title: Lipid-laden monocyte-derived macrophages, mn:224

value: Lidid-Laden Monocyte-derived macrophage


title: Non-lipid-laden monocyte-derived macrophages, mn:224

status: Public on Jun 30 2024

type: SRA

city: Amsterdam

first: Daan

middle: Juri

last: Kloosterman

address: Plesmanlaan 121

department: Tumor Biology & Immunology

country: Netherlands

institute: The Netherlands Cancer

library_source: transcriptomic

data_processing:
A multiplex sequencing pool of all uniquely dual indexed RNA libraries was composed by equimolar pooling before sequencing on the NovaSeq 6000 Illumina sequencing platform. Paired-end sequencing was performed using 54 cycles for Read 1, 10 cycles for Read i7, 10 cycles for Read i5 and 54 cycles for Read 2, using a NovaSeq SP Reagent Kit v1.5 (cat no. 20028401, Illumina). This resulted in, on average, 20 M passing filter (PF) reads per sample.
Assembly: Mus musculus (mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain tumor

extract_protocol:
For RNA-seq samples, FACS-purified (non-) LLMs from MG and MDMs from primary PDG-Ink4a tumors, dTomato+ BMDMs from ex vivo assays (4.000-20.000 cells) or MES-like tumor cells from in vitro assays (20.000-100.000 cells) were homogenized in RLT buffer (79216, Qiagen), total RNA was isolatedusing the RNeasy Micro Kit (74004, Qiagen), including an on-column DNase digestion (79254, Qiagen),according to the manufacturer’s instructions. Quality and quantity of the total RNA was assessed on the 2100 Bioanalyzer instrument following manufacturer’s instructions “Agilent RNA 6000 Pico” (G2938-90046, Agilent Technologies).In general RNA yields of 3-135 ng total RNA and RNA integrity numbers (RIN) above 8 were obtained. RNA samples were concentrated with Agencourt RNAClean XP beads (A63987), according to manufacturer’s instructions (Protocol 001298v001, Agencourt) with modifications. In short, 2.5-5 ng of total RNA for each sample was prepared in a volume of 30 μl by adding nuclease free water (AM9937, Ambion). 1.5 μl of Recombinant RNase inhibitor (2313A, Clontech) was added to each RNA sample. A 1.8x reaction volume RNAClean XP bead cleanup was performed, instead of adding 54 ul RNAClean XP bead suspension, 18 μl RNAClean XP bead suspension and 36 μl RNAClean XP bead buffer (same solution without the beads) were added to each RNA sample. After 3 times wash with 70% ethanol, the bead pellets were dried at 37 degrees Celsius for 3-5 minutes, untill bead pellet begins to show cracks. RNA was eluted by adding 4 μl of NF-H20 and mixing by vortexing. RNA library preparation was performed as previously described with modifications.96 In short, oligo dT primer hybridization was performed by the addition of Oligo dT mix (0.7ul H2O, 0.1 ul RNAse inhibitor (40U/ul), 0.1 ul dNTP mix (100mM) and 0.1 ul Oligo-dT30VN primer (100uM)) to the 4 ul sample-RNA bead suspension. Reverse transcription was performed as described but the MgCl2 concentration was adjusted to 10 mM. Template switching and 7-12 cycles pre-amplification of full length cDNAs with template switching oligo’s was performed using ISPCR primer at a final concentration of 0.08 uM.
The amplified full length cDNA was used for NGS library construction by Tagmentation for Illumina sequencing, using the Illumina Nextera XT DNA sample preparation kit (FC-131-1096, Illumina) and IDT® for Illumina Nextera DNA Unique Dual Indexes (20027216, Illumina). RNA sequencing libraries were quantified and normalized based library QC data generated on the Bioanalyzer system according to manufacturer’s protocols (G2938-90321, Agilent Technologies).

tag: tissue

value: Brain tumor

tag: cell type

value: Monocyte-derived macrophage

tag: genotype

value: Ink4a/ArfKO, PDGFB


title: Week 48 LIDPAD 5

city: Singapore

first: Zun Siong

last: Low

address: 11 Mandalay Rd

country: Singapore

institute: Lee Kong Chian School of Medicine

data_processing:
Alignment done by HISAT2
Raw counts using featurecounts
DEGs determined using DESeq2 with cutoff of log2fc > ±1
Genome_build: grcm38
Supplementary_files_format_and_content: FPM

source_name: Mice from age of 8 weeks

extract_protocol:
TRIzol RNA extraction followed by E.Z.N.A.® HP Total RNA for purification, according to manufacturer’s protocol
Illumina library preparation done by NovogeneAIT

treatment_protocol: Mice from age of 8 weeks were fed either control or LIDPAD

tag: strain

value: Liver

tag: diet

value: LIDPAD

tag: diet duration (weeks)


title: MSCs from MCB, passage 0, donor 197, sequenced by RNAseq

city: Bogota

first: Cristian

middle: Camilo

last: Galindo

state: Bogota DC

address: Cra. 32 #12 - 81 Puente Aranda

country: Colombia

institute: Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud IDCBIS

description:
BM-CEM-GW-197
all_counts_merged.txt

data_processing:
Sequencing data from both RNA-seq and MACE-Seq were uploaded and analyzed on the GenXPro bioinformatics tools platform (https://tools.genxpro.net/).
Sequencing reads were adapter-trimmed, quality-trimmed, and cleaned from library-preparation artifacts using cutadapt (version 3.2).
Expression quantification was done using HTSeq (version 1.99.2) for MACE-Seq data and STAR for RNA-Seq data. QC was done using FASTQC (version 0.11.9), Samtools (version 1.12) and MultiQC (version 1.12).
Normalization and test for differential expression was performed in the statistical programming language R (www.rproject.org) with the DEseq2 package (version 1.34.0).
Assembly: Processed reads were mapped and annotated to the reference human genome GRCh38.p12 from ENSEMBL (version 102) using bowtie2 (version 2.4.3) for MACE-Seq data and using STAR (version 2.7.9a) for RNA-Seq data
Supplementary files format and content: Expression levels are given in transcripts per million (TPM)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Homo sapiens

source_name: Wharton's jelly from umbilical cord

growth_protocol: Wharton's jelly mesenchymal stromal cells were cultured in DMEM with low glucose an 10% human platelet lysate in a humidified atmosphere with CO2 at 37 °C

extract_protocol:
Cells were used and treated with the PureLink RNA Mini Kit (Thermo Fisher). The RNA concentration was measured with nanodrop (Thermo Fisher). Each sample was split into two tubes (25 ul each) and concentration varied between 50 and 2,760 ng/ml.
Conventional RNA-Seq libraries were prepared by Genwiz from Azenta Life Sciences an MACE-seq libraries were prepared by GenXPro GmbH MACE-Kit V2
RNA-seq
Massive Analysis of cDNA Ends (MACE-Seq)-RNA sequencing

treatment_protocol: Upon passage 1, cells were seeded at low (3000 - 4600 cells/cm2) or high denisity (4600 cm2) and expanded until reaching adequate number for cryopreservation

tag: passage

tag: donor

value: donor 197

value: Wharton's jelly from umbilical cord

tag: cell line

value: Primary cells

value: Mesenchymal stromal cells

value: WT

tag: treatment


title: astrocyte-24 h after injury-1

city: Beijing

first: Tingting

last: Li

address: Beichen road

country: China

institute: Chinese Academy of Sciences

data_processing:
The remaining data was aligned against the UCSC D. melanogaster genome (dm6) using Hisat2 with the annotation file of the same version. On average, 92% of the initial reads were mapped to dm6. HTSeq was used to calculate the raw read counts of genes for each sample. DESeq2 was used to normalize the data. Transcripts were considered as significantly differentially expressed if their adjusted p values were less than 0.01 (p < 0.01) by the Benjamini-Hochberg method. Following normalization of the data, DESeq2 was used to perform pairwise comparisons between the control and experimental groups using parametric tests. Genes with absolute value of logarithmic fold change (log2FC) > 1.0 were qualified for the final set of DEGs. Volcano plots and heatmap were constructed for visualization of the resulting expression intensity data following the identification of DEGs and RNA-Seq data normalization by the adjusted p value calculations.
AnnotationHub 2.20.2 biomaRt 0.7 clusterProfiler 3.13 curl 4.3.2 DESeq2 1.30.1 DIOPT 8.0 dplyr 1.0.4 FastQC 0.11.7 ggplot2 3.3.5 ggrepel 0.9.1 org.Dm.eg.db 3.11.4 pheatmap 1.0.12 R 4.0.0 RSEM 1.3.1 RSeQC 2.5 STAR 2.6.0a Trimmomatic 0.39 VennDiagram 1.6.20
Assembly: dm6
Supplementary files format and content: tab-delimited text files include TPM values for each sample

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Flies were maintained on standard cornmeal medium at 25°C otherwise indicated.

extract_protocol:
Brains from adult flies (R86E01-Gal4/UAS-Redstinger) with no injury, 4 h after injury and 24 h after injury were dissected out in freshly prepared adult hemolymph saline (AHS) buffer, as previously described (Yang et al., 2016). Briefly, a total of ∼50 brains for each group was immediately transferred to an Eppendorf tube (1.5 mL) containing 200 µL AHS with Pronase (1 mg/mL; P5147, SigmaAldrich) and Dispase (1 mg/mL; LS02104, Worthington Biochemical Corporation). After tissue digestion for 30 min at 25°C, the enzyme medium was removed, followed by two brief, gentle washes with fresh AHS containing 2% PBS. Brain samples were then triturated by gently pipetting in 1 mL AHS through four fire-polished Pasteur pipettes with descending pore sizes (400 μm, 300 μm, 200 μm, and 100 μm) for a total of ∼20 min. Next, the dissociated cells were centrifuged for 10 min at 100 × g and the AHS was replaced with the same buffer to minimize any RNA content released from damaged cells during the trituration process. Finally, dissociated tissues were filtered through 45 μm filter and then put on ice. FACS sorting was performed according to the following gating procedure with 70 μm nozzle by BD FACS Aria: (1) an initial SSC-A/FSC-A gate to minimize debris; (2) a SSC-A/pe-Texa Ted-A gate to choose only red fluorescence positive cells. At this step, 1600 cells were sorted directly into ice-cold cell lysis buffer (oligo-dT30VN primer, ribonuclease inhibitor, dNTP mix) and stored at -80°C until all samples were ready for RNA extraction and cDNA amplification.
Cell samples were sent to the Anoroad Company for RNA extraction. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step was used to purify the products. Briefly, Smart-Seq2 method was used to amplify cDNA. Concentration and integrity of cDNA was assessed using Qubit 3.0 Flurometer (Life Technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies) to ensure the cDNA length was around 1-2 kbp. After quality control, 40 ng cDNA was used to be fragmented at 350 bp by Bioruptor® Sonication System (Diagenode Inc.). To construct Illumina library, end repair, 3’ ends A-tailing, adaptor ligation, PCR amplification and library validation were performed. PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were used for library quality inspection. Qualified libraries were loaded on Illumina Hiseq platform for PE150 sequencing.

treatment_protocol: Construction and use of the HIT device were described previously (Katzenberger et al., 2013). Deflection of the spring to 90° was the standard angle for strike. Flies were collected at 3 days after eclosion and treated with TBI.

value: brain

value: primary cell

value: astrocyte

value: 24 h after injury


title: Week 48 LIDPAD 10


title: astrocyte-4 h after injury-4

value: 4 h after injury


title: astrocyte-4 h after injury-3


title: Week 48 LIDPAD 3


title: Lipid-laden microglia, mn:224

value: Lipid-Laden Microglia


title: astrocyte-4 h after injury-2


title: MSCs from MCB, passage 0, donor 190, sequenced by RNAseq

description:
BM-CEM-GW-190
all_counts_merged.txt

value: donor 190


title: Co-culture, Tumor cell, 24 hours post myelin, mn:003

source_name: Bone-marrow/brain tumor

value: Bone-marrow/brain tumor

value: PDG-Ink4a Recurrent

value: Tumor cell

value: 24 hour myelin debris


title: Week 48 LIDPAD 4

value: Liver

value: LIDPAD


title: MSCs from MCB, passage 0, donor 195, sequenced by RNAseq

description:
BM-CEM-GW-195
all_counts_merged.txt

value: donor 195

value: Wharton's jelly from umbilical cord


title: MSCs from MCB, passage 0, donor 199, sequenced by RNAseq

description:
BM-CEM-GW-199
all_counts_merged.txt

value: donor 199

value: Primary cells

value: Mesenchymal stromal cells


title: Non-lipid-laden microglia, mn:224

value: Brain tumor

value: Microglia

value: Ink4a/ArfKO, PDGFB


title: astrocyte-4 h after injury-1

value: brain

value: primary cell

value: astrocyte

value: WT

value: 4 h after injury


title: TFK1, combination, biol rep 3

city: Wuhan

first: Ningyu

last: Wang

state: Hubei

address: JIEFANG ROAD1277#

department: Cancer Center, Union Hospital

institute: Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

data_processing:
Clustering and sequencing( Illumina NovaSeq 6000)
Quality control
Reads mapping to the reference genome
Quantification of gene expression level
Differential expression analysis
Enrichment analysis of differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: Cholangiocarcinoma

growth_protocol: TFK1 cells were maintained in RPMI 1640 supplemenied with 10%

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg

treatment_protocol: We used a cholangiocarcinoma cell line TFK1, and set up a blank control group, a radiotherapy group (6Gy), a chemotherapy group  (surufatinib 4.33ng/ml), and a combination treatment group (surufatinib 4.33ng/ml+RT 6Gy). After 24 hours of treatment, total RNA was extracted for transcriptome sequencing in different treatment groups.

value: Cholangiocarcinoma

value: cancer cell line


title: Co-culture, Macrophage, 24 hours post myelin, mn:003

value: Bone-marrow/brain tumor

value: Bone-marrow derived macrophages

value: 24 hour myelin debris


title: astroycte-control-5

value: uninjury


title: TFK1, combination, biol rep 2


title: Week 48 LIDPAD 2

value: Liver

value: LIDPAD


title: Week 48 LIDPAD 1


title: Mono-culture, Tumor cell, 24 hours post myelin, mn:003

value: PDG-Ink4a Recurrent

value: Tumor cell


title: Week 48 control 12

value: Control


title: astroycte-control-4


title: astrocyte-4 h after injury-5


title: TFK1, surufatinib, biol rep 3

value: surufatinib


title: Week 48 control 11


title: TFK1, combination, biol rep 1


title: astroycte-control-3

value: brain


title: Week 48 control 10


title: TFK1, surufatinib, biol rep 2


title: astroycte-control-2

value: primary cell


title: Co-culture, Tumor cell, 6 hours post myelin, mn:003

value: 6 hour myelin debris


title: Co-culture, Macrophage, 6 hours post myelin, mn:003


title: Week 48 control 9


title: TFK1, surufatinib, biol rep 1

value: WT


title: Mono-culture, Tumor cell, 6 hours post myelin, mn:003

value: Brain tumor


title: TFK1, RT_6Gy, biol rep 3

value: Cholangiocarcinoma


title: Lymph glands RpS19a RNAi 3

city: Canberra

first: Olga

last: Zaytseva

state: ACT

address: 131 Garran Road

country: Australia

institute: John Curtin School of Medical Research

data_processing:
Sequence quality was verified using FastQC v0.11.6
Alignment was performed using Tophat2 2.0.13
Gene counts were performed using HTSeq 0.6.1
Significant differential expression was analysed using DESeq2 1.12.0
Assembly: dmel-r6.10 (Flybase)
Supplementary files format and content: Plain text (.txt) files containing raw gene-level counts for each sample
Supplementary files format and content: Microsoft Excel (.xlsx) file containing output of DESeq2 (differential gene expression). Each column contains: FlybaseID, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, geneSymbol, EntrezID

molecule: polyA RNA

source_name: Lymph gland

growth_protocol: Hemese-GAL4 virgin females were crossed to either w1118 or RpS19a RNAi males and the offspring were maintained at 25°C prior to sample collection at larval 3rd instar stage

extract_protocol:
Promega ReliaPrep RNA Tissue miniprep system (Z6010) following the manufacturer’s protocol and eluted in 15 μL nuclease-free water. RNA purity and integrity were assessed using an automated electrophoresis system (2200 TapeStation, Agilent Technologies)
RNA was prepared using the standard TruSeq Illumina protocol preserving strandedness information, with Oligo-dT beads used to enrich for mRNA

treatment_protocol: UAS-RNAi expression prior to microdissection of larval lymph glands (approximately 120 control lymph glands, or 40 RpS19a RNAi lymph glands were pooled for each sample)

value: Lymph gland

tag: developmental stage

value: Larval third instar

value: hemocyte

value: Hemese-GAL4/RpS19a RNAi (VDRC #107188)

value: culture at 25°C


title: Mono-culture, Macrophage, 6 hours post myelin, mn:003

source_name: Bone-marrow

value: Bone-marrow

value: Bone-marrow derived macrophages


title: Week 48 control 7

value: Liver


title: TFK1, RT_6Gy, biol rep 2

value: cancer cell line


title: Week 48 control 6

value: Control


title: Lymph glands RpS19a RNAi 2


title: TFK1, RT_6Gy, biol rep 1


title: Co-culture, Tumor cell, 0 hours post myelin, mn:003

value: Bone-marrow/brain tumor

value: PDG-Ink4a Recurrent

value: Tumor cell


title: Co-culture, Macrophage, 0 hours post myelin, mn:003


title: Mono-culture, Macrophage, 24 hours post myelin, mn:003

value: 24 hour myelin debris


title: Week 48 control 5


title: TFK1, control biol, rep 3

value: WT

value: control


title: Mono-culture, Tumor cell, 0 hours post myelin, mn:003

value: Brain tumor


title: Week 48 control 4


title: Lymph glands RpS19a RNAi 1

value: Lymph gland


title: Lymph glands control 3

value: Larval third instar


title: Lymph glands control 2

value: hemocyte


title: Week 48 control 3


title: TFK1, control biol, rep 2

value: Cholangiocarcinoma


title: TFK1, control, biol rep 1


title: Lymph glands control 1

value: culture at 25°C


title: Co-culture, Tumor cell, 24 hours post myelin, mn:002


title: astroycte-control-1

value: brain

value: primary cell

value: astrocyte

value: uninjury


title: Week 48 control 8

value: Liver

value: Control


title: Week 48 control 2


title: scRNA_HCTRad21D_DMSO_30m

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

country: USA

institute: NIH

library_source: transcriptomic single cell

data_processing:
scRNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
mRNA-seq half-life estimation: htseq count file generation from mRNA-seq aligned both for ERCC spike-in control and genomic sequence
mRNA-seq half-lfe estimation:estimate the decay rate constant (kdecay) by fitting the exponential curve on concentration changes upon timepoints using SSasymp R function. From the decay constant, we calculated the mRNA half-lives using the following equation: ln(2)/kdecay
Assembly: mm9, mm10 (only for scRNAseq), hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigwig file

growth_protocol: HCT-116 degron cell lines: RAD21- mAID-mClover1 and HCT116-OsTIR1-MED26-AID2 were cultured in McCoy's 5A medium supplemented with L-Glutamine (Gibco), 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), at 37 °C; 5% CO2.  ES (E14) RAD213 and CTCF degron4 cell lines were cultured in knock-out DMEM (Gibco), ES cell qualified FBS (ATCC), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 1:10,000LIF (10,000x) on 0.1% gelatin coated dishes at 37 °C; 5% CO2.  Primary WT and Myc knockout B cells were derived from Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (Sigma) (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice).  The deletion of floxed allele was checked as previously5 with PCR or intracellular staining of Myc protein. B cells were isolated from spleen of WT and KO mice, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies) and activated for 4 hours with 50 mg/ml LPS and 2.5 ng/ml IL4 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco), at 37 °C; 5% CO2 B220 positive primary bone marrow B cells were derived from C57BL/6J wild-type mice, enriched with CD45R (B220) MicroBeads Kit (Miltenyi Biotec) and Dead Cell Removal Kit (Miltenyi Biotec). Splenic B cells were derived from C57BL/6J wild-type mice immunized with a keyhole limpet haemocyanin (KLH; 25 µg/footpad, Sigma-Aldrich) in the presence of 10% CFA adjuvant (Sigma-Aldrich). After 5 days B cells were isolated from spleen, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies), and activated for 72 hours with 50 mg/ml LPS, 2.5 ng/ml IL4 and anti-CD180 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco),  at 37 °C; 5% CO2.  CH12 B lymphoma cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco), at 37 °C; 5% CO2. LNK (NK cell line) cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 10 mM HEPES, 1:100 NEAA (Gibco), 1:100 sodium pyruvate (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 200 IU/ml IL-2 (Sigma-Aldrich). Skin cells for scRNA-Seq: whole epidermis from mouse neonates. Keratinocytes were isolated from Fvb neonate (P0-P2) skin (n = 2) as described in Lichti et al., 20086. Cells were subjected to MACS Dead Cell removal kit (Miltenyi Biotech) using the manufacturer’s protocol. Skin cells for mRNA half-lives estimation: primary keratinocyte. Skins from a pool of Fvb neonatal mice were collected at P0-P2 and incubated overnight in 2.0 U/mL Dispase II (Sigma) in KBM-Gold (Lonza) on an end-over-end rotator. The following day, skins were washed twice in 1x PBS (Sigma), and epidermises were separated from dermises. Epidermises were placed basal side down and floated in pre-warmed 0.25% Trypsin-EDTA (Thermo Scientific) for 20min on an orbital shaker at room temperature. An equal volume of pre-warmed 2.5mg/mL Soybean Trypsin Inhibitor (Thermo Scientific) was added to finish trypsinization, and epidermises were rubbed vigorously against bottom of plate using curved forceps to dislodge keratinocytes. Dislodged cells were pooled into a tube on ice in KBM-Gold. Pooled cells were pipetted ~40 times with a 10ml serological pipette and strained with a 100um filter before pelleting cells at 300xg for 10min at 4°C. Cells were resuspended in 4.5mL KBM-Gold per epidermis and cell count was obtained using Cellometer ViaStain AOPI Solution (Sigma). The cells were subjected to Percoll (GE LifeSciences; ratio of 10X PBS:Percoll:KBM-Gold media was 1:4:5, where the cells were at a concentration of 1 million per mL of final volume) gradient ultracentrifugation using a swinging bucket rotor (11,000 rpm for 42 minutes at 4°C) to separate the basal and suprabasal fractions. The cells at the top band were suprabasal cells and separated from the pellet at the bottom of the tube which were basal cells. The basal cell sample was carefully pipetted out, washed twice with 4°C 1x PBS, seeded onto collagen-coated (Collage Type I; Corning) 6-well plates at 1x106 cells per well, and incubated at 37°C overnight to allow cells to attach to the plate before proceeding with experiments.  Mast cells: Mouse bone marrow-derived mast cells (BMMC) were differentiated from the marrow of tibias and femurs of C57/BL6 mice and cultured for 8 weeks in RPMI 1640 containing 10% FBS, 1M HEPES, 100 U/mL penicillin, 100 μg/mL streptomycin, 4 mM l-glutamine, 1 mM sodium pyruvate, non-essential amino acids, 50 μM 2-mercaptoethanol, IL-3 (20 ng/mL) and stem cell factor (SCF) (20 ng/mL). The purity of mast cells was monitored by assessing the expression of the receptors for SCF (CD117;Kit) and for IgE (FcεRI) by flow cytometry. By the end of 6-8 weeks in culture more than 98% of the cultured population was FcεRI+/CD117+ double-positive mast cells.

extract_protocol:
RNA-Seq Cells (0.5M) were harvested and lysed in 100 µl of the lysis solution (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen). RNA was isolated and DNase treated according to manufacturer’s protocol. High RNA quality was confirmed using the Agilent TapeStation system before library preparation. mRNA polyA- purification, reverse transcription and library preparation were performed using NEBNext Poly(A) mRNA Magnetic Isolation Module. For spike-in control ERCC RNA Spike-In Mix (Invitrogen) was added before RNA isolation.   ChIP-Seq Cells were fixed with 1% formaldehyde (Sigma) for 10 min at 37°C, treated with 1/20 volume of 2.5 M Glycine, washed with PBS, snap-frozen on dry ice and stored at -80°C until further processing. After thawing cells were resuspended in RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) supplemented with Complete Mini EDTA free proteinase inhibitor (Roche) and sonicated using ultrasonicator (Covaris) in 1 ml AFA tubes (Covaris): duration (s): 1200, peak power: 75, duty % factor: 15, cycles/burst:1000. Sonicated chromatin was pre-cleared with Dynabeads and incubated overnight at 4˚C with rotation with following antibodies: RAD21: ab992 (Abcam); MED26: 13641S (Cell Signaling Technology); TATA binding protein TBP: ab28175 (Abcam); BRD4: ab128874 (Abcam); RNA Pol II: ab26721 (Abcam). Next day samples were washed (10 min at 4˚C with rotation): 2x with RIPA buffer, 2x with RIPA buffer + 0.3 M NaCl, 2x with 1 ml of LiCl buffer (0.25M LiCl, 0.5% Igepal CA-630, 0.5% NaDOC, store at 4˚C), 1x with 1 ml of TE + 0.2 % Triton X-100, 1x with 1 ml of TE. After washes beads were resuspended with 100 ul of TE, followed by addition of 3 µl of 10% SDS and 5 µl of 20 mg/ml Proteinase K and incubated at 65˚C for 4h. After decrosslinking DNA was purified on columns using ChIP DNA Clean & Concentrator kit (Zymo Research). In the next step DNA was quantified using Qubit system (Invitrogen).  mRNA half-lives estimation  Cells were treated with 5 µg/mL actinomycin D (Sigma) and harvested (0.5M cells) at timepoint 0 hours and up to 24 hours: at 1, 2, 4, 8, 12 and 24 hours timepoints7. After each timepoint the viability of cells was checked with FACS, or Nexcelom cell counter after staining with Acridine Orange/Propidium Iodide (AO/PI) (Nexcelom Bioscience). Some cell types did not survive longer actinomycin D treatment than 8 hours, so the last collected timepoint was determined based on cell type viability (details in Extended Data Fig.1a). Pellets were lysed in 100 µl of the lysis solution (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen), ERCC RNA Spike-In Mix (Invitrogen) was added, RNA isolated (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen), and RNA-Seq was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module.   scRNA-Seq Cells were washed twice with 1x PBS containing 0.04% weight/volume BSA, resuspended in the same buffer and encapsulated into droplets using 10X Genomics system.
RNA-Seq NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NextSeq2000, NextSeq550, HiSeq3000 or NovaSeq6000 (Illumina).  ChIP-Seq Library was prepared using Ovation Ultralow System V2 (Tecan) according to manufacturer’s protocol. Before sequencing high quality was confirmed using the Agilent TapeStation system. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (Illumina).  scRNA-Seq Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeq6000 machine (Illumina).

treatment_protocol: HCT-116 degron cell lines: Starvation: cells were FBS depleted for 14 hours, followed by an additional incubation with FBS free medium for another 6 hours in the presence of DMSO (control), 500 µM auxin (indole-3-acetic acid, IAA) (Sigma-Aldrich) for degradation of the AID-tagged RAD21 and MED26 or 500nM JQ-1 (Sigma-Aldrich) for BRD4 displacement. Cells were analyzed after addition of FBS in the presence of DMSO or drugs at timepoints: 0h (RAD21 degron), 0.5h (RAD21 degron) and 2h (RAD21 and MED26 degron, JQ-1 treatment). ES (E14) For the AID-tagged proteins 500 µM auxin (indole-3-acetic acid, IAA) (Sigma-Aldrich) was added for 6 hours (RAD21) or 24 hours (CTCF). Splenic B cells To measure mRNA half-lives in activated B cells Actinomycin D was added after 2 days of stimulation with LPS, IL4 and anti-CD180 (more details: mRNA half-lives estimation). Skin cells To estimate mRNA half-lives in skin cells we used basal cells.

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 30m


title: Co-culture, Macrophage, 24 hours post myelin, mn:002

value: Bone-marrow/brain tumor

value: Bone-marrow derived macrophages

value: 24 hour myelin debris


title: scRNA_HCTRad21D_DMSO_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: Week 48 control 1


title: Mono-culture, Tumor cell, 24 hours post myelin, mn:002

value: Brain tumor

value: PDG-Ink4a Recurrent

value: Tumor cell


title: scRNA_HCTRad21D_DMSO_0h

value: 10% FBS 14h, noFBS+DMSO 6h


title: Week 32 LIDPAD 19

value: LIDPAD


title: Mono-culture, Macrophage, 24 hours post myelin, mn:002

value: Bone-marrow


title: siALK5 PC, TGFβ 2

city: New Haven

first: Jui

last: Dave

state: CT

address: 300 George St

department: Cardiovascular Research Center

institute: Yale University

description:
invitro PCs_all groups vs Scr_processed data.txt
invitro PCs_siAlk5tgf vs Scrtgf_processed data.txt
invitro PCs_siAlk5tgf vs siAlk5_processed data.txt

data_processing:
Data were analyzed using Partek Flow software.
BOWTIE2 was used to align trimmed reads to the reference genome (hg19).
Gene counts were normalized by Median ratio and differential analysis between controls and mutants was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: There are 4 groups being processed here. Each group is based on a combination of the genotype (Scr or siALK5) and treatment (no treatment or TGFβ treated). In general, all 4 groups are compared against Scr no treatment control which is provided with each raw data file. Moreover, pair-wise comparisons of treatment/genotype derived from the specific group are also provided .
Supplementary files format and content: Each processed data files contain gene name, total counts, pvalue, FDR and fold change between groups being compared. Following datasets are compared for generating processed data files (1) all groups vs. Scr no treatment group (2) Scr no treatement vs. Scr TGFβ (3) Scr no treatment vs. siALK5 no treatment (4) Scr TGFβ vs. siALK5 TGFβ and (5)  siALK5 no treatment vs. siALK5 TGFβ. All features (genes) were included.

growth_protocol: Human brain vascular PCs (ScienCell) were cultured in low-glucose DMEM (Gibco) supplemented with 10% FBS (PC media) up to passage 6.

extract_protocol:
Total RNA was isolated using PureLink RNA Kit (Invitrogen).
Samples with RIN values greater than 9 were used for library preparation. mRNA library was prepared from ~200 ng RNA using KAPA mRNA HyperPrep kit (Roche). Indexed libraries were quantified by KAPA Library Quantification kit (Roche), and insert size distribution was determined with the Agilent 2100 Bioanalyzer. Samples with a yield of  ≥ 0.5 ng/µl and a size distribution of 150-300 bp were used for sequencing using NovaSeq6000 sequencer (Illumina).

treatment_protocol: PCs were transfected with Lipofectamine 2000 (Life Technologies) containing siALK5 (Dharmacon) targeting ALK5 or scrambled control (50 nM) for 6h. Cells were washed and cultured in complete medium for 36h. For TGFβ treatment, following transfection, PCs were serum starved in low-glucose DMEM supplemented with 1% FBS for 24h and then treated with TGFβ1 (5ng/mL, R&D Systems) for 12h.

value: brain

value: pericytes

value: mesenchymal cells

value: TGFβ


title: siALK5 PC, TGFβ 4


title: siALK5 PC, TGFβ 3


title: Week 32 LIDPAD 18

value: Liver


title: Mono-culture, Macrophage, 0 hours post myelin, mn:003

value: Control


title: Co-culture, Tumor cell, 6 hours post myelin, mn:002

value: 6 hour myelin debris


title: Co-culture, Macrophage, 6 hours post myelin, mn:002

value: Bone-marrow/brain tumor


title: Week 32 LIDPAD 17


title: siALK5 PC, no treatment 3

description:
invitro PCs_all groups vs Scr_processed data.txt
invitro PCs_siAlk5 vs Scr_processed data.txt
invitro PCs_siAlk5tgf vs siAlk5_processed data.txt

value: no treatment


title: siALK5 PC, no treatment 4


title: Week 32 LIDPAD 16


title: siALK5 PC, no treatment 2


title: Mono-culture, Tumor cell, 6 hours post myelin, mn:002


title: scRNA_HCTRad21D_AUXIN_2h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+IAA 6h, FBS + IAA 2h


title: scRNA_HCTRad21D_AUXIN_30m

value: 10% FBS 14h, noFBS+IAA 6h, FBS + IAA 30m


title: siALK5 PC, no treatment 1


title: scRNA_HCTRad21D_AUXIN_0h

value: 10% FBS 14h, noFBS+IAA 6h


title: Mono-culture, Macrophage, 6 hours post myelin, mn:002

value: Bone-marrow derived macrophages


title: ChIP-seq-input_NB4-M7_TUM

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

country: France

institute: IGBMC

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using trim_galore (version 0.6.4 options -q 20 –stringency 2)
Reads were mapped to the hg38 genome (only chromosomes 1 to 22, X, Y and M) using bowtie2 (version 2.3.0) and only reads with mapping quality >= 10 were kept.
Read density tracks were generated using bedtools genomecov (version 2.29.0) for each genomic position from reads extended to 200bp and read counts were normalized to one million reads in the library and visualized using the IGV browser.
Peaks were called using MACS2 (version 2.2.5 option --broad-cutoff 0.00001) and peaks located on chromosome M or in ENCODE blacklisted regions were removed.
For comparison across samples, ChIP-seq peak regions were merged using bedtools merge (version 2.29.0) and raw read counts per region were calculated using bedtools intersect (version 2.29.0 option -c). Differentially enriched regions were identified using DESeq2 (version 1.26.0) using the following thresholds: adjusted p-value <= 0.05 and fold change >= 2.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Tumor cells

growth_protocol: The tumor samples were subjected to mechanical and enzymatic dissociation using Tumor Dissociation Kit (Miltenyi Biotec). The dissociated tumor cells were suspended in DMEM/F12 medium supplemented with 1% penicillin-streptomycin, 2% B27 (Invitrogen), and 20ng/ml of human recombinant FGF and   EGF (Peprotech). Adherent cells were cultured in DMEM (catalog no. Gibco) supplemented with 10% of FBS (PAN-Biotech) and 1% of penicillin-streptomycin (Gibco). Cells were maintained at 37°C in humidified, 5% CO2 chambers. Spheroid was grown in ultralow attachment plates (Corning).

extract_protocol:
Single cells from adherent or spheroids cultures counted and diluted to a target of 500’000 cells per ml. Formaldehyde at 1% final concentration was added for 10 minutes at 37°C. Quenching was performed with 125 mM Glycine. The solution was spun at 1500rpm for 5’ at 4C and pellet washed twice with cold PBS + protease inhibitors (PI) before snap freezing. For tumors ~40mg a fragment was put in petri dish on normal ice and cut into small pieces and resuspended in 1ml PBS + protease inhibitors and transferred to a 1.5ml tube. Formaldehyde at 1% final concentration was added for 10 minutes at 37°C. Quenching was performed with 125 mM Glycine.  Pellet was washed once in cold PBS + PI after 5min spin at 2,500 RPM at 4°C. Manual dissociation in PBS + PI was performed with syringe passages: 10up/down with a 18G needle, 10up/down with a 21G needle, 10up/down with a 23G needle (if possible).  The solution was spun down another time and the pellet snap frozen. Lysis was performed at 4°C for 10min in 300ul of 50mM Tris-HCl, 1% SDS, 0.25% DOC (+ PI) and sonication was performed with tip sonicator after dilution in 900ul of dilution buffer  (DB) - 50mM Tris-HCl pH 7.4, 0.1% SDS, 150mM NaCl, 1.84% Triton-X + PI - with the following parameters: sonication time, 3 min; amplitude, 40%; cycle, 0.7s ON and 1.3s OFF. After clearing the solution with 14000rpm spin, the supernatant was further diluted with 1,8ml of DB before IP overnight at 4°C. The equivalent of 2-5M cells or 5-10mg of tumors was used for a single immunoprecipitation (IP) with 0.1-1ug antibody.  After washing once Protein G magnetic beads in DB, the equivalent of 30 ul (50 ul for tumors) of original solution was added to the IPs for 2h at 4°C. Beads were washed 2x with 150 mM NaCl RIPA buffer, 500mM NaCl RIPA, LiCl buffer (10mM Tris-HCl pH 8.1, 250mM LiCl, 0.5% Triton X-100, 0.5% DOC) and once in 10 mM Tris-Cl pH 8.5. Elution was performed with 1X TE pH 8.0, 0.1% SDS, 150mM NaCl, 5mM DTT at 65°C for 1h. RNAse treatment and crosslink reversal with proteinase K were applied on the supernatant, before SPRI beads DNA purification.
After Qubit quantification 5-10ng DNA was used for Illumina TruSeq Library preparation. Sequencing was performed on a Hi-Seq Illumina Genome Analyzer (50 bp single-read).

tag: patient

tag: pdxs

value: Tumor cells

tag: chip antibody


title: Week 32 LIDPAD 15

value: LIDPAD


title: Co-culture, Tumor cell, 0 hours post myelin, mn:002

value: PDG-Ink4a Recurrent

value: Tumor cell


title: ChIP-seq-input_NB4-M7_SPH

source_name: Spheroids

value: Spheroids


title: Week 32 LIDPAD 20


title: siALK5 PC, TGFβ 1

value: brain

value: pericytes

value: mesenchymal cells


title: Week 32 LIDPAD 14

value: Liver


title: Co-culture, Macrophage, 0 hours post myelin, mn:002

value: Control


title: Week 32 LIDPAD 13


title: ChIP-seq-input_NB4-M7_ADH

source_name: Adherent cells

value: Adherent cells


title: ChIP-seq-input_NB1-M11_TUM


title: Mono-culture, Tumor cell, 0 hours post myelin, mn:002

value: Brain tumor


title: Scr PC, TGFβ 3

description:
invitro PCs_all groups vs Scr_processed data.txt
invitro PCs_Scrtgf vs Scr_processed data.txt
invitro PCs_siAlk5tgf vs Scrtgf_processed data.txt

value: Scr

value: TGFβ


title: Scr PC, TGFβ 2


title: Week 32 LIDPAD 12


title: ChIP-seq-input_NB1-M11_ADH


title: ChIP-seq-input_NB1-M11_SPH


title: Week 32 LIDPAD 10


title: Scr PC, no treatment 4

description:
invitro PCs_all groups vs Scr_processed data.txt
invitro PCs_Scrtgf vs Scr_processed data.txt
invitro PCs_siAlk5 vs Scr_processed data.txt

value: no treatment


title: Scr PC, no treatment 3


title: ChIP-seq-H3K4me3_NB4-M7_TUM

value: H3K4me3 (Millipore 07-473)


title: Scr PC, TGFβ 4


title: ChIP-seq-H3K4me3_NB4-M7_ADH


title: Week 32 LIDPAD 8


title: Scr PC, TGFβ 1


title: Scr PC, no treatment 2


title: Co-culture, Tumor cell, 24 hours post myelin, mn:001

value: Bone-marrow/brain tumor

value: 24 hour myelin debris


title: Week 32 LIDPAD 9

value: LIDPAD


title: Co-culture, Macrophage, 24 hours post myelin, mn:001

value: Bone-marrow derived macrophages


title: Mono-culture, Tumor cell, 24 hours post myelin, mn:001

value: PDG-Ink4a Recurrent

value: Tumor cell


title: Week 32 LIDPAD 7


title: ChIP-seq-H3K4me3_NB1-M11_TUM

value: Tumor cells


title: Co-culture, Tumor cell, 6 hours post myelin, mn:001

value: 6 hour myelin debris


title: Week 32 LIDPAD 11


title: ChIP-seq-H3K4me3_NB1-M11_SPH

value: Spheroids


title: Scr PC, no treatment 1

value: brain

value: pericytes

value: mesenchymal cells


title: Week 32 LIDPAD 4

value: Liver


title: Week 32 LIDPAD 6


title: Mono-culture, Macrophage, 0 hours post myelin, mn:002

value: Bone-marrow

value: Control


title: Co-culture, Macrophage, 6 hours post myelin, mn:001


title: ChIP-seq-H3K4me3_NB1-M11_ADH

value: Adherent cells


title: siRNA2

city: Liaocheng

first: Rui

last: Yang

state: Shandong

address: Hunan Road

department: Biomedical Laboratory, Medical School

institute: Liaocheng University

data_processing:
version 0.23.1
Assembly: Homo_sapiens.GCF_000001405.40_GRCh38.p14_genomic.genome.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: glioblastoma cell

growth_protocol: LN229 glioblastoma cell were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
50ul siRNA mixture+750ul Opti MEM, 50ul NC mixture+750ul Opti MEM (siRNA and NC dry powder dissolved in DEPC water; 100ul/1OD, operated on ice), gently mix and let stand at room temperature for 15 minutes. Drop the mixed solution into the corresponding 10cm cell culture dish, return the cells to the incubator for 4-6 hours, and then add 8mL of complete culture medium containing 20% FBS to incubate for 24 hours.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations

treatment_protocol: Treat cells with lipofectamine 3000 and siRNA for 24 hours, respectively

value: glioblastoma cell

value: cancer cell

value: GDH1 gene knockdown

value: GDH1 gene knockdown cells of the glioblastoma cell line LN229 cells


title: Mono-culture, Macrophage, 24 hours post myelin, mn:001

value: Bone-marrow derived macrophages

value: 24 hour myelin debris


title: ChIP-seq-H3K4me3_NB4-M7_SPH

value: H3K4me3 (Millipore 07-473)


title: Mono-culture, Tumor cell, 6 hours post myelin, mn:001

value: Brain tumor

value: PDG-Ink4a Recurrent

value: Tumor cell


title: NC3

value: WT

value: wild-type cells of the glioblastoma cell line LN229 cells


title: siRNA1


title: Week 32 LIDPAD 3

value: LIDPAD


title: NC2


title: RNA-seq_NB4-M9_SPH

data_processing:
RNA-seq reads were mapped to the hg38 genome (only chromosomes 1 to 22, X, Y and M) using hisat2 (version 2.0.5) and the Ensembl gene annotations Homo sapiens GRCh38.87.
Read density tracks were generated using bedtools genomecov (version 2.29.0 option -split) for each genomic position and read counts were normalized to one million reads in the library and visualized using the IGV browser.
Raw read counts and RPKM values were calculated over gene exons using htseq-count (version 0.9.1). Differentially expressed genes were identified using DESeq2 (version 1.26.0) using the following thresholds: adjusted p-value <= 0.001 and fold change >= 2.
Gene ontology annotations were used to calculate the enrichment of biological processes and associated hypergeometric p-values of genes in each class compared to all genes.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was extracted with miRCURY kit (Exiqon) using Lysis buffer + B-mercaptoethanol. For tumor samples, dissociation was performed following gentleMACS Dissociator kit instructions for soft tumors (Miltenyi Biotech).
Minimum 100 ng used for preparing sequencing libraries using the TruSeq mRNA stranded kit (Illumina) and sequencing was performed on a Hi-Seq Illumina Genome Analyzer (100 bp single-read).

value: Spheroids


title: Co-culture, Tumor cell, 0 hours post myelin, mn:001

value: Bone-marrow/brain tumor


title: Week 32 LIDPAD 2

value: Liver


title: RNA-seq_NB4-M7_TUM

value: Tumor cells


title: NC1

value: glioblastoma cell


title: Co-culture, Macrophage, 0 hours post myelin, mn:001

value: Control


title: Week 32 LIDPAD 5


title: Mono-culture, Tumor cell, 0 hours post myelin, mn:001


title: Week 32 LIDPAD 1


title: siRNA3

value: cancer cell

value: GDH1 gene knockdown


title: RNA-seq_NB4-M7_SPH


title: RNA-seq_NB4-M9_TUM


title: Sta Nucleus replicate 4

city: Qingdao

first: Xiaonan

last: Cui

address: 238 Songling Road

institute: The Ocean University of China

description: Standard nucleus RNA-seq,replicate 4

data_processing:
Drop-seq core computational protocol (v.2.0.0)
DESeq2 package of the R project (version 4.1.2)
Assembly: Ensembl mm10 and hg18
Supplementary files format and content: tab-delimited text file includes matrix for each sample

source_name: Hela cell

extract_protocol:
Hela cells were cultured at 37 °C in a humidified 5 % CO2 atmosphere, in high-glucose DMEM (Gibco; 11965092) supplemented with 10 % calf serum (Gibco;10270-106), 1 % penicillin/streptomycin (Nacalai Tesque; 0503), and 1 % L-glutamine (Nacalai Tesque; 16948-04). For cell preparation, Poly-l-lysine-coated chambers were coated with sterile PDL (Sigma Aldrich cat. no. P6407) at 0.3 mg/ml overnight at 4 °C. Afterwards, the chamber was dried for 1 hour, washed with UltraPure water (Invitrogen; 10977023). Chambers were then seeded with cells per well and placed in an incubator (37 °C with 5 % CO2) two days for subcellar resolution validation.Fresh frozen tissue (moouse embryo E14.5 and mouse brain) were OCT embedded, and 10um fozen sections were cut with cryostat. FFPE tissue (mouse embryo E15.5) is sliced with 7um. Different barcode represent different region of light illumination. The library struction is "read2-7bp bar—32fix--8bp-UMI—22bp dTVN-cDNA-read1"
The library was performed by IVT and RT-PCR protocol. Briefly,The RT products (15 μl) were combined with PCR mix, and amplified by PCR . Fragments of 250–1000 bp were then purified and size-selected with Speedbead magnetic capboxylate. The quality of the resulting cDNA library was quantified using a Qubit dsDNA HS assay kit (Invitrogen, Q32854) with Qubit 3.0 Fluorometer (Invitrogen),before sequencing on the Illumina NovaSeq 6000.

value: Hela cell


title: Mono-culture, Macrophage, 0 hours post myelin, mn:001

value: Bone-marrow

value: Bone-marrow derived macrophages


title: Week 32 control 15


title: Mono-culture, Macrophage, 6 hours post myelin, mn:001

value: 6 hour myelin debris


title: RNA-seq_NB1-M16_TUM


title: Week 32 control 16


title: RNA-seq_NB4-M7_ADH

value: Adherent cells


title: Sta Nucleus replicate 2

description: Standard nucleus RNA-seq,replicate 2


title: Week 32 control 13


title: BMDMs Tumor without Myelin, mn:016

source_name: Ex vivo bone-marrow/dissociated brain tumor

value: Tumor without Myelin


title: RNA-seq_NB1-M16_ADH


title: BMDMs Full Tumor, mn:016

value: Ex vivo bone-marrow/dissociated brain tumor

value: Full Tumor


title: Week 32 control 12


title: BMDMs Control, mn:016


title: Week 32 control 11


title: RNA-seq_NB1-M11_SPH


title: Sta Cytoplasm replicate 3

description: Standard cytoplasm RNA-seq,replicate 3


title: BMDMs Myelin Alone, mn:016

value: Myelin Alone


title: RNA-seq_NB1-M16_SPH

value: Spheroids


title: BMDMs Myelin Alone, mn:958


title: Sta Nucleus replicate 1

description: Standard nucleus RNA-seq,replicate 1


title: Week 32 control 14


title: BMDMs Full Tumor, mn:958


title: RNA-seq_NB1-M11_ADH


title: RNA-seq_NB1-M8_TUM


title: Week 32 control 9


title: Sub cell replicate 4

description: Different barcode represent different region of light illumination in Hela cell (Sub-cytoplasm(CAAGCCT)Sub-nucleus(AAACCGG)), replicate 4


title: Week 32 control 8


title: Sta Cytoplasm replicate 2

description: Standard cytoplasm RNA-seq,replicate 2


title: Sta Cytoplasm replicate 1

description: Standard cytoplasm RNA-seq,replicate 1


title: Sub cell replicate 3

description: Different barcode represent different region of light illumination in Hela cell (Sub-cytoplasm(CAAGCCT)Sub-nucleus(AAACCGG)), replicate 3


title: Sta Nucleus replicate 3

description: Standard nucleus RNA-seq,replicate 3


title: BMDMs Myelin Alone, mn:957


title: Week 32 control 10


title: RNA-seq_NB1-M8_ADH


title: Week 32 control 6


title: BMDMs Tumor without Myelin, mn:958


title: RNA-seq_NB1-M11_TUM


title: Sub cell replicate 2

description: Different barcode represent different region of light illumination in Hela cell (Sub-cytoplasm(CAAGCCT)Sub-nucleus(AAACCGG)), replicate 2


title: BMDMs Tumor without Myelin, mn:957


title: Sample40

city: Boston

first: Nikolaos

last: Kalavros

state: Massachusetts

address: 330 Brookline Avenue

department: Pathology

institute: Beth Israel Deaconess Medical Center

data_processing:
Adapters for the QIAgen small RNA kit were removed using cutadapt v4.0
Manatee v1.2 was used to map the FASTQ files to the mm10 genome and transcriptome
Data were loaded into R using data.table
miRNAs with below 5 expression in any condition were removed
Differential expression analysis was conductd using DESeq2
Assembly: mm10
Supplementary files format and content: .tar.gz archive of .tsv files, count matrices derived from manatee. Counts clustered per miRNA, isomiR level results and total count matrix.

source_name: Skin

extract_protocol:
QIAgen miRNeasy
QIAseq miRNA Library Kit

value: Skin

tag: tissue subtype

value: Wound exudate

tag: Sex

value: Male

tag: age

value: 16 weeks

value: db/db

tag: days post_wounding


title: Sta Cytoplasm replicate 4

description: Standard cytoplasm RNA-seq,replicate 4


title: Week 32 control 5

tag: tissue

value: Liver

value: Control


title: BMDMs Full Tumor, mn:957

tag: cell type


title: Sub cell replicate 1

description: Different barcode represent different region of light illumination in Hela cell (Sub-cytoplasm(CAAGCCT)Sub-nucleus(AAACCGG)), replicate 1

value: Hela cell


title: Week 32 control 4

tag: strain


title: RNA-seq_NB1-M8_SPH


title: BMDMs Control, mn:958


title: NCI-H716-Test_rep2

city: Wenzhou

first: LIjun

last: Chen

state: Other

address: Wenzhou Medical University, Wenzhou City, Zhejiang Rrovince,China

institute: Wen Zhou Medical University

data_processing:
We aligned paired-end RNA-seq reads of HCT116 and NCI-H716 to the hg38 reference genome using Bowtie2 v2.5.0 software. Unmapped and non-uniquely mapped reads were removed.   For quantitative analysis, we normalized the read counts by computing the number of RPKMs using BAM files with FeatureCounts.
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
Cells were washed two times in 0.5% BSA-PBS solution.  cDNA was amplified using the Single Cell Full Length mRNA-Amplification Kit(N712, Vazyme) according to the manufacturer’s instructions.
Library preparation was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) according to the manufacturer’s instructions.


title: Week 32 control 7

tag: diet


title: NCI-H716-Control_rep2


title: Sample38

tag: genotype


title: Sample37


title: Sample36


title: Week 32 control 2

tag: diet duration (weeks)


title: Week 32 control 3


title: BMDMs Control, mn:957


title: Week 32 control 1


title: NF_2cell, replicate 2, Input

city: Shanghai

first: Xiaolei

last: Zhang

address: N0.1239 of Siping Road, Shanghai, China

institute: Tongji University

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Trim_galore, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the UCSC mm10 genome using BWA. Only reads with MapQ > 30 and uniquely mapped to genome were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Mouse embryo

extract_protocol:
Cells or embryos were lysed, and chromatin was treated with MNase.
ChIP-seq libraries were prepared using the KAPA HyperPrep Kit. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 200-500 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: Mouse embryo


title: HCT116_Test_rep2


title: HCT116_Control_rep2


title: Sample35


title: Sample39


title: Week 16 LIDPAD 12

value: LIDPAD


title: Sample34


title: NF_2cell, H3K36me3, replicate 2, ChIP

value: H3K36me3 (Abcam, AB9050)


title: NF_2cell, H3K36me3, replicate 1, ChIP


title: NCI-H716-Control_rep1


title: NCI-H716-Test_rep1


title: Sample33


title: NT_2cell, Setd2OE, H3K36me3, replicate 3, ChIP


title: Week 16 LIDPAD 11


title: Week 16 LIDPAD 10


title: HCT116_Test_rep1


title: Sample32


title: NT_2cell, Setd2OE, H3K36me3, replicate 2, ChIP


title: HCT116_Control_rep1


title: Week 16 LIDPAD 9


title: Sample31


title: NT_2cell, Setd2OE, H3K36me3, replicate 1, ChIP


title: NT_2cell, Setd2OE, H3K27me3, replicate 3, ChIP


title: Week 16 LIDPAD 8


title: Sample30


title: HEK293T single cell 3

city: shanghai

first: Guoqiang

last: Zhou

address: Fudan University, Shanghai, 200438, China

institute: Fudan University School of Life Sciences

library_source: other

data_processing:
Following trimming of low-quality reads and removal of sequencing adapters using trim galore the raw data underwent alignment to the hg38 composite reference genome employing bwa mem with default parameters. Subsequently, Numts reads were eliminated using the RtN package, and mitochondrial DNA mutations were analyzed using the MitoMutCall package. Statistical analyses and graphical representations were conducted using R. All statistical comparisons between two samples were performed in an unpaired manner, and two-sided P-values were calculated. Visualization was achieved using both base R plotting functions and ggplot2.
Assembly: hg38
Supplementary files format and content: Comma-Separated Values fiels; Tab-separated values files

molecule: other

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum under standard conditions of 5% CO2 in a humidified atmosphere at 37 ℃.

extract_protocol: The sorted single cells were individually transferred into a 96-well plate containing 5 μL of lysis buffer (final concentration 0.5% CA630). Subsequently, the plate was subjected to heating at 65°C for 10 minutes to ensure optimal release of mtDNA.

value: Human embryonic kidney


title: NF_2cell, replicate 1, Input


title: Week 16 LIDPAD 7


title: HEK293T single cell 2


title: Sample28


title: NT_2cell, Setd2OE, H3K27me3, replicate 1, ChIP


title: Sample29


title: HEK293 genomic DNA 3


title: Sample27


title: NT_2cell, Setd2OE, H3K27me3, replicate 2, ChIP


title: Week 16 LIDPAD 6


title: NT_2cell, Setd2OE, H3K4me3, replicate 3, ChIP

value: H3K4me3 (Cell signaling, #9751)


title: Week 16 LIDPAD 4


title: HEK293 genomic DNA 2


title: HEK293T single cell 1


title: Week 16 LIDPAD 3


title: NT_2cell, Setd2OE, H3K4me3, replicate 2, ChIP


title: Sample26


title: Sample25


title: HEK293 genomic DNA 1


title: Week 16 LIDPAD 2


title: NT_2cell, Setd2OE, H3K4me3, replicate 1, ChIP


title: T Jurkat 2, H3K27ac, ChIP

first: Melissa

middle: McCalley

last: Inge

address: 24 Cummington Mall

department: Biology

institute: Boston University

data_processing:
Reads were trimmed with Trimmomatic v0.36 (SLIDINGWINDOW:4:20, MNLEN: 20).
Trimmed reads were aligned to human genome using Bowtie v2.4.2 (--very-sensitive-local-X 2000)
Peaks were called using Genrich v0.6 and any regions aligning to ENCODE excluded regions, mitochondrial chromosome, and human genome scaffolds were removed.
BigWig files were created using deeptools with sorted Bam files and narrow peak files as input.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Jurkat E6-1

growth_protocol: RPMI + Glutamax, 10% fetal bovine serum, 1mM pyruvate. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quencing and cell lysis, chromatin was sonicated using Epishear probe sonicatior (Active motif).
ChIP-seq libraries were prepared using NEBNext Ultra II Library Prep kit, following manufactors instructions.

treatment_protocol: Cells were treated according to manufacters instructions (25 ul/ml) with ImmunoCult Human CD3/CD28/CD2 T Cell Activator for 45 minutes before fixation.

value: Jurkat E6-1

value: T-cell leukemia

value: 45min TCR stimulation


title: Sample24


title: Week 16 control 12


title: NT_2cell, WDR5-0103, H3K4me3, replicate 2, ChIP


title: Sample23


title: Sample22


title: Week 16 LIDPAD 1


title: Week 16 LIDPAD 5


title: T Jurkat 1, H3K27ac, ChIP


title: NT_2cell, WDR5-0103, H3K4me3, replicate 1, ChIP


title: NT_TE, H3K27me3, replicate 2, ChIP


title: UT Jurkat 2, H3K27ac, ChIP

value: No treatment


title: Week 16 control 11


title: Week 16 control 10


title: UT Jurkat 1, H3K27ac, ChIP


title: Sample21

value: Skin


title: NT_TE, H3K27me3, replicate 1, ChIP


title: Week 16 control 9


title: 10A_JUNM14oe_etoh, IgG, rep4

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

data_processing:
Adapter removal and quality trimming was performed by Cutadapt. Since the carry-over DNA of pAG-MNase purification from E. coli was used as spike-in control, mapping was performed to hg19 and a human repeat-masked E. coli genome by Bowtie2. Paired-end reads mapped to hg19 with inserts <120 bp were extracted using alignment Sieve (deepTools). A scaling factor was inferred by: scaling factor= (mapped reads < 120 bp to hg19)⁄(mapped reads to E.coli).
The scaling factor was used to generate spike-in normalized bigWig files by bamCoverage (deepTools).
Assembly: hg19
Library strategy: CUT&RUN

extract_protocol:
CUT and RUN experiments were performed as described previously (Kim et al., Nat. Commun., 2022). Briefly, for each CUT and RUN reaction 200,000 cells were trypsinized, washed, resuspended in 100 µl wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine) and bound to 10 µl activated BioMag®Plus Concanavalin A magnetic beads (Polysciences) for 10 min at room temperature. The cells were then incubated with antibodies diluted in 100 µl antibody buffer (wash buffer + 0.01% digitonine and 2 mM EDTA) overnight at 4°C. IgG rabbit antibody was used as negative control. After incubation with antibodies, the beads were washed in digitonin wash buffer (wash buffer + 0.01% digitonin) and incubated 1h at 4°C with 1 µg/ml protein A/G Micrococcal Nuclease fusion protein (pA/G MNase). After washing with digitonin wash buffer, beads were rinsed with low salt buffer (20 mM HEPES, pH7.5, 0.5 mM Spermidine, 0.01% digitonine), resuspended in 200 µl incubation buffer (20 mM HEPES, pH7.5, 10 mM CaCl2, 0.01% digitonin) and placed at 0°C to initiate cleavage. After 30 min, reactions were stopped by adding 200 µl STOP buffer (170 mM NaCl, 20 mM EGTA, 0.01% digitonin, 50 µg/ml RNAse A) and the samples were incubated 30 min at 37°C to digest the RNA and release the DNA fragments. The samples were then treated with proteinase K for 1 h at 50°C and the DNA was purified using Phenol/Chloroform/Isoamyl alcohol. After precipitation with glycogen and Ethanol, the DNA pellet was resuspended in 0.1 X TE and used for library preparation.
For DNA library generation, the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) was used. Adaptor ligation was performed with 1:25 diluted adaptor and 15 cycles were used for library amplification using dual indices (NEB dual index kit). Paired-end 2x25 bp sequencing was performed.

treatment_protocol: MCF10A cells expressing a doxycycline-inducible YAP5SA allele were infected with JUN overexpression vectors (WT or M14) or an empty vector control. YAP induction was induced by doxycycline addition (100 ng/ml) and control cells were treated with solvent control (EtOH).

tag: cut&run antibody

value: breast epithelial

value: JUN M14oe

value: etoh


title: NT_TE, H3K4me3, replicate 2, ChIP


title: NT_TE, replicate 2, Input


title: 10A_JUNM14oe_etoh, NCOR1, rep4

tag: cell line


title: LEC, tumor, WT2

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Mapping was done with the STAR v.2.7.0 software to the UCSC mm10 Mus musculus reference.
Biological quality control and summarization were done with the PicardTools (v.1.141).
The read counts were prepared with HTSeq v0.9.1 (htseq-count)
The differential expression analysis was performed with R/Bioconductor package EdgeR(v.3.26.8). The genes having a count above 1 count per million reads (cpm) in at least 3 samples were kept for the analysis. The poorly or not expressed genes were filtered out. The filtered data set consists of 13’454 genes. The differentially expressed genes tests were done with a GLM (general linear model) with a negative binomial distribution. The differentially expressed genes p-values are corrected for multiple testing error with a 5% FDR (false discovery rate). The correction used is Benjamini-Hochberg (BH). The likelihood test was used for the statistical test of differential expression.

source_name: tumor

extract_protocol:
Tumor tissues were cut into small pieces and digested in RPMI containing collagenase IV (1mg/ml; Worthington Biochemical Corporation), DNase I (40 μg/ml; Roche), and 1% FBS for 30 min at 37 °C. Samples were mixed up and down every 10min. Tubes were centrifuged for a few seconds at 1500rpm and supernatants filtered through a 70µm cell strainer in FACS buffer to stop the reaction. Remaining tissue was further digested in RPMI with collagenase D (1 mg/ml; Roche), DNase I (40 μg/ml; Roche) and 1% of FBS for 20 min at 37 °C, with additional two cycles of repeated pipetting. The solution was filtered through a 70µm cell strainer in in FACS buffer and pool into the first collected tubes.digestion was followed by debris removal using Lympholyte®-M (CEDARLANE) according to manufacturer’s instructions. Cells were sorted as CD45-CD31+GP38+ population. Total RNA was isolated using miRNeasy Mini Kit (Qiagen). Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clonetech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 1ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies).

value: tumor

value: lymphatic endothelial cell

value: LEC-CH25h WT


title: Week 16 control 8

first: Zun Siong

last: Low

address: 11 Mandalay Rd

institute: Lee Kong Chian School of Medicine

data_processing:
Alignment done by HISAT2
Raw counts using featurecounts
DEGs determined using DESeq2 with cutoff of log2fc > ±1
Genome_build: grcm38
Supplementary_files_format_and_content: FPM

source_name: Mice from age of 8 weeks

extract_protocol:
TRIzol RNA extraction followed by E.Z.N.A.® HP Total RNA for purification, according to manufacturer’s protocol
Illumina library preparation done by NovogeneAIT

value: Liver

value: Control


title: NT_TE, H3K4me3, replicate 1, ChIP

value: Mouse embryo


title: LEC, tumor, HE1

value: LEC-Ch25h KO


title: NT_ICM, H3K27me3, replicate 2, ChIP


title: 10A_ev_dox, FOS, rep4

tag: treatment

value: empty vector

value: doxycycline


title: LEC, tumor, WT1


title: 10A_JUNM14oe_etoh, JUN, rep4


title: 10A_JUNM14oe_etoh, YAP1, rep4


title: Week 16 control 7


title: Week 16 control 2


title: 10A_ev_dox, YAP1, rep4


title: LEC, tumor, HE3


title: Adipose cDC1s, LFD_DC1

city: Los Angeles

first: Joey

middle: Han Tang

state: CA

address: 615 Charles E. Young Dr S

institute: UCLA

data_processing:
For bulk RNA-seq, the reads were mapped with STAR 2.5.3a to the mouse genome (mm10). The counts for each gene were obtained by using –quantMode GeneCounts commands in STAR, and the other parameters during alignment were set to default.
The counts for all the samples were concatenated to the raw expression matrix.
Assembly: mm10
Supplementary files format and content: txt file contains gene counts for each sample

source_name: Adipose

extract_protocol:
Adipose tissues were physically dissociated using  scissors and incubated in a shaking incubator (225rpm) at 37°C for 45 min in adipose digest solution (2mg/ml type II collagenase in HBSS +MgCl+CaCl, 5% fetal calf serum, 1% L-glutamine, 1% penicillin-streptomycin, and 50ug/mL DNase1). The resulting dissociated tissue was passed through 100μm strainers, and adipocytes were removed from the supernatant by centrifugation. Red blood cells were lysed using ACK lysis buffer and the resulting stromal vascular fraction pellets were processed to single cell suspensions for FACS. cDC1s were sorted to to > 95% purity as via as follows: cDC1: (CD45+Lin–(CD3-TCRβ-CD19-Ly6G-NK1.1-)CD88-HLA-DR+CD11c+CD11b–XCR1+
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were isolated from the visceral adipose tissues of 4-week LFD- or 60% HFD-fed WT mice

value: Adipose

value: WT

value: 4 week LFD


title: NT_TE, replicate 1, Input


title: LEC, tumor, HE2


title: Week 16 control 6

city: Singapore


title: 10A_ev_dox, IgG, rep4


title: 10A_ev_dox, NCOR1, rep4


title: Adipose cDC1s, HFD_DC3

value: 4 week 60% HFD


title: NT_ICM, replicate 2, Input


title: 10A_ev_etoh, NCOR1, rep4


title: Week 16 control 5


title: NT_ICM, H3K4me3, replicate 1, ChIP

value: H3K4me3 (Cell signaling, #9751)


title: LEC, tumor, WT3


title: Week 16 control 4


title: NT_ICM, H3K27me3, replicate 1, ChIP


title: 10A_ev_etoh, FOS, rep4

value: breast epithelial


title: Adipose cDC1s, LFD_DC3


title: NT_ICM, H3K4me3, replicate 2, ChIP


title: 10A_ev_etoh, JUN, rep4


title: Week 16 control 1


title: 10A_ev_dox, JUN, rep4


title: Adipose cDC1s, LFD_DC2


title: 10A_ev_etoh, YAP1, rep4


title: Week 12 LIDPAD 5

value: LIDPAD


title: NT_blastocyst, H3K4me3, replicate 2, ChIP


title: Female Cortex, MaternalExp, rep2

city: College Station

first: Michael

last: Golding

state: TX

address: 588 Raymond Stotzer Pkwy

institute: Texas A&M University

data_processing:
trimmed the sequences of Illumina adapters using Trimmomatic
mapped reads to the Mus musculus reference genome (UCSC version GRCm39/mm39) using RNA STAR
featureCounts   to  determine  read  abundance
Assembly: mm39
Supplementary files format and content: tabular
Supplementary files format and content: counted reads, per gene, per row

source_name: Cortex

extract_protocol:
Qiagen AllPrep Kit (catalog# 80284, Qiagen, Germantown, MD, USA) according to the manufacturer’s instructions
sequencing libraries were generated by the Illumina mouse TruSeq Standard Total RNA kit (catalog# RS-122-2202, Illumina, San Diego, CA, USA)

value: Cortex

value: female

value: Maternal EtOH


title: Week 12 LIDPAD 4


title: NT_blastocyst, replicate 2, Input


title: Week 12 LIDPAD 3


title: Week 16 control 3


title: 10A_ev_etoh, IgG, rep4

value: etoh


title: NT_ICM, replicate 1, Input


title: Week 12 LIDPAD 8

value: Liver


title: Adipose cDC1s, HFD_DC1

last: Li


title: Female Cortex, PaternalExp, rep1

value: Paternal EtOH


title: NT_blastocyst, H3K27me3, replicate 2, ChIP

value: Mouse embryo


title: Week 12 LIDPAD 7


title: NT_blastocyst, H3K4me3, replicate 1, ChIP


title: Female Cortex, DualExp, rep2

value: Dual EtOH


title: NT_blastocyst, H3K27me3, replicate 1, ChIP


title: Female Cortex, Control, rep1

value: Control


title: Week 12 LIDPAD 6


title: NT_morula, H3K4me3, replicate 2, ChIP


title: Female Cortex, MaternalExp, rep1


title: 10A_JUNM14oe_etoh, IgG, rep3

value: JUN M14oe


title: Female Cortex, DualExp, rep1


title: Week 12 LIDPAD 2


title: 10A_JUNM14oe_etoh, NCOR1, rep3


title: NT_blastocyst, replicate 1, Input


title: Female Cortex, PaternalExp, rep2


title: Male Cortex, DualExp, rep2

value: male


title: NT_morula, H3K4me3, replicate 1, ChIP


title: Week 12 control 6


title: NT_morula, replicate 2, Input


title: Male Cortex, DualExp, rep1


title: 10A_JUNM14oe_etoh, JUN, rep3


title: Week 12 control 5


title: NT_morula, H3K27me3, replicate 2, ChIP


title: 10A_ev_dox, JUN, rep3

value: empty vector

value: doxycycline


title: Week 12 LIDPAD 1


title: Week 12 control 8


title: Female Cortex, Control, rep2


title: NT_morula, H3K27me3, replicate 1, ChIP


title: Week 12 control 4


title: 10A_JUNM14oe_etoh, YAP1, rep3


title: Week 12 control 7


title: 10A_ev_dox, IgG, rep3


title: Male Cortex, PaternalExp, rep2


title: Week 12 control 3


title: 10A_ev_dox, NCOR1, rep3


title: 10A_ev_dox, FOS, rep3


title: NT_morula, replicate 1, Input


title: Male Cortex, MaternalExp, rep2


title: NT_8cell, H3K4me3, replicate 1, ChIP


title: Male Cortex, MaternalExp, rep1


title: 10A_ev_dox, YAP1, rep3


title: NT_8cell, replicate 2, Input


title: Week 8 LIDPAD 7


title: NT_8cell, H3K27me3, replicate 2, ChIP


title: 10A_ev_etoh, IgG, rep3


title: B16F10 DAC replicate 3 [RNA-seq]

first: Eric

last: Greer

state: MA

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
Real-Time Analysis (RTA) software
sequencing reads were aligned to the mm10 genombe in RSEM pipeline
Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05.
P-values of differential expression were adjusted for multiple-hypothesis testing using False Discovery Rate (FDR) method.
Assembly: mm10
Supplementary files format and content: Data matrix was generated by RSEM

growth_protocol: B16F10  cell line was a kind gift of Gordon Freeman (Dana-Farber Cancer Institute). 4T1 cells were provided by Fred Miller (Wayne State University). Cells were cultured with Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, VWR), 6 mM HEPES, 1.6 mM L-glutamine, 50 mM 2-mercaptoethanol, 100 U/ml penicillin G and 100 mg/ml streptomycin sulfate (Sigma-Aldrich). All cell lines were verified to be free of mycoplasma by PCR and were authenticated by morphology.

extract_protocol:
genomic DNA was isolated with Quick-DNA Microprep Kit (ZYMO RESEARCH).
12 groups were prepared for RNA-seq libraries using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)

treatment_protocol: B16F10 and 4T1 cells (2x10^4/well in 24 well plates) were treated with 0.1 uM or 1 uM of DAC for 48 hours, respectively. Dead cells were removed with dead cell removal microbeads and live cells were used for RNAseq

value: DAC for 48 h


title: NT_8cell, H3K27me3, replicate 1, ChIP


title: B16F10 DAC replicate 2 [RNA-seq]


title: NT_4cell, H3K27me3, replicate 2, ChIP


title: Male Cortex, PaternalExp, rep1


title: Week 12 control 2


title: Week 12 control 1


title: NT_8cell, H3K4me3, replicate 2, ChIP

value: H3K4me3 (Cell signaling, #9751)


title: 10A_ev_etoh, NCOR1, rep3

value: breast epithelial


title: 10A_ev_etoh, FOS, rep3


title: Male Cortex, Control, rep2


title: Cardiac Myocyte Normoxic Co-Culture 4

first: Megan

middle: L

last: McCain

address: 1024 Downey Way

institute: USC

data_processing:
Samples were trimmed using Phred score and min read lengths of 20 and 25, respectively
Samples were mapped to hg38 genome using STAR (2.7.8a)
Samples were quantified, normalized, and analyzed for differential gene expression using Partek Flow Genomics Software
Assembly: hg38
Supplementary files format and content: text file ("CM_CF_coculture_normalized_counts.txt") includes normalized counts for each sample

source_name: iPSCs N05280 (Coriell)

growth_protocol: Primary human adult cardiac fibroblasts (Lot 3131, Cell Applications Inc., San Diego, CA, USA) were grown in 10% fetal bovine serum (FBS) low glucose (1g/L) DMEM and 1% penicillin-streptomycin in T-75 flasks and passaged at 70-80% confluence. Human induced pluripotent stem cells (N05280, Coriell Institute for Medical Research, Camden, NJ, USA) were maintained in mTESR plus and then differentiated according to the STEMCELL Technologies STEMdiff™ Ventricular Cardiomyocyte Differentiation Kit.

extract_protocol:
Immediately following treatment, the co-culture region was cut to separate hypoxic and normoxic cells with a sterile razor blade and then 0.5 mL TriZOL was added to each of four regions (0% control, 0% co-culture, 10% control, 10% co-culture). TRIzol-chloroform separation followed by RNA purification using a Qiagen miRNA Mini Kit were used to isolate mRNA transcripts.
xGen Broad-Range RNA Library Prep Kit

treatment_protocol: Cells were seeded onto PDMS devices coated with fibronectin. In hypoxic cardiac fibroblasts cocultured with normoxic cardiac fibroblasts, fibroblasts were seeded everywhere at a density of 22,500 cells per square centimeter and serum arrested the following day for 48 hours with 0.1% FBS low glucose DMEM. After serum-arresting, 0.1% FBS low glucose DMEM was replenished, and devices were supplied with oxygen for 24h. In hypoxic cardiac fibroblasts cocultured with normoxic cardiac myocytes, a chamber was temporarily placed in the central coculture region to allow seeding of two distinct cell types. Fibroblasts were seeded at a density of 22,500 cells per square centimeter and cardiac myocytes were seeded at a density of 143,472 cells per square centimeter. The following day, the temporary seeding chamber was removed, media was replenished with 0.1% FBS low glucose DMEM, and then devices were supplied with oxygen for 24h.  Devices were hooked up to gas cylinders that provided 0% oxygen (5% carbon dioxide, bal nitrogen) and 10% oxygen (5% carbon dioxide, bal nitrogen).

value: iPSCs N05280 (Coriell)

value: 10% O2 Co-Cultured with 0% O2 cardiac fibroblasts, 24h


title: NT_4cell, H3K27me3, replicate 1, ChIP


title: B16F10 control replicate 3 [RNA-seq]


title: Week 8 LIDPAD 8

value: LIDPAD


title: 10A_ev_etoh, JUN, rep3


title: NT_4cell, H3K4me3, replicate 2, ChIP


title: Cardiac Myocyte Normoxic Co-Culture 1


title: B16F10 control replicate 2 [RNA-seq]


title: NT_8cell, replicate 1, Input


title: 10A_ev_etoh, YAP1, rep3


title: Male Cortex, Control, rep1

value: Cortex


title: Week 8 LIDPAD 3


title: Week 8 LIDPAD 6


title: Week 8 LIDPAD 1


title: Cardiac Myocyte Normoxic Control 3


title: NT_4cell, replicate 2, Input


title: Week 8 LIDPAD 5


title: Cardiac Myocyte Normoxic Co-Culture 3


title: Cardiac Myocyte Normoxic Control 2


title: Week 8 LIDPAD 4


title: Cardiac Myocyte Normoxic Co-Culture 2


title: NT_2cell, H3K36me3, replicate 2, ChIP

value: H3K36me3 (Abcam, AB9050)


title: Week 8 LIDPAD 2

value: Liver


title: B16F10 control replicate 1 [RNA-seq]


title: NT_4cell, H3K4me3, replicate 1, ChIP


title: NT_4cell, replicate 1, Input


title: Week 8 control 8


title: Week 8 control 6


title: Cardiac Fibroblast Hypoxic Co-Culture 4

source_name: Primary human adult

value: Primary human adult

value: cardiac fibroblasts

value: 0% O2 Co-Cultured with 10% O2 cardiac myocytes, 24h


title: B16F10 DAC replicate 1 [RNA-seq]


title: NT_2cell, H3K27me3, replicate 2, ChIP

value: Mouse embryo


title: Cardiac Myocyte Normoxic Control 4


title: Cardiac Myocyte Normoxic Control 1


title: Week 8 control 5

value: Control


title: Week 8 control 3


title: NT_2cell, H3K4me3, replicate 2, ChIP


title: Cardiac Fibroblast Hypoxic Co-Culture 3


title: NT_2cell, H3K36me3, replicate 1, ChIP


title: Week 8 control 4


title: NT_2cell, H3K4me3, replicate 1, ChIP


title: Cardiac Fibroblast Hypoxic Co-Culture 1


title: NT_2cell, replicate 2, Input


title: Cardiac Fibroblast Hypoxic Co-Culture 2


title: Cardiac Fibroblast Hypoxic Control 3


title: Week 8 control 7


title: Week 8 control 2


title: Cardiac Fibroblast Hypoxic Control 4


title: Cardiac Fibroblast Hypoxic Control 2


title: NT_14hpa, H3K27me3, replicate 2, ChIP


title: Week 8 control 1


title: NT_14hpa, H3K27me3, replicate 1, ChIP


title: prenatally testosterone treated Mouse Testis Replicate 4

type: RNA

city: NANJING

first: YU

last: ZHOU

address: NO. 169, HUSHAN ROAD

institute: THE AFFILIATED JIANGNING HOSPITAL OF NANJING MEDICAL UNIVERSITY

description: Biological replicate 4 of 5. treated mouse testis, prenatally testosterone treated, 3-months-aged.

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10 Blocking Agent and 1 μL of 25 Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2 Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 5 out of 10 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed using the R software. GO analysis was performed using topGO package in R environment for statistical computing and graphics, and Pathway analysis was calculated by fisher's exact test.

source_name: prenatally testosterone treated Mouse

label_protocol: The “IP” RNAs and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

growth_protocol: Female C57BL/6 mice, 6-8 weeks old, were purchased from Charles River Laboratories and housed in temperature-controlled (21–22°C) pathogen-free conditions with 12-hour light 12-hour dark cycle in Nanjing Medical University.

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

treatment_protocol: The F0 pregnant C57BL/6 mice were daily subcutaneously injected with testosterone (T) in a dose of 2.5 mg/kg body weight or equivalent solvent (sesame oil and benzyl benzoate) as control starting from day 14 to 19 post coitum (dpc). After parturition, male offspring of maternal T treated mice were defined as PTF1. Meanwhile, male offspring of maternal solvent treated mice were defined as PCF1. At the age of 12-14 weeks, PTF1 and PCF1 male mice were mated with unrelated healthy female C57BL/6 mice to generate the second generation of maternal T treated mice, which were defined as PTF2 and PCF2, respectively.

tag: condition

value: Supernatant

tag: gender

value: Male

value: testis

value: immunoprecipitated


title: Week 4 LIDPAD 6


title: NT_2cell, replicate 1, Input


title: Week 4 LIDPAD 5


title: NT_2cell, H3K27me3, replicate 1, ChIP


title: Cardiac Fibroblast Hypoxic Control 1


title: Week 4 LIDPAD 4


title: Week 4 LIDPAD 8


title: HCT_mRNA_Rad21Degron_IAA_r1_8h

first: Seolkyoung

last: Jung

address: 10 Center Dr

institute: NIH

data_processing:
scRNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
base calling: illumina CASAVA 1.8.2
Proseq_density: trim: cutadapt 1.14 for adapter and UMI removal with -O 1 --match-read-wildcards -m {20,26}), seqtk trimfq for R1l
Proseq_density: mapping: bowtie2 on combined genome (dm6 (spikein)+ hg19(primary))
Proseq_density: dedup: umitools (http://github.com/CGATOxford/UMI-tools)
Proseq_density: reads seperation with samtools 1.3.1 and convert to bedGraph through bowtie2stdBedgraph.pl (https://github.com/AdelmanLab/NIH_scripts)
mRNA-seq half-life estimation: alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-seq half-life estimation: htseq count file generation from mRNA-seq aligned both for ERCC spike-in control and genomic sequence
mRNA-seq half-lfe estimation:estimate the decay rate constant (kdecay) by fitting the exponential curve on concentration changes upon timepoints using SSasymp R function. From the decay constant, we calculated the mRNA half-lives using the following equation: ln(2)/kdecay
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigwig file

extract_protocol:
RNA-Seq
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NextSeq2000, NextSeq550, HiSeq3000 or NovaSeq6000 (Illumina).
ChIP-Seq
Library was prepared using Ovation Ultralow System V2 (Tecan) according to manufacturer’s protocol. Before sequencing high quality was confirmed using the Agilent TapeStation system. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (Illumina).
scRNA-Seq
Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeq6000 machine (Illumina).
RNA-Seq
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NextSeq2000, NextSeq550, HiSeq3000 or NovaSeq6000 (Illumina).
ChIP-Seq
Library was prepared using Ovation Ultralow System V2 (Tecan) according to manufacturer’s protocol. Before sequencing high quality was confirmed using the Agilent TapeStation system. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (Illumina).
scRNA-Seq
Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeq6000 machine (Illumina).

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 8h


title: NT_14hpa, H3K4me3, replicate 2, ChIP

value: H3K4me3 (Cell signaling, #9751)


title: prenatally testosterone treated Mouse Testis Replicate 5

description: Biological replicate 5 of 5. treated mouse testis, prenatally testosterone treated, 3-months-aged.


title: HCT_mRNA_Rad21Degron_IAA_r1_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 4h


title: Week 4 LIDPAD 7

value: LIDPAD


title: NT_14hpa, H3K4me3, replicate 1, ChIP


title: HCT_mRNA_Rad21Degron_IAA_r1_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 2h


title: prenatally testosterone treated Mouse Testis Replicate 2

description: Biological replicate 2 of 5. treated mouse testis, prenatally testosterone treated, 3-months-aged.


title: prenatally testosterone treated Mouse Testis Replicate 3

description: Biological replicate 3 of 5. treated mouse testis, prenatally testosterone treated, 3-months-aged.


title: prenatally testosterone treated Mouse Testis Replicate 1

description: Biological replicate 1 of 5. treated mouse testis, prenatally testosterone treated, 3-months-aged.


title: HCT_mRNA_Rad21Degron_IAA_r1_12h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 12h


title: Week 4 LIDPAD 3

value: Liver


title: HCT_mRNA_Rad21Degron_IAA_r1_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 24h


title: Week 4 control 8


title: NT_14hpa, replicate 1, Input


title: Week 4 LIDPAD 2


title: NT_6hpa, H3K27me3, replicate 2, ChIP


title: Week 4 LIDPAD 1


title: Week 4 control 6


title: NT_6hpa, H3K27me3, replicate 1, ChIP


title: HCT_mRNA_JQ1_r1_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 4h


title: HCT_mRNA_Rad21Degron_IAA_r1_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 1h


title: Control Mouse Testis Replicate 5

description: Biological replicate 5 of 5. Control mouse testis, prenatally solvent treated, 3-months-aged.

source_name: Control Mouse Testis


title: NT_6hpa, H3K4me3, replicate 2, ChIP

value: Mouse embryo


title: Control Mouse Testis Replicate 4

description: Biological replicate 4 of 5. Control mouse testis, prenatally solvent treated, 3-months-aged.


title: Week 4 control 7

value: Control


title: HCT_mRNA_JQ1_r1_8h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 8h


title: NRVC,Input6 [Input_B3]

last: Jiang

address: 1239 Siping Road, Shanghai, P.R. China

department: Department of life science and technology

institute: Tongji university

data_processing:
For RNAseq, sequenced reads were trimmed for adaptor sequence, then mapped to rn6 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S. Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
For ChIPseq,Basecalls were performed usina bcl2fasta v2.17 for Novasea outout.ChIP_seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trim Galore.ChlP-seq reads were aligned to the UCSC rn6 genome using BWA.Broad peaks were called uing MACS v2.1.0 with the significance cut-off g-value <=0.01.
Assembly: rn6
Supplementary files format and content: tab-dilimited text file include row counts for each sample
Supplementary files format and content: bigwig,broadpeak

organism: Rattus norvegicus

source_name: Neoatal Rat Heart

growth_protocol: For RNA-seq & ChIP-seq,Neonatal rat’s hearts were harvested from 1-day old SD rats. Next, the ventricles were separated and cut into small pieces (around 1 mm2), then they were dissociated in 0.25% trypsin (Gibco, 15090046) at 4 °C overnight. Then the tissue was transferred to 0.2% collagenase type Ⅱ and 0.2% BSA(Worthington, LS004176) to further digest at 37°C at 145 rpm for 3-5min about 4 times, and the supernatant was collected into DMEM medium containing 10% FBS every 5 min. The digestion procedure was repeated 3-4 times. When the tissue was completely digested, the supernatant was centrifuged at 1500 rpm for 6 min. Then, the cells were plated in DMEM medium which containing 10% FBS, 100 unit/ml penicillin and 100 mg/ml streptomycin at 15 cm dishes at an atmosphere of 5% CO2 at 37℃ for 90 min, to remove cells that are easier attached the dishes than cardiomyocytes. Finally, the culture supernatant was collected, plated in the plates which were coated with collagen and then incubated 24 h in an atmosphere of 5% CO2 at 37 ℃ with the same medium. After 24 h, the medium was changed to cardiomyocyte medium: DMEM: F12 (1:1) medium containing 0.25% FBS, 3 mM sodium pyruvate, 0.1 mM Vitamin C and 2 mM L-Glu.

extract_protocol:
For RNA-seq, The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.For ChIP-seq, it performed by ChIP protocol.
For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols; For ChIP-seq, DNA libraries were for sequencing using standard Illumina protocols.

treatment_protocol: For RNA-seq&ChIP-seq, NRVCs were treated with 25μM Blebb and DMSO for 0.5h.

value: Neoatal Rat Heart

value: Neoatal Rat Ventricular Cardiomyocytes

value: cardiomyocytes

value: SD

value: wt

value: 25μm Blebbistatin


title: Week 4 control 5


title: Control Mouse Testis Replicate 3

description: Biological replicate 3 of 5. Control mouse testis, prenatally solvent treated, 3-months-aged.

value: Supernatant

value: Male

value: testis

value: immunoprecipitated


title: Control Mouse Testis Replicate 1

description: Biological replicate 1 of 5. Control mouse testis, prenatally solvent treated, 3-months-aged.


title: Week 4 control 4

value: Liver


title: NT_6hpa, H3K4me3, replicate 1, ChIP

value: H3K4me3 (Cell signaling, #9751)


title: NRVC,Input5 [Input_B2]


title: HCT_mRNA_Rad21Degron_IAA_r1_0h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HCT_mRNA_JQ1_r1_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 2h


title: NRVC,Input4 [Input_B1]


title: CC, H3K36me3, replicate 1, ChIP

source_name: Mouse cumulus cell

value: Mouse cumulus cell

value: H3K36me3 (Abcam, AB9050)


title: DLD-1 cells, control#2

city: Kurume City

first: Toshiyuki

last: Okada

address: 67 Asahi-machi

department: Department of Immunology,

country: Japan

institute: Kurume University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: DLD-1 with a pEGFP-N1 empty vector

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: large intestine


title: DLD-1 cells, AID-OP#1

source_name: DLD-1 with AID overproduction


title: NRVC,Input2 [Input_D2]

first: Rui

value: Neoatal Rat Heart

value: Neoatal Rat Ventricular Cardiomyocytes

value: DMSO


title: NT_6hpa, replicate 1, Input

value: Mouse embryo


title: NRVC,Input3 [Input_D3]

value: cardiomyocytes

value: SD

value: wt


title: HCT_mRNA_JQ1_r1_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 24h


title: CC, H3K36me3, replicate 2, ChIP


title: Week 4 control 3

value: Control


title: HCT_mRNA_JQ1_r1_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 1h


title: HCT_mRNA_JQ1_r1_0h


title: CC, H3K27me3, replicate 1, ChIP


title: CC, H3K27me3, replicate 2, ChIP


title: Week 4 control 2

value: Liver


title: NT_6hpa, replicate 2, Input


title: HCT_mRNA_JQ1_r1_12h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 12h


title: Week 1 LIDPAD 8

value: LIDPAD


title: NRVC,H3K9me3,ChIP5 [K9_B2]

value: 25μm Blebbistatin

tag: antibody

value: H3K9me3 (Active Motif)


title: NRVC,Input1 [Input_D1]


title: CC, H3K4me3, replicate 2, ChIP

value: Mouse cumulus cell

tag: chip antibody

value: H3K4me3 (Cell signaling, #9751)


title: Week 1 LIDPAD 7


title: Week 4 control 1


title: HCT_mRNA_DMSO_r1_8h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 8h


title: HCT_mRNA_DMSO_r1_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 4h


title: NRVC,H3K9me3,ChIP4 [K9_B1]

value: Neoatal Rat Heart

value: Neoatal Rat Ventricular Cardiomyocytes


title: Week 1 LIDPAD 6


title: CC, H3K4me3, replicate 1, ChIP


title: NRVC,H3K9me3,ChIP6 [K9_B3]

value: cardiomyocytes

value: SD


title: HCT_mRNA_DMSO_r1_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 2h


title: CC, replicate 2, Input


title: Week 1 LIDPAD 4


title: CC, replicate 1, Input


title: Week 1 LIDPAD 3


title: HCT_mRNA_DMSO_r1_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 1h


title: Week 1 LIDPAD 2


title: Week 1 LIDPAD 5


title: HCT_mRNA_DMSO_r1_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 24h


title: NRVCs,Treat,Blebb3 [B3]

value: wt


title: scRNA_mBMB220r2

source_name: Bone marrow

value: Bone marrow

value: B220 positive cell

value: WT


title: NRVC,H3K9me3,ChIP1 [K9_D1]

value: DMSO


title: NRVC,H3K9me3,ChIP2 [K9_D2]

value: H3K9me3 (Active Motif)


title: NRVC,H3K9me3,ChIP3 [K9_D3]


title: NRVCs,Treat,Blebb2 [B2]

value: 25μm Blebbistatin


title: HCT_mRNA_DMSO_r1_12h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 12h


title: NT_2cell, Setd2OE, replicate 3

data_processing:
Sequence reads were trimmed from 3' end until the final base had a quality score > 20, using Trim_galore, discarding reads left with < 20 bp.
Sequence reads were aligned to the UCSC mm10 genome using HISAT2. Only reads uniquely mapped to genome were retained.
Read count extraction and normalization were performed using SringTie.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

extract_protocol:
Mouse SCNT embryos were lysed using lysis buffer, followed by reverse transcripted to cDNA.
RNA libraries were prepared using the KAPA HyperPrep Kit. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 200-500 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: Mouse embryo

tag: developmental stage

value: 2 cell embryo

value: Setd2 mRNA injection


title: NRVCs,Control,DMSO3 [D3]

value: Neoatal Rat Heart

value: Neoatal Rat Ventricular Cardiomyocytes

value: cardiomyocytes


title: Week 1 control 7

value: Liver

value: Control


title: Week 1 LIDPAD 1

value: LIDPAD


title: NT_2cell, Setd2OE, replicate 2


title: A375 cells - SEL201+OTX015 - N1

city: MONTREAL

first: Antoine

last: MEANT

state: QC

address: 3755 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

data_processing:
The overall quality of sequencing was assessed before and after trimming with the FastQC package (Babraham Bioinformatics).
Before mapping, reads were trimmed with Trimmomatic (Bolger et al., 2014), with the following parameters: ILLUMINACLIP:$Adapters:2:30:10:8:true, HEADCROP:4, SLIDINGWINDOW:4:30, LEADING:3, TRAILING:3, MINLEN:30.
Sequence alignment was performed with STAR 2.5.4b and compared with hg19 human reference genome using default parameters (Dobin et al., 2013) and converted into bam format using Samtools 1.9 (Li et al., 2009).
Differential expression analysis was generated using the featureCounts matrix (Liao et al., 2014).
Comparison across samples was performed with DESeq2 analysis using default parameters (Love et al., 2014).
Assembly: hg19 human reference genome
Supplementary files format and content: tab-delimited text file containing raw counts for each samples

source_name: melanoma cell line

growth_protocol: A375 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Wisent Inc.) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted using GenElute™ Total RNA Purification Kit (Sigma) as described by the manufacturer.
Extracted RNA was sent to The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) for stranded poly(A) mRNA library preparation (NEBNext) and sequencing using the Illumina NovaSeq S4 flow cell (150 bp paired ends reads; 2/2.5 billion reads total).

treatment_protocol: A375 cells treated for 72 hrs - [SEL201] = 2.5 μM; [OTX015] =  50nM.

value: melanoma cell line

value: BRAF-V600E melanoma


title: A375 cells - SEL201+OTX015 - N3


title: NRVCs,Treat,Blebb1 [B1]

value: SD

value: wt


title: Week 1 control 6


title: NT_2cell, Setd2OE, replicate 1


title: NRVCs,Control,DMSO1 [D1]

value: DMSO


title: A375 cells - OTX015 - N2


title: NT_4cell, WDR5-0103, replicate 1

value: 4 cell embryo


title: Week 1 control 8


title: HCT_mRNA_DMSO_r1_0h

city: bethesda

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: NT_2cell, WDR5-0103, replicate 2

value: Mouse embryo


title: Week 1 control 4


title: Week 1 control 3


title: A375 cells - SEL201+OTX015 - N2


title: NT_4cell, WDR5-0103, replicate 3


title: NRVCs,Control,DMSO2 [D2]


title: NT_2cell, WDR5-0103, replicate 1

value: 2 cell embryo


title: Week 1 control 1


title: A375 cells - OTX015 - N3