title: 4h Enzalutamide treatment rep1

city: Ithaca

first: Haiyuan

last: Yu

address: 335 Weill Hall

department: Department of Computational Biology

institute: Cornell University

data_processing:
PRO-cap reads were preprocessed with fastp verion 0.20.0 to remove adapters, trim UMIs. Only reads longer than 18 nts were kept.
Filtered reads were aligned to the hg38 genome assembly using STAR version 2.7.1a with --alignMatesGapMax 1000 --outFilterMultimapNmax 10 --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --alignIntronMax 1000.
PCR duplicates were removed with umi_tools dedup version 1.0.1.
Assembly: hg38
Supplementary files format and content: bigWig files were generated using PINTS 0.0.1; Scores represent sequencing depth.

source_name: LNCaP

growth_protocol: LNCaP cells (male, ATCC, RRID: CVCL_1379) were maintained in RPMI medium (Gibco, A1049101), supplemented with 10% FBS (Gibco, 10270106), and 1% penicillin-streptomycin (Gibco, 11548876) on poly-L-lysine coated plates. All cell lines were grown at 37 °C with 5% CO2. All cell lines were authenticated by STR analysis and regularly tested for mycoplasma.

extract_protocol:
Cell permeabilization, run-on reactions, and RNA isolation was carried out as previously described (PMID: 27442863)
For PRO-cap, approximately 10 to 30 million cells were processed per sample. Library preparations for two biological replicates each consisting of two technical replicates per condition were processed separately. Cells were permeabilized and run-on reactions were carried out as previously described(PMID: 27442863). Following RNA isolation, two adaptor ligations using T4 RNA Ligase 1 (catalog no. M0204; NEB) and reverse transcription using SuperScript III Reverse Transcriptase (catalog no. 18080044; Invitrogen) were performed. Between adaptor ligations, cap state selection reactions were performed by treating the samples with CIP (catalog no. M0290; NEB) to reduce uncapped RNAs to 5′ hydroxyls and make them incapable of ligating to 5′ adaptor and Cap-Clip (catalog no. C-CC15011H; Cambio) to remove the 5′ cap of transcripts that had undergone guanylation and allow them to be incorporated into the library through 5′ adapter ligation. RNA washes, phenol:chloroform extractions and ethanol precipitations were carried out between reactions. All steps were performed under RNase-free conditions and following manufacturer protocols. Libraries were sequenced on an Illumina HiSeq 3000 following PCR amplification and library clean-up.
PRO-cap

treatment_protocol: LNCaP cells were treated with 10 µM enzalutamide or DMSO for 4 or 24 hrs with each condition consisting of two biological replicates.

value: LNCaP

value: prostate cancer


title: Patient2

status: Public on Apr 27 2022

type: SRA

city: Southampton

first: JAYA

last: THOMAS

address: MP824 Somers Building, Southampton General Hospital, Tremona Road,

department: Cancer Science

country: United Kingdom

institute: University of Southampton

description: Transcriptome primary lung cancer at diagnosis

library_source: transcriptomic

data_processing:
Illumina HiSeq2500 platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using the STAR aligner
FeatureCount was used to get the gene counts from the output bam files

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from snap-frozen tissue (n=17) or tissue stored in RNALater solution (n=2) or cell pellets (n=1). RNA extraction was using the Qiagen RNeasy (n=4) or Allprep DNA/RNA (n=2) kits or the Promega Maxwell® RSC simplyRNA Tissue (n=13) or simply RNA cells (n=1) kits. RNA concentration and quality were assessed by Thermofisher Scientific Qubit Fluorometric quantification and Agilent RNA 6000 Nano Kit for the 2100 Bioanalyzer System.
RNA-Sequencing was undertaken by Edinburgh Genomics, University of Edinburgh, Edinburgh, UK. An automated TruSeq stranded mRNA-seq library was prepared from total RNA and sequencing was by  Illumina NovaSeq system (100bp paired-end; 40million reads/sample).

tag: diagnosis

value: Non small cell lung cancer

tag: histology

value: Squamous cell carcinoma

tag: tissue

value: Primary lung tumor

tag: sampling time-point

value: Baseline (at diagnosis)


title: TSC_HiC_rep1

city: Tsukuba

first: Masashi

last: Hada

state: Ibaraki

address: Koyadai 3-1-1

department: Bioresource Research Center

country: Japan

institute: RIKEN

description: Biological replicate 1 of 2.

library_source: genomic

data_processing:
Hi-C data processing was done by using Docker for 4DN Hi-C pipeline (v43). The pipeline includes alignment (using mm10) and filtering steps. After filtering valid Hi-C alignments with MAPQ > 10 (.pair format file), .cool format Hi-C matrix files were generated by cooler (v0.8.7) (Abdennur and Mirny, 2020). To correct the bias of Hi-C matrices, “cooler balance” command with “—ignore-diags 1” option was applied to each .cool file. The A/B compartment (Hi-C PC1) profiles (in 200-kb bins) in each chromosome were calculated from each .cool file by “cooltools call-compartments” command of cooltools (v0.3.0) with slight modifications to perform the original A/B compartment analysis (Lieberman-Aiden et al., 2009) including the computation of Pearson correlation and covariance matrix followed by the eigen vector decomposition. The sign of Hi-C PC1 in each chromosome was corrected by gene density tracks (the sign of PC1 with higher gene density assigned as A compartment showing positive PC1 values, and the other assigned as B compartment showing negative PC1 values).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: mcool

molecule: genomic DNA

organism: Mus musculus

source_name: Trophoblast stem cell

growth_protocol: ESC and TSC lines were established from blastocysts generated by IVF. IVF was undertaken using oocytes from C57BL/6NCrSlc female mice and spermatozoa from DBA/2 male mice or JF1/Ms male mice. For establishment of ESCs, developing blastocysts were dropped onto Acidic Tyrode (Millipore #MR-004-D) to remove zona pellucida, then transferred to ESC medium containing KnockOut DMEM (Gibco # 10829018), 15% KnockOut serum replacement (KSR, Thermo #10828028), MEM Non-Essential Amino Acids Solution (Gibco #1140050), GlutaMAX supplement (Gibco #35050061), 100 µM 2-mercaptoethanol (2-ME, Sigma-Aldrich #M-7522), ESGRO Recombinant Mouse LIF Protein (Millipore #ESG1107), 1 µM PD0325901 (Stem gent #04-0006), and 1 µM CHIR99021 (Stem gent #04-0004). These blastocysts were putted onto layers of primary mouse embryonic fibroblasts treated with mitomycin-C (MMC-MEFs). After several passages, cell lines with typical ESC colonies were picked up and used for further analysis. In the case of TSCs, developing blastocysts were directory transferred to TSC medium containing the same amount of neurobasal medium (Gibco #21103049) and Dulbecco’s modified Eagle’s medium/F12 (Ham’s) (1:1) (Gibco #11320033), N2 supplement (Gibco #17502048), B27 supplement (Gibco #17504044), GlutaMAX supplement, 150 µM 2-ME, 1 µg/ml heparin (Sigma #H3149), 0.05% bovine serum albumin (Millipore #12657), 1% KSR, 50 ng/ml recombinant mouse basic FGF (Wako #062-05181), 20 ng/ml recombinant human activin A (R&D systems #338-AC), 10 µM XAV939 (Calbiochem #575545), and 5 µM Y27632 (Wako #036-24023) onto MMC-MEFs (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). After several passages, cell lines with typical TSC colonies were used for further experiment.  Established ESC and TSC lines were adapted for feeder-free conditions. Briefly, ESCs were placed onto gelatin coated dish with ESC medium in which PD0325901 and CHIR99021 were removed and 1 µM GSK-3 Inhibitor IX (Millipore #361550) was added. TSCs were placed onto the dishes coated with 15 mg/ml human plasma fibronectin (Millipore #FC010) with TSC medium (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). Medium was replaced every day and cells were passaged every 2 days

extract_protocol:
Libraries for Hi-C were generated as previously described (Kadota et al., 2020). Detailed protocol for Hi-C library preparation is available at Protocols.io (https://www.protocols.io/view/iconhi-c-protocol-ver-1-0-4mjgu4n). Briefly, collected cells were washed by 5% FBS/PBS, then fixed by 1% formaldehyde (Polyscience #18814-10) in 5% FBS/PBS for 10 min. To stop fixation, 2.5 M Glycine was added then incubated for 5 min. Fixed cells were washed and stored at -80 °C. Totally 2x106 fixed cells were lysed, permeabilized, and then digested with DpnII enzyme (4-bps cutter). Digested fragment ends were next filled with biotinylated nucleotides and the resulting blunt-end fragments were ligated.
After reverse cross-linking, ligation products were purified to obtain Hi-C DNA. 1 µg of Hi-C DNA was fragmented by sonication and the biotinylated ligation junctions were pulled down with streptavidin beads. Then, library preparation was performed on beads.

tag: strain


title: HFD_3

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Fastq file Read 1: Cell barcode (position 1) + UMI (position 17). Fastq file Read 2: biological read (cDNA).

data_processing:
Single-cell sequencing FASTQ files were processed using Kallisto (v0.46.0) and BUStools (v0.39.2) for sample demultiplexing, barcode processing, pseudo-alignment to mouse transcriptome (Ensembl release 97) and UMI counting.
UMI counts were extracted and filtered using the dropletUtils Bioconductor package (version 1.6.1). Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes. The package SingleR (v1.0.0) was used for reference-based annotation of the cells using the Immunological Genome Project (ImmGen) mouse microarray dataset as reference. A subset of 377 additional cells not annotated to the broad cell types “Macrophages” or “Monocytes” were filtered out. Low-abundance genes with average normalized log2 counts lower than 0.003 were filtered out. Eventually we used a total of 11,820 genes for 5,420 cells. The UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the scran (v1.14.5) and scatter (v1.14.5) Bioconductor packages, mostly following the steps of the simpleSingleCell  Bioconductor (v3.10) workflow.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with UMI counts for ensembl release 97 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-Chow_9")

source_name: colon monocytes and macrophages from HFD-fed mouse

growth_protocol: Mice were ordered from Charles River Laboratories (Germany) and kept in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.

extract_protocol:
Single cells were extracted from suspensions of lamina propria of each individual mouse replicate.
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for live CD45+Lin-CD11b+CD24-, and Ly6c+ or Cd64+ expression.
Sorted cell suspensions from each mouse were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: 6-7 week-old age-matched mice were fed coconut-based high-fat diet (HFD: 60 %; #D12331, Research Diets) or normal chow diet for 1 week.

tag: cell type

value: monocytes and macrophages

tag: Sex

value: male

tag: diet

value: high fat diet


title: HFD_1


title: DMSO treatment rep2

country: USA

tag: cell line


title: SUIT2, UNTREATED Rep. 3

type: RNA

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix Clariom S Human arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.

label: biotin

source_name: SUIT2 cells, UNTREATED

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: Human glioblastoma multiforme SUT2 cells (ATCC, Manassas, VA) were cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

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

treatment_protocol: Cells were treated with P-bi-TAT (30 µM) for 24 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

value: Human glioblastoma multiforme cells

tag: treatment

value: Control


title: Patient1_TP01

description: Transcriptome lung cancer metastasis post-treatment

value: Adenocarcinoma

value: Parasternal metastasis

value: Post-treatment; 1st line chemotherapy, 2nd line aPD1 immunotherapy


title: SUIT2, UNTREATED Rep. 2


title: Muscle, LacZ/AAV2/2, rep2

city: Miami

first: Zhao-Jun

last: Liu

state: FL

address: 1600 NW 10th Ave, RMSB 1010

department: Surgery

institute: University of Miami Miller School of Medicine

description:
control
SAMPLE 4

data_processing:
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports test/control (i.e., E-selectin/AAV2/2 / LacZ/AAV2/2) ratios.

label: total RNA

source_name: ischemic hindlimb muscle

label_protocol: PCR arrays were performed using the Qiagen RT2 Profiler PCR Array (Angiogenesis, PAMM-011Z) (Germantown, MD), according to manufacturer recommendations.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Hindlimb muscle was treated with intramuscular E-selectin/AAV2/2 (treatment) or LacZ/AAV2/2 (control) prior to induction of ischemia.

value: FVB

tag: stress

value: induction of ischemia

value: ischemic adductor and gastrocnemius muscles

tag: time

value: 21 days


title: Chow_11

source_name: colon monocytes and macrophages from chow-fed mouse

value: control diet (chow)


title: SUIT2, UNTREATED Rep. 1


title: Muscle, E-selectin/AAV2/2, rep2

description:
treatment
SAMPLE 3


title: 24h Enzalutamide treatment rep2

value: LNCaP

value: prostate cancer


title: 24h Enzalutamide treatment rep1


title: Chow_9


title: DMSO treatment rep1


title: Patient1_TP00

source_name: Transcriptome primary lung cancer at diagnosis

value: Non small cell lung cancer

value: Primary lung tumor


title: 4h Enzalutamide treatment rep2


title: Muscle, E-selectin/AAV2/2, rep1

description:
treatment
SAMPLE 1


title: St4_siTNFR2_TNF

status: Public on Apr 26 2022

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna

data_processing:
Reads were mapped using tophat version 2.1.1 with bowtie version 2.2.9.
Reads were counted with featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Fibrobst-like synoviocytes

growth_protocol: FLS were transfected with TNFR2 or non-targeting SMARTpool ON-TARGETplus siRNA pools using Lipofectamine RNAiMAX transfection reagent.

extract_protocol:
RNeasy purification kit (QIAGEN) was used according to the manufacturer's instructions to isolate total RNA.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina).

treatment_protocol: Cells were stimulated or not with TNF for 6 hours.

value: Fibrobst-like synoviocytes

tag: disease

value: Rheumatoid Arthritis

tag: knockdown

value: TNF

tag: patient


title: St4_siTNFR2_ctrl


title: St4_sictrl_ctrl

value: siControl


title: St3_siTNFR2_TNF


title: St3_sictrl_ctrl

value: Control


title: St3_sictrl_TNF


title: Muscle, LacZ/AAV2/2, rep1

description:
control
SAMPLE 2


title: St3_siTNFR2_ctrl


title: St4_sictrl_TNF


title: St1_sictrl_ctrl


title: St2_sictrl_ctrl


title: St2_siTNFR2_ctrl


title: St1_sictrl_TNF


title: St2_sictrl_TNF


title: St1_siTNFR2_TNF


title: M2_r2

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

data_processing:
Raw reads were quality controlled using FastQC (version 0.11.7).
Reads were then trimmed with Trimmomatic (version 0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Reads aligning to mitochondrial DNA or ribosomal RNA, or composed of a single nucleotide, were removed using bowtie2 (version 2.2.3).
The preprocessed reads from the two sequencing runs were merged per sample and aligned to the full Gencode human transcriptome version 27 (for genome version hg38) using STAR (version 2.5.4b) with essential non-default settings: --seedSearchStartLmax 12, --outFilterMismatchNmax 33, --outFilterMatchNminOverLread 0, --outFilterScoreMinOverLread 0.3, and --outFilterType BySJout.
The 2nd strand gene-wise read counts produced by STAR were collected in R (version 3.3.3) using GenomicAlignments::summarizeOverlaps (version 1.6.3).
For batch effect detection (none detected) and visualizations at the sample level, the data were normalizated in R using DESeq2::varianceStabilizingTransformation.
Differentially expressed genes between experimental groups were identified in R (version 3.5.0) using DESeq2 (version 1.20.0) by employing Wald statistic and lfcShrink for fold change shrinkage (type=“normal”).
Genome_build: hg38 with Gencode human transcriptome version 27

source_name: MV3 cells, THP-1 M2 conditioned medium

growth_protocol: MV3 cells were maintained in Dulbecco’s modified Eagle Medium (DMEM) containing 10% FBS supplemented with 1% P/S and 1% L-glutamine and grown in 37°C under 5.0% CO2.

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Valencia, CA) in 3 replicates per group.
RNA-seq libraries were generated using TruSeq Stranded mRNA kit from Illumina and single-end sequenced as 50 nt reads using HiSeq3000 (Illumina) at the Finnish Functional Genomics Centre (Turku, Finland). The libraries were sequenced twice; in the second run the library pooling was adjusted to account for unbalanced yield of the first run.

treatment_protocol: For experimentation, MV3 cells were seeded and pre-incubated for 3 h in RMPI containing 1% FBS, supplemented with 1% P/S, L-glutamine. Medium was then replaced with conditioned RMPI media from differentiated (M0) or further polarized THP-1 cells (M1 and M2) and incubated for 24 h before RNA-extraction.

tag: condition

value: M2 conditioned medium

value: MV3 human melanoma cells, originally isolated from lymph node metastasis

tag: replicate


title: St2_siTNFR2_TNF


title: M2_r1


title: M2_r3


title: St1_siTNFR2_ctrl


title: M1_r1

source_name: MV3 cells, THP-1 M1 conditioned medium

value: M1 conditioned medium


title: M1_r3


title: M1_r2


title: M0_r3

source_name: MV3 cells, THP-1 M0 conditioned medium

value: M0 conditioned medium


title: Ctrl_r2

source_name: MV3 cells, Fresh RPMI medium

value: Fresh RPMI medium


title: Y221 GS single-cell

city: Stockton

first: Yangqi

last: Su

state: CA

address: 4142 E Morada Ln, Apt 6303

department: Bioinformatics

institute: UNC Charlotte

library_source: transcriptomic single cell

data_processing:
The raw reads from FASTQ files of different lanes were first combined based on sample ID
Reads were then mapped to the S. cerevisiae reference genome  using STAR (version 2.5.2) without trimming.
Gene transcription levels were quantified using uniquely mapped reads in TPM(transcript per million mapped reads) by RSEM(v1.2.31) and in raw counts by HTSeq
Differential expression was performed by MAST
promotor motifs were found using Prosampler
Assembly: SGD R64-2-1
Supplementary files format and content: Tab-separated values files

organism: Saccharomyces cerevisiae

growth_protocol: A monoclone of the yeast strain S288C (ATCC) was selected using a YPD based agar (10% yeast extract, 20% peptone, 2% glucose and 20% agar) petri plate and stocked at -80 °C until use. To wake up cells, 30 µl thawed yeast stock inoculated in 3 ml YPD medium (1% yeast extract, 2% peptone and 2% glucose) was incubated overnight at 30 °C and 250 rpm. Cells were then expanded at 30 °C and 250 rpm after a 1:50 dilution in the YPD medium until mid-logarithmic phase (OD600 between 0.5 and 0.8). Five OD unit (ODU) cells were collected by centrifugation (500 g, 5 min) at room temperature. The cells were resuspended in autoclaved water and collected by centrifugation (500 g, 5 min) at room temperature.  The cells were then resuspended in the softening medium (100 mM Hepes-KOH, pH 9.4, 10 mM Dithiothreitol) and incubated in room temperature for 15 min. The cells collected by centrifugation (500 g, 5 min) at room temperature were then resuspended in the Spheroplasts (S) medium (1× YNB, 2% glucose, 1x amino acids, 50 mM Hepes-KOH, pH 7.2, and 1 M sorbitol) [66] to a concentration of 5 ODU/ml. Zymolyase 100T was added to the spheroplasts suspension to a final concentration of 2 μl/ODU, followed by 60 min incubation at 30°C to remove the cell wall.

extract_protocol:
0.5 mL of the spheroplasts were placed on a poly-lysine coated circular cover slip (2 mm diameter) in a petri dish for 5 min at room temperature (23 °C). The cover slip was broken in the center by a forceps, and a small piece of cover slip was transferred to a 30 µl perfusion chamber, which was constantly perfused by a desired solution by gravity feeding. The solution change time in the chamber was about 20 sec. Single cells were harvested using a path clamp electrode pipette using a micromanipulator (ROE-200, Sutter) under an inverted microscope (Olympus 1X71) placed on a vibration isolation table (TMC). A cell was harvested in less than 10 nl perfusion solution.
A harvested cell was quickly transferred using a home-made microinjection system to a 200 µl Eppendorf tube containing 4 µl cell lysis buffer (0.9× PCR Buffer II, 3 mM MgCl2, 0.45% NP40, 4.5 mM DTT, 0.18 U/μl SUPERase-In, 0.36 U/μl RNase Inhibitor, 12.5 nM AUP1 primer, 2 mM dNTP). In most single-cell samples, 0.1 μl (1:2.5x104 dilution) ERCC spike-in mRNA (Thermo Fisher) was added. The cell was lysed at 70 °C for 90 sec, then placed on ice and stored at -80 °C until use. A cell lysate was thawed on ice, and 1 μl reverse transcription mix was added (13.2 U/ μl SuperScript III Reverse transcriptase, 0.4 U/μl Rnase Inhibitor, and 0.07 μg/μl T4 gene 32 protein). The first strand cDNA was synthesized by incubating the tube at 50 °C for 30 min, followed by inactivation of the reverse transcriptase at 70 °C for 10 min, and then the tube was cooled on ice. Free AUP1 primers were removed by adding 1 µl ExoSAP (Affymetrix) to the tube and incubating at 37 °C for 15 min, followed by inactivation of the ExoSAP at 80 °C for 15 min. This step would leave the AUP1 sequences at the 5’-end cDNA intact.  A polyA tail was then added to the 3’-end of the first strand cDNA by adding 6 µl TdT mixture (1× PCR Buffer II, 1.5 mM MgCl2, 3 mM dATP, 0.75 U/μl Terminal Transferase and 0.1 U/μl RNase H) and incubating at 37 °C for 15 min, followed by inactivation of the enzyme at 70 °C for 10 min. The resulting products (12 μl) were then divided into two equal portions (each 6 μl), and each was mixed with 19 μl second strand buffer (1× High Fidelity PCR Buffer, 2 mM MgSO4, 0.2 mM each dNTP, 0.3 μM AUP2 primer, and 0.1 U/μl high fidelity Platinum Taq DNA polymerase). The two tubes were subject to one PCR cycle (30 sec at 95 °C, 2 min at 50 °C and 6 min at 72 °C) to synthesize the second-strand cDNA in the form of 5’-AUP2-T24-cDNA-A24-AUP1-3’. Nineteen μl PCR mixture (1× High Fidelity PCR Buffer, 2 mM MgSO4, 0.25 mM each dNTP, 2 μM AUP1 Primer, 2 μM AUP2 Primer, 0.1 U/μl Platium Taq DNA Polymerase High Fidelity) was added to each tube, which brings the volume of each reaction to 44 μl, and cDNA was amplified by 18 PCR cycles (98 °C for 5 sec, 67 °C for 1 min and 72 °C for 6 min). The resulting cDNA from two reactions were combined (total 88 μl) and were further subject to 12 cycles of PCR with two duplicates, each with 2.4 μl sample and 87.6 μl PCR mixture (1× High Fidelity PCR Buffer, 2 mM MgSO4, 0.375 mM each dNTP, 1 μM AUP1 Primer, 1 μM AUP2 Primer, 0.1 U/μl Platium Taq DNA Polymerase High Fidelity). The products were then combined, and cDNA was revolved on a 1% ager gel (25 μl sample per lane). The band between 300 bases to the loading well was cut and cDNA was purified using a QIA quick gel purification Kit, followed by magnetic beads (GE Health) purification (10:7 sample to beads ratio). After quantification using a Bioanalyzer (Agilent High Sensitivity DNA Kit), the libraries were then prepared using an Illumina Nextera XT or TruSeq  DNA Sample Preparation Kit according to the vender’s guide. The libraries were sequenced on an Illumina HiSeq2000 or HiSeq2500 machine (100 base-paired reads). Bulk mRNA was also extracted from population spheroplasts under AAS using a yeast RiboPureTM RNA Purification Kit (Amion). Different amount of purified bulk mRNA (5pg, 10pg, 20pg, 1,00pg, 1000pg and 10,000pg) were used to construct sequencing libraries in the same way as for single-cell libraries, with the exception that 0.1μl ERCC spike-in mRNA (Thermo Fisher) was added to the lysis buffer, with a concentration of 1:5x105, 1:2.5x105, 1:1.25x105, 1:2.5x104, 1:2.5x103 1:2.5x102  for the 5pg, 10pg, 20pg, 100pg 1,000pg and 10,000pg input RNA, respectively.

treatment_protocol: After two washes in the S medium by centrifugation (500 g, 5 min) at room temperature, spheroplasts were re-suspended to 5 ODU/ml in the desired treatment solution: amino acids starvation (AAS): S medium (with 1.0 M Sorbitol) without amino acid; glucose starvation (GS): S medium (with 1.0 M Sorbitol) without glucose; hypotonic: S medium without sorbitol; isotonic condition: S medium with 1M sorbitol. Cells were exposed to the treatment for at least 30 min (up to 5 hours) before harvest.

value: GS

tag: sample type

value: single-cell


title: Y219 GS single-cell


title: Y220 GS single-cell


title: Young skin

city: Boston

first: Vladimir

last: Botchkarev

state: MA

address: 609 Albany Street

institute: Boston University

data_processing:
The bioinformatics analysis of the RNAseq data was performed by the LC Sciences (Houston, TX). Firstly, Cutadapt (Martin, 2011) and Perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bowtie2 (Langmead and Salzberg, 2012) and Tophat2 (Kim et al., 2013) were used to map reads to the genome of Heterocephalus glaber (https://useast.ensembl.org/Heterocephalus_glaber_female/Info/Index). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown. Ballgown was used to generate a list and heatmaps of differentially expressed genes, and in-house generated Perl scripts (LC Science, Houston, TX) were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
Assembly: Naked Mole-Rat genome (version Ensemble 104.1)
Supplementary files format and content: Excel files include FPKM values for each Sample.  *Sample1.xlsx contains data from only the R1 read. *Sample2.xlsx contains data from only the R2 read.

organism: Heterocephalus glaber

source_name: NMR Dorsal skin

extract_protocol:
Total RNA was extracted from full-thickness dorsal skin samples obtained from young and old animals and purified using Direct-zol RNA purification kit (Zymo Research; Irvine, CA) following by DNAse treatment. Integrity of RNA was assessed on 2100 Bioanalyzer Instrument (Agilent Technologies, Inc.), only samples with RIN factor above 7.5 were used for NGS library preparation.
For RNA sequencing, approximately 10 ug of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). The pair-end 2×150bp sequencing was performed on an Illumina Hiseq 4000 platform in the LC Sciences (Houston, TX).

value: full-thickness skin

tag: age

value: 4 year-old


title: Ctrl_r1


title: Y218 GS single-cell


title: Ctrl_r3


title: Old skin

tag: tissue

value: 19 year-old


title: Y215 GS single-cell


title: Y216 GS single-cell


title: RNAseq_293T-EAF1mut_Rep3_R1

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

institute: Yokohama City University

description: RiboDep-RNAseq.csv

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
For RNA-seq, adapter sequences were trimmed using trimmomatic (v 0.38).
RNA-seq reads were mapped to human genome GRCH38 with hisat2 (version:2.3.4.1) as paired-end, using genecode v28 gene annotation models.
RNA-seq read counts were obtained using Rsubread (version: 2.2.6).
Differential gene expression analysis of RNA-seq was performed using R (v. 4.0.2) package DESeq2 (v. 1.28.1).
Genome_build: GRCH38

source_name: HEK293T EAF1-mutant

growth_protocol: Cells were cultured in 1X DMEM (Nacalai tesque) supplemented with 10% fetal bovine serum and 1X penicillin/streptomycin (Nacalai tesque) in a CO2 incubator (5% CO2) at 37°C.

extract_protocol:
For RNA-seq, total RNA was extracted using miRNeasy Mini Kit (Qiagen #217004) and quantified using RNA 6000 Nano Kit (Agilent Technologies) using Bioanalyzer. One microgram of total RNA was subjected to the depletion of ribosomal RNA (Ribo-Zero rRNA removal kit ,Illumina).
Ribo-depleted RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina) following manufacturer's instructions. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, requantified and sequenced as 100 bp paired-end reads on the Illumina HiSeq 3000 instrument.

tag: genotype

tag: spike-in source

tag: protocol/antibody

value: Ribosome RNA-depleted RNA

tag: sequenced molecule

value: total RNA


title: Y217 GS single-cell

tag: strain


title: RNAseq_293T-WT_Rep3_R1

description: RiboDep-RNAseq.csv

tag: cell line

value: wildtype


title: RNAseq_293T-EAF1mut_Rep1_R1

description: RiboDep-RNAseq.csv


title: Y213 GS single-cell

tag: treatment


title: RNAseq_293T-EAF1mut_Rep2_R1

description: RiboDep-RNAseq.csv


title: RNAseq_293T-WT_Rep2_R1

description: RiboDep-RNAseq.csv


title: Y210 GS single-cell


title: Y209 GS single-cell


title: Y212 GS single-cell


title: Y214 GS single-cell


title: M0_r1

tag: cell type


title: M0_r2


title: Y208 GS single-cell


title: RNAseq_293T-WT_Rep1_R1

description: RiboDep-RNAseq.csv


title: Y207 GS single-cell


title: Y206 GS single-cell


title: E11.5 Endothelial Cells (Reaggregate; 96Hrs) rep1

city: UNSW Sydney

first: Yizhou

last: Huang

state: NSW

address: High Street

country: Australia

institute: University of New South Wales

description: Re-aggregate cells

data_processing:
Raw sequencing reads filtered for adapter contamination, low quality scores, and excluded reads in which more than 10% of bases were unknown.
Filtered paired-end RNA-seq reads aligned to the mouse genome (mm10) using the software package STAR with standard parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for visualization on the UCSC genome browser

source_name: Embryo derived and then Re-aggregate cells

growth_protocol: E11.5- and E13.5 AGM PSCs were isolated from Mesp1DsRed and Wnt1DsRed embryos and cultured as previously described1, 2. Dissected AGMs were transferred into collagenase Type II (263 U/ml; Worthington Biosciences, Lakewood, NJ) and placed on a shaker at 37˚C for 15 min. The supernatant was passed through a 40 µm filter into a fresh tube and inactivated with 100% FCS. Cells were washed twice in 2% FCS in PBS and plated in MEM (Invitrogen, Carlsbad, CA) with 20% FCS, and penicillin/ streptomycin/ glutamine (P/S/G, Invitrogen)2 and cultured in the incubator at 37˚C, 5% CO2 for 72 h. At the end of 72 hrs, cells were washed in PBS to remove non-adherent cells and cultures were continued in fresh medium. Cells were passaged on reaching 80% confluence. After passaging, cells were placed back in tissue culture flasks with MEM + 20% FCS + P/S/G for bulk passaging. Cells were routinely cryopreserved in 10% DMSO and 90% culture medium. Re-aggregates were made by reconstituting FAC sorted cells from one AGM equivalent or 50,000 adult cardiac endothelial cells with 200,000 AGM PSCs. Dissociated cells were resuspended in 10μl of IMDM+ (IMDM Invitrogen) containing 20% fetal calf serum, 4mM L-glutamine, 50units/ml penicillin/streptomycin, 0.1mM mercaptoethanol, 100ng/ml IL, 100ng/ml SCF and 100ng/ml Flt3L (Peprotech). Re-aggregates were made by centrifugation in a yellow tip occluded by parafilm at 300 x g for 5 min and cultured on top of a 0.65μm Durapore filter (Millipore, Cat. No. DVPP02500) at the gas-liquid interface as described3. Tissues were maintained in 5% CO2 at 37C in a humidified incubator.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared by Novogene (Hong Kong) for sequencing using standard Illumina protocols

treatment_protocol: Cells were extracted as either freshly embryo-derived or from co-aggregate cultures.

value: Endothelial Cells

tag: surface marker


title: E13.5 Endothelial Cells (Reaggregate; 96Hrs) rep3

description: Re-aggregate cells


title: Y204 GS single-cell


title: Y203 GS single-cell


title: E13.5 Endothelial Cells (Reaggregate; 96Hrs) rep1

description: Re-aggregate cells


title: E13.5 Endothelial Cells (Reaggregate; 96Hrs) rep2

description: Re-aggregate cells


title: Y211 GS single-cell


title: Y205 GS single-cell


title: Y201 GS single-cell


title: E11.5 Endothelial Cells (Control; 96Hrs) rep2

description: Re-aggregate cells


title: G57 isotonic single-cell

value: isotonic


title: E11.5 Endothelial Cells (Control; 96Hrs) rep1

description: Re-aggregate cells


title: E13.5 Endothelial Cells (Control; 96Hrs) rep3

description: Re-aggregate cells


title: G55 isotonic single-cell


title: E13.5 Endothelial Cells (Control; 96Hrs) rep1

description: Re-aggregate cells


title: E13.5 Wnt1+A+ PSC rep3

description: Embryo-derived cells

source_name: Embryo-derived cells

value: PDGFRA+ stromal cells


title: G50 isotonic single-cell


title: E13.5 Wnt1+A+ PSC rep2

description: Embryo-derived cells


title: E13.5 Wnt1+ B+ PSC rep1

description: Embryo-derived cells


title: F9X hypotonic single-cell

value: hypotonic


title: G53 isotonic single-cell


title: E13.5 Wnt1+ B+ PSC rep2

description: Embryo-derived cells


title: G36 isotonic single-cell


title: F55X hypotonic single-cell


title: F40X hypotonic single-cell


title: E13.5 Fresh Endothelial Cells rep3

description: Embryo-derived cells


title: F30X hypotonic single-cell


title: F3X hypotonic single-cell


title: G56 isotonic single-cell


title: E13.5 Fresh Endothelial Cells rep2

description: Embryo-derived cells


title: E13.5 Endothelial Cells (Control; 96Hrs) rep2

description: Re-aggregate cells


title: E13.5 Fresh Endothelial Cells rep1

description: Embryo-derived cells


title: E11.5 Wnt1+ A+ PSC rep3

description: Embryo-derived cells


title: E11.5 Wnt1+ A+ PSC rep1

description: Embryo-derived cells


title: F24X hypotonic single-cell


title: E11.5 Wnt1+ A+ PSC rep2

description: Embryo-derived cells


title: F22X hypotonic single-cell


title: F21X hypotonic single-cell


title: F23X hypotonic single-cell


title: E13.5 Wnt1+A+ PSC rep1

description: Embryo-derived cells


title: E11.5 Fresh Endothelial Cells rep3

description: Embryo-derived cells


title: F20X hypotonic single-cell


title: E11.5 Fresh Endothelial Cells rep2

description: Embryo-derived cells


title: E10X isotonic single-cell


title: D97X AAS single-cell

value: AAS


title: E11.Mesp1+A+ PSC rep1

description: Embryo-derived cells


title: E11.Mesp1+A+ PSC rep3

description: Embryo-derived cells


title: E11.Mesp1+A+ PSC rep2

description: Embryo-derived cells


title: D96X AAS single-cell


title: D95X AAS single-cell


title: E11.5 Fresh Endothelial Cells rep1

description: Embryo-derived cells


title: E11X isotonic single-cell


title: D94X AAS single-cell


title: Y719 isotonic single-cell


title: Y718 isotonic single-cell


title: Y720 isotonic single-cell


title: D93X AAS single-cell


title: D91X AAS single-cell


title: D7 AAS single-cell


title: D9 AAS single-cell


title: Y717 isotonic single-cell


title: Y716 isotonic single-cell


title: D30 AAS single-cell


title: D3 AAS single-cell


title: D29 AAS single-cell


title: Y714 isotonic single-cell


title: Y713 isotonic single-cell


title: D28 AAS single-cell


title: Y712 isotonic single-cell


title: Y710 isotonic single-cell


title: D26X AAS single-cell


title: D24 AAS single-cell


title: Y707 isotonic single-cell


title: Y706 isotonic single-cell


title: D23 AAS single-cell


title: Y705 isotonic single-cell


title: D20 AAS single-cell


title: D27 AAS single-cell


title: Y704 isotonic single-cell


title: D19 AAS single-cell


title: Y703 isotonic single-cell


title: C80X hypotonic single-cell


title: D22 AAS single-cell


title: Y701 isotonic single-cell


title: Y709 isotonic single-cell


title: D1 AAS single-cell


title: Y700 isotonic single-cell


title: Y530 GS single-cell


title: A35 isotonic single-cell


title: Y532 GS single-cell


title: Y526 GS single-cell


title: A7 isotonic single-cell


title: Y702 isotonic single-cell


title: C81X hypotonic single-cell


title: Y525 GS single-cell


title: Y708 isotonic single-cell


title: A34 isotonic single-cell


title: Y531 GS single-cell


title: A47 isotonic single-cell


title: A29 isotonic single-cell


title: Y524 GS single-cell


title: A44 isotonic single-cell


title: Y527 GS single-cell


title: A28 isotonic single-cell


title: Y522 GS single-cell


title: A27 isotonic single-cell


title: Y521 GS single-cell


title: A26 isotonic single-cell


title: A25 isotonic single-cell


title: Y515 GS single-cell


title: H6P15 AAS bulk

data_processing:
The raw reads from FASTQ files of different lanes were first combined based on sample ID
Reads were then mapped to the S. cerevisiae reference genome  using STAR (version 2.5.2) without trimming.
Gene transcription levels were quantified using uniquely mapped reads in TPM(transcript per million mapped reads) by RSEM(v1.2.31) and in raw counts by HTSeq
Assembly: SGD R64-2-1
Supplementary files format and content: Tab-separated values files

extract_protocol:
0.5 mL of the spheroplasts were placed on a poly-lysine coated circular cover slip (2 mm diameter) in a petri dish for 5 min at room temperature (23 °C). The cover slip was broken in the center by a forceps, and a small piece of cover slip was transferred to a 30 µl perfusion chamber, which was constantly perfused by a desired solution by gravity feeding. The solution change time in the chamber was about 20 sec. Single cells were harvested using a path clamp electrode pipette using a micromanipulator (ROE-200, Sutter) under an inverted microscope (Olympus 1X71) placed on a vibration isolation table (TMC). A cell was harvested in less than 10 nl perfusion solution.
Bulk mRNA was extracted from population spheroplasts under AAS using a yeast RiboPureTM RNA Purification Kit (Amion). Different amount of purified bulk mRNA (5pg, 10pg, 20pg, 1,00pg, 1000pg and 10,000pg) were used to construct sequencing libraries in the same way as for single-cell libraries, with the exception that 0.1μl ERCC spike-in mRNA (Thermo Fisher) was added to the lysis buffer, with a concentration of 1:5x105, 1:2.5x105, 1:1.25x105, 1:2.5x104, 1:2.5x103 1:2.5x102  for the 5pg, 10pg, 20pg, 100pg 1,000pg and 10,000pg input RNA, respectively.

treatment_protocol: After two washes in the S medium by centrifugation (500 g, 5 min) at room temperature, spheroplasts were re-suspended to 5 ODU/ml in the desired treatment solution: amino acids starvation (AAS): S medium (with 1.0 M Sorbitol) without amino acid; Cells were exposed to the treatment for at least 30 min (up to 5 hours) before harvest.

value: bulk


title: Y517 GS single-cell


title: A23 isotonic single-cell


title: H6P16 AAS bulk


title: H6P14 AAS bulk


title: H6P12 AAS bulk


title: Y514 GS single-cell


title: Y509 GS single-cell


title: Y510 GS single-cell


title: Y508 GS single-cell


title: Y507 GS single-cell


title: E11.5 Endothelial Cells (Reaggregate; 96Hrs) rep2

description: Re-aggregate cells


title: Y506 GS single-cell


title: Y512 GS single-cell


title: Y518 GS single-cell


title: H6P11 AAS bulk


title: Y513 GS single-cell


title: Y511 GS single-cell


title: Y505 GS single-cell


title: Y504 GS single-cell


title: Y503 GS single-cell


title: Y501 GS single-cell


title: Y502 GS single-cell


title: Y5p9 AAS bulk


title: Y516 GS single-cell


title: Y5p8 AAS bulk


title: Y5p7 AAS bulk


title: Y5p6 AAS bulk


title: Y5p4 AAS bulk


title: Y5p5 AAS bulk


title: Y5p10 AAS bulk


title: Y5p2 AAS bulk


title: Y5p3 AAS bulk


title: Y20p8 AAS bulk


title: Y5p1 AAS bulk


title: Y20p7 AAS bulk


title: Y20p6 AAS bulk


title: Y20p5 AAS bulk


title: Y20p4 AAS bulk


title: Y20p3 AAS bulk


title: 3541B

type: genomic

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Genome Studio

source_name: Placenta

label_protocol: Standard Illumina Protocol

extract_protocol: Placental genomic DNA was extracted using Invitrogen PureLinkTM Genomic DNA kit. The genomic DNA was converted to bisulfite DNA using Zymo EZ DNA methylation kit.

treatment_protocol: Placentas were collected at delivery and then stored at −80 °C until DNA extractions were performed.

value: Placenta

tag: gender

value: Female

value: Frozen autologous


title: 725.11.07

value: Male

value: Fresh autologous


title: 650.11.06


title: 803.11.06


title: Y20p2 AAS bulk


title: VC_Pool_C_GE_scRNA-seq

city: Sydney

first: Dominik

last: Beck

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

institute: University of Technology Sydney

description: scRNA-seq

data_processing:
Raw sequencing data was processed by Cell Ranger (v3.1.0) for initial analysis and quality control.
Reads from multiple channels (gemgroups) of the 10X run were combined using 10X Genomics Cellranger (cellranger aggr)
Feature-barcode and hashing matrices were subject to bioinformatics analysis using the R package Seurat (v3.1.5)
Genome_build: mm10
Supplementary_files_format_and_content: Summary of raw/normalized counts per gene per sample (.txt)

source_name: fresh adult cardiac endothelium and co-aggregated culture with E11.5 Mesp1(der) PSCs

growth_protocol: All the co-aggregate were cultured in floting membrane in 10 µl of IMDM+ (IMDM Invitrogen) containing 20% fetal calf serum, 4 mM L glutamine, 50 U/ml penicillin/streptomycin, 0.1 mM mercaptoethanol, 100 ng/ml IL, 100 ng/ml SCF, and 100 ng/ml Flt3L (Peprotech)

extract_protocol:
10X Genomics Chromium
10X Genomics Gene expression v3 Chemistry


title: Y20p9 AAS bulk


title: 549.11.06.00


title: Y20p10 AAS bulk


title: VC_Pool_B_GE_scRNA-seq

description: scRNA-seq

value: fresh adult cardiac endothelium and co-aggregated culture with E11.5 Mesp1(der) PSCs


title: 3985A


title: 208B


title: 4221


title: 4014


title: 2727B


title: 589.11.06


title: Tumor 11

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

country: Germany

institute: University Medical Center - Mainz

description:
Tumor11
geosub_dasgupta_counts.tsv

data_processing:
Quality control on the sequencing data was performed with the FastQC tool (version 0.11.2, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0j).
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (Marini et al., 2019).
Differential expression analysis was performed with DESeq2 (version 1.22.1), setting the False Discovery Rate to 0.1, using the ideal package [Marini et al. 2020].
Genome_build: GRCm38
Supplementary_files_format_and_content: geosub_dasgupta_counts.tsv: Tab-delimited text file includes raw counts as input matrix to DESeq2.

source_name: single cell suspension of B progenitor cells

extract_protocol:
RNA extraction from primary tumour samples and FACS sorted B220+ mIgM- pro/preB cells was performed using Trizol extraction. Quality control was performed using the Bioanalyzer RNA 6000 NanoChip (Agilent Technologies).
Library preparation was performed at the Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz using the NEBNext Ultra Library Prep kit (New England Biolabs).

value: lymphoma (lymph node)

value: primary leukemia


title: Y20p1 AAS bulk


title: 527.11.07.5


title: 208A


title: 2727A


title: 3973


title: 4006


title: 3541A


title: 3881


title: 362.11.07


title: 556.11.06.00


title: 3913


title: BM IRF4 r1

description:
KM_IRF4_r1
geosub_dasgupta_counts.tsv

value: bone marrow

value: FACS sorted B220+ mIgM- pro/preB cells


title: T11 IRF4 r2

growth_protocol: 2.5 x 10^5 T11 cells were cultured in 500 µL RPMI medium in 48 well plates.

treatment_protocol: For viral transduction, 5 x 10^5 T11 cells were resuspended in 400 µL DMEM medium (D5030, Sigma-Aldrich) with 600 µL viral supernatant plus 1.5 µL polybrene and spun in culture plates at 2700 RPM for 90 min at 37 °C.

value: pB-ALL cell line

value: IRF4-RV transduced


title: 3919


title: Y1n7 AAS bulk


title: T11 IRF4 r1


title: 3871


title: Y1n5 AAS bulk


title: T11 GFP r2

value: EV transduced


title: Tumor 14

description:
Tumor14
geosub_dasgupta_counts.tsv


title: T11 GFP r1


title: 4019


title: Tumor 10

description:
Tumor10
geosub_dasgupta_counts.tsv


title: Y1n4 AAS bulk


title: 3878


title: Y1n3 AAS bulk


title: 416B_emptyV_rep3

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16279

data_processing:
QC perfomed with custom R script (available upon request). Samples were thresholded based on minimal fraction of mapped reads (15%), minimal number of reads (200,000), maximal number of mitochondrial reads (20%) and number of expressed genes (3000 genes > 10 cpm)
Reads were aligned to mouse genome (mm10) using GSNAP and reads overlapping exons (ENSEMBL m38.81) were counted using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with counts for each gene (how many aligned reads overlap its exons) generated using HTSeq

growth_protocol: 416B cells were cultured in media consisting of: RPMI1640, 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
75 cells sorted directly into lysis buffer (Smart-Seq2 protocol Picelli et al. 2014)
As in Smart-Seq2 protocol (Picelli et al. 2014), with 13 PCR amplification cycles

treatment_protocol: 416B cells stably expressing Cas9 protein were infected with lentiviruses (made in Perturb-Seq GBC plasmid background) containing expression cassettes for sgRNAs targeting Chd7, Runx1 or GFP  genes (control). After 4 days in culture the cells were harvested for RNA-Seq

value: emptyV


title: 416B_emptyV_rep2

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16276


title: 416B_emptyV_rep4

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16282


title: 416B_Runx1_sg1_rep4

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16290


title: 416B_emptyV_rep1

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16273


title: Y1n2 AAS bulk


title: 416B_Runx1_sg1_rep3

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16288


title: Y1n10 AAS bulk


title: 416B_Runx1_sg1_rep2

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16286


title: 3886


title: 416B_Runx1_sg1_rep1

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16284


title: 416B_Chd7_sg3_rep4

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16281


title: VC_Pool_A_GE_scRNA-seq

description: scRNA-seq


title: 416B_Chd7_sg3_rep1

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16272


title: Y10p9 AAS bulk


title: Y1n1 AAS bulk


title: 416B_Chd7_sg3_rep2

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16275


title: 416B_Chd7_sg2_rep4

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16289


title: Y10p8 AAS bulk


title: Y10p7 AAS bulk


title: BM IRF4 r2

description:
KM_IRF4_r2
geosub_dasgupta_counts.tsv


title: 416B_Chd7_sg2_rep1

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16283


title: 416B_Chd7_sg2_rep3

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16287


title: 3985B


title: Y10p6 AAS bulk


title: 416B_Chd7_sg1_rep3

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16277


title: Y10p5 AAS bulk


title: 416B_Chd7_sg1_rep4

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16280


title: 416B_Chd7_sg1_rep2

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16274


title: Y10p4 AAS bulk


title: 155.11.07


title: Y10p3 AAS bulk


title: Control Population 20 (Illumina HiSeq 4000)

city: Detroit

first: Grace

middle: Michelle

last: Swanson

state: MI

address: 275 E. Hancock, C.S. Mott Center room 271

institute: Wayne State University

description: Control Population 20

data_processing:
Sequences were aligned to the human genome using HISAT2.
BAM files were visualized on the UCSC genome browser for transcript intactness.
BAM files were processed using the transcript integrity index algorithm.
Intact transcripts from manual and computational analysis were compared for similarity.
Interquartile range was used to define a cut-off for intact transcripts and sample RNA quality.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains the transcript integrity index value for the merged data of the 22 transcripts used to define transcript integrity.

source_name: sperm

extract_protocol:
RNA was extracted as previously described in the publications Goodrich R et al. 2007; Goodrich RJ et al. 2013; Mao et al. 2013; Jodar et al. 2015 using a PureSperm gradient.
Libraries were constructed as previously described in the publications Goodrich R et al. 2007; Goodrich RJ et al. 2013; Mao et al. 2013; Jodar et al. 2015.

value: sperm


title: Control Population 19 (Illumina HiSeq 4000)

description: Control Population 19


title: 3850


title: 3709


title: Control Population 17 (Illumina HiSeq 4000)

description: Control Population 17


title: 3811


title: 3849


title: Y1n9 AAS bulk

value: AAS


title: Y10p2 AAS bulk

value: bulk


title: 416B_Chd7_sg2_rep2

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16285


title: Y10p10 AAS bulk


title: Control Population 14 (Illumina HiSeq 4000)

description: Control Population 14


title: Control Population 13 (Illumina HiSeq 4000)

description: Control Population 13


title: Control Population 12 (Illumina HiSeq 4000)

description: Control Population 12


title: 3697

value: Placenta


title: Y10n9 AAS bulk


title: Y10p1 AAS bulk


title: Control Population 15 (Illumina HiSeq 4000)

description: Control Population 15


title: Control Population 16 (Illumina HiSeq 4000)

description: Control Population 16


title: 3706

value: Female


title: 3585


title: 416B_Chd7_sg3_rep3

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16278


title: Control Population 11 (Illumina HiSeq 4000)

description: Control Population 11


title: 3550

value: Frozen autologous


title: Y10n7 AAS bulk


title: Control Population 9 (Illumina HiSeq 4000)

description: Control Population 9


title: Control Population 8 (Illumina HiSeq 4000)

description: Control Population 8


title: Control Population 6 (Illumina HiSeq 4000)

description: Control Population 6


title: Control Population 5 (Illumina HiSeq 4000)

description: Control Population 5


title: Y10n6 AAS bulk


title: Control Population 4 (Illumina HiSeq 4000)

description: Control Population 4


title: 416B_Chd7_sg1_rep1

description:
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16271


title: Y10n5 AAS bulk


title: Control Population 7 (Illumina HiSeq 4000)

description: Control Population 7


title: Control Population 3 (Illumina HiSeq 4000)

description: Control Population 3


title: Y10n4 AAS bulk


title: 3740


title: 3616

value: Male


title: 3521


title: Control Population 1 (Illumina HiSeq 4000)

description: Control Population 1


title: 3518

value: Fresh autologous


title: 3735


title: Y10n3 AAS bulk


title: Y10n2 AAS bulk


title: Control Population 10 (Illumina HiSeq 4000)

description: Control Population 10


title: 3457


title: U937_honokiol_3 [UH_3]

city: Weifang

first: Yanli

last: Sun

state: Shandong

address: No. 7166, Baotong West Street

department: Department of Clinical Laboratories

country: China

institute: Stem cell institution of Weifang Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: THP-1 and U-937 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 and U-937 cells were  incubated with 20 µM or 35 µM of honokiol or 0.1% DMSO for 24 h.

value: acute myeloid leukemia

value: Complex karyotype

value: honokiol


title: U937_honokiol_2 [UH_2]


title: U937_honokiol_1 [UH_1]


title: Y10n10 AAS bulk


title: U937_DMSO_3 [UC_3]

value: DMSO


title: 3303


title: 3493


title: U937_DMSO_2 [UC_2]


title: 3280


title: SCCC-52

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

description: microdissected SCCC tissue

data_processing: The  expression (Ct value ) of a specific miRNA in a sample was normalized to the median Ct of all detectable miRNAs in that sample (ΔCt= Ct target-Ct median). Subsequently the normalized relative expression (2^-ΔCT) was calculated for each miRNA. The normalized miRNA expression data were log 2 transformed and median centered to acquire the relative expression values that were used for hierarchical clustering analyses using Cluster-3.0 and Java TreeView for visualization. The clustering was based on the uncentered correlation as a distance metric using average linkage. A Mann-Whitney U test  was used to determine statistical significance between distinct groups of expression data and the Benjamini-Hochberg false discovery rate (FDR) was used to control for multiple testing.  In the matrix templates blue cells designate flagged wells whereas green cells indicate wells with undetermined value which were arbitrarily set at the highest Ct value measured in that particular sample.

label: FAM

source_name: formalin-fixed paraffin embedded tumor material

label_protocol: The miRNA expression profiles were determined in FFPE samples using TaqMan™ Low Density Array (TLDA) Human MicroRNA Cards (A card v2.0; Applied Biosystems/Thermo Fisher Scientific). First, a pool of cDNA was prepared using Megaplex™ RT Primer Human Pool  (pool A v2.1) and a TaqMan™ microRNA Reverse Transcription kit (Applied Biosystems/Thermo Fisher Scientific). Second, a pre-amplification step was conducted using Megaplex™ PreAmp Primers Human Pools (pool A v2.1) Applied Biosystems/Thermo Fisher Scientific) together with the TaqMan™ PreAmp Master Mix (Applied Biosystems/Thermo Fisher Scientific). The resulting products were mixed with TaqMan™ Universal PCR Master Mix No AmpErase™ UNG and individually added to human microRNA A cards.  The TLDA cards were analyzed using a 7900HT Fast Real-Time PCR system (Applied Biosystems).

extract_protocol: Total RNA was extracted from microdissected material of multiple 4 µm sections from each FFPE tumor and controle sample using the RecoverAll total nucleic acid isolation kit (Ambion / Life Technologies) according to the manufacturer’s recommendations.

treatment_protocol: Ocular sebaceous carcinoma (OSC) and squamous cell carcinoma of the conjunctiva (SCCC) resection samples and corresponding control tissues (Meibomian glands for OSC and conjunctival squamous epithelium of the eyelid for SCCC) were identified at the department of Pathology in the Erasmus Medical Center. Formalin-fixed paraffin-embedded (FFPE) tissue blocks from resection material of control tissue and of the untreated, primary tumors were collected from the Erasmus MC tissue bank. Hematoxylin-eosin-stained sections of these samples were examined by an expert pathologist to confirm the initial histopathological diagnosis and to precisely locate the required tissues.

value: Conjunctival squamous cell carcinoma


title: U937_DMSO_1 [UC_1]


title: SCCC-50

description: microdissected SCCC tissue


title: Y100p7 AAS bulk


title: SCCC-49

description: microdissected SCCC tissue


title: Y100p5 AAS bulk


title: Control Population 18 (Illumina HiSeq 4000)

description: Control Population 18


title: Y100p4 AAS bulk


title: SCCC-46

description: microdissected SCCC tissue


title: Control Population 2 (Illumina HiSeq 4000)

description: Control Population 2


title: 3269


title: Y10n1 AAS bulk


title: THP1_honokiol_2 [TH_2]


title: Y100p2 AAS bulk


title: THP1_DMSO_3 [TC_3]


title: THP1_DMSO_2 [TC_2]


title: Y100p3 AAS bulk


title: THP1_honokiol_1 [TH_1]


title: Y100p10 AAS bulk


title: Y100p1 AAS bulk


title: 3350


title: 3293


title: WSU-DLCL2-INPUT

city: New York

first: Laura

last: Pasqualucci

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10^-15
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively.

source_name: DLBCL cell line

growth_protocol: Cells were grown in IMDM medium supplemented with 10% FBS and 1% Penicillin/Streptomicin at 37C and 5% CO2. Cells in log phase of growth were harversted and used for H3K27Ac ChIP-Seq experiments.

extract_protocol:
Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp.
ChIP-seq libraries were constructed starting from 3ng of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 15nM, pooled and sequenced in an Illumina HiSeq 4000 instrument as paired-end 150 bp reads, obtaining on average 25x10^6 reads/sample.

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen.

value: DLBCL cell line

value: WSU

tag: antibody

value: INPUT no Antibody


title: sgSV40 mESC_without_DOX _rep2

city: HangZhou

first: hao

last: wu

address: YuHang street

institute: Zhejiang University

data_processing:
Raw reads were first trimmed using Trimmomatic (v.0.36). Illumina sequence adaptors were removed, the leading and tailing low-quality base pairs (fewer than 3) were trimmed, and a 4-bp   sliding window was used to scan the reads and trim when the window mean quality dropped below 15. Only reads having at least 50-bp were kept.
The resulting reads were mapped to the mm10 genome using STAR (v.2.5.2b) with the following parameters: -outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout -outSAMattributes NH HI AS NM MD -outFilterMultimapNmax 20 -outFilterMismatchNmax 999 -quantMode TranscriptomeSAM GeneCounts.
Then the ‘Trimmed Mean of M values’ normalization (TMM) method from the R/Bioconductor package edgeR package (v3.24.0) was used to calculate the normalized expression
The R/Bioconductor edgeR package (v3.24.0)was used to detect the differentially expressed genes between the different samples using the generalized linear model-based method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Count for each Sample

growth_protocol: The E14 cells were cultured on 0.1% gelatin-coated plates with standard leukemia inhibitory factor (LIF) /serum medium containing 10% FBS (HAKATA, cat. no. HB-FBS-500), 1,000 U/ml mouse LIF (Biolegend, cat. no. 554002), 0.1 mM non-essential amino acids (Gibco, cat. no. 11140), 0.055 mM β-mercaptoethanol (Gibco, cat. no. 21985023), 2 mM GlutaMAX (Gibco, cat. no. 35050), 1 mM sodium pyruvate (Gibco, cat. no. 11360) and penicillin/streptomycin (100 U/ml) (Gibco, cat. no. 15140) in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol:
Cellular RNA was collected using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, cat. no. RC112).
Total RNA was used as input material for the RNA sample preparations. Briefly,mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments,Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: embryonic stem cell

value: WT

value: DOX minus


title: WSU-DLCL2-H3K27Ac-Diagenode

value: H3K27Ac Diagenode #A1723-0041D


title: SCCC-40

description: microdissected SCCC tissue


title: SCCC-41

description: microdissected SCCC tissue


title: SCCC-45

description: microdissected SCCC tissue


title: 3178

value: Placenta


title: THP1_honokiol_3 [TH_3]


title: SCCC-42

description: microdissected SCCC tissue


title: SCCC-43

description: microdissected SCCC tissue


title: 3156


title: SCCC-44

description: microdissected SCCC tissue


title: THP1_DMSO_1 [TC_1]


title: 3860

value: Female


title: WSU-DLCL2-H3K27Ac-Active Motif

value: H3K27Ac Active Motif #39135


title: sgSV40 mESC_without_DOX _rep1


title: sgSV40 mESC_DOX _rep2

value: DOX plus


title: SCCC-36

description: microdissected SCCC tissue


title: 3049

value: Male

value: Frozen autologous


title: U2932-INPUT


title: 3004

value: Fresh autologous


title: 2852


title: U2932-H3K27Ac-Diagenode_Lib-6_LE057


title: 3131


title: SCCC-20

description: microdissected SCCC tissue


title: sgSV40 mESC_DOX _rep1


title: U2932-H3K27Ac-Active Motif_Lib-5_LE047


title: SCCC-18

description: microdissected SCCC tissue


title: SCCC-17

description: microdissected SCCC tissue


title: sgZfp281 mESC_without_DOX _rep2

value: Zfp281 KO


title: sgZfp281 mESC_without_DOX _rep1


title: SCCC-16

description: microdissected SCCC tissue


title: TMD8--INPUT


title: 2950


title: SCCC-15

description: microdissected SCCC tissue


title: 2872


title: sgZfp281 mESC_DOX _rep1


title: sgZfp281 mESC_DOX _rep2


title: TMD8-H3K27Ac-Active Motif


title: 2747


title: SUDHL7-INPUT


title: Spatial transcriptome of immune cells in  a 16-day B78ChOVA melanoma GEX

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gene and ZipSeq barcode counts in the Matrix Exchange format.

source_name: skin

growth_protocol: Adherent B78ChOVA tumor cells were grown to confluency and harvested using 0.05% Trypsin-EDTA (GIBCO) and washed 3x with PBS (GIBCO). 1.0x105 – 2.5x105 cells in PBS were resuspended in a 1:1 ratio with Growth Factor Reduced Matrigel (Corning) and a final volume of 50μl was injected subcutaneously into the flanks of anaesthetized and shaved mice.  Tumors were harvested 16 days post-injection.

extract_protocol:
Tumors were sectioned while live using a compresstome (Precisionary Instruments VFZ-310-0Z) to generate ~160 μm sections.
The sectioning, imaging, spatial barcoding, tumor dissociation, sorting, 10X encapsulation and library construction were identical to the methods described in (Hu et al., 2020).

value: Immune

value: skin

tag: time

value: 16 days


title: Spatial transcriptome of immune cells in  a 16-day B78ChOVA melanoma ADT

description: 10x Genomics


title: SUDHL7-H3K27Ac-Diagenode

value: DLBCL cell line


title: OSC-48

description: microdissected OSC tissue

value: Ocular sebaceous carcinoma


title: SCCC-13

description: microdissected SCCC tissue

value: Conjunctival squamous cell carcinoma


title: OSC-38

description: microdissected OSC tissue


title: Day 14 exhausted OT-I T cell-3

data_processing:
Reads were trimmed and quality filtered using fastp.
Reads were aligned to mm10 using hisat2
Aligned reads were de-duplicated using Picard
Mitochondrial reads and Y chromosome reads were removed
Peaks were called for each sample using MACS2, merged into a union peak set, and the peak by count matrix was loaded into DESeq2 for differential analysis
Assembly: mm10
Supplementary files format and content: normalized genome coverage (bigwig) file for each sample

source_name: T cells

growth_protocol: C57Bl6/J mice bearing B78ChOVA melanomas received adoptively transferred OT-I T cells 4 or 14 days prior to sacrifice. Tumor-infiltrating CD44+ OT-I T cells were isolated by FACS sorting in lysis buffer for RNAseq. Naïve OT-I T cells were directly isolated from lymph nodes of tumor-naive OT-I mice. Effector OT-I T cells were generated in vitro upon 5 days of antigenic stimulation.

extract_protocol:
5x104 cells per replicate were lysed in 50 µL ATAC resuspension buffer supplemented with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. After lysis, nuclei were transposed using 2.5 µl Tn5 transposase in a 50 µl reaction for 30 min at 37°C. Finally, the transposed DNA was purified using a commercial PCR cleanup kit and libraries were prepared for sequencing. 2x75 paired end sequencing was performed on an Illumina sequencer
ATAC-seq samples were processed according to the Omni-ATAC

treatment_protocol:
N/A
N/A

value: T cells

value: OT-I

value: Day 14


title: Day 14 exhausted OT-I T cell-2


title: TMD8-H3K27Ac-Diagenode_Lib-6_LE056

value: H3K27Ac Diagenode #A1723-0041D


title: SUDHL7-H3K27Ac-Active Motif


title: OSC-37

description: microdissected OSC tissue


title: Day 14 exhausted OT-I T cell-8


title: Day 14 exhausted OT-I T cell-7


title: SUDHL6_H3K27Ac-Diagenode


title: SUDHL6_Input

value: INPUT no Antibody


title: OSC-35

description: microdissected OSC tissue


title: 2658

value: Placenta

value: Female


title: OSC-34

description: microdissected OSC tissue


title: 2488


title: SUDHL5-INPUT_Lib-4_LE036


title: SCCC-14

description: microdissected SCCC tissue


title: Naive CD8 OT-I T cell-5

value: Day 0


title: 2692

value: Frozen autologous


title: 2509

value: Male


title: Naive CD8 OT-I T cell-6


title: 2403

value: Fresh autologous


title: OSC-31

description: microdissected OSC tissue


title: OSC-33

description: microdissected OSC tissue


title: 2489


title: 2631


title: 2536


title: SUDHL5-H3K27Ac-Active Motif

value: H3K27Ac Active Motif #39135


title: Naive CD8 OT-I T cell-4


title: SUDHL5-H3K27Ac-Diagenode


title: OSC-28

description: microdissected OSC tissue


title: Naive CD8 OT-I T cell-1


title: OSC-30

description: microdissected OSC tissue


title: Day 14 exhausted OT-I-3

data_processing:
Raw fastq reads were QC’d and trimmed to remove adapter contamination, and poly-G artifacts using using fastp version 0.19.6. Reads with fewer than 20bp post-trimming were discarded.
Trimmed reads were aligned to the GRCm38 reference sequence annotated with Gencode V25 using STAR version 2.6.1b (Dobin et al., 2013) with the following parameters (--quantMode GeneCounts –outFilterMismatchNoverLmax 0.04 --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with CPM values for each Sample as reported by the STAR aligner.

extract_protocol:
Cells were directly sorted in lysis buffer, RNA was extracted using Dynabead Direct.
mRNA was converted into amplified cDNA using the Tecan Ovation RNA-Seq System V2 kit, following the manufacturer guidelines. The dsDNA is tagmented, amplified and undergoes clean up with AMPure XP bead, using the Illumina Nextera XT DNA Library Prep Kit. The resulting sequencing library is QC’d using an Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration. Libraries were pooled prior to single-end sequencing on and Illumina MiSeq/MiniSeq to ensure quantify library complexity. Libraries with less than 10 percent of the reads aligned to coding regions, or fewer than 1,000 unique reads in total were rejected. The validated libraries were re-pooled based on the percentage of reads in coding regions and submitted for sequencing.


title: 2221


title: 2292


title: SUDHL4_Input


title: SUDHL4_H3K27Ac-Diagenode


title: Day 14 exhausted OT-I-2


title: OSC-27

description: microdissected OSC tissue


title: 2369


title: 2423


title: 2197


title: 2079


title: 2114


title: Day 14 exhausted OT-I-1


title: SUDHL2--INPUT


title: Day 4 exhausted OT-I-3

value: Day 4


title: SUDHL4-H3K27Ac-Active Motif


title: 2105


title: OSC-25

description: microdissected OSC tissue


title: OSC-24

description: microdissected OSC tissue


title: 2058


title: SUDHL6_H3K27Ac-Active Motif


title: SUDHL2-H3K27Ac-Diagenode


title: OSC-23

description: microdissected OSC tissue


title: Day 4 exhausted OT-I-2


title: 2009


title: Day 4 exhausted OT-I-1


title: Control 12

description: microdissected normal control tissue to SCCC

source_name: formalin-fixed paraffin embedded material

value: Conjunctival squamous epithelium of the eyelid


title: SUDHL2-H3K27Ac-Active Motif

value: DLBCL cell line


title: OSC-22

description: microdissected OSC tissue

value: Ocular sebaceous carcinoma


title: SUDHL10-H3K27Ac-Diagenode


title: Effector OT-I-3


title: 2097


title: SUDHL10-H3K27Ac-Active Motif


title: Control 11


title: Control 10


title: Effector OT-I-1


title: SUDHL10-INPUT


title: RL-INPUT

value: RL


title: Control 9


title: 2004


title: Naïve OT-I-3

value: T cells


title: RL-H3K27Ac-Diagenode


title: Naïve OT-I-2

value: OT-I


title: Control 7


title: 1973


title: Control 8


title: RL-H3K27Ac-Active Motif


title: Naïve OT-I-1


title: 1999


title: RIVA-H3K27Ac-Diagenode

value: RIVA


title: Control 5

description: microdissected normal control tissue to OSC

value: Meibomian gland


title: P2Y₂ KO cADSC+UTP 1

city: Brussels

first: Didier

last: Communi

address: Route de Lennik 808

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic)
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR software to generate read alignments.
The annotation file Mus_musculus.GRCm38.90.gtf was obtained from the ftp.Ensembl.org server
Following transcript assembly, gene level counts were obtained using HTSeq
Assembly: GRCm38.p4/mm10
Supplementary files format and content: Excel xlsx file includes counts per 20 millions of aligned reads values for each sample.

source_name: adipose-derived stem cells isolated from cardiac adipose tissue

growth_protocol: Cardiac adipose tissue was freshly harvested from WT or P2Y₂ KO mice, washed in phosphate-buffered saline (PBS) and minced, followed by a digestion in collagenase A (2.5 g/L) at 37°C for 45 min. The digested tissue was filtered through a 100 μm cell strainer (Corning) and centrifuged at 500 g for 5 min. The supernatant containing adipocytes and debris was discarded. A red blood cell lysis was performed on the pelleted cells by an osmotic shock. After a last centrifugation at 500 g for 5 min, the resultant pellet, named the stromal vascular fraction, was suspended in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin, plated and incubated at 37°C in a humidified 95% air - 5% CO2 atmosphere for 7 days. cADSC were selected by their high plastic adhesion, non-adherent cells were removed after 24 h and the culture medium was subsequently replaced every two days.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) after cells had been lysed using TRI Reagent Solution (Invitrogen).
TruSeq Stranded mRNA (Illumina)
RNA-Seq 2x100 bases Paired-End

treatment_protocol: cADSC cultures were untreated or treated daily with UTP (100 µM) for 7 days in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

value: cardiac adipose tissue

value: cardiac adipose-derived stem cells

value: P2Y2 KO

tag: culture medium

value: UTP 100 uM for 7 days


title: Control 4


title: Control 6


title: P2Y₂ KO cADSC 2

value: DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

value: untreated


title: RIVA-H3K27Ac-Active Motif


title: Effector OT-I-2


title: 1927

value: Placenta

value: Male

value: Frozen autologous


title: RCK8--INPUT

value: INPUT no Antibody


title: P2Y₂ KO cADSC 1


title: Control 3


title: 1876

value: Female

value: Fresh autologous


title: RCK8-H3K27Ac-Diagenode

value: DLBCL cell line

value: H3K27Ac Diagenode #A1723-0041D


title: WT cADSC+UTP 2

value: wild type


title: Control 2


title: RCK8-H3K27Ac-Active Motif

value: H3K27Ac Active Motif #39135


title: 1891


title: Control 1

value: Meibomian gland


title: P2Y₂ KO cADSC+UTP 2

value: cardiac adipose tissue


title: PFEIFFER-INPUT

value: PFEIFFER


title: 1845


title: WT cADSC+UTP 1

value: cardiac adipose-derived stem cells


title: RIVA-INPUT

value: RIVA


title: 1688


title: KO3 HFD

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

institute: University of Geneva

data_processing:
4 RNA-seq reads files per sample were merged
RNA-seq reads were aligned to rmm10 using hisat2 version 2.1.0 using the default parameters
Counts were obained using htseq-count function of HTSeq 0.13.5 using the parameters -a 20 -s no
mm10refGene.gtf (prepared from ://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz) was used as gff input for htseq-count
Counts were normalized using DESeq2 v1.26 R package
Assembly: mm10
Supplementary files format and content: raw counts

source_name: inguinal white adipose tissue

extract_protocol:
Total iWAT RNA was extracted using TRIzolTM
RNA-seq libraries were prepared with the illumina TruSeq RNA v2 kit using 500ng of total RNA, checked with the Agilent bioanalyzer DNA1000 chip, quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing. Approximately 25Million, 75 bp long, Single-End reads were generated for each sample with illumina NextSeq500 sequencer.

value: inguinal white adipose tissue

value: Mpst knockout

value: High fat diet (HFD)


title: 1654

value: Placenta


title: WT cADSC 2

value: DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

value: untreated


title: PFEIFFER-H3K27Ac-Diagenode


title: WT3 HFD

value: WT


title: KO1 HFD


title: 1331

value: Female

value: Fresh autologous


title: 1921


title: PFEIFFER-H3K27Ac-Active Motif

value: DLBCL cell line


title: 1503

value: Frozen autologous


title: WT2 HFD


title: 1640


title: ATAC_Smyd5KO_Smyd5delC_E14_rep1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Assembly: mm9, hg19
Supplementary files format and content: BigWig files

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM-mercaptoethanol and 1000 U/ml recombinant leukemia inhibitory factor (LIF). K562 cells were cultured in RPMI1640 supplemented with 1% glutamax, 1% antibiotic solution (penicillin/streptomycin) and 10% FBS. All cells were grown at 37 °C and 5% CO2.

extract_protocol:
CUT&Tag libraries are constructed from nuclei extraction and antibody binding, transposome tagmentation. ATAC-seq libraries are constructed from nuclei extraction and transposome tagmentation.
CUT&Tag and ATAC-seq libraries are prepared from directely PCR.

value: native

tag: chip antibody

value: Smyd5 KO, overexpression Smyd5delC


title: NU-DHL1-INPUT

value: NU

value: INPUT no Antibody


title: 1020

tag: sample type


title: NU-DHL1-H3K27Ac-Diagenode

value: H3K27Ac Diagenode #A1723-0041D


title: 1285


title: ATAC_Smyd5KO_Smyd5delC_E14_rep2

tag: age


title: 1196

tag: tissue

value: Male


title: ATAC_Smyd5KO_Smyd5FL_E14_rep2

tag: genotype

value: Smyd5 KO, overexpression Smyd5


title: 131


title: ATAC_Smyd5KO_E14_rep2

value: Smyd5 KO


title: NU-DHL1-H3K27Ac-Active Motif

value: H3K27Ac Active Motif #39135


title: ATAC_Smyd5KO_Smyd5FL_E14_rep1


title: LY8--INPUT


title: N_KPSC_3

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity sequence, then mapped to mm10 whole genome.
Reads Per Kilobase of exon per Megabase of library size were calculated using a protocol from Chepeleve et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: neutrophils

extract_protocol:
Briefly, neutrophils were cultured with 20% CM from KPC or KPSC cells for 20 hr.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: Freshly isolated neutrophils from bone marrow

value: Wild type

value: KPSC


title: WT cADSC 1

value: cardiac adipose tissue

value: cardiac adipose-derived stem cells

value: wild type

value: DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

value: untreated


title: N_KPSC_2


title: WT1 HFD

value: inguinal white adipose tissue

value: WT

value: High fat diet (HFD)


title: KO2 HFD

value: Mpst knockout


title: LY8-H3K27Ac-Active Motif

value: DLBCL cell line


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 Rep1 5C

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Library strategy: 5C-seq
5C analysis steps were performed as described (Gilgenast et al., 2019; Beagan et al., 2020; Fernandez et al., 2020). Briefly, paired-end reads were aligned to the 5C primer pseudo-genome using Bowtie, allowing only reads with one unique alignment to pass filtering. Only reads for which one paired end mapped to a forward/left-forward primer and the other end mapped to a reverse/left-reverse primer were tallied as true counts. Primer-primer pairs with outlier count totals, resulting primarily from PCR bias, were identified as those with a count at least 8-fold higher (100-fold for the lower-quality Arc region) than the median count of the 5x5 subset of the counts matrix centered at the primer-primer pair in question; outlier counts were removed.  Primer-primer pair counts were then converted to fragment-fragment interaction counts by averaging the primer-primer counts that mapped to each fragment-fragment pair (max of 2 if both a forward/left-forward and a reverse/left-reverse primer were able to be designed to both fragments and were not trimmed during outlier removal). We then divided our 5C regions into adjacent 4 kb bins and computed the relative interaction frequency of two bins (i,j) by summing the counts of all fragment-fragment interactions for which the coordinates of one of the constituent fragments overlapped (at least partially) a 12 kb window surrounding the center of the 4 kb ith bin and the other constituent fragment overlapped the 12 kb window surrounding the center if the jth bin. Binned count matrices were then matrix balanced using the ICE algorithm69,71 and quantile normalized across all 8 replicates (2 per condition) within each experimental set (neuronal activation and cohesin-rescue experimental datasets were quantile normalized separately) as previously described (Beagan et al., 2020), at which point we considered each entry (i,j) to represent the Observed Interaction Frequency of the 4 kb bins i and j. Finally, the background contact domain ‘expected’ signal was calculated using the donut background mode (Su et al., 2017) and used to normalize the relative interaction frequency data for the background interaction frequency present at each bin-bin pair. The resulting background-normalized interaction frequency (“observed over expected”) counts were fit with a logistic distribution from which p-values were computed for each bin-bin pair and converted into ‘Background-corrected Interaction Scores’ (interaction score = -10*log2(p-value)), which have previously shown to be informatively comparable across replicates and conditions (Beagan et al., 2020).
Genome_build: mm9 5C primer psuedogenome
Supplementary_files_format_and_content: BED_6715-mm9-ERneuro.bed' is the bed file containing the coordinates for each 5C primer used in the neuronal activity experiments. 'BED_6718-mm9-synapt.bed' is the bed file containing the coordinates for each 5C primer used in the cohesin rescue experiments.   '[Rep_name].counts.txt' contains the number of reads mapped to each pair of 5C primers (see 5C processing) for each replicate.

source_name: Primary neuron

extract_protocol:
Neuronal cultures were fixed in 1% formaldehyde for 10 minutes (room temp) via the addition (1:10 vol/vol) of the following fixation solution: 50 mM Hepes-KOH (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 11% Formaldehyde. Fixation was quenched via the addition of 2.5 M glycine (1:20 vol/vol) and scraped into pellets. Each pellet was washed once with cold PBS, flash frozen, and stored at -80oC. For each condition, in situ 3C was performed on 2 replicates of 4-5 million cells as described (Beagan et al., 2020). Briefly, cells were thawed on ice and resuspended (gently) in 250 L of lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) with 50 L protease inhibitors (Sigma P8340). Cell suspension was incubated on ice for 15 minutes and pelleted. Pelleted nuclei were washed once in lysis buffer (resuspension and spin), then resuspended and incubated in 50 L of 0.5% SDS at 62oC for 10 min. SDS was inactivated via the addition of 145L H2O, 25 uL 10% Triton X-100, and incubation at 37oC for 15 min. Subsequently, chromatin was digested overnight at 37oC with the addition of 25 L 10X NEBuffer2 and 100U (5 L) of HindIII (NEB, R0104S), followed by 20 min incubation at 62oC to inactivate the HindIII. Chromatin was re-ligated via the addition of 100 L 10% Triton X-100, 120 L NEB T4 DNA Ligation buffer (NEB B0202S), 12L 10 mg/mL BSA, 718 L H2O, and 2000 U (5 L) of T4 DNA Ligase (NEB M0202S) and incubation at 16oC for 2 hours. Following ligation nuclei were pelleted, resuspended in 300 L of 10 mM Tris-HCl (pH 8.0), 0.5 M NaCl, 1% SDS, plus 25 L of 20 mg/mL proteinase K (NEB P8107), and incubated at 65oC for 4 hours at which point an additional 25 L of proteinase K was added and incubated overnight. 3C templates were isolated next day via RNaseA treatment, phenol-chloroform extraction, ethanol precipitation, and Amicon filtration (Millipore MFC5030BKS). Template size distribution and quantity were assessed with a 0.8% agarose gel.
5C primers were designed according to the double-alternating design scheme using the My5C primer design software (http://my5c.umassmed.edu/my5Cprimers/5C.php)10 with universal “Emulsion” primer tails. Regions were designed to capture TAD structures immediately surrounding the genes of interest (Bdnf, Fos, Arc, Neurexin-1, Neuroligin-3, Synaptotagmin-1) in published mouse cortex HiC data. 5C reactions were carried out as previously described. 600 ng (~200,000 genome copies) of 3C template for each replicate was mixed with 1 fmole of each 5C primer and 0.9 ug of salmon sperm DNA in 1x NEB4 buffer, denatured at 95oC for 5 min, then incubated at 55oc for 16 hours. Primers which had then annealed in adjacent positions were ligated through the addition of 10 U (20 uL) Taq ligase (NEB M0208L) and incubation at 55oC for 1 hour then 75oC for 10 min. Successfully ligated primer-primer pairs were amplified using primers designed to the universal tails (FOR = CCTCTC TATGGGCAGTCGGTGAT, REV = CTGCCCCGGGTTCCTCATTCTCT) across 30 PCR cycles using Phusion High-Fidelity Polymerase. Presence of a single PCR product at 100 bp was confirmed via agarose gel, then residual DNA <100 bp was removed through AmpureXP bead cleanup at a ratio of 2:1 beads:DNA (vol/vol). 100 ng of the resulting 5C product was prepared for sequencing on the Illumina NextSeq 500 using the NEBNext Ultra DNA Library Prep Kit (NEB E7370) following the manufacturer’s instructions with the following parameter selections: during size selection, 70 uL of AMPure beads was added at the first step and 25 at the second step; linkered fragments were amplified using 8 PCR cycles. A single band at 220 bp in each final library was confirmed using an Agilent DNA 1000 Bioanalyzer chip, and library concentration was determined using the KAPA Illumina Library Quantification Kit (#KK4835). Finally, libraries were evenly pooled and sequenced on the Illumina NextSeq 500 using 37 bp paired-end reads.

value: TTX-Kcl


title: 428

data_processing: Genome Studio

extract_protocol: Placental genomic DNA was extracted using Invitrogen PureLinkTM Genomic DNA kit. The genomic DNA was converted to bisulfite DNA using Zymo EZ DNA methylation kit.

value: Placenta

value: Female

value: Frozen autologous


title: 1111


title: 124

value: Male

value: Fresh autologous


title: ATAC_WT_E14_rep2

value: native


title: LY7-INPUT

value: INPUT no Antibody


title: N_KPC_3

value: Freshly isolated neutrophils from bone marrow

value: Wild type

value: KPC


title: ATAC_Smyd5KO_E14_rep1

value: Smyd5 KO


title: ATAC_WT_E14_rep1


title: N_KPSC_1

value: KPSC


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 Rep2 5C

value: wt

value: TTX


title: 95


title: LY7-H3K27Ac-Diagenode

value: H3K27Ac Diagenode #A1723-0041D


title: N_KPC_2


title: N_KPC_1


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep2 5C


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 Rep2 5C


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 Rep1 5C


title: LY7-H3K27Ac-Active Motif

value: DLBCL cell line

value: H3K27Ac Active Motif #39135


title: LY3-INPUT


title: LY3-H3K27Ac-Diagenode


title: 71

value: Placenta


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep2 5C


title: N_CON_2

value: control


title: Rad21tev+VEH24h_primary_neuron_culture Rep2 Synaptic 5C


title: 65

value: Frozen autologous


title: 27

value: Male


title: Rad21tev+VEH7D_primary_neuron_culture Rep2 Synaptic 5C


title: 723


title: LY18-INPUT


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep1 5C

value: TTX-Kcl


title: N_CON_1


title: N_CON_3


title: H3K9me3_E14_rep2

data_processing:
Library strategy: CUT&TAG
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Assembly: mm9, hg19
Supplementary files format and content: BigWig files

value: native

value: Rabbit monoclonal anti-Histone H3K9me3 (Abcam, Cat. #ab8898)

value: WT


title: GOLGA8N 1

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

data_processing:
Raw reads were mapped against the human genome Grch38 using STAR version 0.7.2
Mapped reads were annotated with overlapping genes using FeatureCounts
PCR duplicates were then discarded on a per-gene basis using UMI_Tools
Gene Counts were then computed using Salmon version 0.7.2 and human gene models from Ensembl build 96
Assembly: hg38
Supplementary files format and content: quant.sf files are default salmon output (tab-deliminited, indexed by ensembl transcript ID)

growth_protocol: K562 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using the Zymo direct-zol RNA kits
Libraries constructed using Lexogen 3' QuantSeq kit (cat# XXXXXXX) using modified oligo-dT primers containing 12bp UMIs

treatment_protocol: K562 were electroporated with CRISPR plasmids, followed by ASO treatment, and processed on Day 6 for DGE analysis

value: lymphoblasts

tag: plasmids


title: H3K9me3_E14_rep1


title: GOLGA8N 2


title: LY3-H3K27Ac-Active Motif


title: LY18-H3K27Ac-Diagenode


title: LY10-INPUT

value: INPUT no Antibody


title: Rad21tev+DOX24h_primary_neuron_culture Rep2 Synaptic 5C


title: Rad21tev+DOX7D_primary_neuron_culture Rep2 Synaptic 5C


title: Rad21tev+VEH7D_primary_neuron_culture Rep1 Synaptic 5C


title: 13


title: Rad21tev+DOX7D_primary_neuron_culture Rep1 Synaptic 5C


title: COL6A6


title: UBE2V1


title: LY10-H3K27Ac-Diagenode


title: LY1-INPUT


title: ADORA2A


title: 126

value: Female