,000 × g to pellet insoluble material. 5% of the supernatant was set aside as input, and the remainder was incubated at 4°C overnight with antibodies (6 µL anti-Zld, 8 µL anti-Grh, 10 µg anti-Twi, 7.5 µL anti-HA). 20 µL protein A beads (Dynabeads Protein A, ThermoFisher Scientific) blocked with BSA were added and samples were incubated at 4°C for 4 hours. Beads were separated on a magnet and washed 3× with low salt wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton-X 100, 150 mM NaCl), 2× high salt wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton-X 100, 300 mM NaC), 2× LiCl wash buffer (0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate), and 1× with TE buffer with NaCl (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). Beads were resuspended in elution buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) and incubated at 65°C for 10 minutes. The IP and input samples were treated with 4.5 µL RNAse A for 30 minutes. 5 µL Proteinase K was added and samples were incubated overnight at 65°C to reverse crosslinking. DNA was isolated by phenol:chloroform extraction, precipitated with EtOH, and resuspended in 20 µL H2O.
Preparation of sequencing libraries was performed using NEBNext Ultra II kit (NEB) with 7 PCR cycles for library amplification. Sequencing was performed on the Illumina Hi-Seq4000 using 50bp single-end reads, or on the Illumina NovaSeq 6000 using 150bp paired-end reads.

treatment_protocol: Transcription factor expression was induced by adding CuSO4 to the cell culture media. For all induction experiments, cells were plated at 1×10^6 cells per mL. Experiments were performed with cells harvested 48 hours after induction.

value: 80 uM CuSO4

tag: antibody

value: anti-Grh


title: ATAC.09_MRTK.60_CTRL_rep3

value: MRT organoids P60

value: Malignant rhabdoid tumor cells

value: Luciferase plasmid


title: A45 MSCs 3M: Three months blood MNCs

value: Multiple sclerosis (MS)

value: Male

value: blood MNCs

value: three months timepoint post UC-MCSs treatment


title: PO_F_15822_hippocampus

value: brain

value: hippocampus

value: F


title: S2-Grh-DBD_aGrh_80uM_rep1


title: PO_F_15822_hindbrain

value: hindbrain

value: PO


title: S2-Grh-DBD_aGrh_20uM_rep2

value: 20 uM CuSO4


title: HeLa cells, Untreated CR4/5 amplicon hTR WT transfection

value: HeLa cell culture

value: HeLa

value: Cervical cancer

value: WT


title: HeLa cells, DMS lipofectamine control

value: DMS


title: HeLa cells, Untreated CR4/5 amplicon hTR G270C C277G A218T transfection

value: hTR G270C C277G A281T


title: S2-Grh-DBD_aGrh_20uM_rep1

value: anti-Grh


title: PO_F_15822_cerebellum

value: cerebellum


title: 134, CSF

value: in vitro patient-derived glioblastoma cell line

value: Glioblastoma

value: CSF

value: Primary

value: Gene Expression


title: PO_F_15823_hippocampus

value: brain

value: hippocampus

value: F


title: PO_F_15821_thalamus

value: thalamus

value: PO


title: S2-Zld-DBD_aZld_400uM_rep2

value: 400 uM CuSO4

value: anti-Zld


title: 111, CSF


title: HeLa cells, Untreated CR4/5 amplicon hTR C277G A218T transfection

value: HeLa cell culture

value: HeLa

value: Cervical cancer

value: hTR C277G A281T


title: S2-Zld-DBD_aZld_400uM_rep1


title: S020

city: Rochester

first: Ryan

middle: Christian

last: Augustin

state: MN

address: 200 1st St SW

department: Oncology

institute: Mayo Clinic

data_processing:
Raw FastQ files (76 bp PE reads for both cohorts) and processed all data to generate count matrices in house using kallisto (v0.48.0). In brief, after quality control, reads were pseudoaligned via kallisto (v0.48.0) with human reference transcriptome (GRCh38) and Gencode annotation (v28), summarized into gene level by tximport (v1.22.0). From here, raw count matrices were directly downloaded (sources above), followed by TMM normalization. All expression values were log2-transformed before statistical analysis.
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Acral melanoma tumor

extract_protocol:
The dissected, deparaffinized tissue was air dried prior to adding 240 μL of Qiagen Buffer PKD (Qiagen, Germantown, MD, catalog #: 1034963), and 10 μL of QIAGEN Proteinase K (catalog #19131). RNA was extracted using the RNeasy FFPE kit (Qiagen, Germantown, MD, catalog #:73504) according to the manufacturer’s instructions. RNA concentration was determined using the High Sensitivity RNA Qubit kit (ThermoFisher Scientific, Pittsburgh, PA, catalog#: Q32855) and the RNA quality was determined using the NanoDrop and the Agilent Pico RNA Bioanalyzer kit (Agilent, Santa Clara, CA, catalog#:5067-1513). 100 ng of total RNA underwent library prep using the TruSeq® RNA Library Prep for Enrichment (Illumina, San Diego, CA, catalog#:20020189) assay for library construction according to the manufacturer’s instructions (Illumina TruSeq RNA Exome reference guide: document # 1000000039582 v01, March 2018). As per the protocol recommendations for FFPE RNA, the samples were not fragmented prior to cDNA synthesis.
Samples underwent 15 cycles of pre-hybridization PCR using the following protocol: 98°C/30sec, then 15 cycles of: 98°C/10sec, 60°C/30sec, 72°C/30sec, then 72°C/5min, 4°C Hold. The concentration and size distribution of the pre-hybridization PCR product was determined using the double stranded High Sensitivity DNA Qubit kit (ThermoFisher Scientific, Pittsburgh, PA, catalog#: 32854) and the Agilent High sensitivity DNA Bioanalyzer kit (Agilent, Santa Clara, CA, catalog#: 5067-4626). Samples had an average distribution of approximately 260 base pairs. 200 ng of cDNA per sample was used for individual hybridizations (Illumina TruSeq® RNA Enrichment kit, catalog #: 20020490) and the Illumina exome panel (Illumina catalog #: 20020183). Final library amplification of 10 cycles using the following protocol: 98°C- 30sec, then 10 cycles of 98°C-10sec, 60°C-30sec, 72°C-30sec, 72°C-5min, 10°C Hold. Upon the final library PCR clean-up, each library was individually interrogated using the double stranded High Sensitivity DNA Qubit kit (ThermoFisher Scientific, Pittsburgh, PA, catalog#: 32854) and the Agilent High sensitivity DNA Bioanalyzer kit (Agilent, Santa Clara, CA, catalog#: 5067-4626). Prior to sequencing, the concentration of each sample was confirmed using the double stranded high sensitivity DNA Qubit kit (ThermoFisher Scientific, Pittsburgh, PA, catalog#: 32854). Individual samples were then diluted down to 4 nM, following the Illumina NextSeq Denature and dilution guide (Illumina Document # 15048776 v18). The pooled library was denatured and diluted to 1.5 pM final library concentration. Sequencing was in batches of sixteen on the Illumina NextSeq 500/550 using a 150-cycle high output kit. The sequencing run was set on the NextSeq using the Illumina NextSeq Local Run Manager with the following parameters: paired end, R1 76 base pair X R2 76 base pair, with single 8 base pair index.

value: Acral melanoma tumor

tag: patient id

tag: cbl id

tag: biopsy site

value: vulvectomy, partial

tag: prim met

value: met

tag: age dx

tag: stage dx

value: IIA

tag: braf v600e_mut

value: No

tag: nras mut

tag: ckit mutation

tag: nf1 mutation

tag: ici treatment

value: Yes

tag: pre post_ici

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

tag: group

value: intermediate

tag: clinical benefit_(cb)


title: S019

tag: tissue

value: heel, right

value: primary

tag: gender

value: F

value: IIIB

value: non-T cell-inflamed


title: PO_F_15821_striatum

value: brain

tag: brain subregion

value: striatum

tag: strain

value: PO

tag: Sex


title: HeLa cells, Untreated lipofectamine control

value: HeLa cell culture

tag: cell line

value: HeLa

tag: cell type

value: Cervical cancer

tag: genotype

value: WT

tag: treatment


title: PO_F_15821_septum

value: septum


title: S017

value: Acral melanoma tumor

tag: patient id

tag: cbl id

tag: biopsy site

value: foot

tag: prim met

tag: age dx

tag: stage dx

tag: braf v600e_mut

value: No

tag: nras mut

tag: ckit mutation

value: T cell-inflamed


title: PO_F_15821_mPFC

tag: tissue

value: mPFC


title: S2-Zld-DBD_aZld_100uM_rep1

value: 100 uM CuSO4

tag: antibody

value: anti-Zld


title: PO_F_15821_midbrain

tag: brain subregion

value: midbrain

tag: strain

value: F


title: 111, TME (GM)

value: in vitro patient-derived glioblastoma cell line

value: Glioblastoma

value: TME (GM)

tag: tumor type

value: Primary

tag: library type

value: Gene Expression


title: caroli_M_input

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

data_processing:
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
deeptools was used to calculate RPKM normalized signal of each epigenetic mark across the genome and at TAD boundaries
ChromHMM was used to annotate chromatin states using the mouse alignments
Assembly: mm10, mPah1, mCar1, nomLeu4, hMol2
Supplementary files format and content: bigWig; bed

organism: Mus caroli

source_name: Liver

extract_protocol: ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.

value: Liver

value: ChIP

value: Ryukyu Mouse

tag: Sex

value: M

tag: chip antibody

value: input


title: PO_F_15821_hypothalamus

value: brain

value: hypothalamus

value: PO


title: S015

value: Acral melanoma tumor

tag: patient id

value: foot

value: primary

tag: gender

value: IV

tag: nf1 mutation

tag: ici treatment

value: Yes

tag: pre post_ici

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

tag: group

value: intermediate

tag: clinical benefit_(cb)


title: PO_F_15821_amygdala

tag: tissue

value: amygdala

value: F


title: caroli_F_input

value: Liver


title: DSP-2

city: Marburg

first: Martin

last: Thanbichler

address: Karl-von-Frisch-Str. 10

country: Germany

institute: MPI for Terrestrial Microbiology

data_processing:
Base-calling was performed online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.0.2.2
Quality and adapter trimming was performed with Timmomatic v0.36:  SE -threads 24 -phred33 ILLUMINACLIP:TruSeq3-vertis.fa:2:30:10 (contains Illumina TruSeq adapter sequences and a 80 nt langen polyA-tail) SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:30
Mappings against reference CP001340 were performed with bowtie2 with the --local parameter
Expression values were calculated using FeatureCounts with the following parameters: Feature type  -t gene Attribute type  -g gene_id Strand type  -s 1 (fwd) Feature level  -f (yes) Multi-mapping reads will be counted  -M (yes) fractional count 1/n  --fraction (yes) Minimum overlap  --minOverlap 30
Assembly: CP001340
Supplementary files format and content: Tab-delimited text files include raw counts and RPKM values of each sample

organism: Caulobacter vibrioides NA1000

source_name: conditional expression of PitA in JK158 strain (MAB259)

growth_protocol: Αll strains' precultures were grown overnight at 28 oC with constant shaking at 220 rpm in PYE medium until late exponential phase (OD600 =0.8-1), apart from ΔphoB and ΔpstS, which required 1.5 and 3 days respectively to reach that state. Samples cultures were diluted from the precultures at a starting OD600=0.05 in PYE medium supplemented with 0.3% xylose and cell pellets were collected in early exponential phase (OD600=0.3-0.5). All strains reached the desired OD after 3.5h, apart from ΔphoB and ΔpstS which required 10h and 12h respectively.

extract_protocol:
Τotal RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including Dnase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Remonal Kit for bacteria (Epicentre).
From the rRNA-depleted RNA samples, first strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illlumina TruSeq sequencing adpaters (containing barcode sequences) were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR using a proof-reading enzyme. For Illumina NextSeq sequencing, the cDNA were pooled in approximately equimolar amounts. The cDNA pool was eluted from a preparative agarose gel in the size range of 200-500 bp. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina, with a total length of the flanking sequences  of 122 bp. The cDNA pool was sequenced on an Illumina NextSeq500 system using 75 bp read length.

treatment_protocol: Addition of the xylose inducer was kept constant throughout the samples to eliminate any xylose-specific effect from the comparative trasncriptome analysis. Cell pellets collected for each strain, were snap-frozen in liquid nitrogen and stored  at -80 oC

tag: genotype

value: deltapstS::omega Pxyl::Pxyl-pitA

tag: treatment

value: PYE medium + 0.3% xylose


title: DSP-1

tag: strain

value: conditional expression of PitA in JK158 strain (MAB259)


title: DPP-2

source_name: conditional expression of PitA in JK2 strain (MAB258)

value: deltaphoB Pxyl::Pxyl-pitA


title: S013

tag: cbl id

tag: biopsy site

value: wide excision, left foot

tag: prim met

value: M

tag: age dx

tag: stage dx

value: IIB

tag: braf v600e_mut

tag: nras mut

value: No

tag: ckit mutation


title: S014

value: Acral melanoma tumor

tag: patient id

value: heel, Left

tag: gender

value: IIIA

tag: nf1 mutation

tag: ici treatment

tag: pre post_ici

value: non-T cell-inflamed


title: CBP-2

source_name: conditional expression of PitA in wild-type strain (MAB257)

value: CB15N Pxyl::Pxyl-pitA


title: PO_F_15818_thalamus

tag: tissue

value: brain

tag: brain subregion

value: thalamus

value: PO

tag: Sex


title: PO_F_15818_striatum

value: striatum

tag: strain

value: F


title: S018

tag: cbl id

value: metatarsal head, left foot

value: primary

value: Yes

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

tag: group

value: intermediate

tag: clinical benefit_(cb)


title: caroli_M_H3K27ac

value: Liver

value: ChIP

value: Ryukyu Mouse

value: M

tag: chip antibody


title: PO_F_15818_septum

value: septum


title: S016

value: Acral melanoma tumor

tag: biopsy site

value: Neck dissection

tag: prim met

value: met

tag: age dx

tag: stage dx

value: III

tag: braf v600e_mut

value: No

tag: nras mut

value: T cell-inflamed


title: S012

tag: patient id

value: primary, punch

tag: gender

value: IIIC

tag: ckit mutation

tag: nf1 mutation

tag: ici treatment

tag: pre post_ici


title: DPP-1

tag: strain

value: conditional expression of PitA in JK2 strain (MAB258)

tag: genotype

value: deltaphoB Pxyl::Pxyl-pitA

tag: treatment

value: PYE medium + 0.3% xylose


title: PO_F_15818_mPFC

tag: tissue

value: brain

tag: brain subregion

value: mPFC

value: PO

tag: Sex

value: F


title: caroli_F_H3K27ac

value: Liver

value: ChIP

value: Ryukyu Mouse

tag: chip antibody


title: S010

value: Acral melanoma tumor

tag: cbl id

tag: biopsy site

value: right foot, partial amputation + SLN bx

tag: prim met

value: primary

value: M

tag: age dx

value: Yes

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

tag: group

value: non-T cell-inflamed

tag: clinical benefit_(cb)


title: S2-Zld-DBD_aZld_100uM_rep2

tag: cell line

value: 100 uM CuSO4

tag: antibody

value: anti-Zld


title: DS-1

source_name: deletion of pstS (JK158)

tag: strain

value: deletion of pstS (JK158)

value: deltapstS::omega cassette

value: PYE medium + 0.3% xylose


title: S009

tag: patient id

value: heel, left

tag: gender

tag: stage dx

value: IIIC

tag: braf v600e_mut

value: No

tag: nras mut

tag: ckit mutation

tag: nf1 mutation

tag: ici treatment

tag: pre post_ici


title: caroli_M_H3K4me1

tag: tissue

value: Liver

value: ChIP

tag: Sex

tag: chip antibody


title: PO_F_15818_midbrain

value: brain

tag: brain subregion

value: midbrain

value: PO

value: F


title: caroli_M_CTCF

description: caroli-CTCF.bigwig

data_processing:
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
deeptools was used to calculate RPKM normalized signal of each epigenetic mark across the genome and at TAD boundaries
ChromHMM was used to annotate chromatin states using the mouse alignments
Assembly: mm10, mPah1, mCar1, nomLeu4, hMol2
Supplementary files format and content: bigWig; bed
Supplementary files format and content: *-CTCF-peaks-combined-merge200bp-sorted.bed: bed files contain all CTCF peaks unionized between one male and one female replicate, and merged within 200bp.

value: Ryukyu Mouse

value: M

value: CTCF


title: DP-2

source_name: deletion of phoB (JK2)

value: deletion of phoB (JK2)

tag: genotype

value: deltaphoB

tag: treatment


title: caroli_F_H3K4me1


title: PO_F_15818_hypothalamus

value: hypothalamus


title: caroli_M_H3K27me3


title: caroli_F_CTCF

description: caroli-CTCF.bigwig


title: DP-1


title: S007

value: Acral melanoma tumor

tag: cbl id

tag: biopsy site

value: foot

tag: prim met

value: primary

tag: age dx

value: IIA

value: Yes

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

tag: group

value: intermediate

tag: clinical benefit_(cb)


title: S008

tag: patient id

value: femur met, right

value: met

tag: gender

tag: stage dx

value: IIB

tag: braf v600e_mut

value: No

tag: nras mut

tag: ckit mutation

tag: nf1 mutation

value: T cell-inflamed


title: caroli_F_H3K27me3

tag: tissue

value: Liver

value: ChIP

value: Ryukyu Mouse

tag: Sex

value: F

tag: chip antibody


title: CB-2

source_name: wild-type strain CB15N (LS101)

tag: strain

value: wild-type strain CB15N (LS101)

tag: genotype

tag: treatment

value: PYE medium + 0.3% xylose


title: PO_F_15818_amygdala

source_name: brain

value: brain

tag: brain subregion

value: amygdala

value: PO


title: PO_F_15764_thalamus

value: thalamus


title: CBP-1

value: conditional expression of PitA in wild-type strain (MAB257)

value: CB15N Pxyl::Pxyl-pitA


title: DS-2

value: deletion of pstS (JK158)

value: deltapstS::omega cassette


title: CB-1


title: S011

value: Acral melanoma tumor

tag: cbl id

tag: biopsy site

value: foot, right

tag: prim met

value: primary

value: M

tag: age dx

value: IIIC

tag: ici treatment

value: Yes

tag: pre post_ici

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

value: intermediate


title: S006

tag: patient id

value: primary, L index finger amputation

tag: gender

tag: stage dx

value: IIIB

tag: braf v600e_mut

value: No

tag: nras mut

tag: ckit mutation

tag: group

tag: clinical benefit_(cb)


title: PO_F_15764_striatum

tag: tissue

value: brain

tag: brain subregion

value: striatum

tag: strain

value: PO

tag: Sex

value: F


title: caroli_M_H3K4me3

value: Liver

value: ChIP

value: Ryukyu Mouse

tag: chip antibody


title: caroli_F_H3K4me3


title: BW_M_16947_wholebrain

value: wholebrain

value: BW


title: S004

value: Acral melanoma tumor

tag: cbl id

tag: biopsy site

value: foot, left

tag: prim met

value: primary

value: M

tag: age dx

value: II

tag: nf1 mutation

tag: ici treatment


title: PO_F_15764_septum

value: septum


title: caroli_mouse_M_HiC

data_processing:
HiC data were subject to quality control and alignment with bowtie2 using the HiCUP pipeline.
Bam files were paired and converted to .cool format using cooltools.
TADs were called using HicExplorer, HicFindTADs with parameters --minDepth 100000, --maxDepth 600000, --delta 0.01, --correctForMultipleTesting fdr
Supplementary_files_format_and_content: BED files with TAD boundary regions

extract_protocol: Arima HiC

tag: protocol

value: Arima


title: S003

tag: patient id

value: primary, initial

tag: gender

tag: stage dx

value: IIIC

tag: braf v600e_mut

value: No

value: Yes

tag: pre post_ici

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

value: intermediate


title: PO_F_15764_mPFC

tag: tissue

value: brain

tag: brain subregion

value: mPFC

tag: strain

value: PO

value: F


title: caroli_mouse_F_HiC

value: Liver

value: Ryukyu Mouse


title: S002

value: Acral melanoma tumor

tag: cbl id

value: wide local

value: primary

value: IIA

tag: nras mut

tag: ckit mutation

tag: group

tag: clinical benefit_(cb)


title: BW_M_16894_wholebrain

value: wholebrain

value: BW

tag: Sex

value: M


title: BW_M_16687_wholebrain


title: S001

tag: biopsy site

value: R plantar foot

tag: prim met

tag: age dx

value: IIIA

value: No

tag: nf1 mutation

tag: ici treatment

value: T cell-inflamed


title: BW_M_16634_wholebrain

value: brain


title: PO_F_15764_hypothalamus

value: hypothalamus


title: PO_F_15764_amygdala

value: amygdala

value: PO


title: MCF-7 mammospheres, DMSO, 72 h

city: Yogyakarta

first: Adam

last: Hermawan

state: DI Yogyakarta

address: Sekip Utara II

department: Pharmacy

country: Indonesia

institute: Universitas Gadjah Mada

data_processing:
The qualities of cleaned reads were assessed using FastQC version 0.11.9 (https://github.com/s-andrews/FastQC)
the reports were compiled using MultiQC version 1.1 (https://multiqc.info).
The transcript were quantified using the pseudo-alignment method employing kallsito version 0.461
Supplementary files format and content: tab-delimited text files

source_name: Breast

growth_protocol: MCF-7 cells were culture in Poly HEMA-coated plate using DMEM supplemented with EGF, insulin, B27 in 5% CO2 incubator

extract_protocol:
RNA was harvested using Bioline - Isolate II RNA Mini Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: DMSO or Nobiletin

value: Breast

tag: cell line

tag: cell type

value: epithelial

tag: genotype

value: WT

tag: treatment

value: DMSO


title: young shoots, low tempreture, rep1

status: Public on Oct 19 2023

city: Hangzhou

first: Kexin

last: Zhang

address: No.9, Meiling South Road

country: China

institute: Tea Research Institute,Chinese Academy of Agricultural Science

description: treatment

data_processing:
Illumina Casava v1.8.2 software used for base calling.
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 package (version 1.20.0) with R (version 4.1.0).
Assembly: Longjing43 (Camellia sinensis var. sinensis)
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Camellia sinensis

source_name: young shoots

growth_protocol: Plants were grown in two artificial climate chambers in the two growth chamber for 1 month, 12h light / 12h dark at 22°C and illuminated with 200 μmol m-2 s-1 fluorescent lights.

extract_protocol:
Total RNA was harvested using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: The temperature of one artificial climate chamber was set to 12h / light at 26 °C and 12h / dark at 22 °C, and the temperature of the other artificial climate chamber was set to 12h / light at 18 °C and 12h / dark at 14 °C. When the leaves turn yellow (about a month) under LT treatment, both the green and the etiolated young shoots  were collected for analysis.

tag: tissue

value: young shoots

value: zhonghuang 2

value: low tempreture


title: young shoots, low tempreture, rep3

description: treatment


title: young shoots, high tempreture, rep3

description: control

value: high tempreture


title: young shoots, high tempreture, rep2

description: control


title: S005

value: Acral melanoma tumor

tag: patient id

value: CLND, inguinal

value: met

tag: gender

value: F

tag: stage dx

value: IIIC

tag: braf v600e_mut

value: Yes

tag: pre post_ici

value: Pre

tag: tmb

tag: cd8 til_ihc_pct

value: intermediate


title: young shoots, low tempreture, rep2

description: treatment


title: lib62378

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
A base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
FASTQs were aligned to the GRCh38 human reference genome using STAR v.2.4.2a.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using htseq-count.
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: whole blood in Tempus

extract_protocol:
Whole blood was collected in Tempus Blood RNA Tubes (ThermoFisher), and RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit, followed by globin reduction using GlobinClear Human (ThermoFisher). To generate sequencing libraries, total RNA (0.5 ng) was added to reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 59-base reads, using a NextSeq P2 sequencing kit (Illumina) with a target depth of 5 million reads per sample.

tag: donorid

tag: disease status

value: systemic lupus erythematosus

tag: Sex

value: female

tag: sledai score

tag: normalized fcar gmfi on pdcs


title: lib62379


title: young shoots, high tempreture, rep1

description: control


title: lib62349


title: lib62348


title: lib62377


title: lib62375


title: lib62347


title: BW_M_16807_wholebrain

value: brain

tag: brain subregion

value: wholebrain

tag: strain

value: BW

value: M


title: lib57797


title: PO_F_15764_midbrain

value: midbrain

value: PO


title: lib57794


title: lib57791


title: MCF-7 mammospheres, Nobiletin, 72 h

value: Breast

tag: cell line

tag: cell type

value: epithelial

tag: genotype

value: WT

value: Nobiletin


title: lib57790


title: lib57787


title: lib57795


title: lib57784


title: lib57776


title: lib57773


title: lib62373


title: TT-Seq ML1, IBRD9, 6h, TTseq_Rep1

city: Pittsburgh

first: David

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description: ML1, IBRD9, 6h, TTseq_Rep1

data_processing:
Barcode adapter sequences removed
Reads mapped to hg38 genome using STAR, with options --outFilterMismatchNoverReadLmax 0.02 and --outFilterMultimapNmax 1
Aligned reads were processed in deepTools by using the bamCoverage command to generate stranded bigwig files detailing coverage genome-wide in 5 bp bins with BPM normalization
Assembly: hg38
Supplementary files format and content: bigwig

source_name: cell line

growth_protocol: Human AML-derived cell lines were grown in RPMI-1640 medium, supplemented with 10% Fetal Bovine Serum, 1X sodium pyruvate and 2 mM L-glutamine. Cells were passaged every 48 hours by dilution in fresh medium. Routine anti-mycoplasma cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened by PCR to confirm no mycoplasma presence.

extract_protocol:
Cells were pelleted, washed with DPBS, and RNA was extracted with TRIzol per manufacturer's instructions.
RNA-seq; built with NEBNext Directional kit

treatment_protocol: Cells were centrifuged for 5 minutes at 600xG. Medium was aspirated and cells were resuspended in fresh medium containing 10 µM I-BRD9 or an equivalent volume of 100% DMSO. Plates were then left at 37 degrees Celsius with 5% CO2 for 6 hours before extraction.

tag: tissue

value: cell line

value: AML cell

tag: time

value: 6 hours

tag: treatment


title: TT-Seq KG1, IBRD9, 6h, TTseq_Rep1

description: KG1, IBRD9, 6h, TTseq_Rep1


title: TT-Seq KG1, DMSO, 6h, TTseq_Rep1

description: KG1, DMSO, 6h, TTseq_Rep1

value: DMSO


title: TT-Seq KG1, DMSO, 6h, TTseq_Rep2

description: KG1, DMSO, 6h, TTseq_Rep2


title: TT-Seq MV411, DMSO, 6h, TTseq_Rep2

description: MV411, DMSO, 6h, TTseq_Rep2


title: TT-Seq KG1, IBRD9, 6h, TTseq_Rep2

description: KG1, IBRD9, 6h, TTseq_Rep2


title: TT-Seq U937, DMSO, 6h, TTseq_Rep2

description: U937, DMSO, 6h, TTseq_Rep2


title: TT-Seq ML1, DMSO, 6h, TTseq_Rep2

description: ML1, DMSO, 6h, TTseq_Rep2


title: TT-Seq MV411, IBRD9, 6h, TTseq_Rep1

description: MV411, IBRD9, 6h, TTseq_Rep1


title: TT-Seq MV411, DMSO, 6h, TTseq_Rep1

description: MV411, DMSO, 6h, TTseq_Rep1


title: TT-Seq U937, DMSO, 6h, TTseq_Rep1

description: U937, DMSO, 6h, TTseq_Rep1


title: TT-Seq MV411, IBRD9, 6h, TTseq_Rep2

description: MV411, IBRD9, 6h, TTseq_Rep2


title: TT-Seq ML1, IBRD9, 6h, TTseq_Rep2

description: ML1, IBRD9, 6h, TTseq_Rep2


title: TT-Seq U937, IBRD9, 6h, TTseq_Rep2

description: U937, IBRD9, 6h, TTseq_Rep2


title: TT-Seq Kasumi1, IBRD9, 6h, TTseq_Rep2

description: Kasumi1, IBRD9, 6h, TTseq_Rep2


title: TT-Seq ML1, DMSO, 6h, TTseq_Rep1

description: ML1, DMSO, 6h, TTseq_Rep1


title: TT-Seq Kasumi1, IBRD9, 6h, TTseq_Rep1

description: Kasumi1, IBRD9, 6h, TTseq_Rep1


title: lib57775


title: TT-Seq Kasumi1, DMSO, 6h, TTseq_Rep1

description: Kasumi1, DMSO, 6h, TTseq_Rep1


title: TT-Seq U937, IBRD9, 6h, TTseq_Rep1

description: U937, IBRD9, 6h, TTseq_Rep1


title: TT-Seq Kasumi1, DMSO, 6h, TTseq_Rep2

description: Kasumi1, DMSO, 6h, TTseq_Rep2


title: CUT&Run U937, IBRD9, 6h, No primary antibody, Rep2

description:
U937, IBRD9, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.

extract_protocol:
Cells were pelleted, washed with DPBS, and nuclei were extracted with a hypotonic buffer. Unfixed nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodies followed by proteinA/proteinG-MNase. Cleavage of Mnase was initiated by Ca2+ addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.
CUT&RUN

tag: cut&run antibody


title: CUT&Run MV411, IBRD9, 6h, No primary antibody, Rep2

description:
MV411, IBRD9, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run U937, DMSO, 6h, No primary antibody, Rep1

description:
U937, DMSO, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run U937, DMSO, 6h, No primary antibody, Rep2

description:
U937, DMSO, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run U937, IBRD9, 6h, No primary antibody, Rep1

description:
U937, IBRD9, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run MV411, IBRD9, 6h, No primary antibody, Rep1

description:
MV411, IBRD9, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run MV411, DMSO, 6h, No primary antibody, Rep1

description:
MV411, DMSO, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run ML1, IBRD9, 6h, No primary antibody, Rep2

description:
ML1, IBRD9, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run MV411, DMSO, 6h, No primary antibody, Rep2

description:
MV411, DMSO, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run ML1, IBRD9, 6h, No primary antibody, Rep1

description:
ML1, IBRD9, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run ML1, DMSO, 6h, No primary antibody, Rep1

description:
ML1, DMSO, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run ML1, DMSO, 6h, No primary antibody, Rep2

description:
ML1, DMSO, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run MV411, IBRD9, 6h, anti-H3K27ac, Rep2

description: MV411, IBRD9, 6h, anti-H3K27ac, Rep2

value: Abcam ab4729


title: CUT&Run U937, IBRD9, 6h, anti-H3K27ac, Rep1

description: U937, IBRD9, 6h, anti-H3K27ac, Rep1


title: CUT&Run U937, DMSO, 6h, anti-H3K27ac, Rep2

description: U937, DMSO, 6h, anti-H3K27ac, Rep2


title: CUT&Run U937, IBRD9, 6h, anti-H3K27ac, Rep2

description: U937, IBRD9, 6h, anti-H3K27ac, Rep2


title: CUT&Run Kasumi1, DMSO, 6h, No primary antibody, Rep2

description:
Kasumi1, DMSO, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run Kasumi1, DMSO, 6h, No primary antibody, Rep1

description:
Kasumi1, DMSO, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run MV411, DMSO, 6h, anti-H3K27ac, Rep2

description: MV411, DMSO, 6h, anti-H3K27ac, Rep2


title: CUT&Run MV411, DMSO, 6h, anti-H3K27ac, Rep1

description: MV411, DMSO, 6h, anti-H3K27ac, Rep1


title: CUT&Run ML1, IBRD9, 6h, anti-H3K27ac, Rep2

description: ML1, IBRD9, 6h, anti-H3K27ac, Rep2


title: CUT&Run ML1, IBRD9, 6h, anti-H3K27ac, Rep1

description: ML1, IBRD9, 6h, anti-H3K27ac, Rep1


title: CUT&Run U937, DMSO, 6h, anti-H3K27ac, Rep1

description: U937, DMSO, 6h, anti-H3K27ac, Rep1


title: CUT&Run Kasumi1, IBRD9, 6h, No primary antibody, Rep2

description:
Kasumi1, IBRD9, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run KG1, IBRD9, 6h, No primary antibody, Rep1

description:
KG1, IBRD9, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run KG1, DMSO, 6h, No primary antibody, Rep1

description:
KG1, DMSO, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run Kasumi1, IBRD9, 6h, No primary antibody, Rep1

description:
Kasumi1, IBRD9, 6h, No primary antibody, Rep1
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run KG1, DMSO, 6h, No primary antibody, Rep2

description:
KG1, DMSO, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run ML1, DMSO, 6h, anti-H3K27ac, Rep1

description: ML1, DMSO, 6h, anti-H3K27ac, Rep1


title: CUT&Run ML1, DMSO, 6h, anti-H3K27ac, Rep2

description: ML1, DMSO, 6h, anti-H3K27ac, Rep2


title: CUT&Run KG1, IBRD9, 6h, anti-H3K27ac, Rep2

description: KG1, IBRD9, 6h, anti-H3K27ac, Rep2


title: CUT&Run KG1, DMSO, 6h, anti-H3K27ac, Rep2

description: KG1, DMSO, 6h, anti-H3K27ac, Rep2


title: CUT&Run Kasumi1, IBRD9, 6h, anti-H3K27ac, Rep1

description: Kasumi1, IBRD9, 6h, anti-H3K27ac, Rep1


title: CUT&Run KG1, IBRD9, 6h, anti-H3K27ac, Rep1

description: KG1, IBRD9, 6h, anti-H3K27ac, Rep1


title: CUT&Run Kasumi1, DMSO, 6h, anti-H3K27ac, Rep2

description: Kasumi1, DMSO, 6h, anti-H3K27ac, Rep2


title: CUT&Run KG1, DMSO, 6h, anti-H3K27ac, Rep1

description: KG1, DMSO, 6h, anti-H3K27ac, Rep1


title: CUT&Run Kasumi1, IBRD9, 6h, anti-H3K27ac, Rep2

description: Kasumi1, IBRD9, 6h, anti-H3K27ac, Rep2


title: CUT&Run KG1, IBRD9, 6h, No primary antibody, Rep2

description:
KG1, IBRD9, 6h, No primary antibody, Rep2
Bigwig files containing control reads belonging to distinct size classes (1-200 bp and 150-500 bp). 1-200 bp files should be used for most comparisons, while 150-500 bp should be used as controls for H3K27ac files.


title: CUT&Run MV411, IBRD9, 6h, anti-H3K27ac, Rep1

description: MV411, IBRD9, 6h, anti-H3K27ac, Rep1


title: CUT&Run Kasumi1, DMSO, 6h, anti-H3K27ac, Rep1

description: Kasumi1, DMSO, 6h, anti-H3K27ac, Rep1


title: CUT&Run U937, IBRD9, 6h, anti-BAF57, Rep2

description: U937, IBRD9, 6h, anti-BAF57, Rep2

value: Bethyl A300-810A


title: CUT&Run U937, IBRD9, 6h, anti-BAF57, Rep1

description: U937, IBRD9, 6h, anti-BAF57, Rep1


title: CUT&Run U937, DMSO, 6h, anti-BAF57, Rep2

description: U937, DMSO, 6h, anti-BAF57, Rep2


title: CUT&Run MV411, DMSO, 6h, anti-BAF57, Rep2

description: MV411, DMSO, 6h, anti-BAF57, Rep2


title: CUT&Run MV411, IBRD9, 6h, anti-BAF57, Rep1

description: MV411, IBRD9, 6h, anti-BAF57, Rep1


title: CUT&Run MV411, IBRD9, 6h, anti-BAF57, Rep2

description: MV411, IBRD9, 6h, anti-BAF57, Rep2


title: CUT&Run KG1, DMSO, 6h, anti-BAF57, Rep1

description: KG1, DMSO, 6h, anti-BAF57, Rep1


title: CUT&Run KG1, DMSO, 6h, anti-BAF57, Rep2

description: KG1, DMSO, 6h, anti-BAF57, Rep2


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BAF57, Rep2

description: Kasumi1, IBRD9, 6h, anti-BAF57, Rep2


title: CUT&Run KG1, IBRD9, 6h, anti-BAF57, Rep2

description: KG1, IBRD9, 6h, anti-BAF57, Rep2


title: CUT&Run Kasumi1, DMSO, 6h, anti-BAF57, Rep2

description: Kasumi1, DMSO, 6h, anti-BAF57, Rep2


title: CUT&Run Kasumi1, DMSO, 6h, anti-BAF57, Rep1

description: Kasumi1, DMSO, 6h, anti-BAF57, Rep1


title: CUT&Run ML1, IBRD9, 6h, anti-BAF57, Rep2

description: ML1, IBRD9, 6h, anti-BAF57, Rep2


title: CUT&Run ML1, DMSO, 6h, anti-BAF57, Rep1

description: ML1, DMSO, 6h, anti-BAF57, Rep1


title: CUT&Run U937, IBRD9, 6h, anti-BRM, Rep1

description: U937, IBRD9, 6h, anti-BRM, Rep1

value: Cell Signaling 11966S


title: CUT&Run U937, IBRD9, 6h, anti-BRM, Rep2

description: U937, IBRD9, 6h, anti-BRM, Rep2


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BAF57, Rep1

description: Kasumi1, IBRD9, 6h, anti-BAF57, Rep1


title: CUT&Run U937, DMSO, 6h, anti-BRM, Rep2

description: U937, DMSO, 6h, anti-BRM, Rep2


title: CUT&Run ML1, DMSO, 6h, anti-BAF57, Rep2

description: ML1, DMSO, 6h, anti-BAF57, Rep2


title: CUT&Run U937, DMSO, 6h, anti-BAF57, Rep1

description: U937, DMSO, 6h, anti-BAF57, Rep1


title: CUT&Run U937, DMSO, 6h, anti-BRM, Rep1

description: U937, DMSO, 6h, anti-BRM, Rep1


title: CUT&Run MV411, DMSO, 6h, anti-BRM, Rep1

description: MV411, DMSO, 6h, anti-BRM, Rep1


title: CUT&Run MV411, DMSO, 6h, anti-BRM, Rep2

description: MV411, DMSO, 6h, anti-BRM, Rep2


title: CUT&Run KG1, IBRD9, 6h, anti-BAF57, Rep1

description: KG1, IBRD9, 6h, anti-BAF57, Rep1


title: CUT&Run MV411, IBRD9, 6h, anti-BRM, Rep1

description: MV411, IBRD9, 6h, anti-BRM, Rep1


title: CUT&Run ML1, IBRD9, 6h, anti-BRM, Rep2

description: ML1, IBRD9, 6h, anti-BRM, Rep2


title: CUT&Run MV411, DMSO, 6h, anti-BAF57, Rep1

description: MV411, DMSO, 6h, anti-BAF57, Rep1


title: CUT&Run ML1, IBRD9, 6h, anti-BAF57, Rep1

description: ML1, IBRD9, 6h, anti-BAF57, Rep1


title: CUT&Run ML1, DMSO, 6h, anti-BRM, Rep2

description: ML1, DMSO, 6h, anti-BRM, Rep2


title: CUT&Run KG1, IBRD9, 6h, anti-BRM, Rep1

description: KG1, IBRD9, 6h, anti-BRM, Rep1


title: CUT&Run MV411, IBRD9, 6h, anti-BRM, Rep2

description: MV411, IBRD9, 6h, anti-BRM, Rep2


title: CUT&Run ML1, IBRD9, 6h, anti-BRM, Rep1

description: ML1, IBRD9, 6h, anti-BRM, Rep1


title: CUT&Run KG1, DMSO, 6h, anti-BRM, Rep1

description: KG1, DMSO, 6h, anti-BRM, Rep1


title: CUT&Run KG1, IBRD9, 6h, anti-BRM, Rep2

description: KG1, IBRD9, 6h, anti-BRM, Rep2


title: CUT&Run KG1, DMSO, 6h, anti-BRM, Rep2

description: KG1, DMSO, 6h, anti-BRM, Rep2


title: CUT&Run U937, IBRD9, 6h, anti-BRG1, Rep2

description: U937, IBRD9, 6h, anti-BRG1, Rep2

value: Bethyl A300-813A


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BRM, Rep1

description: Kasumi1, IBRD9, 6h, anti-BRM, Rep1


title: CUT&Run MV411, IBRD9, 6h, anti-BRG1, Rep1

description: MV411, IBRD9, 6h, anti-BRG1, Rep1


title: CUT&Run U937, DMSO, 6h, anti-BRG1, Rep1

description: U937, DMSO, 6h, anti-BRG1, Rep1


title: CUT&Run Kasumi1, DMSO, 6h, anti-BRM, Rep2

description: Kasumi1, DMSO, 6h, anti-BRM, Rep2


title: CUT&Run U937, IBRD9, 6h, anti-BRG1, Rep1

description: U937, IBRD9, 6h, anti-BRG1, Rep1


title: CUT&Run MV411, IBRD9, 6h, anti-BRG1, Rep2

description: MV411, IBRD9, 6h, anti-BRG1, Rep2


title: CUT&Run Kasumi1, DMSO, 6h, anti-BRM, Rep1

description: Kasumi1, DMSO, 6h, anti-BRM, Rep1


title: CUT&Run ML1, DMSO, 6h, anti-BRG1, Rep1

description: ML1, DMSO, 6h, anti-BRG1, Rep1


title: CUT&Run U937, DMSO, 6h, anti-BRG1, Rep2

description: U937, DMSO, 6h, anti-BRG1, Rep2


title: CUT&Run MV411, DMSO, 6h, anti-BRG1, Rep2

description: MV411, DMSO, 6h, anti-BRG1, Rep2


title: CUT&Run ML1, IBRD9, 6h, anti-BRG1, Rep2

description: ML1, IBRD9, 6h, anti-BRG1, Rep2


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BRM, Rep2

description: Kasumi1, IBRD9, 6h, anti-BRM, Rep2


title: CUT&Run ML1, DMSO, 6h, anti-BRM, Rep1

description: ML1, DMSO, 6h, anti-BRM, Rep1


title: CUT&Run KG1, IBRD9, 6h, anti-BRG1, Rep2

description: KG1, IBRD9, 6h, anti-BRG1, Rep2


title: CUT&Run ML1, IBRD9, 6h, anti-BRG1, Rep1

description: ML1, IBRD9, 6h, anti-BRG1, Rep1


title: CUT&Run KG1, IBRD9, 6h, anti-BRG1, Rep1

description: KG1, IBRD9, 6h, anti-BRG1, Rep1


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BRG1, Rep2

description: Kasumi1, IBRD9, 6h, anti-BRG1, Rep2


title: CUT&Run ML1, DMSO, 6h, anti-BRG1, Rep2

description: ML1, DMSO, 6h, anti-BRG1, Rep2


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BRG1, Rep1

description: Kasumi1, IBRD9, 6h, anti-BRG1, Rep1


title: CUT&Run KG1, DMSO, 6h, anti-BRG1, Rep1

description: KG1, DMSO, 6h, anti-BRG1, Rep1


title: CUT&Run KG1, DMSO, 6h, anti-BRG1, Rep2

description: KG1, DMSO, 6h, anti-BRG1, Rep2


title: CUT&Run Kasumi1, DMSO, 6h, anti-BRG1, Rep2

description: Kasumi1, DMSO, 6h, anti-BRG1, Rep2


title: CUT&Run U937, IBRD9, 6h, anti-BRD9, Rep1

description: U937, IBRD9, 6h, anti-BRD9, Rep1

value: Invitrogen PA5-113488


title: CUT&Run U937, IBRD9, 6h, anti-BRD9, Rep2

description: U937, IBRD9, 6h, anti-BRD9, Rep2


title: CUT&Run MV411, DMSO, 6h, anti-BRG1, Rep1

description: MV411, DMSO, 6h, anti-BRG1, Rep1


title: CUT&Run U937, DMSO, 6h, anti-BRD9, Rep1

description: U937, DMSO, 6h, anti-BRD9, Rep1


title: CUT&Run MV411, IBRD9, 6h, anti-BRD9, Rep2

description: MV411, IBRD9, 6h, anti-BRD9, Rep2


title: CUT&Run U937, DMSO, 6h, anti-BRD9, Rep2

description: U937, DMSO, 6h, anti-BRD9, Rep2


title: CUT&Run MV411, IBRD9, 6h, anti-BRD9, Rep1

description: MV411, IBRD9, 6h, anti-BRD9, Rep1


title: CUT&Run MV411, DMSO, 6h, anti-BRD9, Rep2

description: MV411, DMSO, 6h, anti-BRD9, Rep2


title: CUT&Run ML1, IBRD9, 6h, anti-BRD9, Rep2

description: ML1, IBRD9, 6h, anti-BRD9, Rep2


title: CUT&Run ML1, IBRD9, 6h, anti-BRD9, Rep1

description: ML1, IBRD9, 6h, anti-BRD9, Rep1


title: CUT&Run MV411, DMSO, 6h, anti-BRD9, Rep1

description: MV411, DMSO, 6h, anti-BRD9, Rep1


title: CUT&Run KG1, IBRD9, 6h, anti-BRD9, Rep1

description: KG1, IBRD9, 6h, anti-BRD9, Rep1


title: CUT&Run KG1, IBRD9, 6h, anti-BRD9, Rep2

description: KG1, IBRD9, 6h, anti-BRD9, Rep2


title: CUT&Run ML1, DMSO, 6h, anti-BRD9, Rep2

description: ML1, DMSO, 6h, anti-BRD9, Rep2


title: CUT&Run ML1, DMSO, 6h, anti-BRD9, Rep1

description: ML1, DMSO, 6h, anti-BRD9, Rep1


title: ATAC-Seq U937, IBRD9, 6h, ATACseq_Rep2

description: U937, IBRD9, 6h, ATACseq_Rep2

extract_protocol:
Cells were pelleted, washed with DPBS, and nuclei were extracted with a hypotonic buffer. Extracted nuclei were transposed for 30 minutes with Tn5 transposome in buffer containing digitonin, NP-40, and Tween-20.
ATAC-seq libraries were amplified by high-fidelity PCR with barcoded Nextera indices.


title: CUT&Run Kasumi1, DMSO, 6h, anti-BRD9, Rep1

description: Kasumi1, DMSO, 6h, anti-BRD9, Rep1


title: ATAC-Seq U937, IBRD9, 6h, ATACseq_Rep1

description: U937, IBRD9, 6h, ATACseq_Rep1


title: CUT&Run KG1, DMSO, 6h, anti-BRD9, Rep2

description: KG1, DMSO, 6h, anti-BRD9, Rep2


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BRD9, Rep2

description: Kasumi1, IBRD9, 6h, anti-BRD9, Rep2


title: CUT&Run Kasumi1, IBRD9, 6h, anti-BRD9, Rep1

description: Kasumi1, IBRD9, 6h, anti-BRD9, Rep1


title: CUT&Run Kasumi1, DMSO, 6h, anti-BRD9, Rep2

description: Kasumi1, DMSO, 6h, anti-BRD9, Rep2


title: ATAC-Seq U937, DMSO, 6h, ATACseq_Rep2

description: U937, DMSO, 6h, ATACseq_Rep2


title: CUT&Run Kasumi1, DMSO, 6h, anti-BRG1, Rep1

description: Kasumi1, DMSO, 6h, anti-BRG1, Rep1


title: ATAC-Seq MV411, IBRD9, 6h, ATACseq_Rep2

description: MV411, IBRD9, 6h, ATACseq_Rep2


title: ATAC-Seq U937, DMSO, 6h, ATACseq_Rep1

description: U937, DMSO, 6h, ATACseq_Rep1


title: ATAC-Seq MV411, IBRD9, 6h, ATACseq_Rep1

description: MV411, IBRD9, 6h, ATACseq_Rep1


title: ATAC-Seq MV411, DMSO, 6h, ATACseq_Rep1

description: MV411, DMSO, 6h, ATACseq_Rep1


title: ATAC-Seq ML1, IBRD9, 6h, ATACseq_Rep2

description: ML1, IBRD9, 6h, ATACseq_Rep2


title: ATAC-Seq ML1, IBRD9, 6h, ATACseq_Rep1

description: ML1, IBRD9, 6h, ATACseq_Rep1


title: ATAC-Seq KG1, DMSO, 6h, ATACseq_Rep2

description: KG1, DMSO, 6h, ATACseq_Rep2


title: ATAC-Seq KG1, IBRD9, 6h, ATACseq_Rep2

description: KG1, IBRD9, 6h, ATACseq_Rep2


title: ATAC-Seq KG1, IBRD9, 6h, ATACseq_Rep1

description: KG1, IBRD9, 6h, ATACseq_Rep1


title: ATAC-Seq ML1, DMSO, 6h, ATACseq_Rep2

description: ML1, DMSO, 6h, ATACseq_Rep2


title: ATAC-Seq KG1, DMSO, 6h, ATACseq_Rep1

description: KG1, DMSO, 6h, ATACseq_Rep1


title: ATAC-Seq Kasumi1, DMSO, 6h, ATACseq_Rep2

description: Kasumi1, DMSO, 6h, ATACseq_Rep2


title: ATAC-Seq Kasumi1, IBRD9, 6h, ATACseq_Rep1

description: Kasumi1, IBRD9, 6h, ATACseq_Rep1


title: ATAC-Seq Kasumi1, IBRD9, 6h, ATACseq_Rep2

description: Kasumi1, IBRD9, 6h, ATACseq_Rep2


title: CUT&Run KG1, DMSO, 6h, anti-BRD9, Rep1

description: KG1, DMSO, 6h, anti-BRD9, Rep1


title: ATAC-Seq Kasumi1, DMSO, 6h, ATACseq_Rep1

description: Kasumi1, DMSO, 6h, ATACseq_Rep1


title: OMPiGFP/OMPtTA, RNA-seq, r3

first: Ariel

last: Pourmorady

address: 3227 Broadway

department: Neurobiology and Behavior

description:
RNA-seq performed on FAC sorted cells from the main olfactory epithelium of adult mice using the following kit: SMARTER Stranded Total RNA-Seq Kit- Pico Input Mammalian v2.
rna.OMPM71nc_v_OMPGFPOMPtTA_rlog_rna.txt

data_processing:
Data processing and analysis was performed as described in "Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons" (Monahan et al. 2017). Briefly Adapter sequences were removed from raw sequencing data with CutAdapt. RNA-seq reads were aligned to the mouse genome (mm10) using STAR. Samtools was used to select uniquely aligning reads by remove reads with alignment quality alignments below 30 (-q 30). RNA-seq data analysis was performed in R with the DESeq2 package.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Olfactory Sensory Neurons

extract_protocol: All RNA-seq experiments were performed under RNA clean conditions. For RNA-seq, live cells were sorted into RNase free 1x PBS, pelleted at 600-g, for 5-min, at 4 ̊C, then resuspended in 500-uL Trizol, flash frozen in liquid nitrogen and stored O/N at -80 ̊C. RNA extraction was performed the next day. Trizol suspensions were thawed on ice, 1/5V of 1-bromo-3-chloropropane was added, and tubes were shook vigorously to combine phases. Phases were allowed to separate for 2-min at room temperature and then tubes were centrifuged at 10,500 rpm, for 15-min at 4  ̊C in an Eppendorf centrifuge C5424R. We collected the upper aqueous phase which was transferred to a new tube. 1/2V of Isopropanol and 1-uL of linear polyacrylamide (Sigma Aldrich 56575) were added, tube was inverted to mix, and RNA was allowed to precipitate for 10-min at RT. Tubes were centrifuged for 10-min at 10,500 rpm and 4- ̊C. The supernatant was removed and 1V of 75% EtOH was added to the pellet, which was dislodged by flicking the tube. Tubes were centrifuged for another 5-min, at 10,500-rpm, and 4  ̊C. EtOH was removed and tubes were allowed to air dry for 5-min until the pellet turned clear. Next we added 26- uL of RNase free water, 3-uL of Ambion DNase I 10x buffer and 1-uL of DNase I (AM2222) to remove all DNA, and incubated tubes at 37  ̊C for 30-min. RNA was purified doing a 1.5x AMPure bead cleanup, measured on a nanodrop, and used as the input for library preparation with SMARTER Stranded Total RNA-Seq Kit- Pico Input Mammalian v2 (Takara Bio USA). OMP-tTA>tetO-GFP and gg8-tTA>tetO-GFP libraries were prepared with the TruSeq kit. However, mature OSN samples were compared to both OMP-tTA>tetO-GFP (TruSeq prep) and OMP-IRES-GFP (Takara Bio USA), which label the same neurons, and produced the same results. Libraries were sequenced on either a NextSeq550 or a NextSeq2000 and were sequenced to a targeted coverage of ~25M reads. All RNA-seq experiments were performed with 2-3 biological replicates.

value: OMPiresGFP/OMPtTA

value: Olfactory Sensory Neurons


title: OMPiGFP/OMPtTA, RNA-seq, r1


title: ATAC-Seq MV411, DMSO, 6h, ATACseq_Rep2

description: MV411, DMSO, 6h, ATACseq_Rep2


title: OMPiGFP/OMPtTA, RNA-seq, r2


title: OMPiGFP, RNA-seq, r1

description:
RNA-seq performed on FAC sorted cells from the main olfactory epithelium of adult mice using the following kit: SMARTER Stranded Total RNA-Seq Kit- Pico Input Mammalian v2.
rna.OMPM71nc_v_OMPGFP_rlog_rna.txt

value: OMPiresGFP


title: Trx_20wk_Mut, rep 1, scRNAseq

city: HOUSTON

first: Margaret

last: Goodell

state: TX

address: 1 Baylor Plz, Rm N1030

institute: Baylor College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Paired-end sequencing data were mapped and quantified using Cell Ranger Single Cell Suite v3.1.0 to the mouse genome (mm10) provided by 10x Genomics’ Cell Ranger.
Cell Ranger count files of each Sample were combined and normalized using Cell Ranger aggregate.
Cells with 6,500-30,000 detected genes and less than 10% total mitochondrial gene expression were filtered and retained for analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
20,000 donor (CD45.2) HSPCs in the bone marrow were isolated after competitive transplantation for 20 weeks. Each independent Sample were used as input for 10X platform droplet-based library construction.
Library was performed using 10x platform 3v31 assay using chromium Single Cell 3’ solution without multiplexing according to the manufacter’s instructions.

value: Isolated Srcap mutant HSPCs

value: Bone marrow

tag: age

value: 20 weeks post-transplantation


title: Trx_20wk_Mut, rep 2, scRNAseq

description: 10x Genomics


title: OMPiGFP, RNA-seq, r3


title: OMPiGFP, RNA-seq, r2


title: Isolated T cells, Transplantation, 2-weeks_1 Srcap mutant

data_processing:
Fastq files quality were controlled using fastqc/multizc
Duplicate reads were removed and unique sequence reads were trimmed for adaptor sequence/low-quality sequence
Paired-end bulk RNA-sequencing reads were mapped to the STAR mouse reference genome index (mm39) using STAR
Quantification of mapped reads for RNA-sequencing was performed using Subread package (featureCount) to obtain count files
Assembly: mm10
Supplementary files format and content: tab-delimited text files including feature counts for each Sample

source_name: T cells in bone marrow

extract_protocol:
RNA was harvested from 30,000 sorted HSPCs in the bone marrow and isolated using Allprep DNA/RNA Micro Kit (Qiagen) of each independent Sample for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using True-Seq Stranded mRNA library preparation kit (Illumina, 20020594) based on manufacturer’s protocol.

value: T cells in bone marrow

value: Srcap mutant

value: Transplantation

value: 2 weeks


title: Trx_20wk_WT, rep 1, scRNAseq

description: 10x Genomics

value: Isolated WT HSPCs


title: Trx_20wk_WT, rep 2, scRNAseq

description: 10x Genomics


title: Isolated T cells, Transplantation, 2-weeks_2 WT

value: WT


title: Isolated T cells, Transplantation, 2-weeks_1 WT


title: ATAC-Seq ML1, DMSO, 6h, ATACseq_Rep1

description: ML1, DMSO, 6h, ATACseq_Rep1

value: cell line

value: AML cell

value: 6 hours

value: DMSO


title: Isolated T cells, Transplantation, 2-weeks_2 Srcap mutant


title: Isolated B cells, Transplantation, 2-weeks_1 Srcap mutant

source_name: B cells in bone marrow

value: B cells in bone marrow


title: Isolated B cells, Transplantation, 2-weeks_2 WT


title: Isolated B cells, Transplantation, 2-weeks_1 WT


title: Isolated HSPCs, Doxorubicin IP, 12-hours_2 Srcap mutant

source_name: Hematopoietic stem and progenitor cells (HSPCs)

value: Doxorubicin

value: 12 hours


title: Isolated HSPCs, Transplantation, 2-weeks_1 Srcap mutant

value: Hematopoietic stem and progenitor cells (HSPCs)


title: Isolated HSPCs, Transplantation, 2-weeks_2 Srcap mutant


title: Isolated HSPCs, Doxorubicin IP, 12-hours_2 WT


title: Isolated B cells, Transplantation, 2-weeks_2 Srcap mutant


title: Isolated HSPCs, Transplantation, 2-weeks_2 WT


title: Isolated HSPCs, Doxorubicin IP, 12-hours_1 WT


title: Isolated HSPCs, Transplantation, 20-weeks_2 Srcap mutant

value: Competitive transplantation

value: 20 weeks


title: Isolated HSPCs, Doxorubicin IP, 12-hours_1 Srcap mutant


title: Isolated HSPCs, Transplantation, 2-weeks_1 WT


title: Isolated HSPCs, Germline, no treatment_1 Srcap mutant

value: No treatment


title: Isolated HSPCs, Transplantation, 20-weeks_2 WT


title: Isolated HSPCs, Transplantation, 20-weeks_1 WT


title: Isolated HSPCs, Germline, no treatment_2 Srcap mutant


title: CaR, HSPC, Mut, Trx, SRCAP, rep2

data_processing:
Fastq files quality were controlled using fastqc/multizc
Cut-and-run paired-end reads were trimmed from 3' end using Trimmomatic and unique reads were mapped to the mouse genome (mm10) using Bowtie2
BigWig file for each biological replicates were generated using deepTools (bamCoverage) with counts-per-miillion (CPM) normalization and blacklist subtraction
Cut-and-run reads from biological replicates were then merged for peak calling using MACS3
Quantification of peaks for Cut-and-run sequencing was performed using Subread package (featureCounts)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut-and-run sequencing

source_name: Isolated Srcap mutant HSPCs

extract_protocol:
50,000 sorted HSPCs from the bone marrow were permeabalized with 0.05% Digtonin to perform antibody binding and Mnase digestion. The antibody-enriched DNA fragments were released and used for library construction
Cut-and-run sequencing library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) according to the manufacturer’s protocol.

value: Isolated Srcap mutant HSPCs

tag: antibody

value: SRCAP (Kerafast, #ESL103)


title: CaR, HSPC, Mut, Trx, SRCAP, rep1


title: CaR, HSPC, WT, Trx, SRCAP, rep2

source_name: Isolated WT HSPCs


title: Isolated HSPCs, Germline, no treatment_1 WT


title: CaR, HSPC, WT, Trx, SRCAP, rep1


title: CaR, HSPC, Mut, Trx, H2AZ, rep2


title: CaR, HSPC, WT, Trx, H2AZ, rep2


title: CaR, HSPC, Mut, Trx, mIgG

value: mIgG (Abcam, #ab46540)


title: CaR, HSPC, Mut, Trx, H2AZ, rep1


title: CaR, HSPC, WT, Trx, H3K27me3


title: CaR, HSPC, WT, Trx, H2AZ, rep1


title: CaR, HSPC, Mut, NT, SRCAP, rep2

description: Germline


title: CaR, HSPC, WT, Trx, mIgG


title: CaR, HSPC, WT, NT, SRCAP, rep2

description: Germline


title: Isolated HSPCs, Transplantation, 20-weeks_1 Srcap mutant

value: Srcap mutant


title: CaR, HSPC, Mut, NT, mIgG

description: Germline


title: CaR, HSPC, WT, NT, SRCAP, rep1

description: Germline

value: Isolated WT HSPCs


title: CaR, HSPC, WT, NT, H2AZ, rep1

description: Germline


title: CaR, HSPC, Mut, NT, H2AZ, rep1

description: Germline


title: CaR, HSPC, Mut, NT, SRCAP, rep1

description: Germline


title: CaR, HSPC, WT, NT, mIgG

description: Germline


title: CaR, HSPC, WT, NT, H2AZ, rep2

description: Germline


title: Isolated HSPCs, Germline, no treatment_2 WT

value: WT


title: CaR, HSPC, Mut, NT, H3K27me3

description: Germline


title: CaR, HSPC, WT, NT, H3K27me3

description: Germline


title: ATAC, HSPC, Mut, Trx, rep 1

data_processing:
Fastq files quality were controlled using fastqc/multiqc
Cut-and-run paired-end reads were trimmed from 3' end using Trimmomatic and unique reads were mapped to the mouse genome (mm10) using Bowtie2
BigWig file for each biological replicates were generated using deepTools (bamCoverage) with counts-per-miillion (CPM) normalization and blacklist subtraction
Cut-and-run reads from biological replicates were then merged for peak calling using MACS3
Quantification of peaks for Cut-and-run sequencing was performed using Subread package (featureCounts)
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Isolated HSPCs

extract_protocol:
20,000 sorted HSPCs from the bone marrow were washed, permeabalized, and treated with Tn5 transposase. The treated genomic DNA were isolated and used for library construction
ATAC-seq library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) according to the manufacturer’s protocol.

value: Isolated HSPCs


title: ATAC, HSPC, WT, Trx, rep 3


title: CaR, HSPC, Mut, Trx, H3K27me3


title: ATAC, HSPC, WT, Trx, rep 1


title: ATAC, HSPC, Mut, NT, rep 2


title: ATAC, HSPC, Mut, NT, rep 1


title: ATAC, HSPC, Mut, Trx, rep 3


title: ATAC, HSPC, WT, NT, rep 2


title: ATAC, HSPC, WT, Trx, rep 2


title: ATAC, HSPC, WT, NT, rep 1


title: CaR, HSPC, Mut, NT, H2AZ, rep2

description: Germline


title: 2 Pediatric food anaphylaxis

city: Madrid

first: Vanesa

last: Esteban

state: State...

address: Av. Reyes Catolicos 2

department: Immunology

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

data_processing:
Quality controls were determined using the Bioanalyzer 2100 or the TapeStation 4200 (Agilent Technologies).
miRNAs data were normalized to equimolar ratios depending on the quality of the library, the quality of the inserts and the concentration measurements.
Raw data files (FASTQ) were generated for each sample using the bcl2fastq program (Illumina Inc.) and Cutadapt (1.11) software was utilized to remove adapter sequences and collapse the reads by UMIs.
Assembly: mirbase_20
Supplementary files format and content: scRNA_AX_rawcounts.xls

source_name: sera

extract_protocol:
Total RNA was isolated from 200 μl of serum using the miRNeasy Serum/Plasma Kit (Qiagen) according to manufacturer’s instructions
Libraries were performed with the QIAseq miRNA Library Kit (Qiagen). RNA was retrotranscribed to copy DNA (cDNA), amplified by PCR (22 cycles) and purified from samples. Libraries were carried out by a gel-free system through the addition of Unique Molecular Identifiers (UMIs) and were specific for small RNA species ranging from 15-40 nucleotides.

value: sera


title: 5 Pediatric food anaphylaxis_basal


title: 3 Pediatric food anaphylaxis_basal


title: 3 Pediatric food anaphylaxis


title: 4 Pediatric food anaphylaxis_basal


title: 4 Pediatric food anaphylaxis


title: 1 Pediatric food anaphylaxis


title: 5 Adult drug anaphylaxis


title: ATAC, HSPC, Mut, Trx, rep 2


title: 5 Adult drug anaphylaxis_basal


title: 3 Adult drug anaphylaxis_basal


title: 3 Adult drug anaphylaxis


title: 4 Adult drug anaphylaxis


title: 1 Pediatric food anaphylaxis_basal


title: 2 Adult drug anaphylaxis_basal


title: 2 Adult drug anaphylaxis


title: 1 Adult drug anaphylaxis_basal


title: 1 Adult drug anaphylaxis


title: 5 Pediatric food anaphylaxis


title: 2 Pediatric food anaphylaxis_basal


title: 4 Adult drug anaphylaxis_basal


title: Primary breast tumor, scRNA-seq, Tumor_08_Tamoxifen

city: Chapel Hill

first: Philip

last: Spanheimer

state: NC

address: 101 Manning Drive (Campus Box 7213)

department: UNC School of Medicine - Surgery

institute: University of North Carolina at Chapel Hill

data_processing:
The filtered feature barcode matrices were generated by Cell Ranger from 10x Genomics.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 (10x Genomics)

source_name: tissue

extract_protocol:
Primary tissue specimens were obtained in the operating room and placed in DMEM/F12 (Gibco) media with 1% Penicillin-Streptomycin (Life Technologies). Specimens were transferred immediately to the laboratory and processed into single cell suspensions by sharply mincing into 2-4 mm fragments. Enzymatic dissociation was then performed using Gentle Collagenase/Hyaluronidase (Stemcell Technologies Inc. 07919) in DMEM/F12 supplemented with 5% BSA (Sigma Aldrich), Hydrocortisone (Stemcell Technologies Inc.), HEPES (Corning), and Glutamax (Gibco) for 16 hours at 37⁰C with cell agitation. The cells were gently centrifuged and washed twice with PBS (Gibco) supplemented with Fetal Bovine Serum (FBS) and HEPES buffer. Cells were resuspended in cold ammonium chloride solution (Stemcell Technologies Inc. 07800) and incubated at room temperature to remove red blood cells. Cells were centrifuged and briefly trypsinized in warm 0.05% Trypsin-EDTA (Gibco) and DNase I (Stemcell Technologies Inc. 07900). Cells were further dissociated with dispase (Stemcell Technologies Inc. 07923) and DNase I. Cells were centrifuged and washed then resuspended in DMEM/F12 with 10% FBS and 1% Penicillin-Streptomycin. Cells were then strained using multiple rounds of sequential straining with 40 µm mini strainers (Pluriselect USA Inc.) to remove cell debris.
scRNA-seq was done with the 10x Genomics Chromium Next GEM Single Cell 30 v3.1 reagent kits according to the manufacturer’s revision D user guide. After 12-hour suspension, viability was assessed using trypan blue, quantified using the Countess, and 7,000 to 10,000 viable cells were targeted per library. Libraries were sequenced on the NextSeq500 and NextSeq2000 (Illumina) platforms with pair-end sequencing and single indexing according to the recommended manufacturer’s protocols.

value: tissue

value: Tamoxifen

value: Female

tag: race

value: Black

tag: er status

value: ER positive

tag: her2 status

value: HER2 negative

tag: body site

value: Breast

tag: analyte type

value: RNA

tag: is tumor

value: Y

tag: histological type

value: Invasive Ductal Carcinoma

tag: primary metastatic_tumor

value: Primary Tumor

tag: primary tumor_location

tag: tumor stage

tag: tumor grade


title: Primary breast tumor, scRNA-seq, Tumor_06_Control

tag: cell type

value: Control

tag: Sex

value: White

value: Invasive Lobular Carcinoma


title: Primary breast tumor, scRNA-seq, Tumor_05_Tamoxifen

tag: treatment


title: Primary breast tumor, scRNA-seq, Tumor_03_Tamoxifen


title: Primary breast tumor, scRNA-seq, Tumor_04_Tamoxifen


title: Primary breast tumor, scRNA-seq, Tumor_08_Control


title: Primary breast tumor, scRNA-seq, Tumor_07_Control


title: Primary breast tumor, scRNA-seq, Tumor_09_Tamoxifen


title: Primary breast tumor, scRNA-seq, Tumor_10_Tamoxifen


title: Primary breast tumor, scRNA-seq, Tumor_05_Control


title: Primary breast tumor, scRNA-seq, Tumor_06_Tamoxifen


title: Primary breast tumor, scRNA-seq, Tumor_09_Control


title: Primary breast tumor, scRNA-seq, Tumor_03_Control


title: Primary breast tumor, scRNA-seq, Tumor_02_Control

value: Other


title: Primary breast tumor, scRNA-seq, Tumor_01_Tamoxifen


title: Primary breast tumor, scRNA-seq, Tumor_02_Tamoxifen


title: Cell line, scRNA-seq, T47D_Tamoxifen

tag: cell line

value: cell line

value: Unknown

value: Cell line

value: Cell Line


title: Primary breast tumor, scRNA-seq, Tumor_10_Control

value: tissue

value: Female


title: Primary breast tumor, scRNA-seq, Normal_02_Tamoxifen

value: Tamoxifen

value: Black

value: Not applicable

value: N

value: Normal Breast


title: Primary breast tumor, scRNA-seq, Normal_01_Tamoxifen

value: Breast

value: RNA


title: Primary breast tumor, scRNA-seq, Tumor_07_Tamoxifen

value: ER positive

value: HER2 negative

value: Y

value: Invasive Ductal Carcinoma

value: Primary Tumor


title: slan_neg_mono_3

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
reads were mapped onto the Ensembl human transcriptome (version 96) and quantified at the transcript level using kallisto
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2
Gene abundance was indicated as FPKM, and genes with FPKM equal or higher than 1 in at least one sample were considered as expressed and further analysed
Differentially expressed genes were identified using DESeq2, by using as selection parameter an adjusted p-values (padj) lower than 0.01
Assembly: hg38
Supplementary files format and content: Expression_FPKM.xls

source_name: blood

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation
Libraries for transcriptome analysis were prepared using Smart-seq protocol (PMID: 24056875)

tag: tissue

value: blood

value: slan- -monocytes

value: Freshly isolated cells


title: slan_neg_mono_2


title: slan_neg_mono_1


title: Primary breast tumor, scRNA-seq, Normal_02_Control

value: tissue

value: Control


title: Primary breast tumor, scRNA-seq, Normal_01_Control

value: Female

value: White


title: Primary breast tumor, scRNA-seq, Tumor_04_Control


title: Monocytes subsets,donor 2, scRNA

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
FASTQ files obtained from sequencing were provided to the BD Rhapsody WTA Analysis Pipeline Targeted Multiplex Rhapsody Pipeline v1.0 with default settings
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence. Putative cells information were combined together with RSEC-adjusted molecules to generate a single-cell expression matrix.
Raw gene expression matrices were read into R (version ) separately and converted to Seurat objects using the Seurat R package (3.2.2)
Assembly: Genome_build: hg38
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

source_name: Blood

extract_protocol:
The different cell populations (CL, INT, NC, slan neg/NC and slan pos/NC) were sorted from peripheral blood by using a Becton Dickinson FACS Aria Fusion (BD Biosciences) and then labelled with the BD Single-Cell Multiplexing Kit (BD Biosciences), strictly following the manufacturer's protocol. Both cell viability and counts were then evaluated, and only samples with high viability (> 85 %) were used for sequencing. Approximately 15000 cells were pooled together and loaded in a single BD Rhapsody cartridge. The procedure described above was repeated for two different donors
cDNA Libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification kit and BD Single-Cell Multiplexing kit (BD Biosciences) following the manufacturer's protocol

value: Blood

value: innate immunity cells (CL, INT, NC, slan neg/NC and slan pos/NC)

tag: individual

value: donor 2


title: Primary breast tumor, scRNA-seq, Tumor_01_Control

tag: race

value: Black

value: Breast


title: Cell line, scRNA-seq, T47D_Control

value: cell line

value: Unknown

tag: er status

value: ER positive

value: RNA

value: Cell line

value: Cell Line


title: Monocytes subsets,donor 1, scRNA

value: donor 1


title: LAIV_036_Curettage_4

city: London

last: Thwaites

state: London

address: St Mary's Hospital

country: United Kingdom

institute: Imperial College London

data_processing:
Fastp (v 0.20.1) was used to trim the adapters and reads were mapped against human GRCh38 Ensembl 99
Quantification was performed using the Salmon tool
DeSEQ2 (v 1.34.0) was used to normalize the counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include  counts values for each Sample

source_name: nasal epithelium

extract_protocol:
Lexogen SPLIT RNA extraction kit per manufacturers protocol
Lexogen QuantSeq FWD kit per manufacturers protocol

value: nasal epithelium

value: Primary nasal epithelial

tag: time point


title: LAIV_047_Curettage_1

value: Baseline


title: LAIV_043_Curettage_1


title: LAIV_042_Curettage_4


title: LAIV_038_Curettage_4


title: LAIV_045_Curettage_1


title: LAIV_035_Curettage_1


title: LAIV_034_Curettage_4


title: LAIV_042_Curettage_1


title: LAIV_049_Curettage_1


title: LAIV_044_Curettage_4


title: LAIV_044_Curettage_1


title: LAIV_046_Curettage_1


title: LAIV_034_Curettage_1


title: LAIV_029_Curettage_Visit1


title: LAIV_033_Curettage_Visit4


title: LAIV_030_Curettage_1


title: LAIV_028_Curettage_1


title: LAIV_026_Curettage_1


title: LAIV_027_Curettage_4


title: LAIV_027_Curettage_Visit1


title: LAIV_025_Curettage_1


title: LAIV_048_Curettage_Visit1


title: LAIV_047_Curettage_4


title: LAIV_031_Curettage_1


title: LAIV_024_Curettage_1


title: LAIV_031_Curettage_4


title: LAIV_041_Curettage_1


title: LAIV_029_Curettage_4


title: LAIV_021_Curettage_4


title: LAIV_017_Curettage_4


title: LAIV_022_Curettage_4


title: LAIV_016_Curettage_4


title: LAIV_020_Curettage_4


title: LAIV_021_Curettage_1


title: LAIV_015_Curettage_1


title: LAIV_023_Curettage_1


title: LAIV_012_Curettage_4


title: LAIV_022_Curettage_1


title: LAIV_011_Curettage_1


title: LAIV_020_Curettage_1


title: LAIV_014_Curettage_Visit4


title: LAIV_018_Curettage_4


title: LAIV_014_Curettage_1


title: LAIV_018_Curettage_1


title: LAIV_008_Curettage_4


title: LAIV_010_Curettage_4


title: LAIV_008_Curettage_1


title: LAIV_010_Curettage_1


title: LAIV_007_Curettage_4


title: LAIV_002_Curettage_4