title: hbca_n08,P17,replicate_1,blank,nuclei

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_n08
nuclei samples

molecule: nuclear RNA

extract_protocol:
RNAs are extracted from single nuclei suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

value: breast

value: 10x Genomics 3' end V2 nuclei


title: Tumor, Combo2L15

status: Public on Jun 29 2023

type: SRA

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

country: USA

institute: University of Iowa

library_source: transcriptomic

data_processing:
Reads were processed with ‘bcbio-nextgen.py’ genomics pipeline run in “RNA-seq” mode with the ‘mm10’ key as the selected genome build (internally referencing Ensembl GRCm38.p6 v94, GENCODE M19).
The pipeline aligned reads to the GRCm38 genome using the splice-aware ‘hisat2’ aligner (2.2.1) and concurrently quantified reads to the GENCODE M19 transcriptome using ‘salmon’ (1.4.0) aligner.
Salmon-derived transcript quantifications (TPM) were imported and summarized to estimated counts at the gene level using ‘tximport’ (1.12.3).
Differential gene expression analysis was then conducted with DESeq2 (1.24.0) on estimated gene-level counts using a model conditioned on animal sex and tumor classification factor (‘vehicle’, ‘resistant’, or ‘sensitive’).
Assembly: GRCm38 / GENCODE M19
Supplementary files format and content: flat text, gene counts

molecule: total RNA

organism: Mus musculus

source_name: Malignant Peripheral Nerve Sheath Tumor

growth_protocol: Tumors were generated via adenoviral delivery of a cas9 system targeting mouse Nf1 and Cdk2na

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep (Illumina) kits in accordance with manufacturer guideliens

treatment_protocol: Mice were treated daily with 100 mg/kg Palbociclib + 1 mg/kg Mirdametinib or the vehicle control by oral gavage

tag: tissue

value: Malignant Peripheral Nerve Sheath Tumor

tag: strain

tag: genotype

value: WT

tag: treatment

value: Palbociclib (100 mg/kg) + Mirdametinib (1 mg/kg)

tag: harvest time

value: Terminal


title: ST_Pt15

city: Guangzhou

first: Guangshuai

last: Jia

address: Dongfengxi Rd, Yuexiu Campus

country: China

institute: Guangzhou Medical University

description: Raw matrix for ST_Pt15

data_processing:
The Space Ranger toolkit (v1.2.1) with GRCh38 reference genomes was used to align and quantify the raw fastq files. Seurat was used to process the Space Ranger output files.
The ST data from individual patients and tumor/para-tumor regions were merged, and the function SCTransform implemented in Seurat was used to normalize the data. Because each ST spot contained several cells, we used the R package SPOTlight28 to deconvolute mixtures of cells using the scRNA-seq data as a reference.
The ST cell types were inferred from the scRNA-seq data, and the proportions of corresponding cell types for each spot were obtained with the NMF regression model.
Assembly: GRCh38 (for human)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json:scalefactors in ison format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: GBM.spatial.rds: Processed Seurat object for all ST data
Library strategy: Visium Spatial Transcriptomics

molecule: polyA RNA

organism: Homo sapiens

source_name: brain

extract_protocol:
Cryosections of GBM tissues (10-μm thick) were embedded in OCT using the 2-methylbutane (isobutene) method. Tissue permeabilization for different times (8, 12, 16, or 20 min) was performed, and 16 min permeabilization resulted in the maximum fluorescence signal in both the tumor core and the para-tumor regions. The RNA quality of tissue sections was checked (RIN > 7.0).
ST experiment was performed using Visium Spatial Gene Expression Kits (10x Genomics) following standard manufacturer protocols. The libraries were sequenced on an Illumina HiSeq X Ten sequencer.

value: brain

tag: age(year)

tag: Sex

value: male

value: Neoadjuvant


title: hbca_n07,P12,replicate_1,left and right breast,nuclei

city: Houston

first: Nicholas

last: Navin

state: TX

address: 6767 Bertner Ave

department: System Biology

institute: MD Anderson Cancer Center

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_n07
nuclei samples

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger 10XRNA Vcellranger-3.1.0 mkfastq
cellranger 10XRNA Vcellranger-3.1.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: H5

source_name: breast

tag: paper participant_number

tag: assay


title: hbca_n10,P19,replicate_1,left and right breast,nuclei

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_n10
nuclei samples


title: ST_Pt12

description: Raw matrix for ST_Pt12

value: TMZ+RT


title: ST_Pt14

description: Raw matrix for ST_Pt14


title: Tumor, VehLL1

value: Vehicle Control


title: Patient_26_D0_Pfsz

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

data_processing:
Reads were assessed for quality, trimmed if PHRED scores fell below 20, and any remaining adapter sequences were removed
Processed paired-end reads were aligned to human reference genome GRCh38 using HISAT2, and counts were generated using the HTseq analysis package
Reads that successfully mapped to the reference genome were used for downstream analyses
Assembly: GRCh38
Supplementary files format and content: htseq output with gene counts for each sample

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
RNA was isolated using QIAzol and the Direct-zol RNA Mini Prep Plus Kit per manufacturer's instructions. RNA quality was assessed using the Agilent Bioanalyzer 2100, and only samples with RNA integrity numbers (RIN) greater than 7 or total RNA concentration greater than 100 ng were selected for RNA sequencing racted using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
PolyA-enriched, strand-specific RNA libraries were constructed and 100bp paired-end reads were sequenced on an Illumina NovaSeq 6000 platform

treatment_protocol: Samples were stimulated with Plasmodium falciparum schizonts, or SEB, or were left unstimulated.

tag: subject

tag: time

tag: cell type

value: Peripheral Blood Mononuclear Cells

value: P. falciparum schizonts


title: ST_Pt13

description: Raw matrix for ST_Pt13

value: female


title: hbca_n03,P10,replicate_1,contra,nuclei

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_n03
nuclei samples


title: ST_Pt11

description: Raw matrix for ST_Pt11


title: Tumor, ComboUR7


title: hbca_n06,P134,replicate_1,left and right breast,nuclei

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_n06
nuclei samples


title: Patient_26_D0_Med

value: Media


title: Tumor, VehUB6


title: ST_Pt10

description: Raw matrix for ST_Pt10


title: ST_Pt9_Pt8

description: Raw matrix for ST_Pt9_Pt8

value: male,male

value: newly_diagnosed, TMZ+RT


title: Patient_22_D150_SEB

value: SEB


title: Patient_22_D150_Pfsz


title: hbca_n01,P01,replicate_1,contra,nuclei

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_n01
nuclei samples

value: breast

value: 10x Genomics 3' end V2 nuclei


title: hbca_n02,P08,replicate_1,contra,nuclei

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 126 cycles.
hbca_n02
nuclei samples


title: Patient_22_D150_Media


title: ST_Pt8

description: Raw matrix for ST_Pt8


title: Patient_22_D90_Pfsz


title: hbca_n09,P18,replicate_1,left and right breast,nuclei

description:
76PE
Read1 26cycles, i7: 8cycles, Read2: 98 cycles.
hbca_n09
nuclei samples


title: Tumor, VehUR8FFT

value: Malignant Peripheral Nerve Sheath Tumor

value: WT


title: Tumor, ComboLB10FFT

value: Palbociclib (100 mg/kg) + Mirdametinib (1 mg/kg)

value: Terminal


title: Tumor, Veh2R9FFT


title: ST_Pt6

description: Raw matrix for ST_Pt6

value: brain

value: male


title: Patient_22_D90_Media


title: ST_Pt7

description: Raw matrix for ST_Pt7

value: TMZ+RT


title: Patient 10, lesion

city: Hasselt

first: Tim

last: Vanmierlo

address: Martelarenlaan 40

country: Belgium

institute: Universiteit Hasselt

description:
full_table_counts_QC_normalized.xlsx
10A

data_processing:
Normalisation and transformation of counts to log counts-per-million, using the Trimmed Mean of M-values (TMM) normalisation method.
Assembly: GRCh37
Supplementary files format and content: XLSX file with LogCPM for all samples

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen)
Lexogen 3’mRNA-Seq Library Prep Kit

tag: cell line

value: bulk sample

tag: age

tag: seks

value: M

tag: pmi (minutes)


title: Patient 9, lesion

description:
full_table_counts_QC_normalized.xlsx
9A

value: F


title: Patient 9, NAWM

description:
full_table_counts_QC_normalized.xlsx
9B


title: Patient 7, NAWM

description:
full_table_counts_QC_normalized.xlsx
7B


title: Patient 10, NAWM

description:
full_table_counts_QC_normalized.xlsx
10B


title: ST_Pt5_Pt7

description: Raw matrix for ST_Pt5_Pt7

value: female,female


title: 4C-seq of Cyp26-E2 in Mus musculus: RARX-DKO-Cyp26-E2-4C-bait-Rep1

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

library_source: genomic

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to mm10 using Bowtie2(2.3.1)
Peak calling using MACS2(2.2.7.1)
Clean reads of 4C-seq were removed primer using the "demultiplex.py" script in fourCseq and then mapped to mm10 using Bowtie2(2.3.1)
The interactions were identified using R package fourCseq and r3Cseq
Assembly: mm10
Supplementary files format and content: csv files include genes counts values,ChIP signal peaks for each sample,bam file for each  4C-seq sample
Library strategy: 4C-seq

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: Mouse ESCs were grown in culture dishes coated with 0.1% gelatin in Glasgow Minimum Essential Medium (GMEM) supplemented with 15% fetal bovine serum (FBS), 100 nM nonessential amino acids, 1 % sodium pyruvate, 200 mM glutamate, 1% penicillin-streptomycin, 50 μM β-mercaptoethanol, 10 ng/mL LIF, 1 μM PD0325901 (a MEK inhibitor) and 3 μM CHIR99021 (a GSK inhibitor). The medium was replaced every day

extract_protocol:
1. For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions.   2. For Chip-seq, 10 M cells cells were crosslinked with 1% formaldehyde (methanol free) in DMEM at a volume of 1 mL of formaldehyde for every one million cells. Cells were cross-linked 10 min at room temperature with rotation. Glycine was added into a final concentration of 125 mM to quench the formaldehyde. Samples were washed ywice using cold PBS. Then according the ChIP-seq Kit (Byotime)  manufacturer's instructions. The volume of pelleted material was brought up to 800 μL in SDS Lysis Buffer and incubated 15 min on ice. Samples were then divided equally into 4 parts, sheared for 30 cycles (30 s “ON” and 30 s of “OFF”), and then spun down at 12000 g for 10 min. Supernatant were collected into new low-adsorption 1.5mL EP tubes and diluted using ChIP dilution buffer. Then, add 7.5 μg antibodies incubated at 4 °C overnight with rotation.  The next day, 60 μL Protein A/G beads were washed and added to samples and then rotated 2 h at 4 °C. Beads were washed three times each with Low Salt Wash Buffer, High Salt Wash Buffer, and LiCl Wash Buffer. Chip-DNA was de-crosslinking with Proteinase K and purification using AmpureXP beads. Then the purified products were sequenced at Novogene (Tianjin city, China).                                                                                3. For 4C-seq：Briefly, 10^7 ESCs were trypsinised into single cells and resuspended in 9.5 ml of DMEM/15% FBS. Cells were then cross-linked by adding 0.6 ml of 16% formaldehyde for 10 min. After centrifugation at 4 degrees (2000 g), cells were lysed in 5 ml of lysis buffer (10 mM Tris-HCl [pH 7.5]; 10 mM NaCl; 5 mM MgCl2; 0.1 mM EGTA; 1 x protease inhibitor) for 10 min (placed ice with constant light shaking) and centrifuged to remove the supernatant. The nuclei were then digested with DpnII at 37°C. After inactivation with 1.6% SDS for 20 minutes at 65°C, samples were diluted in 6.125 ml of 1.15× ligation buffer and 100 U T4 ligase and incubated for 4 hours at 16°C, followed by 30 minutes at 25°C. The ligated chromatin was digested by proteinase K, purified by phenol-chloroform extraction and the DNA was precipitated by ethanol. The purified product was further digested with NlaIII and then cyclised with T4 ligase. After purification, PCR reactions containing 100 ng DNA were performed using the bait-primers. PCR products were purified by Agencourt AMPure XP paramagnetic beads and the purified products were sequenced at Novogene (Tianjin city, China).
1. RNA-seq Library. Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.                                                                                2. ChIP-seq:  DNA libraries were generated using a FS DNA Library Prep Kit (QIAGEN). The sequencing platform used was HiSeq XTen (Illumina). Mapping of ChIP-seq data to mm10 was performed using bowtie2. Peaks were called using MACS2  with default parameters and annotated with annotatePeaks in Homer : callpeak -t treated.bam -c input.bam -n sample -g mm -B -q 0.05. Co-localization of histone modifications was detected with ChromHMM.   3. 4C-seq Library. After the DNA samples were tested and passed, the DNA fragments specifically enriched by the 4C technique were subjected to end repair, addition of A-tails, addition of sequencing connectors, purification and PCR amplification to complete the entire library preparation. After library construction, initial quantification was performed using Qubit 2.0 to dilute the library, followed by detection of the insert fragment using Agilent 2100. After the insert fragment size met the expectation, the effective concentration of the library was accurately quantified using Q-PCR method to ensure the quality of the library. After the libraries passed the assay, the different libraries were pooled into flowcell according to the effective concentration and the target downstream data volume. cBOT was clustered and sequenced using Illumina high-throughput sequencing platform NovaSeq 6000.

treatment_protocol: For RA treatment, ESCs were induced to differentiate by LIF/2i withdrawal and addition of 2 μM RA (Sigma). Culture medium was replaced every day.

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 24 h


title: Patient_22_D0_Pfsz

value: Peripheral Blood Mononuclear Cells

value: P. falciparum schizonts


title: Tumor, Regress2L4FFT

value: During Regression


title: ST_Pt5

description: Raw matrix for ST_Pt5

value: female


title: Patient_22_D0_SEB

value: SEB


title: Patient_22_D90_SEB


title: 4C-seq of Cyp26-E2 in Mus musculus: Rxrα-KO-Cyp26-E2-4C-bait-Rep2


title: 4C-seq of Cyp26-E2 in Mus musculus: RARX-DKO-Cyp26-E2-4C-bait-Rep2


title: ST_Pt4

description: Raw matrix for ST_Pt4


title: Patient_22_D0_Media

value: Media


title: ST_Pt3

description: Raw matrix for ST_Pt3


title: 4C-seq of Cyp26-E2 in Mus musculus: Rxrα-KO-Cyp26-E2-4C-bait-Rep1


title: Patient 6, NAWM

description:
full_table_counts_QC_normalized.xlsx
6B


title: Patient 6, lesion

description:
full_table_counts_QC_normalized.xlsx
6A


title: Patient_21_D150_Pfsz


title: ST_Pt2

description: Raw matrix for ST_Pt2

value: Neoadjuvant


title: Patient_21_D150_SEB


title: 4C-seq of Cyp26-E2 in Mus musculus: Rarα-KO-Cyp26-E2-4C-bait-Rep1


title: Patient_21_D150_Media


title: 4C-seq of Cyp26-E2 in Mus musculus: Rarα-KO-Cyp26-E2-4C-bait-Rep2


title: Patient 5, NAWM

description:
full_table_counts_QC_normalized.xlsx
5B


title: 4C-seq of Cyp26-E2 in Mus musculus: WT-Cyp26-E2-4C-bait-Rep2


title: ST_Pt1

description: Raw matrix for ST_Pt1


title: Patient_21_D90_Pfsz


title: 4C-seq of Cyp26-E2 in Mus musculus: WT-Cyp26-E2-4C-bait-Rep1


title: ST_Pt9

description: Raw matrix for ST_Pt9


title: Contra 24h

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

country: Sweden

institute: Lund University

description: high output 150 cycle kit, Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 single index

data_processing:
The cells from the sequenced data were counted with cell ranger v.5 set to default for contra- or IPSI - 1h, -12h or -24h samples. The individual .h5 - files were aggregated in cell ranger aggr
Assembly: mm10
Supplementary files format and content: Cell Ranger Aggr matrix. Aggregated Cell ranger file with all the conditions in the experiments, e.g,, 1h, 12h or 24h contra- or IPSI-lateral single cells from mouse brain cortex.
Supplementary files format and content: Order of files and cell indentifying suffixes in the matrix:
Supplementary files format and content: 1: Contra 1h
Supplementary files format and content: 2: IPSI 1h
Supplementary files format and content: 3: Contra 12h
Supplementary files format and content: 4: IPSI 12h
Supplementary files format and content: 5: Contra 24h
Supplementary files format and content: 6: IPSI 24h

extract_protocol:
Brain cortex from stroke (penumbra or stroke tissue ,IPSI) or contra (nonstroke corresponding brain cortex tissue area)
According to the 10x Library & Gel Bead Kit v3 single index or Library & Gel Bead Kit v3.1 dual index protocols, respectively

value: Endothelial cells, Astrocytes, Oligodendrocytes, Microglia, Immune cells, Pericytes, Neuronal progenitors

value: RGS5::GFP het

value: Contra (stroke)


title: 4C-seq of Cyp26-E1 in Mus musculus: RARX-DKO-Cyp26-E1-4C-bait-Rep2


title: Patient 7, lesion

description:
full_table_counts_QC_normalized.xlsx
7A

value: brain


title: 4C-seq of Cyp26-E1 in Mus musculus: RARX-DKO-Cyp26-E1-4C-bait-Rep1


title: WTIGG

city: Cincinnati

first: Shreyasi

last: Mukherjee

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: CUT&RUN

data_processing:
Raw reads were quality-checked using FASTQC  and adapters were trimmed using cutadapt
Sequences were aligned to the mm10 genome using bowtie2 v2.2.3 with the following parameters: --local, --very-sensitive, --no-mixed, --no-discordant. –q –phred33, --minIns 10 –maxIns 1000.
For V5 CUT&RUN, the resultant bam files were then split to retain <120bp fragments indicative of TF binding signature. BAM files were then sorted, indexed and converted to BigWig files for data visualizing using deeptools.
Tracks were visualized using IGV.
BAM files were then converted to bedgraph files for peak calling using bedtools genomecov
Peaks were called using SEACR and the following parameters: signal threshold ‘stringent’ and normalization control ‘norm’.
Assembly: mm10
Supplementary files format and content: .bw files are bigWig files for visualization of CUT&RUN data
Library strategy: CUT&RUN

growth_protocol: All animals were maintained in accordance with the National Institutes of Health Guide for Care and Use of Laboratory Animals and the Cincinnati Children’s Medical Center Animal Care and Use Committee (IACUC2020-0060) approved all animal procedures.

extract_protocol:
CUT&RUN experiments were performed according to Meers et. al. 2019 with minor modifications. Briefly, nuclei were isolated from ~250,000 VECs by resuspending cells in ice-cold NE buffer [20mM HEPES, pH 7.9, 10mM KCl, 0.1% Triton X-100, 20% Glycerol, 1mM MnCl2, supplemented with protease inhibitors and 0.5mM Spermidine]. Cells were incubated on ice for 10 mins, and then centrifuged at 600xg for 3 min at 4°C. The supernatant was discarded and the nuclear pellet resuspended in 100ml NE buffer per reaction. Simultaneously, Concanavalin A beads [PolySciences, 86057] were activated by washing in ice cold Bead Activation Buffer [20mM HEPES pH 7.9, 10mM KCl, 1mM CaC2, 1mM MnCl2] twice. After two washes, activated ConA beads were resuspended in 10ml/reaction Bead Activation Buffer and kept on ice until needed. After nuclei isolation, 100ml of nuclei were added to 10ml activated ConA beads and the bead-nuclei slurry was incubated at RT for 10 mins for cells to adsorb. The beads were then pelleted on a magnet, and the supernatant was discarded. 50ml/reaction Antibody Buffer [20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.01% digitonin, 2mM EDTA supplemented with fresh protease inhibitors] was added to each reaction and the beads were gently vortexes to thoroughly resuspend. The following antibodies were added: V5 (Invitrogen, 46-0705), mouse IGG (Milipore Sigma, 12-371), H3K27ac (Active Motif, 39133), or Rabbit IGG (Cell Signaling Technology, 2729). The bead-antibody reactions were incubated on a rotator overnight at 4°C. The next day, the beads were washed twice with Wash Buffer [20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.01% digitonin]. The beads were then pelleted and 2.5ml pAG-MNase [Epicypher, Cat#15-1016] was added to each IP in 50ml of Wash buffer and incubated for 10 mins at RT to allow pAG-MNase to bind to the bead slurry. After 10 mins, the bead slurry was washed twice with Wash Buffer and targeted chromatin digestion was performed by adding 1ml 100mM CaCl2 per reaction in 50ml Wash Buffer. The beads were then rotated for 2 hours at 4°C for chromatin release to occur. After 2 hours, 33ml of STOP buffer [340mM NaCl, 20mM EDTA, 4mM EGTA, 50mg/ml RNase A, 50mg/ml Glycogen] was added per reaction, and the beads were incubated for 10 min at 37°C. The beads were pelleted to collect supernatant, and DNA was purified using the Minelute PCR Purification Kit [Qiagen, 28004]. DNA concentration was measured using the Qubit fluorometer.
The libraries were constructed using the CUTANA CUT&RUN Library Prep kit [Epicypher, 14-1001] with the following modifications: 1) Enzyme activation during end repair PCR was performed at 50C for 1 hour. 2) PCR cleanup was performed using 1.8x reaction volume of SPRI beads.  DNA was eluted in a final volume of 10l 0.1xTE buffer and libraries were pooled in equimolar concentration. Purified libraries were sequenced using a NextSeq 500 instrument with a 2x75bp read length.

treatment_protocol: Mice were euthanized with isoflurane and sacrificed using cervical dislocation. Murine hearts were harvested quickly and washed in ice-cold PBS to remove blood. Each AoV was carefully isolated under a microscope. The tissue was than disassociated to optimize VEC isolation with a light digestion buffer. For V5-tagged NFATc1enCre Prox1 GoF CUT&RUN, 4 AoVs were placed in 400l digestion buffer (composed of 2mg/mL collagenase type IV (Worthington Biochemical Corporation), 1.2 U/mL dispase II (Sigma-Aldrich) in Hanks' Balanced Salt Solution (HBSS)) for 20minutes at 37C with rocking. Supernatant was collected and placed in a separate tube. 400l of fresh digestion buffer was added to AoVs and rocked for 20minutes at 37C and the supernatant was collected again. This process was repeated for a total of 3 times. The 1600l of collected supernatant was than filtered using a 40L cell strain and centrifuged at 400g for 10minutes. The supernatant was removed and discarded. The cell pellet was resuspended in 500L ice-cold PBS. The cells were counted using a Bio-Rad TC20 Automated Counter. The H3K27ac CUT&RUN was completed using a similar process, in which 17 control mice were used and 1% trypsin was added to the digestion buffer for the last two 20minute incubations.

value: wildtype

tag: developmental stage

value: aortic valve cells

tag: chip antibody

value: rabbit IGG Cell Signaling Technology 2729


title: Patient 3, NAWM

description:
full_table_counts_QC_normalized.xlsx
3B

tag: tissue

value: bulk sample

value: F


title: Patient_21_D90_Media


title: 4C-seq of Cyp26-E1 in Mus musculus: Rxrα-KO-Cyp26-E1-4C-bait-Rep2

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 24 h


title: Patient_21_D0_Pfsz

value: Peripheral Blood Mononuclear Cells

value: P. falciparum schizonts


title: Patient 3, lesion

description:
full_table_counts_QC_normalized.xlsx
3A


title: WTH3

description: CUT&RUN

tag: strain

tag: genotype

value: H3K27ac Active Motif 39133


title: 4C-seq of Cyp26-E1 in Mus musculus: Rxrα-KO-Cyp26-E1-4C-bait-Rep1

tag: treatment


title: Patient 5, lesion

description:
full_table_counts_QC_normalized.xlsx
5A


title: Patient_21_D0_SEB

value: SEB


title: GoFV5

description: CUT&RUN

source_name: NFATc1enCre Prox1 KI/+ (C57BL/6)

value: NFATc1enCre Prox1 KI/+

value: V5 Invitrogen 46-0705


title: IPSI 24h

value: male

value: Endothelial cells, Astrocytes, Oligodendrocytes, Microglia, Immune cells, Pericytes, Neuronal progenitors

value: IPSI (stroke)


title: Patient 2, lesion

description:
full_table_counts_QC_normalized.xlsx
2A

value: brain

value: M


title: GoFIGG

description: CUT&RUN

value: aortic valve cells

value: mouse IGG Milipore Sigma 12-371


title: X15_5__RNA.islets.13 (8.5 months, Plexxikon)

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the mouse genome mm10 assembly with STAR (version 2.7.0c) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax =10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”). The featureCounts function fron the Bioconductor rsubread package was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (gene annotation: Ensembl release 96).
All subsequent RNA-seq data analysis was performed using the R software (version 4.0.0) and Bioconductor 3.11 packages.
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts.tsv.gz: gzipped text file with tab-separated RNA-seq read counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Ensembl ID, 2.-14. read counts per gene and sample.

source_name: Pancreatic islets

extract_protocol:
Total RNA was extracted using NucleoSpin RNA kit from Macherey Nagel and was quantified and quality-controlled on a Fragment Analyzer instrument.
RNA-seq library preparation (Illumina Truseq stranded kit) was performed at the Genomics Facility Basel of the ETH Zurich, Basel, starting from 80 ng of total RNA. Sequencing was performed on the Illumina NextSeq 500 platform to produce paired-end 38nt reads.

treatment_protocol: Mice were kept on AIN-76A diet. Either as control diet or supplemented with 1200mg PLX5622/kg diet.

value: Pancreatic islets

value: Male

tag: treatment duration

value: 8.5 months

tag: treatment group

value: Plexxikon


title: Patient_21_D0_Media

value: Peripheral Blood Mononuclear Cells

value: Media


title: Patient 4, NAWM

description:
full_table_counts_QC_normalized.xlsx
4B

value: bulk sample


title: 4C-seq of Cyp26-E1 in Mus musculus: Rarα-KO-Cyp26-E1-4C-bait-Rep1

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 24 h


title: Patient 2, NAWM

description:
full_table_counts_QC_normalized.xlsx
2B


title: Patient_21_D90_SEB

value: SEB


title: Patient_25_D150_Pfsz

value: P. falciparum schizonts


title: Patient 4, lesion

description:
full_table_counts_QC_normalized.xlsx
4A


title: X15_4__RNA.islets.12 (8.5 months, Plexxikon)

tag: Sex


title: Patient_25_D150_SEB


title: Patient 1, lesion

description:
full_table_counts_QC_normalized.xlsx
1A


title: 4C-seq of Cyp26-E1 in Mus musculus: WT-Cyp26-E1-4C-bait-Rep1


title: 4C-seq of Cyp26-E1 in Mus musculus: WT-Cyp26-E1-4C-bait-Rep2


title: 4C-seq of Hoxb-E2 in Mus musculus: RARX-DKO-Hoxb-E2-4C-bait-Rep2


title: Patient_25_D150_Media


title: X14_7__RNA.islets.9 (5.5 months, Plexxikon)

value: 5.5 months


title: M74, scRNAseq

city: Beijing

first: Jiawe

last: Chen

state: Beijing

address: Peking university

institute: Peking university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
PBMCs were isolated from human peripheral blood samples. 5 mL fresh peripheral blood was drawn per individual and mixed with 5 mL PBS, and then was gently layered over 5 mL Ficoll (GIBCO, USA) in a Falcon tube. Samples were centrifuged at 400g for 30 min without brake. After centrifugation, PBMCs in the white layer were carefully transferred to a new tube. After being washed with PBS twice, samples were then centrifuged at 400g for 10 min, and the pellets were resuspended with cryopreservation medium (1 mL FBS supplemented with 120 μL DMSO) for long-term storage in liquid nitrogen.
To perform single-cell RNA sequencing (scRNA-seq), thawed PBMCs were captured using the 10X Chromium system (10X Genomics, USA) according to the manufacturer’s protocol. Cells were loaded onto a Chromium Controller Instrument to generate Gel Bead-In-Emulsions (GEM). Afterward, barcoding and complementary DNA (cDNA) libraries were prepared using the Single-Cell 3’ Library and Gel Bead Kit (Cat#120237, 10X Genomics). GEM-reverse transcription (RT) was performed in a Mastercycler Nexus Thermal cycler (Eppendorf), then GEMs were broken. cDNA was cleaned up with Dynabeads MyOne Silane Beads (Thermo Fisher Scientific, USA) and amplified. Amplified cDNA product was then cleaned up using the SPRIselect Reagent Kit (0.6× SPRI, Beckman Coulter). Indexed sequencing libraries were constructed using the Chromium Single-Cell 3’ Library Kit, and subsequently sequenced using an Illumina HiSeq PE150 at Novogene (Beijing, China) with average sequencing depth of >15M reads per cell.

value: Mononuclear cells

value: peripheral blood


title: 4C-seq of Cyp26-E1 in Mus musculus: Rarα-KO-Cyp26-E1-4C-bait-Rep2


title: X14_8__RNA.islets.10 (5.5 months, Plexxikon)


title: Patient_25_D90_SEB


title: M45, scRNAseq

description: 10x Genomics


title: X14_6__RNA.islets.8 (8.5 months, Control)

value: Control


title: X14_5__RNA.islets.7 (8.5 months, Control)


title: Patient_25_D90_Media


title: M66, scRNAseq

description: 10x Genomics


title: 4C-seq of Hoxb-E2 in Mus musculus: Rxrα-KO-Hoxb-E2-4C-bait-Rep2


title: M60, scRNAseq

description: 10x Genomics


title: Patient 1, NAWM

description:
full_table_counts_QC_normalized.xlsx
1B

value: brain

value: M


title: 4C-seq of Hoxb-E2 in Mus musculus: Rxrα-KO-Hoxb-E2-4C-bait-Rep1


title: X15_2__RNA.islets.5 (5.5 months, Plexxikon)

value: Pancreatic islets


title: Patient_25_D0_Pfsz


title: M28, scRNAseq

description: 10x Genomics

value: Male


title: X15_3__RNA.islets.6 (5.5 months, Plexxikon)


title: Patient_23_D90_SEB


title: Patient_25_D90_Pfsz


title: 4C-seq of Hoxb-E2 in Mus musculus: Rarα-KO-Hoxb-E2-4C-bait-Rep2


title: Patient_25_D0_Media


title: Patient_25_D0_SEB


title: Patient_24_D150_Pfsz


title: F65, scRNAseq

description: 10x Genomics

value: Female


title: X15_1__RNA.islets.11 (5.5 months, Plexxikon)

value: Plexxikon


title: M36, scRNAseq

description: 10x Genomics


title: F46, scRNAseq

description: 10x Genomics


title: 4C-seq of Hoxb-E2 in Mus musculus: RARX-DKO-Hoxb-E2-4C-bait-Rep1


title: 4C-seq of Hoxb-E2 in Mus musculus: Rarα-KO-Hoxb-E2-4C-bait-Rep1


title: Patient_24_D150_SEB

value: Peripheral Blood Mononuclear Cells


title: 4C-seq of Hoxb-E2 in Mus musculus: WT-Hoxb-E2-4C-bait-Rep2


title: F60, scRNAseq

description: 10x Genomics


title: F55, scRNAseq

description: 10x Genomics


title: X14_3__RNA.islets.3 (5.5 months, Control)


title: X14_2__RNA.islets.2 (5.5 months, Control)


title: 4C-seq of Hoxb-E2 in Mus musculus: WT-Hoxb-E2-4C-bait-Rep1


title: F77, scRNAseq

description: 10x Genomics


title: X14_1__RNA.islets.1 (5.5 months, Control)


title: X14_4__RNA.islets.4 (5.5 months, Control)


title: Patient_24_D90_Pfsz


title: F66, scRNAseq

description: 10x Genomics


title: 4C-seq of Hoxb-E1 in Mus musculus: RARX-DKO-Hoxb-E1-4C-bait-Rep1


title: Patient_24_D90_SEB


title: 4C-seq of Hoxb-E1 in Mus musculus: Rxrα-KO-Hoxb-E1-4C-bait-Rep1


title: 4C-seq of Hoxb-E1 in Mus musculus: Rxrα-KO-Hoxb-E1-4C-bait-Rep2


title: Patient_24_D90_Media

value: Media


title: F40, scRNAseq

description: 10x Genomics


title: 4C-seq of Hoxb-E1 in Mus musculus: Rarα-KO-Hoxb-E1-4C-bait-Rep1


title: F58, scRNAseq

description: 10x Genomics


title: 4C-seq of Hoxb-E1 in Mus musculus: Rarα-KO-Hoxb-E1-4C-bait-Rep2


title: Patient_24_D0_Pfsz


title: Patient_24_D150_Media


title: 4C-seq of Hoxb-E1 in Mus musculus: RARX-DKO-Hoxb-E1-4C-bait-Rep2


title: Patient_24_D0_SEB


title: 4C-seq of Hoxb-E1 in Mus musculus: WT-Hoxb-E1-4C-bait-Rep1


title: hbca_n24,P41,replicate_1,right,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n24
nuclei samples

value: breast

tag: paper participant_number

tag: assay

value: 10x Genomics 3' V3 nuclei


title: RNA-Seq of Seher-2006 leaves

city: Islamabad

first: Saman

last: Maqbool

address: Shahdra Road

department: Plant Sciences

country: Pakistan

institute: Quaid-i-Azam University, Islamabad

description: RNA-Seq using single end sequencing library

data_processing:
Adapters with unknown bases (N’s > 5%) and low quality were removed from raw reads to produce ‘clean data’ as FastQ data files
High quality single-end reads were mapped to the reference genome of bread wheat
Alignment of the reference sequence with reads was performed
Quantification of the reads was performed using featureCounts software program and differentially expressed genes (DEGs) were identified using DeSEQ2
Assembly: IWGSC, INSDC AssemblyGCA_900519105.1
Supplementary files format and content: tab delimited text files include gene counts of each sample
Supplementary files format and content: tab delimited text files include tpm values of each sample

organism: Triticum aestivum

source_name: leaf

growth_protocol: The wheat seedlings were grown under optimum growth conditions

extract_protocol:
RNA was extracted using EasyPure Plant RNA Kit (ER301-01) following manufacturer instructions
mRNAs were isolated and fragmented from total RNA using the oligo (dT) method for cDNA synthesis. The single-end sequencing libraries were constructed, and sequencing was performed on BGISEQ-500 using standard protocols.

treatment_protocol: No treatment was applied

value: leaf


title: RNA-Seq of Ujala-2016 leaves


title: RNA-Seq of TJ-83 leaves


title: RNA-Seq of Zincol-2016 leaves


title: RNA-Seq of T-9 leaves


title: RNA-Seq of Rawal-87 leaves


title: F47, scRNAseq

description: 10x Genomics


title: 4C-seq of Hoxb-E1 in Mus musculus: WT-Hoxb-E1-4C-bait-Rep2

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 24 h


title: C62_S47

city: Fayetteville

first: Francielly

last: Morena da Silva

state: AR

address: 155 Stadium Dr

institute: University of Arkansas

data_processing:
Sequenced reads were mapped to mm10 mouse genome assembly using STAR 2.7.8a with default parameters.
Aligned reads were quantified for gene counts, filtered to exclude genes  with high noise or a maximum count of less than or equal to 50.
The filtered counts were median ratio normalized and tested for statistical significance using DESeq2.
All steps were performed using the Partek® Flow® Software.
Assembly: mm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Gastrocnemius

extract_protocol:
Gastrocnemius muscles were flash frozen in liquid nitrogen and RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 million Lewis Lung Carcinoma Cells were injected bilaterally in 8-week-old male and female mice. Animals were harvested at 1-, 2-, 3-, 4-weeks of tumor progression. Gastrocnemius was collected and further processed.

value: Skeletal Muscle

tag: conditions

value: High tumor mass >=2g


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-RARX-DKO-H3K27Ac-input2

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to mm10 using Bowtie2(2.3.1)
Peak calling using MACS2(2.2.7.1)
Clean reads of 4C-seq were removed primer using the "demultiplex.py" script in fourCseq and then mapped to mm10 using Bowtie2(2.3.1)
The interactions were identified using R package fourCseq and r3Cseq
Assembly: mm10
Supplementary files format and content: csv files include genes counts values,ChIP signal peaks for each sample,bam file for each  4C-seq sample


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rxrα-KO-H3K27Ac-input2


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-RARX-DKO-H3K27Ac-input1


title: F36, scRNAseq

description: 10x Genomics

tag: cell type

value: Mononuclear cells

value: peripheral blood


title: C60_S44


title: RNA-Seq of Punjab-96 leaves

value: Control


title: RNA-Seq of S-24 leaves


title: RNA-Seq of Sonalika leaves


title: hbca_n21,P40,replicate_1,left,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n21
nuclei samples


title: Patient_24_D0_Media

tag: subject

tag: time


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rxrα-KO-H3K27Ac-input1

tag: cell line


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rarα-KO-H3K27Ac-input2


title: RNA-Seq of Pothowar-70 leaves


title: hbca_n23,P41,replicate_1,left,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n23
nuclei samples


title: RNA-Seq of Pasban-90 leaves


title: hbca_n19,P39,replicate_1,left,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n19
nuclei samples


title: hbca_n22,P40,replicate_1,right,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n22
nuclei samples


title: C48_S23

tag: age


title: RNA-Seq of Parwaz-94 leaves


title: C46_S20


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rarα-KO-H3K27Ac-input1


title: C38_S5


title: C55_S35


title: F30, scRNAseq

description: 10x Genomics


title: C54_S32


title: hbca_n20,P39,replicate_1,right,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n20
nuclei samples


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-H3K27Ac-input2


title: C57_S41

value: Low tumor mass <=1.2g


title: hbca_n15,P24,replicate_1,right,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n15
nuclei samples


title: RNA-Seq of Pak-81 leaves


title: hbca_n14,P23,replicate_1,contra,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n14
nuclei samples


title: C56_S38


title: hbca_n17,P38,replicate_1,left,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n17
nuclei samples


title: RNA-Seq of NARC-2009 leaves


title: hbca_n18,P38,replicate_1,right,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n18
nuclei samples


title: hbca_n16,P59,replicate_1,right,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n16
nuclei samples


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-H3K27Ac-input1


title: C53_S29


title: RNA-Seq of Pak-13 leaves


title: RNA-Seq of Pari-73 leaves


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-RARX-DKO-H3K27Ac-Rep1


title: RNA-Seq of Maxipak-65 leaves


title: RNA-Seq of Inquilab-91 leaves


title: C51_S26


title: ChIP-seq of H3K27Ac in Mus musculus: RA 0 h-H3K27Ac-input1

value: Normal growth condition


title: ChIP-seq of H3K27Ac in Mus musculus: RA 0 h-H3K27Ac-input2


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-RARX-DKO-H3K27Ac-Rep2


title: C44_S17


title: hbca_n13,P22,replicate_1,contra,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n13
nuclei samples


title: RNA-Seq of Hope leaves


title: RNA-Seq of Gabo leaves


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rxrα-KO-H3K27Ac-Rep2


title: hbca_n05,P133,replicate_1,contra,nuclei

description:
S2-100
Read1 26cycles, i7: 8cycles, Read2: 91cycles
hbca_n05
nuclei samples

value: 10x Genomics 3' end V2 nuclei


title: hbca_n12,P135,replicate_1,rm,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 91cycles
hbca_n12
nuclei samples


title: C37_S2


title: hbca_n11,P20,replicate_1,rm,nuclei

description:
S2-100
Read1 28cycles, i7: 8cycles, Read2: 89cycles
hbca_n11
nuclei samples


title: RNA-Seq of Dirk leaves


title: P82, replicate_1, right, frozen tissue OCT, visium

description:
hbca_v10
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 90 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI

library_source: other

data_processing:
Basecalls performed using CASAVA version 1.8.1
Spatial 3' v1 spaceranger-1.2.0 mkfastq
Spatial 3' v1 spaceranger-1.2.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels by area
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: H5

molecule: other

extract_protocol:
visism protocol
from fresh frozen tissue slides using visium

value: Spatial Transcriptomics, 10x visium ST


title: C43_S14


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-H3K27Ac-Rep2


title: C39_S8


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rxrα-KO-H3K27Ac-Rep1


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rarα-KO-H3K27Ac-Rep2


title: RNA-Seq of GA-2002 leaves


title: P85, replicate_1, right, frozen tissue OCT, visium

description:
hbca_v08
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 90 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: ChIP-seq of H3K27Ac in Mus musculus: RA 0 h-H3K27Ac-Rep2


title: RNA-Seq of Chakwal-86 leaves

description: RNA-Seq using single end sequencing library


title: hbca_n04,P37,replicate_1,contra,nuclei

description:
S2-100
Read1 26cycles, i7: 8cycles, Read2: 91cycles
hbca_n04
nuclei samples


title: C33_S61

value: 2-week tumor progression


title: C42_S11


title: P79, replicate_1, left, frozen tissue OCT, visium

description:
hbca_v09
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 90 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: RNA-Seq of Dharabi-2011 leaves


title: ChIP-seq of H3K27Ac in Mus musculus: RA 0 h-H3K27Ac-Rep1


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-Rarα-KO-H3K27Ac-Rep1


title: ChIP-seq of H3K27Ac in Mus musculus: RA 24 h-H3K27Ac-Rep1


title: C31_S57


title: C34_S63


title: P67, replicate_1, right, frozen tissue OCT, visium

description:
hbca_v06
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 90 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: C32_S59


title: P127, replicate_1, right, frozen tissue OCT, visium

description:
hbca_v07
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 90 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-E2-Rep3


title: RNA-Seq of Chakwal-97 leaves


title: RNA-Seq of C-271 leaves


title: P65, replicate_1, right, frozen tissue OCT, visium

description:
hbca_v05
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 90 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: C30_S55


title: RNA-Seq of Chakwal-50 leaves


title: RNA-Seq of C-518 leaves


title: RNA-Seq of C-217 leaves


title: P47, replicate_1, left, frozen tissue OCT, visium

description:
hbca_v04
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 120 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-E2-Rep2


title: C28_S51


title: C29_S53


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-E2-Rep1


title: P46, replicate_1, left, frozen tissue OCT, visium

description:
hbca_v03
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 120 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: P35, replicate_1, contra, frozen tissue OCT, visium

description:
hbca_v02
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 120 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI


title: C20_S46

value: 1-week tumor progression


title: RNA-Seq of Barani leaves+B59:B88


title: C27_S49


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-E1-KO-Rep3


title: RNA-Seq of Zincol-2016 roots

source_name: root

value: root


title: C19_S43


title: RNA-Seq of Ujala-2016 roots


title: P10, replicate_1, contra, frozen tissue OCT, visium

description:
hbca_v01
S2-100
28 cycles read 1, 10 cycles of i7 index,10 cycles of i5 index and 120 cycles read 2
processed data here are just the h5 files other information can be gotten from CZI

value: breast


title: MCF7 cells, glucose starvation, Biol rep4

city: Shenzhen

first: FengFeng

last: Rao

address: 1088 Xueyuan Road

institute: Southern University of Science and Technology

data_processing:
Clean reads were aligned to hg38 using HISAT2.
FeatureCounts was applied to quantify the number of reads mapped to each gene.
Assembly: hg38
Supplementary files format and content: raw_count_rs.csv: Comma-separated values file includes raw count for all the samples.

source_name: MCF7 cells

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Invitrogen TRIzol according to manufacturer's instruction.
1.0 ug of total RNA was used for the construction of sequencing libraries. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: MCF7 cells are seeded on culture plate 2 days prior of experiment. On the day of the experiment, for the fast group, the cells were changed to fresh DMEM complete medium for 4h before treatment to ensure the viability. Then the cells were changed to glucose-free DMEM medium for 4 hours before collection. For the refed group, cells were also changed to fresh DMEM medium for 4h and followed by glucose-free DMEM medium for 4 hours. Then the cells were refed by changing to complete DMEM before collection.

value: MCF7 cells

value: epithelial breast cancer cell line

value: WT

value: Glucose withdraw


title: MCF7 cells, glucose starvation, Biol rep3


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-E1-KO-Rep1

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 24 h


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-Rep3


title: C17_S37

value: Skeletal Muscle


title: RNA-Seq of T-9 roots


title: C18_S40


title: RNA-Seq of Mus musculus: ESCs-Rxrα-OE-Rep2


title: C16_S34


title: MCF7 cells, refeed, Biol rep4

value: Glucose refeed after glucose withdraw


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-E1-KO-Rep2


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-Rep2


title: RNA-Seq of Sonalika roots

value: Control


title: RNA-Seq of Mus musculus: ESCs-WT-Cyp26-Rep1


title: MCF7 cells, glucose starvation, Biol rep1


title: RNA-Seq of Mus musculus: ESCs-Rxrα-OE-Rep1


title: RNA-Seq of Seher-2006 roots


title: MCF7 cells, glucose starvation, Biol rep2


title: C15_S31


title: RNA-Seq of Rawal-87 roots


title: MCF7 cells, refeed, Biol rep3


title: C14_S28


title: RNA-Seq of Mus musculus: ESCs-Rarα-OE-Rep2


title: MCF7 cells, refeed, Biol rep2


title: C13_S25


title: RNA-Seq of Punjab-96 roots


title: MCF7 cells, refeed, Biol rep1


title: RNA-Seq of Pothowar-70 roots


title: MCF7 cells, Fast, Biol rep3

data_processing:
Clean reads were aligned to hg38 using HISAT2.
FeatureCounts was applied to quantify the number of reads mapped to each gene.
Assembly: hg38
Supplementary files format and content: raw_count_cf.csv: Comma-separated values file includes raw count for all the samples.

treatment_protocol: MCF7 cells are seeded on culture plate 2 days prior of experiment. On the day of the experiment, for the control group, the cells were changed to fresh medium and cultured for 4h before collection. For the fast group, cells were also changed to fresh DMEM medium for 4 hours first and then changed to glucose-free DMEM before collection.

value: Glucose withdrawal


title: RNA-Seq of Mus musculus: ESCs-Rarα-OE-Rep1


title: C10_S19


title: RNA-Seq of S-24 roots


title: C11_S22


title: RNA-Seq of Mus musculus: ESCs-V-OE-Rep1


title: RNA-Seq of Mus musculus: ESCs-RARX-DKO-Rep2


title: C9_S16


title: C8_S13


title: MCF7 cells, Fast, Biol rep1


title: RNA-Seq of Pari-73 roots


title: RNA-Seq of Parwaz-94 roots


title: MCF7 cells, Fast, Biol rep2


title: RNA-Seq of Pak-13 roots


title: RNA-Seq of Mus musculus: ESCs-RARX-DKO-Rep1


title: RNA-Seq of Mus musculus: ESCs-Rxrα-KO-Rep2


title: C5_S7


title: RNA-Seq of Pasban-90 roots


title: RNA-Seq of Pak-81 roots


title: RNA-Seq of Mus musculus: ESCs-Rxrα-KO-Rep1


title: RNA-Seq of Mus musculus: ESCs-V-OE-Rep2


title: Copper-exposed female biol rep 3 [AORF-1-12]

city: Le Havre

first: Caroline

last: Arcanjo

address: 25, rue Philippe Lebon

country: France

institute: UMR-I02 SEBIO

description: Cu-F

data_processing:
Reads quality score (Phread score above 30) was accecced with FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (Bolger, A. et al. 2014)
Trimmed sequence reads were aligned against the Eurytemora affinis genome GCA_000591075.2 Eaff_2.0 using STAR (Dobin, A. et al. 2012)
Read count extraction was performed using FeatureCounts (Liao, Y. et al. 2013)
Read count normalization and the differential analysis was perfomed using DESeq2 R package
Assembly: Eaff_2.0
Supplementary files format and content: Tab-delimited text files matrix with gene counts for each samples

organism: Eurytemora affinis

source_name: entire adults

growth_protocol: Copepods were kept under optimal conditions (i.e. 15°C, 15 psu, 18h/6h light-dark cycle) in laboratory prior to exposure

extract_protocol:
Total RNA was extracted with the Quick-RNA Tissue/Insect Microprep Kit (Zymo Research, Mülhauser, Germany) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (Tecan) following manufacturer's protocols.

treatment_protocol: Copepods were exposed 72h to 25 µg/L of copper by balneation (15°C, 15 psu, acidified water 0,2%). Water (15°C, 15 psu) for the control condition was also acidified (0,02%)

value: entire adults

value: female

tag: exposure time

tag: developmental stage

value: adult

value: Cu 25 µg/L


title: MCF7 cells, Ctrl, Biol rep2


title: MCF7 cells, Ctrl, Biol rep3


title: MCF7 cells, Ctrl, Biol rep1


title: RNA-Seq of NARC-2009 roots

tag: tissue


title: C6_S10


title: C2_S1


title: RNA-Seq of Inquilab-91 roots


title: RNA-Seq of Mus musculus: ESCs-Rarα-KO-Rep2


title: RNA-Seq of Maxipak-65 roots


title: RNA-Seq of Mus musculus: ESCs-Rarα-KO-Rep1


title: RNA-Seq of Gabo roots


title: C9_3

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
clean data were mapped to mouse genome mm10 by hisat2
reads count per gene is caculated by featurecount
Assembly: mm10
Supplementary files format and content: gene annotation with reads count

source_name: Cortex

extract_protocol:
Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol.

value: Cortex

tag: strain

value: C9orf72+/-;C9-BAC with AAV-C9orf72


title: RNA-Seq of Mus musculus: ESCs-WT-RARX-Rep2


title: Copper-exposed female biol rep 1 [AORF-1-10]

description: Cu-F


title: Liver_C57Bl6/J_THRB-KO_sample5

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  SOAPnuke
Trimmed sequence reads were mapped to GRCm38/mm10 (Ensembl release 102) using HISAT2 v2.2.1, default options
Read count extraction were performed using Htseq-count v0.9.1 and Ensembl annotation GRCm38 /mm10 – release 102, options : -s no -f bam -m union -a 10 --nonunique none
Count normalization and Differential expression was performed using EdgeR v3.36.0 (using Galaxy Europe Interface), options : filter lowly expressed genes ( 1cpm in at least 5 samples), adjustement method= Benjamini-Hochberg, nomalization method = TMM, Robust=True
Assembly: Mm10
Supplementary files format and content: tab-delimited text files include Ensembl IDs and count values for each Sample
Supplementary files format and content: Differential expression Matrix table obtained from EdgeR (output from EdgeR ; "DE_Thrb-KO_WT.tabular" file)

source_name: Liver

growth_protocol: Mice were housed in standard cages in a temperature-controlled room (22–24°C) with a 12-h dark–light cycle. They had ad libitum access to tap water and standard chow.

extract_protocol:
Liver RNA was harvested using Nucleospin RNA kit (Macherey Nagel)
RNA libraries for RNA-seq were prepared by BGI platform (DNBSEQ stranded mRNA library)

value: Liver

tag: genotype

value: Liver-specificTHRBKO


title: Liver_C57Bl6/J_THRB-KO_sample4


title: C4_S4


title: PDAC macrophages (Flt3_YFPnegative)

city: St. Louis

first: David

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

data_processing:
The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50,000 mean reads per cell. Cellranger mkfastq pipeline (10X Genomics) was used to demultiplex illumina base call files to FASTQ files. Afterward, fastq files from each sample were processed with Cellranger counts and aligned to the mouse mm10 reference genome (Cellranger v.4.0.0, 10X Genomics, mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) to generate feature barcode matrix.
Genome_build: mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Mouse pancreas macrophages

extract_protocol:
Mice were sacrificed by cardiac perfusion with ~10-15mL PBS-heparin under isofluorane anesthesia. Pancreas or tumor tissue was then isolated, minced with scissors, and digested in ~15-25mL Dulbecco’s Modified Eagle Medium (DMEM) with 2mg/mL Collagenase A and 1x DNase I for either 15 minutes (steady-state pancreas and cerulein treated pancreas) or 25 minutes (tumor tissue) at 37°C with constant stirring. Digestion buffer was quenched with 3mL fetal bovine serum (FBS) and filtered through 100uM Nylon mesh, pelleted by centrifugation (2000rmp for 5 min) and resuspended in FACS buffer (1% BSA in PBS). Cells were then resuspended in FACS Buffer containing CD16/CD32 antibodies to block for 10 minutes on ice, pelleted by centrifugation, then resuspended in fluorophore-conjugated antibodies, stained for 25 minutes on ice, then washed with FACS Buffer. Cells were then immediately sorted on Aria-II (BD Biosciences).  For homeostatic pancreas, pancreatitis, and pancreatic tumors, live macrophages (CD45+CD11b+CD3-CD19-B220-SiglecF-Ly6G-Ly6C-7AAD-F4/80+MHCIIHI/Lo) were sorted. After cells were sorted into FACS Buffer, they were pelleted by centrifugation, resuspended in 0.04% BSA in PBS, and cell counts were obtained.
Single-cell RNA-sequencing library preparation was then conducted by the Genome Technology Access Center at Washington University. Briefly, cells from each sample were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’v3 Reagent kits according to the manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).

treatment_protocol: For steady-state samples, no treatment was done. For pancreatitis samples, mice were treated with by administering 6 hourly intraperitoneal injections (i.e. once per hour for six hours) of cerulein at a dose of 100ug/kg given every other day for one week. For PDAC samples, orthotopic pancreas KPC tumor models were established by implanting mice with 100,000 KPC-1 cells in 5uL serum-free DME/F-12 and 45uL Cultrex (Trevigen) by injecting cells directly into the pancreas.

value: Flt3-Cre;LSL-YFP (C57BL/6)

value: pancreas

value: macrophages

tag: cell subset

value: YFP-negative macrophage

tag: disease state

value: Pancreatic ductal adenocarcinomas (PDAC)


title: Copper-exposed female biol rep 2 [AORF-1-11]

description: Cu-F

tag: treatment


title: Copper-exposed male biol rep 3 [AORF-1-9]

description: Cu-M

tag: Sex

value: male


title: Copper-exposed male biol rep 2 [AORF-1-8]

description: Cu-M


title: RNA-Seq of Dirk roots

value: root


title: RNA-Seq of GA-2002 roots

value: Control


title: Copper-exposed male biol rep 1 [AORF-1-7]

description: Cu-M


title: Liver_C57Bl6/J_THRB-KO_sample3


title: PDAC macrophages (Flt3_YFPpositive)

value: YFP-positive macrophage


title: Liver_C57Bl6/J_THRB-KO_sample2


title: RNA-Seq of Chakwal-97 roots


title: Liver_C57Bl6/J_THRB-KO_sample1


title: Control female biol rep 2 [AORF-1-5]

description: Ctrl-Cu-F

value: entire adults

value: control


title: Control female biol rep 3 [AORF-1-6]

description: Ctrl-Cu-F

value: female

value: adult


title: RNA-Seq of Mus musculus: ESCs-WT-RARX-Rep1

source_name: Embryonic stem cell

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 24 h


title: Liver_C57Bl6/J_WT_sample5

value: Liver

value: WT


title: Control female biol rep 1 [AORF-1-4]

description: Ctrl-Cu-F


title: Pancreatitis macrophages (Flt3_YFPnegative)

value: Flt3-Cre;LSL-YFP (C57BL/6)

value: Pancreatitis


title: Liver_C57Bl6/J_WT_sample4


title: Steady-state pancreas macrophages (Flt3_YFPpositive)

value: pancreas

value: macrophages

value: Steady-state


title: Pancreatitis macrophages (Flt3_YFPpositive)


title: RNA-Seq of Chakwal-50 roots


title: RNA-Seq of C-271 roots


title: Liver_C57Bl6/J_WT_sample2


title: RNA-Seq of C-217 roots


title: Liver_C57Bl6/J_WT_sample3


title: RNA-Seq of C-518 roots


title: Control male biol rep 3 [AORF-1-3]

description: Ctrl-Cu-M

value: male


title: Control male biol rep 2 [AORF-1-2]

description: Ctrl-Cu-M


title: RNA-Seq of Dharabi-2011 roots

value: root


title: Liver_C57Bl6/J_WT_sample1


title: RNA-Seq of Chakwal-86 roots

value: Control


title: RNA-Seq of Barani roots


title: Control male biol rep 1 [AORF-1-1]

description: Ctrl-Cu-M


title: CAVD_5

status: Public on Jun 28 2023

city: Jinan

first: guo

last: chenghu

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

description: ZFR

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRnor_6.0.100 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: human GRCh38

source_name: Aortic valve

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Aortic valve

value: Disease


title: non_CAVD_2

description: LGQ


title: non_CAVD_3

description: RGM


title: non_CAVD_4

description: ZMY


title: CAVD_4

description: LCL


title: non_CAVD_1

description: YJP


title: CAVD_2

description: FSH


title: CAVD_1

description: LHY


title: Tg-3 C

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

country: Germany

institute: Universitätsklinikum Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fastq version 2.19.1.
For adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_04 was used.
Trimmed read sequences were aligned with STAR version 2.5.4a
Read counting for exonic regions was performed with subread featureCounts version 2.0.0.
Assembly: Rnor6
Supplementary files format and content: subread featureCounts tab-separated, per-gene raw counts

organism: Rattus norvegicus

source_name: colon

extract_protocol: NEBNext Ultra II Directional RNA, NEBNext Poly(A) mRNA Magnetic Isolation

value: colon

value: 3 months

value: colon epithelial

value: transgenic


title: Tg-1 C


title: WT-2 Ab

value: wild type

value: antibiotics


title: WT-2 C


title: Tg-2 C


title: WT-1 Ab


title: Tg-1 Ab


title: WT-1 C


title: Tg-2 Ab


title: WT-3 C


title: Tg-3 Ab


title: WT-3 Ab


title: Steady-state pancreas macrophages (Flt3_YFPnegative)

value: YFP-negative macrophage


title: SF3B1_DMSO_r3

city: Philadelphia

first: Peter

middle: S

last: Klein

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania School of Medicine

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq were converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification
Fastq files were counted against transcripts defined in Gencode v35 using Salmon.
Assembly: Gencode v35, built against GRCh38
Supplementary files format and content: Ensembl gene IDs with raw counts for each sample - comma separated values

source_name: cell line

growth_protocol: K562 cells were cultured in IMDM supplemented with 10% FBS.

extract_protocol:
RNeasy/DNaseI/RNeasy/polyA selection
NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: Cells were treated with DMSO or 3uM Chir99021 for 24 hours.

value: cell line

value: leukemia

value: SF3B1-K700E/wt knockin

value: CHIR


title: SRSF2_CHIR_r3


title: SRSF2_DMSO_r3

value: vehicle


title: PA_DMSO_r3


title: SF3B1_CHIR_r3


title: SF3B1_CHIR_r2

value: SRSF2-P95H/wt knockin


title: PA_CHIR_r3


title: CAVD_3

description: LXH


title: SF3B1_DMSO_r2


title: SRSF2_CHIR_r1

value: parental K562 cells


title: PA_CHIR_r2


title: PA_DMSO_r2


title: SF3B1_CHIR_r1


title: SRSF2_DMSO_r2


title: SF3B1_DMSO_r1


title: SRSF2_DMSO_r1


title: PA_DMSO_r1


title: PA_CHIR_r1


title: CLS085_popD_VDJ

city: Atlanta

first: Frances

middle: Eun-Hyung

last: Lee

state: GA

address: 615 Michael Street, Suite 205

department: Department of Medicine

institute: Emory University

description:
10x Genomics
B cell receptor

data_processing:
Analysis of single cell VDJ data was conducted using Cellranger v3.1.0 via the 10x Genomics cloud interface and an in-house developed informatics pipeline for clonal clustering and SHM analysis
Fasta files from the Cellranger output were annotated with metadata and aligned to germline sequences using the IMGT/HighV-QUEST web portal. All data from IMGT/HighV-QUEST were retained through the process and were used for mutation calculations and alignment analyses
Assembly: GRCh38
Supplementary files format and content: Single cell  BCR sequencing data for each sample were saved in a csv file, which is generated by 'cellranger vdj' function and in-house pipeline.
Library strategy: scVDJ-seq

source_name: Human Bone Marrow

extract_protocol:
Bone marrow aspirate was obtained under sterile conditions from the iliac crest from each of the 5 healthy adults. Mononuclear cells were isolated by Ficoll density gradient centrifugation and enriched by a custom-designed negative selection EasySep cell isolation kit from StemCell that removes CD66b+/GPA+/CD3+/CD14+ cells to limit sorting time of fragile BM ASC. Enriched mononuclear cells were stained with the following anti-human antibodies: IgD–FITC (Cat. no. 555778; BD Biosciences), CD3-BV711 (Cat. no. 317328; BioLegend), CD14-BV711 (Cat. no. 301838; BioLegend), CD19-PE-Cy7 (Cat. no. 560911; BD Biosciences), CD38-V450 (Cat. no. 561378; BD Biosciences), CD138-APC (Cat. no. 130-117-395; Miltenyi Biotech), CD27-APC-e780 (Cat. no. 5016160; eBiosciences), and LiveDead (L34966; Invitrogen). ASC subsets were FACS-sorted on a BD FACSAria II using a standardized sorting procedure with rainbow calibration particles to ensure consistency of sorts between individuals. ASC subsets were sorted as: popA (CD19+CD38hiCD138-), popB (CD19+CD38hiCD138+) and popD (CD19-CD38hiCD138-)
Cells were counted using a Bio-Rad TC10 cell counter and verified via hemocytometer. Cell numbers were adjusted to 1,000 cells per μl to allow for 10,000 single cells per sample loaded in the 10x Genomics Chromium device. The manufacturer’s standard protocol for Chromium Next GEM Single Cell 5’ Reagent Kit, v2 and Chromium Single Cell Human BCR Amplification kit was used to generate libraries. Libraries were sequenced on an Illumina NovaSeq (paired-end; 2 × 150 bp; read 1:26 cycles; i7 index: 8 cycles, i5 index: 0 cycles; read 2: 98 cycles) such that more than 70% saturation could be achieved with a sequence depth of 5,000 reads per cell for VDJ libraries

value: Pop D

value: Human Bone Marrow

tag: donor

value: healthy


title: CLS085_popB_VDJ

description:
10x Genomics
B cell receptor

value: Pop B


title: CLS085_popA_VDJ

description:
10x Genomics
B cell receptor

value: Pop A


title: CLS084_popA_VDJ

description:
10x Genomics
B cell receptor


title: CLS084_popB_VDJ

description:
10x Genomics
B cell receptor


title: CLS055_popD_VDJ

description:
10x Genomics
B cell receptor


title: CLS058_popB_VDJ

description:
10x Genomics
B cell receptor


title: CLS058_popA_VDJ

description:
10x Genomics
B cell receptor


title: CLS055_popB_VDJ

description:
10x Genomics
B cell receptor


title: CLS085_popD_GEX

description: 10x Genomics

data_processing:
The 10x Genomics single-cell transcriptomic sequenced raw reads were aligned to GRCh38 reference and quantified per cell barcode using Cellranger v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)
Genes expressed in at least 0.1% - 0.3% (depending on the sample size) of the total cell population were regarded as expressed genes and retained for downstream analysis
To filter low-quality cells, we excluded cells with greater or equal than 30% of their UMIs coming from mitochondrial genes, or less than 800 total number of detected genes, or less than total number of UMIs 1000
Moreover, we removed cells with total number of genes or UMIs greater or equal than 6,000 or 60,000, respectively, to control for potential doublets.
Assembly: GRCh38
Supplementary files format and content: Each scRNA-seq sample contains a .h5 file including Gene Expression profile.

extract_protocol:
Bone marrow aspirate was obtained under sterile conditions from the iliac crest from each of the 5 healthy adults. Mononuclear cells were isolated by Ficoll density gradient centrifugation and enriched by a custom-designed negative selection EasySep cell isolation kit from StemCell that removes CD66b+/GPA+/CD3+/CD14+ cells to limit sorting time of fragile BM ASC. Enriched mononuclear cells were stained with the following anti-human antibodies: IgD–FITC (Cat. no. 555778; BD Biosciences), CD3-BV711 (Cat. no. 317328; BioLegend), CD14-BV711 (Cat. no. 301838; BioLegend), CD19-PE-Cy7 (Cat. no. 560911; BD Biosciences), CD38-V450 (Cat. no. 561378; BD Biosciences), CD138-APC (Cat. no. 130-117-395; Miltenyi Biotech), CD27-APC-e780 (Cat. no. 5016160; eBiosciences), and LiveDead (L34966; Invitrogen). ASC subsets were FACS-sorted on a BD FACSAria II using a standardized sorting procedure with rainbow calibration particles to ensure consistency of sorts between individuals. ASC subsets were sorted as: popA (CD19+CD38hiCD138-), popB (CD19+CD38hiCD138+) and popD (CD19-CD38hiCD138-)
FACS-sorted cells were kept on ice until proceeding with 10x Genomics processing. Cells were centrifuged at 500xg for 10 minutes at 4C to remove media. Cells were then washed twice in 0.04% BSA in PBS. During last wash, media was aspirated and cell volume was measured using a pipette. The whole sample was then taken for processing using the 10x Genomics 5’ v1 Single Cell platform. V(D)J and 5’ Gene Expression (GEX) libraries were constructed for each sample, following 10x Genomics protocol. QC for each library was performed at each step by Bioanalyzer. Final libraries were quantified by kappa qPCR and sequenced on a NovaSeq.


title: CLS028_popA_VDJ

description:
10x Genomics
B cell receptor


title: CLS055_popA_VDJ

description:
10x Genomics
B cell receptor


title: CLS028_popD_VDJ

description:
10x Genomics
B cell receptor


title: CLS085_popB_GEX

description: 10x Genomics


title: SRSF2_CHIR_r2


title: CLS028_popB_VDJ

description:
10x Genomics
B cell receptor


title: CLS085_popA_GEX

description: 10x Genomics


title: CLS084_popD_GEX

description: 10x Genomics


title: CLS084_popB_GEX

description: 10x Genomics


title: CLS084_popA_GEX

description: 10x Genomics


title: CLS058_popD_VDJ

description:
10x Genomics
B cell receptor


title: CLS058_popB_GEX

description: 10x Genomics


title: CLS058_popA_GEX

description: 10x Genomics


title: CLS055_popD_GEX

description: 10x Genomics


title: CLS084_popD_VDJ

description:
10x Genomics
B cell receptor


title: CLS028_popD_GEX

description: 10x Genomics


title: CLS028_popA_GEX

description: 10x Genomics


title: shNT, 3

city: Helsinki

first: Juuso

last: Taskinen

address: Tukholmankatu 8

country: Finland

institute: Minerva Foundation Institue for Medical Research

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Pair ended reads were clipped with Triommatic (phred >= 30)
Aligned to the human genome with STAR
reads were counted using HTSeq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include non-normalized transcript counts

source_name: Primary cell

growth_protocol: P6 HUVECs grown in media with lentiviral particles at aproximately 30 MOI containing two different VAPA shRNAs one VAPB shRNA or non-targeting shRNA

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
NEB Next Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions

treatment_protocol: Cells were treated for 48 h with lentiviral particles and then selected with 2.5 ug/mL of puromycin for 72 h

value: Primary cell

value: Human umbilical vein endothelial cell

value: shRNA non-targeting


title: shVAPAB, 3

value: shRNA VAPA/B


title: shVAPAB, 2


title: shNT, 1


title: CLS028_popB_GEX

description: 10x Genomics


title: shNT, 4


title: shVAPAB, 4


title: SAS, AQ-ac1M, 0h rep2

city: Kitakyushu

first: Shigeori

last: Takenaka

state: Fukuoka

address: 1-1 Sensui-cho, Tobataku

department: Department of Applied Chemistry

country: Japan

institute: Kyushu Institute of Technology

data_processing:
The run data were demultiplexed and converted to FASTQ files using Illumina’s bcl2fastq2 Conversion Software (v2.20)
The RNA-Seq analysis was performed according to ENCODE4 Uniform Processing bulk RNA-seq pipeline　(https://www.encodeproject.org/pipelines/ENCPL002LPE/), with some customizations for this data.
FASTQ raw sequencing files were preprocessed using RabbitQC to remove the adapter contamination and poor quality sequences.
FASTQ files were mapped to the human reference genome GRCh38 using the RNA-seq aligner STAR.
Gene counts were calculated using HTSeq
Assembly: GRCh38/GENCODE v29
Supplementary files format and content: tab-delimited text files include read counts

source_name: tongue

growth_protocol: The cells were maintained in the Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
The total RNA of the cells were extracted using NucleoSpin RNA (Takara Bio, Shiga, Japan) according to the manufacture’s protocol.
The cDNAs were prepared by the SMART (Switching Mechanism At 5'End of RNA Template) method.

treatment_protocol: SAS cells at 70% confluence were incubated in the presence or absence of cAQ-mBen or AQ-Ac at the concentrations of 1 and 5 µM for 6 or 24 h

value: tongue

value: SAS

value: Squamous cell carcinoma

value: WT

value: treated with 1 M AQ-ac for 0 hours


title: SAS, cAQ-mBen5M, 24h rep2

value: treated with 5 M cAQ-mBen for 24 hours


title: SAS, AQ-ac1M, 24h rep2

value: treated with 1 M AQ-ac for 24 hours


title: SAS, cAQ-mBen1M, 0h rep2

value: treated with 1 M cAQ-mBen for 0 hours


title: SAS, control, 24h rep2

value: no treated for 24 hours


title: SAS, control, 0h rep2

value: no treated for 0 hours


title: SAS, AQ-ac1M, 24h rep1


title: CLS058_popD_GEX

description: 10x Genomics

value: Pop D

value: Human Bone Marrow

value: healthy


title: SAS, control, 24h rep1


title: CLS055_popB_GEX

description: 10x Genomics

value: Pop B


title: CLS055_popA_GEX

description: 10x Genomics

value: Pop A


title: shVAPAB, 1

value: Primary cell

value: Human umbilical vein endothelial cell


title: C68 day13 6uM CHIR99021_rep 2

city: Aurora

first: Kunhua

last: Song

state: Colorado

institute: University of Colorado Anschutz Medical Campus

description: RNA-seq_counts_normalized_64_human_by_gene_with_ID.xlsx

data_processing:
FastQC was used for the raw RNA-seq reads for the control of sequence quality, GC content, the presence of adaptor sequences and duplicated reads and ensure homogeneity of sequencing reads between samples.
Reads that passed quality control were aligned to NCBI GRCh38 human reference genome or GRCm38/mm10 mouse reference genome using the splice-aware STAR aligner v2.7.
The read counts were generated from the aligned reads with featureCounts function in the RsubRead package.
The read counts were normalized with DESeq2 R package.
Assembly: NCBI GRCh38 or GRCm38/mm10
Supplementary files format and content: Excel files include normalized RPKM values for each sample

extract_protocol:
Total RNA from cells or mouse tissues was isolated by using TRIzol reagent (Invitrogen) according to manufacturer’s instructions. 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by BGI Genomics or Novogene Corporation.

value: induced pluripotent stem cell derived cell

tag: human cells derived from

value: healthy control

value: Disomy 21

value: Mono-layer cardiac differentiation

tag: agent

value: 6uM CHIR99021


title: SAS, AQ-ac1M, 0h rep1

value: tongue

value: SAS

tag: cell type

value: Squamous cell carcinoma

value: WT

value: treated with 1 M AQ-ac for 0 hours


title: SAS, cAQ-mBen5M, 24h rep1

value: treated with 5 M cAQ-mBen for 24 hours


title: D49 day7 10uM CHIR99021_rep 3

value: patient with Down syndrome as well as congenital heart defects

value: Trisomy 21


title: D7 day13 6uM CHIR99021_rep 2


title: SAS, cAQ-mBen1M, 24h rep2

value: treated with 1 M cAQ-mBen for 24 hours


title: SAS, cAQ-mBen5M, 0h rep1

value: treated with 5 M cAQ-mBen for 0 hours


title: D7 day7 10uM CHIR99021_rep 3


title: C68 day7 6uM CHIR99021_rep 3


title: D7 day7 10uM CHIR99021_rep 2


title: shNT, 2

value: Primary cell

value: shRNA non-targeting


title: C62 day13 6uM CHIR99021_rep 2

value: induced pluripotent stem cell derived cell


title: SAS, control, 0h rep1

value: no treated for 0 hours


title: SAS, cAQ-mBen1M, 24h rep1


title: D49 day13 6uM CHIR99021_rep 2


title: C68 day7 10uM CHIR99021_rep 2

value: healthy control

value: Disomy 21


title: C68 day7 10uM CHIR99021_rep 3

value: Mono-layer cardiac differentiation


title: D7 day7 6uM CHIR99021_rep 2

value: 6uM CHIR99021


title: D49 day7 6uM CHIR99021_rep 2


title: SAS, cAQ-mBen5M, 0h rep2

value: tongue

value: SAS


title: FL_CS16_and_W9

city: Lund

first: Charlotta

last: Böiers

state: Lund

address: BMC B12

institute: Lund University,

description: CITEseq

data_processing:
Library strategy: CITE-seq
Libraries were processed using Cellranger version 3.0.2 to generate the count matrices. The count matrices were demultiplexed into individual samples based on HTO UMIs. Cells that had minimum 50% reads from one of the HTO were assigned to that corresponding sample.
Genome_build: hg38
Supplementary_files_format_and_content: The count matrices were saved in MTX format along with Barcodes (TSV format file) and gene names (TSV format file). For each sample, for three files were zipped together and deposited in GEO

source_name: Fetal liver CS16 and W9

extract_protocol:
For CITE-seq; cell were stained with CITEseq antibodies, sorted and 10x genomics 3' RNA was performed.
Libaries were prepered according to 10x genomics 3’ V2 kit with the addition of CITEseq protocol. Libraries were sequenced on a Illumina Nextseq or Illumina Novaseq6000.

value: fetal liver

tag: cell population

value: FACS sorted

tag: molecule subtype

value: 3' RNA+epitope


title: C62 day7 10uM CHIR99021_rep 3

tag: cell line

tag: time


title: D49 day7 10uM CHIR99021_rep 2

value: patient with Down syndrome as well as congenital heart defects


title: D49 day7 6uM CHIR99021_rep 3

value: Trisomy 21


title: SAS, cAQ-mBen1M, 0h rep1

value: Squamous cell carcinoma

value: WT

value: treated with 1 M cAQ-mBen for 0 hours


title: FL1_hpc

description: CITEseq

source_name: Fetal Liver CS22 sample1


title: C62 day7 10uM CHIR99021_rep 2


title: FL2_hpc

description: CITEseq

source_name: Fetal Liver CS22 sample2


title: D49_Day 13 6uM CHIR99021_1uM JAKi-3

description: RNA-seq_counts_normalized_18_human_day_13_by_gene.xlsx

value: 6uM CHIR99021_1uM JAKi

value: day 13


title: D49_Day 13 6uM CHIR99021_1uM JAKi-2

value: induced pluripotent stem cell derived cell


title: D49_Day 13 6uM CHIR99021_1uM JAKi-1


title: C62 day7 6uM CHIR99021_rep 2

value: healthy control


title: C62 day7 6uM CHIR99021_rep 3

value: Disomy 21


title: D49_Day 13 6uM CHIR99021_DMSO-1

value: Mono-layer cardiac differentiation

value: 6uM CHIR99021_DMSO


title: D49_Day 13 6uM CHIR99021_DMSO-2


title: C68 day7 6uM CHIR99021_rep 2

value: 6uM CHIR99021


title: D49_Day 13 6uM CHIR99021_DMSO-3


title: C68_Day 13 6uM CHIR99021_DMSO-1


title: D7_Day 13 6uM CHIR99021_1uM JAKi-2


title: D7 day7 6uM CHIR99021_rep 3


title: D7_Day 13 6uM CHIR99021_1uM JAKi-3


title: D7_Day 13 6uM CHIR99021_DMSO-1


title: C62_Day 13 6uM CHIR99021_DMSO-3


title: C62_Day 13 6uM CHIR99021_DMSO-2


title: C62_Day 13 6uM CHIR99021_DMSO-1


title: C68_Day 13 6uM CHIR99021_DMSO-3


title: D7_Day 13 6uM CHIR99021_DMSO-3


title: D7_Day 13 6uM CHIR99021_1uM JAKi-1


title: D7_Day 13 6uM CHIR99021_DMSO-2


title: D7 Day13 10uM CHIR99021


title: D49 Day13 10uM CHIR99021


title: D7 Day7 10uM CHIR99021


title: D49 Day3 10uM CHIR99021


title: D49 Day7 10uM CHIR99021


title: D49 Day2 10uM CHIR99021


title: C68_Day 13 6uM CHIR99021_DMSO-2


title: C68 Day13 6uM CHIR99021


title: D7 Day5 10uM CHIR99021


title: D49 Day13 6uM CHIR99021


title: D49 Day5 10uM CHIR99021


title: D7 Day1 10uM CHIR99021


title: D49 Day1 10uM CHIR99021


title: D7 Day13 6uM CHIR99021


title: D7 Day2 10uM CHIR99021


title: D49 Day7 6uM CHIR99021


title: C62 Day7 6uM CHIR99021


title: C62 Day13 6uM CHIR99021


title: D7 Day3 6uM CHIR99021


title: C68 Day7 6uM CHIR99021


title: D7 Day7 6uM CHIR99021


title: C62 Day2 6uM CHIR99021


title: C62 Day3 6uM CHIR99021


title: D49 Day0 6uM CHIR99021


title: C68 Day0 6uM CHIR99021


title: D49 Day5 6uM CHIR99021


title: C68 Day5 6uM CHIR99021


title: D7 Day5 6uM CHIR99021


title: C68 hiPSC

value: induced pluripotent stem cell


title: C62 Day5 6uM CHIR99021


title: C68 Day3 6uM CHIR99021


title: C68 Day2 6uM CHIR99021


title: D7 Day3 10uM CHIR99021


title: 4-hTSC-si-set8-48h

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

data_processing:
Zebracall software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Tophat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: hg38

source_name: humen TSC

growth_protocol: Advanced DMEM/F12 supplemented with 0.1mM 2-mercaptoethanol, 0.2% FBS, 1% ITS-X supplement, 0.3% BSA, 0.5% Penicillin -Streptomycin, 1.5 μg/ml L-ascorbic acid, 0.5 μM A83-01, 50 ng/ml EGF, 1μM SB431542, 2 μM CHIR99021, 5 μM Y27632 and 0.8 mM VPA

extract_protocol:
hTSCs were harvested  and extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hTSCs were treated with or without siRNA against PR-SET7 for 48h

tag: age

value: trophoblast stem cells

value: Set8 ko


title: D49 Day2 6uM CHIR99021


title: D49 Day3 6uM CHIR99021


title: D49 Day1 6uM CHIR99021


title: D7 hiPSC


title: C68 Day1 6uM CHIR99021


title: 1-hTSC-si-NC


title: D7 Day2 6uM CHIR99021


title: C62 Day1 6uM CHIR99021


title: D7 Day1 6uM CHIR99021


title: D7 Day0 6uM CHIR99021


title: D49 hiPSC


title: C62 Day0 6uM CHIR99021


title: C62 hiPSC


title: 3-hTSC-si-NC


title: 2-hTSC-si-set8-48h


title: Control parasite line at schizont stage Replicate 3

type: RNA

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

institute: University of South Florida

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_4.txt
Biological replicate 3 of 3. Control malaria parasite, untreated, harvested at schizont stage.

hyb_protocol: Hybridization was performed by Genomics Core Facility of Pennsylvania State University according to the manufacturer’s instructions (Agilent).

scan_protocol: Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in DNASTAR software-ArrayStar 11 (dnastar.com).

organism: Plasmodium falciparum

source_name: wildtype malaria parasite

label_protocol: Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Amplify 1ug of each sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit. Dye couple 15 ug of aRNA with Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions.(AM1753).

growth_protocol: P. falciparum parasites were maintained as described previously (Trager and Jensen, 1976)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Schizont stage (46h)

value: wildtype


title: PfPRMT5 knockout parasite line at late trophozoite stage Replicate 3

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_3.txt
Biological replicate 3 of 3. PfPRMT5 KO malaria parasite, harvested at late trophozoite stage.

source_name: PfPRMT5 KO malaria parasite

value: Late trophozoite stage (36h)

value: PfPRMT5 KO


title: Control parasite line at late trophozoite stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_3.txt
Biological replicate 2 of 3. Control malaria parasite, untreated, harvested at late trophozoite stage.


title: Control parasite line at schizont stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_4.txt
Biological replicate 2 of 3. Control malaria parasite, untreated, harvested at schizont stage.


title: PfPRMT5 knockout parasite line at schizont stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_4.txt
Biological replicate 1 of 3. PfPRMT5 KO malaria parasite, harvested at schizont stage.


title: Patient 8 Slide E19 ROI 016

city: Seattle

first: Rich

middle: A

last: Klinghoffer

state: WA

address: 530 Fairview Ave N

institute: Presage Biosciences

scan_protocol: Nanostring GeoMx Digital Spatial Profiling (DSP) Platform

data_processing: Raw probe level counts from the NanoString DSP machine were subjected to QC and normalization as follows. ROIs with deduplicated read counts of <10,000 were excluded. Count data was then normalized using TMM normalization(26) prior to performing limma analysis

source_name: head and neck carcinoma

label_protocol: Nanostring

extract_protocol: Tissue sections were baked, deparaffinized, washed in PBS, and targets were retrieved for 20 minutes in 1x Tris-EDTA pH 9.0 buffer (Invitrogen #00-4956-58) at 100 °C. Next, tissues were washed in PBS, incubated in 0.1 μg/ml proteinase K (Thermo Fisher Scientific, #AM2546) in PBS for 15 minutes at 37 °C and washed again in PBS. Protein targets were post-fixed in 10% neutral-buffered formalin for 5 minutes, followed by two 5-minute incubations in 12.25 mg/ml Tris base, 7.5 mg/ml Glycine stop buffer diluted in DEPC-treated water. Tissues were incubated overnight at 37 °C with hybridization solution (Human Cancer Transcriptome Atlas probe mix (NanoString #121400101), Buffer R (NanoString #121300313), and DEPC-treated water). During incubation, slides were covered with HybriSlip hybridization covers (Grace BioLabs #714022). After incubation, HybriSlip covers were gently removed by soaking in 2x SSC buffer. Two 25 minute stringent washes were performed using 50% formamide in 2x SSC at 37 °C. Tissues were washed for 5 minutes in 2× SSC and incubated in blocking buffer W (NanoString #121300313) for 30 minutes at room temperature in a humidity chamber. Primary antibody targeted against MIL113 was diluted in buffer W and incubated with the tissues for 1 hour followed by a 1 hour incubation with fluorescently-labeled secondary antibody diluted in buffer W. After the slides were washed twice for 5 minutes in 5x SSC buffer they were incubated for 1 hour in SYTO13 (50 nM) and fluorescently conjugated antibody targeting PanCK in blocking  8  buffer. Following staining the sections were washed for 5 minutes in fresh 2x SSC. Following whole slide imaging, multiple geometric ROIs of 400 μm2 were placed in regions of subasumstat drug exposure according to MIL113 signal intensity and regions of vehicle or background. Indexing oligonucleotides were then cleaved and quantified via next gen sequencing on a NovaSeq 6000 Illumina sequencer as previously described(25)

value: head and neck carcinoma

tag: gender

value: Male

tag: anatomical location

value: Right parotid

tag: tumor level

value: med


title: Patient 8 Slide E19 ROI 020

tag: tissue

value: Background

value: negative


title: PfPRMT5 knockout parasite line at early trophozoite stage Replicate 3

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_2.txt
Biological replicate 3 of 3. PfPRMT5 KO malaria parasite, harvested at early trophozoite stage.

tag: strain

value: Early trophozoite stage (24h)

tag: genotype


title: Patient 8 Slide E19 ROI 019

tag: treatment


title: PfPRMT5 knockout parasite line at early trophozoite stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_2.txt
Biological replicate 1 of 3. Control malaria parasite, untreated, harvested at schizont stage.


title: PfPRMT5 knockout parasite line at late trophozoite stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_3.txt
Biological replicate 2 of 3. PfPRMT5 KO malaria parasite, harvested at late trophozoite stage.


title: Control parasite line at early trophozoite stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_2.txt
Biological replicate 1 of 3. Control malaria parasite, untreated, harvested at late trophozoite stage.


title: Control parasite line at ring stage Replicate 3

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_1.txt
Biological replicate 3 of 3. Control malaria parasite, untreated, harvested at ring stage.

value: Ring stage (12h)


title: Patient 8 Slide E19 ROI 015

value: high


title: PfPRMT5 knockout parasite line at schizont stage Replicate 3

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_4.txt
Biological replicate 3 of 3. PfPRMT5 KO malaria parasite, harvested at schizont stage.


title: Control parasite line at schizont stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_4.txt
Biological replicate 1 of 3. PfPRMT5 KO malaria parasite, harvested at late trophozoite stage.


title: PfPRMT5 knockout parasite line at ring stage Replicate 3

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_1.txt
Biological replicate 3 of 3. PfPRMT5 KO malaria parasite, harvested at ring stage.


title: Control parasite line at ring stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_1.txt
Biological replicate 2 of 3. Control malaria parasite, untreated, harvested at ring stage.


title: Control parasite line at late trophozoite stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_3.txt
Biological replicate 1 of 3. PfPRMT5 KO malaria parasite, harvested at ring stage.


title: PfPRMT5 knockout parasite line at ring stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_1.txt
Biological replicate 1 of 3. Control malaria parasite, untreated, harvested at early trophozoite stage.


title: Patient 8 Slide E19 ROI 018


title: Control parasite line at early trophozoite stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_2.txt
Biological replicate 2 of 3. Control malaria parasite, untreated, harvested at early trophozoite stage.


title: Control parasite line at late trophozoite stage Replicate 3

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_3.txt
Biological replicate 3 of 3. Control malaria parasite, untreated, harvested at late trophozoite stage.


title: Control parasite line at ring stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_1.txt
Biological replicate 1 of 3. Control malaria parasite, untreated, harvested at ring stage.


title: PfPRMT5 knockout parasite line at early trophozoite stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_2.txt
Biological replicate 2 of 3. PfPRMT5 KO malaria parasite, harvested at early trophozoite stage.


title: Control parasite line at early trophozoite stage Replicate 3

description:
SG12454250_254853210010_S001_GE2_1105_Oct12_1_2.txt
Biological replicate 3 of 3. Control malaria parasite, untreated, harvested at early trophozoite stage.


title: PfPRMT5 knockout parasite line at schizont stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_4.txt
Biological replicate 2 of 3. PfPRMT5 KO malaria parasite, harvested at schizont stage.


title: PfPRMT5 knockout parasite line at ring stage Replicate 2

description:
SG12454250_254853210007_S001_GE2_1105_Oct12_1_1.txt
Biological replicate 2 of 3. PfPRMT5 KO malaria parasite, harvested at ring stage.


title: Patient 8 Slide E19 ROI 017


title: PfPRMT5 knockout parasite line at late trophozoite stage Replicate 1

description:
SG12454250_254853210001_S001_GE2_1100_Jul11_1_3.txt
Biological replicate 1 of 3. PfPRMT5 KO malaria parasite, harvested at early trophozoite stage.


title: Patient 8 Slide D19 ROI 015


title: Patient 8 Slide D19 ROI 016


title: Patient 8 Slide D19 ROI 014


title: Patient 8 Slide E19 ROI 014


title: Patient 8 Slide C19 ROI 024


title: Patient 8 Slide C19 ROI 025


title: Patient 8 Slide C19 ROI 023


title: Patient 8 Slide D19 ROI 013


title: Patient 8 Slide E19 ROI 013


title: Patient 8 Slide D19 ROI 019


title: Patient 8 Slide D19 ROI 018


title: Patient 8 Slide D19 ROI 020


title: Patient 8 Slide B369 ROI 068


title: Patient 8 Slide D19 ROI 017


title: Patient 8 Slide B369 ROI 064


title: Patient 8 Slide B369 ROI 065


title: Patient 8 Slide B369 ROI 067


title: Patient 8 Slide B369 ROI 058

value: low


title: Patient 8 Slide B369 ROI 060


title: Patient 8 Slide B369 ROI 061


title: Patient 8 Slide B369 ROI 066


title: Patient 8 Slide B369 ROI 063