title: IL-4/IL-13 L48199_M2_1_02_C04

description:
IL-4/IL-13
IL-4/IL-13


title: Sample 187

status: Public on Jan 11 2022

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 9 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata_q.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

organism: Homo sapiens

growth_protocol:
Human samples: Samples of tumor and adjacent normal lung tissues were obtained from treatment-naive surgical specimens of NSCLC patients undergoing resection at the Mount Sinai Medical Center (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai
Mouse samples: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol:
treatment protocol (1): Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
treatment protocol (2): mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

tag: organ

value: lung tumor

tag: cell type

value: T cells

tag: selection marker

tag: co-culture conditions

tag: time point

tag: patient id

tag: replicate id


title: C0014FL

city: Paris

first: Jean-David

last: Bouaziz

address: Hôpital Saint-Louis 1, avenue Claude Vellefaux

department: Skin Research Center Service de Dermatologie

country: France

institute: INSERM U976

description: Lichen planus

data_processing:
Fastq files produced after RNA-seq sequencing have been processed by in-house CNRGH (Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France ) tools in order to assess quality of raw and genomic-aligned nucleotides
Quality control was performed on a random selection of 2 x 10 million reads, including the following steps: removal of adapters and poor-quality sequences to evaluate the % of usable reads (use of trimmomatic); alignment on the reference genome (Hisat2) as well as on the transcriptome and rRNAs (Bowtie2)
Use of rseqc and picardTools to evaluate the % of mapping on the genome and transcriptome, the % of duplicate sequences, the % of rRNA and the total number of usable sequences
Fastq files were aligned against the human GRCh38 genome assembly using STAR-2.6.0 according to author’s procedure (Dobin et al. 2016)
Genome_build: human GRCh38 genome assembly
Supplementary_files_format_and_content: table count

molecule: total RNA

source_name: Skin biopsy

extract_protocol:
RNeasy Plus Universal Kit (Qiagen, Hilden, Germany)
Libraries have been prepared using the "TruSeq stranded mRNA” Kit from Illumina

tag: tissue

value: skin

tag: sample type (cgvhd or healthy)

value: lichen planus lesion of cGVHD

tag: age

tag: gender

value: M

tag: cohort

value: Local cohort - Saint-Louis Hospital


title: IL-4/IL-13 L48198_M2_1_02_C03

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

description:
IL-4/IL-13
IL-4/IL-13

data_processing:
Bbasecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
Read alignment: Fragments were aligned to the mouse reference genome mm10 using the aligner gsnap (2019-06-10) with Ensembl 98 splice sites as support (parameters: --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0  --action-if-cigar-error noprint).
Counts per feature: Uniquely mapped fragments were compared based on their overlap to Ensembl 98 gene annotations using featureCounts (v1.6.3) to create a table of counts per gene and cell (parameters:  -a EnsemblGene-98.mm10.TR.gtf -s 0 -p -o bfx1341.mm10.e98.txt -Q 1).
Samples were processed and analyzed in R (4.0.0) using Seurat (v3)
Genes from specific metabolic pathways were retrieved from KEGG
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells.

organism: Mus musculus

source_name: Bone marrow

growth_protocol: In the presence of M-CSF

extract_protocol:
Wild-type BMDMs were stimulated with 10ng/ml IL4, IL13 and TNF. Cells were scraped and stained for live/dead staining with LDFA. Single cells were flow-sorted into 384-well plates containing nuclease-free water with 0.2% Triton X-100 and 1 U murine RNase inhibitor, centrifuged, and frozen at −80°C. After thawing, the primer mix and 1 U murine RNase inhibitor was added to each well. The reverse transcription reaction was performed, cDNA was amplified and purified. The concentration of samples was measured using a plate reader (Infinite 200 PRO, Tecan).
Then, pre-amplified cDNA was used for library preparation (TruePrep DNA library preparation kit V2 for Illumina, Vazyme) in a 1-μL reaction volume. Illumina indices were added during the PCR reaction with 1 × KAPA Hifi HotStart Ready Mix and dual indexing primers. After PCR, the libraries were quantified with AccuBlue Broad Range kit, pooled in equimolar amounts, and purified twice with Sera-Mag SpeedBeads. The libraries were sequenced on the Novaseq 6000 Illumina platform to obtain 50 bp paired-end reads aiming at an average sequencing depth of 0.5 million reads per cell.
Single Cell RNA seq

treatment_protocol: 10ng/ml IL4, IL13 and/or TNF

tag: strain

value: BMDM

tag: treatment


title: AB9569

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: A*.txt file:  includes mRNA molecule count values for each Sample (single cell expression matrix)
metadata_q.txt:  Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: C57BL/6, TCR-transgenic OT-II, and OVA-expressing B16 cell line

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
[human samples]  Samples of tumor and adjacent normal lung tissues were obtained from treatment-naive surgical specimens of NSCLC patients undergoing resection at the Mount Sinai Medical Center (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
(1) Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
(2) mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

value: tumor draining lymph node

value: OT-II T cells

value: day 10 post tumor injection

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection

tag: mouse age

value: 6-8 weeks


title: C0014FJ

description: Lichen planus

value: F


title: IL-4/IL-13 L48197_M2_1_02_C02

description:
IL-4/IL-13
IL-4/IL-13


title: Sample 183

value: doublets of T cells and myeloid cells


title: AB9568


title: IL-4/IL-13 L48196_M2_1_02_C01

description:
IL-4/IL-13
IL-4/IL-13


title: AB9567

value: in vitro

value: TCRb+

value: OT-II T mono-culture

value: 20 hours


title: AB9573

value: Myeloid cells


title: Sample 185

value: lung tumor


title: IL-4/IL-13 L48195_M2_1_02_B24

description:
IL-4/IL-13
IL-4/IL-13


title: AB9566

value: Doublets of T cells and myeloid cells

value: B16-OVA + OT-II T cells + B6 DC co-culture


title: AB9564

value: T cells

value: B16-OVA + OT-II T cells co-culture


title: AB9565


title: IL-4/IL-13 L48193_M2_1_02_B22

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: Skin biopsy-C5 [C5_PT_5]

city: New Orleans

first: Nakhle

last: Saba

state: LA

address: 1415 Tulane Ave, Room 118

department: Internal Medicine/Hematology

country: USA

institute: Tulane University

data_processing:
We used STAR(v.2.6.1d) to algin reads to hg38, Strelka(v.2.9.2) to call INDELs, and Kallisto(v.0.46.0) for expression measurement.
Analysis of gene expression profiling was performed using the following programs and software: JMP statistical software package 16 (SAS Institute), Cluster and Tree View programs (Eisen Laboratory, Stanford University), Gene Set Enrichment Analysis (GSEA) version 4.1 (Broad Institute).
Genome_build: human genome hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin biopsy-C

extract_protocol:
Skin biopsies were flash frozen on dry ice and  mechanically broken down using TissuLyser followed by RNA extraction using the RNeasy extraction Kit (Qiagen). RNA was then subjected to RNA sequencing.
library construction and paired-end sequencing of 100 bp reads on Illumina HiSeq-2500.

treatment_protocol: Skin biopsies were collected from patients before treatment and 3.months after treatment with apremilast

value: Skin

tag: disease

value: Dermatomyositis

value: Untreated


title: Skin biopsy-C6 [C6_PT_6]


title: Skin biopsy-T5 [T5_PT_5]

source_name: Skin biopsy-T

value: Treated


title: Skin biopsy-T8 [T8_PT_8]


title: Skin biopsy-T6 [T6_PT_6]


title: C0014FT

description: Lichen planus

value: skin

value: lichen planus lesion of cGVHD

value: F

value: Local cohort - Saint-Louis Hospital


title: IL-4/IL-13 L48191_M2_1_02_B20

description:
IL-4/IL-13
IL-4/IL-13


title: AB9570

value: tumor draining lymph node

value: OT-II T cells

value: day 10 post tumor injection

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection

value: 6-8 weeks


title: AB9562

value: in vitro

value: TCRb+

value: B16-OVA + OT-II T cells + B6 DC co-culture

value: 20 hours


title: Sample 182

value: lung tumor

value: doublets of T cells and myeloid cells


title: Skin biopsy-T4 [T4_PT_4]

value: Skin

value: Dermatomyositis


title: IL-4/IL-13 L48189_M2_1_02_B18

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: Skin biopsy-C4 [C4_PT_4]

value: Untreated


title: AB9560

value: T cells


title: Skin biopsy-C8 [C8_PT_8]


title: Skin biopsy-T3 [T3_PT_3]

value: Treated


title: IL-4/IL-13 L48188_M2_1_02_B17

description:
IL-4/IL-13
IL-4/IL-13


title: Skin biopsy-C3 [C3_PT_3]


title: IL-4/IL-13 L48187_M2_1_02_B16

description:
IL-4/IL-13
IL-4/IL-13


title: ZI418,stress,non-deletion,replicate 1 [ZI418s_L1]

city: Planegg-Martinsried

first: Sonja

last: Grath

address: Grosshaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

data_processing:
From RNA-sequencing we obtained from 29.3 – 67.6 million reads per library, and an average of 97% of these reads were successfully mapped to the D. melanogaster transcriptome (FlyBase,  release 6.31)  using NextGenMap (version 0.5.5) .
Differentially expressed genes were called with DESeq2 (version 1.28.1)  as implemented in R (version 4.0.0)  .
Genome_build: dmel-all-transcript-r6.31
Supplementary_files_format_and_content: text file with sample- and gene-wise expression table
Supplementary_files_format_and_content: text file with sample information

organism: Drosophila melanogaster

source_name: ZI418_stress_non-deletion_whole head

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Poly-A mRNA purification, reverse transcription, and high-throughput sequencing were performed by Novogene (Cambridge, UK) using a Novaseq 6000 sequencer (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads.

tag: population

value: Siavonga, Zambia

value: stress

tag: genotype

value: non-deletion

value: whole head


title: ZI418,control ,non-deletion,replicate 2 [ZI418c_L3]

source_name: ZI418_control _non-deletion_whole head

value: control


title: IL-4/IL-13 L48194_M2_1_02_B23

description:
IL-4/IL-13
IL-4/IL-13

tag: cell type


title: Skin biopsy-T2 [T2_PT_2]


title: IL-4/IL-13 L48186_M2_1_02_B15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48192_M2_1_02_B21

description:
IL-4/IL-13
IL-4/IL-13


title: AB9563

tag: organ

value: in vitro

tag: selection marker

value: 6-8 weeks


title: ZI418,control,non-deletion,replicate 1 [ZI418c_L2]

source_name: ZI418_control_non-deletion_whole head


title: Skin biopsy-C2 [C2_PT_2]


title: IL-4/IL-13 L48184_M2_1_02_B13

description:
IL-4/IL-13
IL-4/IL-13


title: ZI273,stress,non-deletion,replicate 3 [ZI273s_K5]

source_name: ZI273_stress_non-deletion_whole head


title: IL-4/IL-13 L48185_M2_1_02_B14

description:
IL-4/IL-13
IL-4/IL-13


title: Skin biopsy-T1 [T1_PT_1]


title: ZI273,stress,non-deletion,replicate 2 [ZI273s_K2]


title: IL-4/IL-13 L48183_M2_1_02_B12

description:
IL-4/IL-13
IL-4/IL-13


title: ZI273,stress,non-deletion,replicate 1 [ZI273s_K1]


title: Skin biopsy-C1 [C1_PT_1]


title: MCF7_IgG_VGLL3_OE

city: La Jolla

first: Shenghong

last: Ma

state: CA

address: 2880 TORREY PINES SCENIC DR, Sanford Consortium

institute: UCSD

library_source: genomic

data_processing:
library strategy: CUT&Tag-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v2.3.5.1 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
For RNA-seq data: Transcripts per Million (TPM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
For ATAC-seq data: peaks were called using Genrich version 0.6.1 with the following setting: -j -y -r -e chrM -v.Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
For ChIP-seq data: peaks were called using MACS3 version 3.0.0a6 with the following setting: -g hs -f BAM. Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
For CUT&Tag-seq data: peaks were called using SEACR version 1.3 with the following setting: -norm strigent. Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: For ATAC-seq, ChIP-seq and CUT&Tag-seq: bigwid files for display in hg38 genome browser track

molecule: genomic DNA

source_name: MCF7 breast cancer cell lines

growth_protocol: DMEM with 10% FBS

extract_protocol:
Wash cells, isolate nuclei, sequential primary antibody, secondary antibody, proteinA-Tn5 incubation and tagmention with addition of Mg2+
Tn5 tagmentation based PCR amplification

value: breast cancer cell line

tag: passage

tag: origin tissue

value: breast

tag: genotype/variation

value: wild type

tag: chip antibody

value: anti-rabbit IgG

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody cat. #

tag: chip antibody lot/batch #

value: Lentivirus expression of VGLL3


title: AB9561

value: TCRb+

tag: co-culture conditions

value: B16-OVA + OT-II T cells co-culture

tag: time point

value: 20 hours

tag: patient id

tag: replicate id


title: Hap1 WT H3K27me3 ChIPseq

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads were mapped to hg19 using Bowtie2.1.0 with default settings.
Peak calling was performed using MACS2 (v2.1.1) (Feng et al., 2012).
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: Hap1 WT

growth_protocol: Hap1 cells were cultered in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptomycin (Invitrogen) and 0.5% UltraGlutamin (Lonza). NMuMG cells (Gift of J. Jonkers) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptocmycin (Invitrogen) and 0.5% UltraGlutamin (Lonza).

extract_protocol:
Cells were fixed in 1% formaldehyde; 50mM Hepes-KOH; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA. Cell lysis was performed in LB1 buffer with final pH 7,5 (50 mM Hepes-KOH; 140mM NaCl; 1mM EDTA, 10% Glycerol, 0.5% NP-40; 0,25% Triton X-100; Proteinase inhibitor) for 20 minutes at 4°C. Subsequently, nuclei were lysed using LB2, pH 8,0 (10mM Tris-HCl; 200 mM NaCl; 1mM EDTA; 0,5mM EGTA; Proteinase inhibitor) for 10 minutes at 4°C. Pellets were resuspended in LB3 pH8,0 (10mM Tris-HCl; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine; Proteinase inhibitor). Cross-linked chromatin was sheared (400-800 bp) using a Covaris S2 with Tube and Caps (Covaris, 520048), using the following settings: duty cycle: 10%, intensity: 4, cycles per burst: 200 time 40 seconds with 20 cycles. Chromatin precipitation was performed overnight using antibody-bound (CTCF 5 μl, SMC1 10 μl, Igg 10 μl per IP) proteinA coupled DynaBeads (Invitrogen). Elution and decrosslinking was performed overnight at 65°C in EB pH 8,0 (50mM Tris-HCl; 10mM EDTA; 1% SDS). Samples were treated with Proteinase K and RNAseA for 2 hours. DNA was isolated using phenol extraction and ethanol precipitation.
Library preparation was done using a KAPA Library preparation kit using the manufacturer’s protocol.

treatment_protocol: Hap1 MED12 knock-out cells were generated using gRNA’s targeting MED12 exon 3 (primer: ;5’CCCTTCCTGACACTGGTCGC-3’) which were cloned into PX330. HAP1 wild type or ∆WAPL cells (Haarhuis et al. 2017), were transfected with PX330 and pDonorTia containing a puromycin resistance gene (Blomen et al., 2015). Clones were selected using puromycin (2 µg/µl). Colonies were screened for the loss of MED12 using PCR and western blot analysis.

tag: cell line

tag: antibody

value: WT


title: IL-4/IL-13 L48190_M2_1_02_B19

description:
IL-4/IL-13
IL-4/IL-13

tag: strain

value: BMDM

tag: treatment


title: ZI273,control,non-deletion,replicate 2 [ZI273c_K4]

source_name: ZI273_control_non-deletion_whole head

tag: population

value: Siavonga, Zambia

tag: genotype

tag: tissue


title: MCF7_IgG_VGLL3_CTR

tag: cell type

tag: passage

tag: origin tissue

value: Lentivirus expression of a control vector


title: IL-4/IL-13 L48181_M2_1_02_B10

description:
IL-4/IL-13
IL-4/IL-13


title: MCF7_H3K4M3_VGLL3_OE

tag: genotype/variation

tag: chip antibody

tag: chip antibody vendor


title: ZI273,control ,non-deletion,replicate 1 [ZI273c_K3]

source_name: ZI273_control _non-deletion_whole head

value: non-deletion

value: whole head


title: Hap1 MED12 H3K4me3 ChIPseq

source_name: Hap1 MED12

value: MED12 knock-out


title: IL-4/IL-13 L48180_M2_1_02_B09

description:
IL-4/IL-13
IL-4/IL-13


title: Hap1 MED12 H3K27me3 ChIPseq


title: MCF7_H3K4M3_VGLL3_CTR

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: Hap1 MED12 H3K36me3 ChIPseq


title: IL-4/IL-13 L48179_M2_1_02_B08

description:
IL-4/IL-13
IL-4/IL-13


title: ZI254,stress,non-deletion,replicate 2 [ZI254s_J2]

source_name: ZI254_stress_non-deletion_whole head

value: stress


title: IL-4/IL-13 L48178_M2_1_02_B07

description:
IL-4/IL-13
IL-4/IL-13


title: Hap1 WT H3K36me3 ChIPseq


title: MCF7_H3K27M3_VGLL3_OE

value: breast cancer cell line

value: Millipore


title: Hap1 WT H3K4me3 ChIPseq


title: ZI254,stress,non-deletion,replicate 1 [ZI254s_J1]


title: MCF7_H3K27M3_VGLL3_CTR

value: breast

value: wild type


title: IL-4/IL-13 L48177_M2_1_02_B06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48176_M2_1_02_B05

description:
IL-4/IL-13
IL-4/IL-13


title: ZI254,control,non-deletion,replicate 2 [ZI254c_J4]

source_name: ZI254_control_non-deletion_whole head

value: control


title: ZI254,control,non-deletion,replicate 1 [ZI254c_J3]


title: MCF7_H3K27AC_VGLL3_OE

value: Cell Signaling Technology

value: Lentivirus expression of VGLL3


title: IL-4/IL-13 L48182_M2_1_02_B11

description:
IL-4/IL-13
IL-4/IL-13


title: 34_616_FGFRL1_sh11

city: Turku

first: Pirkko

last: Härkönen

state: Finland

address: Medisiina D, 5th floor, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
For RNAseq analysis of the cell lines, the workflow was written in R v3.3, where Unix command line interface (CLI) tools were called by means of dedicated wrapper functions.
Sequence quality was assessed with FastQC v0.11.2 (RRID:SCR_014583).
Reads were aligned to the reference genome version GRCh38.81 using TopHat2 v2.1.0. Alignment files were sorted and converted for down-stream analysis using SAM v1.3 tools (RRID:SCR_010951) and reads were counted using HTSeq v0.6.1p1 (RRID:SCR_005514).
Counts were filtered according to Anders et al. 2013, Nat Protoc 2013;8:1765-86. Features without at least 1 read per million in n of the samples were removed, where n is the size of the smallest group of replicates.
Voom with sample quality weights, and quantile-normalization was applied to the filtered counts (Law et al. 2014; Genome Biol. 15: R29).
Genome_build: GRCh38.81
Supplementary_files_format_and_content: Matrix table (txt) with quantile-normalised log2-cpm for every gene and every sample

source_name: PrCa cell line PC3M

growth_protocol: PC3M cells with stable sh-RNA transfection were cultured in DMEM containing 10% fetal bovine serum (FBS, Gibco) and 1% antibiotics (Lonza). The cultures were maintained in a humidified incubator at 37 °C with 5 % CO2.

extract_protocol:
Total RNA was extracted from cell cultures using an RNeasy Mini Kit (Qiagen, Germany) according to the protocol and DNAse treated in the RNEasy column. The quality of the total RNA samples was ensured with Agilent Bioanalyzer 2100 and Advanced Analytical Fragment Analyzer. Sample concentration was measured with Nanodrop ND-2000, Thermo Scientific.
The library preparation was started from 100 ng of total RNA. Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047): The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification, because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix (FSA) prevents spurious DNA-dependent synthesis, while allowing RNA-dependent synthesis, improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library. Unique Illumina TruSeq indexing adapter was ligated to each sample during adapter ligation step to be able to later pool several samples in one flow cell lane.

tag: shRNA

value: FGFRL1 targeted shRNA transfection


title: 33_615_FGFRL1_sh11


title: MCF7_H3K27AC_VGLL3_CTR


title: MCF7_H3K4M1_VGLL3_OE

value: Abcam


title: ZI197,stress,non-deletion,replicate 1 [ZI197s_I1]

source_name: ZI197_stress_non-deletion_whole head


title: IL-4/IL-13 L48175_M2_1_02_B04

description:
IL-4/IL-13
IL-4/IL-13

source_name: Bone marrow


title: IL-4/IL-13 L48174_M2_1_02_B03

description:
IL-4/IL-13
IL-4/IL-13


title: ZI254,stress,non-deletion,replicate 3 [ZI254s_J5]


title: ZI197,control,non-deletion,replicate 2 [ZI197c_I3]

source_name: ZI197_control_non-deletion_whole head


title: MCF7_H3K4M1_VGLL3_CTR


title: 30_511_FGF13_sh21

value: FGF13 targeted shRNA transfection


title: 29_512_FGF13_sh21


title: MCF7_VGLL3_HA_6KO

value: LATS1/2 and TEAD1-4 six genes knock-out

value: anti-HA


title: ZI197,control,non-deletion,replicate 1 [ZI197c_I2]

value: Siavonga, Zambia


title: 28_614_FGF13_sh19


title: IL-4/IL-13 L48172_M2_1_02_B01

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L48173_M2_1_02_B02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48171_M2_1_02_A24

description:
IL-4/IL-13
IL-4/IL-13


title: 27_613_FGF13_sh19


title: M9N1,stress,non-deletion,replicate 1 [M9N1s_A1]

source_name: M9N1_stress_non-deletion_whole head

value: Munich, Germany

value: non-deletion

value: whole head


title: IL-4/IL-13 L48170_M2_1_02_A23

description:
IL-4/IL-13
IL-4/IL-13


title: 26_612_FGF13_sh13


title: M9N1,control,non-deletion,replicate 2 [M9N1c_A4]

source_name: M9N1_control_non-deletion_whole head


title: MCF7_VGLL3_HA_WT

value: breast cancer cell line


title: 25_611_FGF13_sh13


title: IL-4/IL-13 L48169_M2_1_02_A22

description:
IL-4/IL-13
IL-4/IL-13


title: MCF7_TEAD2_HA_L12KO

value: LATS1 and LATS2 double knock-out


title: MCF7_TEAD2_HA_WT

value: breast

value: treat doxcycline for 14 days


title: M9N1,control,non-deletion,replicate 1 [M9N1c_A3]

value: control


title: IL-4/IL-13 L48168_M2_1_02_A21

description:
IL-4/IL-13
IL-4/IL-13


title: 24_610_ctrl_sh8

value: scrambled shRNA transfection


title: M9D3,stress,deletion,replicate 2 [M9D3s_B2]

source_name: M9D3_stress_deletion_whole head

value: stress

value: deletion


title: MCF7_VGLL3_HA_D14

value: wild type

value: Cell Signaling Technology

value: treat doxcycline for 7 days


title: 23_609_ctrl_sh8


title: IL-4/IL-13 L48167_M2_1_02_A20

description:
IL-4/IL-13
IL-4/IL-13


title: M9D3,stress,deletion,replicate 1 [M9D3s_B1]


title: M9D3,control,deletion,replicate 2 [M9D3c_B4]

source_name: M9D3_control_deletion_whole head


title: MCF7_VGLL3_HA_D2

value: anti-HA


title: M9N1,stress,non-deletion,replicate 2 [M9N1s_A2]


title: 21_492_ctrl_sh5


title: IL-4/IL-13 L48165_M2_1_02_A18

description:
IL-4/IL-13
IL-4/IL-13


title: M9D3,control,deletion,replicate 1 [M9D3c_B3]


title: MCF7_VGLL3_HA_L12KO


title: MCF7_IgG_2_L12KO

value: anti-rabbit IgG


title: Hap1 CCNC CTCF ChIPseq

source_name: Hap1 CCNC

value: CCNC knock-out

value: CTCF (3418S, Cell Signaling)


title: IL-4/IL-13 L48164_M2_1_02_A17

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L48163_M2_1_02_A16

description:
IL-4/IL-13
IL-4/IL-13


title: Hap1 MED12 CTCF ChIPseq

value: MED12 knock-out


title: M12N3,stress,non-deletion,replicate 1 [M12N3s_D1]

source_name: M12N3_stress_non-deletion_whole head

value: Munich, Germany

value: non-deletion

value: whole head


title: MCF7_H3K36M3_L12KO

source_name: MCF7 breast cancer cell lines

value: breast cancer cell line

value: breast

value: LATS1 and LATS2 double knock-out


title: MCF7_IgG_2_WT


title: IL-4/IL-13 L48162_M2_1_02_A15

description:
IL-4/IL-13
IL-4/IL-13


title: M12N3,control,non-deletion,replicate 2 [M12N3c_D4]

source_name: M12N3_control_non-deletion_whole head

value: control


title: Hap1 WT CTCF ChIPseq


title: IL-4/IL-13 L48161_M2_1_02_A14

description:
IL-4/IL-13
IL-4/IL-13


title: MCF7_H3K36M3_WT


title: Hap1 CCNC SCC1 ChIPseq

value: SCC1 (ab992, Abcam)


title: Hap1 MED12 SCC1 ChIPseq


title: MCF7_H3K9M3_L12KO

value: Abcam


title: 22_493_ctrl_sh5

value: scrambled shRNA transfection


title: IL-4/IL-13 L48166_M2_1_02_A19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48160_M2_1_02_A13

description:
IL-4/IL-13
IL-4/IL-13


title: M12D3,stress,deletion,replicate 2 [M12D3s_C2]

source_name: M12D3_stress_deletion_whole head

value: stress

value: deletion


title: MCF7_VGLL3_HA_D7

value: wild type

value: anti-HA

value: Cell Signaling Technology

value: treat doxcycline for 2 days


title: Hap1 SCC1 ChIPseq


title: MCF7_H3K9M3_WT


title: MCF7_H4K20M1_L12KO


title: Hap1 MED12 ChIPseq

value: MED12 (A300-774A  Bethyl)


title: IL-4/IL-13 L48158_M2_1_02_A11

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: M12D3,stress,deletion,replicate 1 [M12D3s_C1]

value: Munich, Germany


title: M12D3,control,deletion,replicate 2 [M12D3c_C4]

source_name: M12D3_control_deletion_whole head

value: whole head


title: IL-4/IL-13 L48159_M2_1_02_A12

description:
IL-4/IL-13
IL-4/IL-13


title: MCF7_H4K20M1_WT

value: breast cancer cell line


title: IL-4/IL-13 L48157_M2_1_02_A10

description:
IL-4/IL-13
IL-4/IL-13


title: MCF7_CTCF_L12KO

value: breast

value: anti-CTCF


title: Hap1 WT H3K9me3 ChIPseq

value: WT

value: H3K9me3 (PAB-193-050, Diagenode)


title: KL02,stress,non-deletion,replicate 2 [KL02s_F2]

source_name: KL02_stress_non-deletion_whole head

value: Kuala Lumpur, Malaysia

value: non-deletion


title: IL-4/IL-13 L48156_M2_1_02_A09

description:
IL-4/IL-13
IL-4/IL-13


title: MCF7_CTCF_WT


title: IL-4/IL-13 L48155_M2_1_02_A08

description:
IL-4/IL-13
IL-4/IL-13


title: Hap1 MED12 H3K4me1 ChIPseq

value: H3K4me1 (PAB-037-050, Diagenode)


title: MCF7_pPolIIS2_L12KO

value: LATS1 and LATS2 double knock-out

value: Abcam


title: M12N3,control,non-deletion,replicate 1 [M12N3c_D3]

value: control


title: IL-4/IL-13 L48154_M2_1_02_A07

description:
IL-4/IL-13
IL-4/IL-13


title: KL02,control,non-deletion,replicate 2 [KL02c_F4]

source_name: KL02_control_non-deletion_whole head


title: Hap1 WAPL H3K9me3 ChIPseq

value: WAPL


title: Hap1 MED12 H3K9me3 ChIPseq


title: Hap1 WAPL/MED12 H3K9me3 ChIPseq


title: KL02,stress,non-deletion,replicate 1 [KL02s_F1]

value: stress


title: MCF7_pPolIIS2_WT

value: wild type


title: KL02,control,non-deletion,replicate 1 [KL02c_F3]


title: Hap1 WAPL H3K4me1 ChIPseq


title: IL-4/IL-13 L48153_M2_1_02_A06

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: MCF7_PolII_WT

value: anti-PolII

value: Active Motif


title: KL01,stress,deletion,replicate 2 [KL01s_E2]

source_name: KL01_stress_deletion_whole head

value: deletion

value: whole head


title: IL-4/IL-13 L48152_M2_1_02_A05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48151_M2_1_02_A04

description:
IL-4/IL-13
IL-4/IL-13


title: Hap1 WAPL/MED12 H3K4me1 ChIPseq


title: KL01,stress,deletion,replicate 1 [KL01s_E1]


title: MCF7_IgG_L12KO

value: breast cancer cell line

value: breast

value: anti-rabbit IgG

value: Cell Signaling Technology


title: M12D3,control,deletion,replicate 1 [M12D3c_C3]

value: Munich, Germany


title: Hap1 WT H3K4me1 ChIPseq

value: WT

value: H3K4me1 (PAB-037-050, Diagenode)


title: IL-4/IL-13 L48150_M2_1_02_A03

description:
IL-4/IL-13
IL-4/IL-13


title: KL01,control,deletion,replicate 2 [KL01c_E4]

source_name: KL01_control_deletion_whole head

value: Kuala Lumpur, Malaysia


title: IL-4/IL-13 L48149_M2_1_02_A02

description:
IL-4/IL-13
IL-4/IL-13


title: MCF7_IgG_WT


title: MED12 rep 3C RNAseq

data_processing:
Reads were mapped to hg19 using TopHat 2.0.9 and HTSeq-count was used to generate transcript-counts.
DESeq2 1.10.1 was used to infer differentially expressed genes with basic settings.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq output

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 1% Ultraglutamin (Lonza).

extract_protocol:
Total RNA from cultured cells was extracted using TRIzol reagent (Invitrogen).
Strand-specific libraries were generated using the TruSeq PolyA Stranded mRNA sample preparation kit (iIlumina). In brief, polyadenylated RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random-primed and reserve transcribed using SuperScript II Reverse Transcriptase (Invitrogen). The generated cDNA was 3’ end-adenylated and ligated to Illumina Paired-end sequencing adapters and amplified by PCR using HiSeq SR Cluster Kit v4 cBot (Illumina).

treatment_protocol: CRISPRs targeting WAPL (5’-CACCGCGTTCCATAGTATCCTGTA-3’) and SCC4 (5’-CACCGTACGGGCCTCGATGCGCTG-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL and ∆SCC4 HAP1 clones were generated by insertion of a Blasticidine or Puromycin cassette respectively, as previously described (Blomen et al., 2015). ∆WAPL/∆SCC4 cells were generated by knocking out SCC4 in ∆WAPL cells.


title: KL01,control,deletion,replicate 1 [KL01c_E3]

value: control


title: MCF7_H3K27AC_L12KO

value: LATS1 and LATS2 double knock-out


title: IL-4/IL-13 L48148_M2_1_02_A01

description:
IL-4/IL-13
IL-4/IL-13


title: MED12 rep 3B RNAseq


title: C2N1,stress,non-deletion,replicate 2 [C2N1s_G2]

source_name: C2N1_stress_non-deletion_whole head

value: Nicosia, Cyprus

value: stress

value: non-deletion


title: MCF7_H3K27AC_WT

value: wild type


title: C2N1,stress,non-deletion,replicate 1 [C2N1s_G1]


title: MCF7_PolII_L12KO

value: anti-PolII

value: Active Motif


title: MCF7_H3K4M1_L12KO

value: Abcam


title: MED12 rep 3A RNAseq


title: Skull

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the bone marrow niche of 5 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Skull bone marrow

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

tag: age

value: 8 weeks

tag: Sex

value: male


title: Tibia

source_name: Tibia bone marrow


title: C2N1,control,non-deletion,replicate 2 [C2N1c_G4]

source_name: C2N1_control_non-deletion_whole head

value: whole head


title: MCF7_H3K4M1_WT

value: breast cancer cell line

value: breast


title: C2N1,control,non-deletion,replicate 1 [C2N1c_G3]


title: MCF7_H3K27M3_L12KO

value: Millipore


title: WAPL rep 3A RNAseq

value: WAPL


title: WAPL rep 3B RNAseq


title: Cd45+ Day_7_T

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

country: China

institute: Pharmaceutical Informatics Institute

data_processing: The global-scaling method was used to normalize the gene expression with a default scale factor. The normalized expression was scaled through the function of ScaleData to remove unwanted sources of variation.

source_name: Cardiac immune cells

extract_protocol: After washing and resuspending in an appropriate volume of cold PBS, purified Cd45+ cells were processed in the Chromium single cell gene expression platform (10x Genomics). In brief, Single Cell 3′ Reagent Kit v2 (10X Genomics) was used to generate droplets encapsulating single cell and barcoded bead. Following lysis, reverse transcription was performed in a thermal cycler (ProFlexTM PCR). cDNA was purified with Dynabeads (provided by 10x) and amplified for 10 or 14 cycles (ProFlexTM PCR). The amplified-cDNA was fragmented, ligated with adapter and sample index, and selected with SPRI beads (Beckman). The constructed library was sequenced on the NovaSeq 6000 Illumina sequencing platform.

treatment_protocol: Single-cell RNA sequencing (scRNA-seq) was used to map the Cd45+ immune cell composition at different time points (0, 3, 7 and 14 days) after MI within a mouse left anterior descending coronary artery (LAD) ligation model. A time course-analysis was performed to characterize dynamic changes in cell populations. Multiparameter flow cytometry, immunohistochemistry, and immunofluorescence were performed using the same mouse model.

value: Cardiac immune cells

tag: time after mi (days)


title: C2D3,stress,deletion,replicate 2 [C2D3s_H2]

source_name: C2D3_stress_deletion_whole head

value: deletion


title: MCF7_H3K27M3_WT


title: Cd45+ Day_3_T

tag: strain


title: WT rep 3C RNAseq

value: WT


title: C2D3,stress,deletion,replicate 1 [C2D3s_H1]

value: Nicosia, Cyprus

tag: treatment


title: MCF7_H3K4M3_L12KO

value: LATS1 and LATS2 double knock-out

value: Cell Signaling Technology


title: WT rep 3B RNAseq


title: C2D3,control,deletion,replicate 2 [C2D3c_H4]

source_name: C2D3_control_deletion_whole head

tag: population

value: control


title: BALBc-2

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

description: 10x 5' single cell VDJ sequencing

data_processing:
Raw sequencing data were processed using Cell Ranger v3.1.0 with default settings, aligning the reads to the GRCm38 mouse VDJ reference. Outputs from Cell Ranger were then visualized using the Loupe V(D)J Browser for quality control assessment and to identify the top enriched clonotypes. The consensus amino acid sequences for the top-ranked heavy/light chain pairs in each sample were then extracted and codon-optimized for human expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: VDJ gene usage, population frequency, and CDR3 sequences for clonotypes called by CellRanger

source_name: spleen, draining lymph nodes, and bone marrow

extract_protocol:
The enriched CD138+ plasma cells and progenitor B cells were loaded on a 10X Chromium Next GEM Chip G. The target cell number was 10,000 cells per sample. Single-cell lysis and RNA first-strand synthesis were performed using Chromium Next GEM Single Cell 5’ Gel Bead V3.1 according to the manufacturer’s protocol.
The following RNA and V(D)J library preparation was performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell V(D)J reagent kit, mouse BCR). The resulting VDJ-enriched libraries were sequenced following the reading mode recommended by 10x Genomics. Sequencing was performed on a NovaSeq targeted for 10,000 reads/cell, with a total of 100 million reads.

value: BALB/c

tag: cell enrichment

value: CD138+ B cells

tag: immunization

value: RBD-His-tag


title: MCF7_H3K4M3_WT

tag: cell type

value: wild type


title: BALBc-1

description: 10x 5' single cell VDJ sequencing


title: WT rep 3A RNAseq


title: C2D3,control,deletion,replicate 1 [C2D3c_H3]

tag: genotype

tag: tissue


title: MCF7_L12KO_ATAC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v2.3.5.1 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
For RNA-seq data: Transcripts per Million (TPM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
For ATAC-seq data: peaks were called using Genrich version 0.6.1 with the following setting: -j -y -r -e chrM -v.Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
For ChIP-seq data: peaks were called using MACS3 version 3.0.0a6 with the following setting: -g hs -f BAM. Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
For CUT&Tag-seq data: peaks were called using SEACR version 1.3 with the following setting: -norm strigent. Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: For ATAC-seq, ChIP-seq and CUT&Tag-seq: bigwid files for display in hg38 genome browser track

extract_protocol:
Wash cells, isolate nuclei, tagment accessible genomic loci using in-house generated Tn5 assembly
Tn5 tagmentation based PCR amplification

tag: passage

tag: origin tissue

tag: genotype/variation


title: T6-4

description: xenografts_norm_counts_disambiguated.txt

data_processing:
Image analysis, base calling, and quality check were performed with the Illumina data analysis pipeline RTA3.4.4 and the program Bcl2fastq v2.20
trimming of adapter sequences using the ‘ILLUMINACLIP’ step from ‘Trimmomatic’ version 0.36
Alignment of reads with TopHat v2.0.14
disambiguation of human/mouse reads performed with Disambiguate 1.0
gene level raw counts calculation using ‘HTSeq’ version 0.9.1 and GRCh37.75/ GRCm38.p4 annotation files (.gtf) for human and mouse reads respectively
gene and transcripts level FPKM calculation using cufflinks-2.2.1 and GRCh37.75/GRCm38.p4 gtfs for human and mouse reads respectively
Genome_build: GRCh37.75 and GRCm38.p4
Supplementary_files_format_and_content: Matrix txt-table with disambiguated and normalized counts for every gene and every sample

organism:
Homo sapiens
Mus musculus

source_name: Human prostate cancer cell xenograft in mouse

growth_protocol: Cells were collected at the log growth phase and subcutaneously injected into mice (1 x 106 cells in 100 µl of PBS). Mice were housed under controlled conditions (12 h light/12 h dark cycles, temperature 21 ± 3 ℃) and fed standard chew food and tap water ad libitum. Tumors were grown for 45 days, and the tumor sizes and body weights of mice were measured every five days. After sacrificing the mice with CO2 asphyxiation followed by cervical dislocation, tumors were excised and divided into two parts: one for fixation with 10 % neutral-buffered formalin, and another for protein analysis and RNA sequencing.

extract_protocol:
Tumors were snapfrozen in liquid nitrogen. The total RNA was isolated using Qiagen RNeasy mini kit according to manufacturer's instructions.
NEB #E7760S/L

tag: sh-rna transfection

value: FGFRL1 sh-RNA

tag: cells


title: T6-5


title: C57-BM

description: 10x 5' single cell VDJ sequencing

source_name: bone marrow


title: MCF7_WT_ATAC

source_name: MCF7 breast cancer cell lines


title: WAPL/MED12 rep 3B RNAseq


title: C57-spleen

description: 10x 5' single cell VDJ sequencing

source_name: spleen and draining lymph nodes


title: WAPL/MED12 rep 3C RNAseq


title: T47D_L12KO-rep03

source_name: T47D breast cancer cell lines

extract_protocol:
Remove media, harvest RNA using Qiagen RNeasy Mini Kit.
NEBNext Ultra II RNA Library Prep Kit (E7770) was used with 1 ug of total RNA for the construction of sequencing libraries.


title: WAPL/MED12 rep 3A RNAseq


title: Cd45+ Day_14_T


title: SC_Ythdc2_iKO_3

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Reads were mapped to the mouse genome (GRCm38 , Ensembl release 95) using salmon v1.3.0 (salmon quant with options -l A –validateMappings–gcBias) (https://doi.org/10.1038/nmeth.4197). Further analysis was performed using R (https://www.r-project.org/) version 3.6.3 and Bioconductor (https://bioconductor.org/). The DESeq function of DESeq2_1.25.10 bioconductor package (https://doi.org/10.1186/s13059-014-0550-8) was used to obtain log2 fold changes of gene expression between wild-type and mutant samples and the adjusted p-values. Adjusted p-value 0.1 was used as a threshold for statistical significance. Only protein-coding genes with average expression >= 50 reads across samples were further processed, and those which were significantly differentially expressed with the log2 fold change >= 0.5 or <= (-0.5) in the mutant were considered to be dysregulated.
Genome_build: mouse GRCm38 – Ensembl release 95
Supplementary_files_format_and_content: The xlsx file summarizes the gene statistics obtained by DESeq2.

source_name: pachytene spermatocytes

growth_protocol: Pachytene spermatocytes were purified by Staput (sedimentationt at unit gravity)

extract_protocol:
Total RNA of the purified pachytene spermatocytes was extracted using Trizol reagent (Ambion).
The cDNA library was constructed with 3 μg of input total RNA for each sample using the Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Ythdc2fl/- and Ythdc2 fl/- Ddx4-CreERT2 males between 10-25 weeks were injected with tamoxifen (2 mg/30 g body weight) daily for five consecutive days. At 2 days post treatment (2 dpt), pachytene spermatocytes were purified by Staput.

tag: purification

value: STAPUT

value: 10-25 weeks old

value: 129/C57BL/6 hybrid

value: iKO (inducible KO)


title: T47D_L12KO-rep02

value: breast cancer cell line

value: breast


title: MED12 rep 2B RNAseq


title: SC_Ythdc2_iKO_2

tag: age


title: T5-5


title: WAPL rep 2B RNAseq

value: WAPL


title: SC_Ythdc2_iKO_1


title: T5-2


title: WT rep 2B RNAseq

value: WT


title: M12N3,stress,non-deletion,replicate 2 [M12N3s_D2]

source_name: M12N3_stress_non-deletion_whole head

value: Munich, Germany

value: stress

value: non-deletion

value: whole head


title: SC_Ythdc2_HT_3

value: Heterozygous


title: T2-4

value: scrambled ctrl sh-RNA


title: T47D_WT-rep03


title: WAPL/MED12 rep 2A RNAseq


title: SC_Ythdc2_HT_2


title: T47D_WT-rep02


title: T2-3


title: T47D_WT-rep01


title: WAPL rep 2A RNAseq


title: macrophages

city: Leipzig

first: Manuela

last: Rossol

address: Liebigstr. 19

institute: University of Leipzig

data_processing:
Both libraries were sequenced on an Illumina Novaseq 6000 in 100 bp paired-end mode, thus generating ~400 mio. fragments for the transcript library and 45 mio. fragments for the hashtag library.
The raw data were processed and aligned in the Dresden-concept Genome Center, Center for Regenerative Therapies Dresden (CRTD), Cluster of Exellence at TU Dresden, Germany The raw sequencing data was processed with the ‘count’ command of the Cell Ranger software (v5.0.1) provided by 10X Genomics with the option ‘--expect-cells’ set to 10,000 (all other options were used as per default).
Genome_build: Genome Reference Consortium Human Build 38 (GRCh38)
Supplementary_files_format_and_content: Zipped filtered_feature_bc_matrix folder containing .mtx.gz, and .tsv.gz files for reading into R using the Seurat Pipeline. The .rds dataset is a R dataset containing the filtered and processed data as final Seurat object.

source_name: monocyte-derived macrophages (GM-CSF), monocyte-derived macrophages (M-CSF), monocyte-derived macrophages (danger signal)

growth_protocol: Monocytes were in vitro differentiated into macrophages for 7 days.

extract_protocol:
scRNA-seq was performed in the Dresden-concept Genome Center, Center for Regenerative Therapies Dresden (CRTD), Cluster of Exellence at TU Dresden, Germany. Cells were mixed with the reverse transcription mix before loading them in a Chromium Single Cell G Chip on the 10X Genomics Chromium device and processed further following the guidelines of the 10x Genomics user manual (v3.1). The droplets were directly subjected to reverse transcription, the emulsion was broken and cDNA was purified using silane beads. After amplification of cDNA with 11 cycles using primers to enrich cDNA as well as Totalseq-B hashtag, it underwent a cleanup, including a fractionation of small fragments (up to 400 bp) to enrich the hashtag sequences and larger fragments (>400 bp) to separate cDNA fragments.
RNA libraries were prepared for sequencing using standard 10x protocols. For the gene expression library 10 µl cDNA were used involving fragmentation, dA-Tailing, adapter ligation and a 12 cycles indexing PCR was performed based on the manufacturer’s protocol. The hashtag library was prepared with 5 µl FBC-fraction by a 12-cycles index PCR. For both libraries Chromium SC NextGem 3 Lib prep v3.1 was used.

value: blood

tag: phenotype

value: healthy


title: SC_Ythdc2_HT_1


title: MED12 rep 2A RNAseq


title: CD45+ Day_14

value: Cardiac immune cells

tag: time after mi (days)


title: T2-1


title: T1-6


title: T6-1

value: FGFRL1 sh-RNA


title: CD45+ Day_7

tag: strain


title: T1-5


title: HREC_EGTA_CPE_Inhibition_rep2

city: Chicago

first: Jan

last: Kitajewski

state: Illinois

address: 909 South Wolcott Avenue

department: Department of Physiology and Biophysics

institute: University of Illinois, Chicago

description:
HR_p13_1_5C
HREC_EGTA_1.5C_counts.txt

data_processing:
fastq files were aligned to human (ENSEMBL/GRCh38) or mouse (UCSC/mm10) genome using STAR (version 2.5.0a for in-vitro screens or version 2.5.2b for RiboTag screening)
Aligned files were converted to Sam and Bam format using Samtools (version 1.4.1)
Raw counts were extracted from the Bam files using FeatureCounts (version 1.5.2)
Normalized read counts and analysis to generate a list of differentially expressed genes was done using DESeq2 (version 1.18.1)
Panther Db was used for identifying over representation of genes using Panther pathways.
Genome_build: Human Genome (ENSEMBL/GRCh38); Mouse Genome (UCSC/mm10)
Supplementary_files_format_and_content: Raw count files (.txt) were generated using FeatureCounts (v1.5.2) ; Normalized count files (.xlsx) were generated by DESeq2 (version 1.18.1)

source_name: Human Microvascular Retinal Endothelial Cells (HREC)

growth_protocol:
TLA: HUVECs and HRECs were grown using EGM2 supplemented with FBS until 80% onfluency
EGTA Induction: ECs were grown using EGM2 supplemented with FBS until 80% confluency. CpE was added to the media the previous evening before treatment and replaced with fresh media the following morning.
EGTA + CpE Inhibition: ECs were grown using EGM2 supplemented with FBS until 80% confluency. CpE was added to the media the previous evening before treatment and replaced with fresh media the following morning.
RiboTag: Mouse strains used include Rpl22tm1.1Psam (a.k.a. RiboTag, MGI:4355967), Cdh5-CreERT2 (MGI:3848982), CBF:H2B-Venus (MGI:5487759), and wildtype C57BL6/J mice on a fully backcrossed C57BL6/J genetic background. Mice were maintained as breeding trios in a barrier facility under standard housing conditions with daily health monitoring, weekly cage and bedding changes, and chewable nestlet enrichment. All genotyping was performed by Transnetyx. Animals for P8 endothelial RiboTag isolation  were generated from mating trios of doubly homozygous Rpl22tm1.1Psam; Cdh5-CreERT2 mice.

extract_protocol:
Ribosomal protein was precipitated by anti-HA from tissue lysate and ribosome binding RNA and total RNA from all samples were extracted using Qiagen kits as per manufacturer's protocol.
RNA libraries were prepared using standard protocols recommended by Illumina at either NovogeneCorp. Or at the Genome Centre at Columbia University.

treatment_protocol:
TLA: Cells were detached by trypsinization and seeded on Fc (Control) or DLL4 coated plates for 6h from the time of seeding.
EGTA Induction: Cells were treated with EGTA for 15mins, washed with PBS ad resuspended in EGM2 supplemented with FBS for 75mins.
EGTA + CpE Inhibition: Cells were treated with EGTA for 15mins, washed with PBS and resuspended in EGM2 supplemented with FBS and CpE for 75mins.
RiboTag: Mice were injected with tamoxifen at p1-3 and treated with DAPT for 6h before collection of the tissue at p8.

tag: treatment

value: Primary Cells (Human Microvascular Retinal Endothelial Cells)


title: WT rep 2A RNAseq


title: WAPL/MED12 rep 2C RNAseq


title: HREC_EGTA_CPE_Inhibition_rep3

description:
HR_p8_1_5C
HREC_EGTA_1.5C_counts.txt


title: CD45+ Day_3


title: T47D_L12KO-rep01

value: LATS1 and LATS2 double knock-out


title: HREC_EGTA_CPE_Inhibition_rep1

description:
HR_p12_1_5C
HREC_EGTA_1.5C_counts.txt


title: WAPL rep 2C RNAseq


title: CD45+ Sham


title: HREC_EGTA_Induction_rep2

description:
HR_p13_1_5
HREC_EGTA_0vs1.5counts.txt


title: WT rep 2C RNAseq


title: Brain_EC_DAPTtreated_rep2

description:
BJ011
brain_IPcounts_table_raw.txt

source_name: P8 Rpl22HA/HA;Cdh5CreERT2 (RiboTagEC) mice

value: DAPTtreated

value: P8 Whole Brain EC

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2


title: control_3

city: Guangzhou

first: Xiaoping

last: Liu

address: No. 9 Jinsui Road, Tianhe District, Guangzhou, Guangdong, China

institute: Guangzhou Women and Children’s Medical Center

data_processing:
Basecalls performed using bcl2fastq V2.19
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Genome_build: hg18
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: glioma cell

growth_protocol: Human glioma cell line U251 was provided  grown in DMEM containing with 10% FBS at 37 °C containing 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol® reagent.
Strand-specific adapters were added to fragmented RNA (average fragment length 200 nt) before reverse transcription followed the manufacturer's instructions. The quality of cDNA libraries was quality evaluated on an Agilent 2100 Bioanalyzer and sequenced by Shanghai Genergy Co. Ltd.

treatment_protocol: U251 cells were treated with 1.7%, 3.4% and 5.1% Sev gas for 2h.

tag: cell line

value: untreated


title: sev_3

value: sevoflurane 2h-treatment


title: sev_1


title: sev_2


title: Brain_EC_DAPTtreated_rep1

description:
BJ010
brain_IPcounts_table_raw.txt


title: WAPL/MED12 rep 2B RNAseq


title: control_2


title: HREC_EGTA_control_rep3

description:
HR_p8_0
HREC_EGTA_0vs1.5counts.txt


title: MED12 rep 1B RNAseq


title: HREC_EGTA_Induction_rep1

description:
HR_p12_1_5
HREC_EGTA_0vs1.5counts.txt


title: HREC_EGTA_control_rep2

description:
HR_p13_0
HREC_EGTA_0vs1.5counts.txt


title: Brain_EC_Control_rep2

description:
BJ008
brain_IPcounts_table_raw.txt

value: Control


title: Day 10 erythroblasts - Ser2-Pol2 - Rep 3

city: Rochester

first: Zachary

middle: C

last: Murphy

state: NY

address: 601 Elmwood Ave box 703

institute: University of Rochester

data_processing:
Library strategy: CUT&Tag
Bowtie2 hg19 alignment
samtools view sam to bam conversion
samtools sort
bamCoverage bigwig conversion, RPKM normalization, bs 5, ignore duplicates
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: primary terminally maturing erythroblasts

growth_protocol: as described in Gautier Cell Reo9rts 2016

extract_protocol:
phenol chloroform
CUT&Tag TN5 tagmentation

value: CD36+ selected erythroid maturation

tag: time point

value: Day 10

tag: cut&tag antibody

value: Cell Signaling Phospho-Rpb1 CTD (Ser2) (E1Z3G) Rabbit mAb #13499


title: HREC_EGTA_control_rep1

description:
HR_p12_0
HREC_EGTA_0vs1.5counts.txt


title: MED12 rep 1A RNAseq

tag: cell type


title: Brain_EC_Control_rep1

description:
BJ007
brain_IPcounts_table_raw.txt

tag: tissue


title: WAPL rep 1C RNAseq

value: WAPL


title: control_1


title: HREC_TLA_DLL4_rep3

description:
Retinal_DLL4_3
TLA-HRECcounts.txt


title: Day 10 erythroblasts - Ser2-Pol2 - Rep 2


title: MED12 rep 2C RNAseq


title: Brain_Homogenate_DAPTtreated_rep3

description:
BJ006
brain_INcounts_table_raw.txt

value: P8 Whole Brain


title: HREC_EGTA_Induction_rep3

description:
HR_p8_1_5
HREC_EGTA_0vs1.5counts.txt


title: Brain_EC_DAPTtreated_rep3

description:
BJ012
brain_IPcounts_table_raw.txt


title: Day 10 erythroblasts - Ser2-Pol2 - Rep 1


title: WAPL rep 1A RNAseq


title: Brain_Homogenate_DAPTtreated_rep1

description:
BJ004
brain_INcounts_table_raw.txt


title: WT rep 1C RNAseq

value: WT


title: Day 7 erythroblasts - Ser2-Pol2 - Rep 2

value: Day 7


title: Day 7 erythroblasts - Ser2-Pol2 - Rep 3


title: HREC_TLA_DLL4_rep1

description:
Retinal_DLL4_1
TLA-HRECcounts.txt


title: HREC_TLA_Control_rep3

description:
Retinal_Fc_3
TLA-HRECcounts.txt


title: WT rep 1B RNAseq


title: Brain_Homogenate_Control_rep3

description:
BJ003
brain_INcounts_table_raw.txt


title: Day 7 erythroblasts - Ser2-Pol2 - Rep 1


title: Brain_Homogenate_Control_rep2

description:
BJ002
brain_INcounts_table_raw.txt


title: WT rep 1A RNAseq


title: Day 10 erythroblasts - Ser5-Pol2 - Rep 3

value: Cell Signaling Phospho-Rpb1 CTD (Ser5) (D9N5I) Rabbit mAb #13523


title: HREC_TLA_Control_rep1

description:
Retinal_Fc_1
TLA-HRECcounts.txt


title: Brain_EC_Control_rep3

description:
BJ009
brain_IPcounts_table_raw.txt


title: Brain_Homogenate_Control_rep1

description:
BJ001
brain_INcounts_table_raw.txt


title: WAPL/MED12 rep 1C RNAseq


title: Day 10 erythroblasts - Ser5-Pol2 - Rep 2


title: HUVEC_TLA_DLL4_rep3

description:
JJ0012
TLA_HUVEC_SE_counts.txt

source_name: Human Umbilical Vein Endothelial Cells (HUVEC)

value: Primary Cells (Human Umbilical Vein Endothelial Cells)


title: WAPL/MED12 rep 1B RNAseq


title: MKO_GC_4: Ckmm-Cre; USP21 flox/flox, rep 3

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.38, then mapped to mm10 whole genome using HISTAT2 v2.1.0 and Bowtie2 v2.3.4.1
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v1.3.4d.
Genome_build: mm10

source_name: Muscle

extract_protocol:
Gastrocnemius muscles tissues were excised from mice and stored in RNAlater solution. Total RNA was extracted using Trizol.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (#RS-122-2101)

value: Gastrocnemius muscle

value: 12 weeks

tag: genotype

value: Muscle-specific USP21 KO


title: Day 10 erythroblasts - Ser5-Pol2 - Rep 1


title: HUVEC_TLA_DLL4_rep2

description:
JJ009
TLA_HUVEC_SE_counts.txt


title: WAPL rep 1B RNAseq


title: MKO_GC_2: Ckmm-Cre; USP21 flox/flox, rep 2


title: WAPL/MED12 rep 1A RNAseq


title: Day 7 erythroblasts - Ser5-Pol2 - Rep 3


title: HREC_TLA_DLL4_rep2

description:
Retinal_DLL4_2
TLA-HRECcounts.txt

value: Primary Cells (Human Microvascular Retinal Endothelial Cells)


title: HUVEC_TLA_DLL4_rep1

description:
JJ006
TLA_HUVEC_SE_counts.txt


title: HUVEC_TLA_Control_rep3

description:
JJ0011
TLA_HUVEC_SE_counts.txt


title: Brain_Homogenate_DAPTtreated_rep2

description:
BJ005
brain_INcounts_table_raw.txt

value: DAPTtreated

value: Rpl22HA/HA x Cdh5CreERT2


title: HUVEC_TLA_Control_rep2

description:
JJ008
TLA_HUVEC_SE_counts.txt


title: L_GC_7: USP21 flox/flox, rep 2

value: Litter


title: HUVEC_TLA_Control_rep1

description:
JJ005
TLA_HUVEC_SE_counts.txt

value: Control


title: MED12 Hi-C

description: TruSeq libraries prepared from 3C template

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

extract_protocol:
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.


title: HREC_TLA_Control_rep2

description:
Retinal_Fc_2
TLA-HRECcounts.txt


title: WAPL rep 3C RNAseq


title: Mpfad5_vs_Tak-1_repl3

type: RNA

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation

scan_protocol: Images were scanned at 2um resolution in an Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and  were with Feature Extraction 9.0 software (Agilent Technologies).

data_processing: Raw intensities were background-subtracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were  normalized by LOWESS algorithm followed by quantile normalization

organism: Marchantia polymorpha

label_protocol: 200 ng of total RNA were reverse transcribed used T7 primer and the cDNA converted to aRNA using T7 RNA polymerase, incorporating cyanine 3- or cyanine 5-labeled CTP, according to 'Two color Microarray-Based Gene Expression Analysis Protocol' (Agilent)

growth_protocol: Marchantia polymorpha accession Takaragaike-1 (Tak-1; male) and mutant Mpfad5 were used in this work. Plants were subcultivated on 0.5 Gamborg’s B5 medium containing 1% agar for 3 weeks. Apical fragments of the plants, excluding gemma cups, were ground in liquid nitrogen prior RNA extraction. Every independent biological replicate contained 6-8 plants.

extract_protocol: Total RNA from Marchantia was extracted with Favorgen Plant RNA Extraction and DNase on-column digestion (Qiagen) was performed to remove genomic DNA contamination.

treatment_protocol: Leaflets were wounded with tweezers and frozen 90 min after treatment

tag: cultivar

value: leaflet

value: Wound

value: control


title: HKU Meningioma 96 (methylation)

status: Public on Jan 10 2022

type: genomic

city: San Francisco

first: Abrar

last: Choudhury

state: California

institute: University of California, San Francisco

description:
meningioma
QM96
203219750085_R07C01

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

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

data_processing:
Analysis was performed in R v3.5.3 with the SeSAMe package. Probes were filtered and analyzed using the standard SeSAMe preprocessing pipeline, including normal-exponential out-of-band background correction, nonlinear dye bias correction, p-value with out-of-band array hybridization masking, and beta value calculation
Processed data file meningioma_betas.csv represents SeSAMe-computed average beta values.

label: Cy5 and Cy3

source_name: Meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and DNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224)

value: meningioma

tag: institution

value: HKU

tag: Sex

tag: grade


title: HKU Meningioma 99 (methylation)

description:
meningioma
QM99
204081730051_R06C01


title: HKU Meningioma 95 (methylation)

description:
meningioma
QM95
203219750085_R06C01


title: HKU Meningioma 9 (methylation)

description:
meningioma
QM9
203219750010_R02C01


title: HKU Meningioma 89 (methylation)

description:
meningioma
QM89
204081730051_R05C01


title: Mpfad5_vs_Tak-1_repl4

tag: genotype/variation


title: Mpfad5_vs_Tak-1_repl2


title: HKU Meningioma 93 (methylation)

description:
meningioma
QM93
203219750085_R04C01

tag: age


title: Day 7 erythroblasts - Ser5-Pol2 - Rep 2

value: CD36+ selected erythroid maturation


title: HKU Meningioma 88 (methylation)

description:
meningioma
QM88
204081730051_R04C01


title: HKU Meningioma 92 (methylation)

description:
meningioma
QM92
203219750085_R03C01


title: HKU Meningioma 90 (methylation)

description:
meningioma
QM90
203219750085_R01C01


title: HKU Meningioma 87 (methylation)

description:
meningioma
QM87
203219750026_R08C01


title: HKU Meningioma 84 (methylation)

description:
meningioma
QM84
204081730051_R02C01


title: Mpfad5_vs_Tak-1_repl1


title: HKU Meningioma 86 (methylation)

description:
meningioma
QM86
203219750026_R07C01


title: L_GC_8: USP21 flox/flox, rep 3


title: HKU Meningioma 81 (methylation)

description:
meningioma
QM81
204081730051_R01C01


title: WAPL/MED12 Hi-C


title: HKU Meningioma 85 (methylation)

description:
meningioma
QM85
204081730051_R03C01


title: Day 7 erythroblasts - Ser5-Pol2 - Rep 1

value: Day 7


title: MKO_GC_1: Ckmm-Cre; USP21 flox/flox, rep 1


title: HKU Meningioma 83 (methylation)

description:
meningioma
QM83
203219750026_R06C01


title: HKU Meningioma 80 (methylation)

description:
meningioma
QM80
203219750026_R05C01


title: HKU Meningioma 98 (methylation)

description:
meningioma
QM98
203219750085_R08C01


title: HKU Meningioma 8 (methylation)

description:
meningioma
QM8
203064760075_R02C01


title: L_GC_6: USP21 flox/flox, rep 1


title: HKU Meningioma 94 (methylation)

description:
meningioma
QM94
203219750085_R05C01


title: HKU Meningioma 91 (methylation)

description:
meningioma
QM91
203219750085_R02C01


title: HKU Meningioma 79 (methylation)

description:
meningioma
QM79
203219750026_R04C01


title: HKU Meningioma 78 (methylation)

description:
meningioma
QM78
203219750026_R03C01


title: HKU Meningioma 73 (methylation)

description:
meningioma
QM73
204367410032_R07C01


title: HKU Meningioma 76 (methylation)

description:
meningioma
QM76
203219750026_R01C01


title: HKU Meningioma 74 (methylation)

description:
meningioma
QM74
204367410032_R08C01


title: HKU Meningioma 77 (methylation)

description:
meningioma
QM77
203219750026_R02C01


title: HKU Meningioma 71 (methylation)

description:
meningioma
QM71
203219750011_R08C01


title: HKU Meningioma 7 (methylation)

description:
meningioma
QM7
203064760075_R01C01


title: HKU Meningioma 66 (methylation)

description:
meningioma
QM66
203219750011_R05C01


title: HKU Meningioma 72 (methylation)

description:
meningioma
QM72
204367410032_R06C01


title: HKU Meningioma 68 (methylation)

description:
meningioma
QM68
204367410032_R05C01


title: HKU Meningioma 67 (methylation)

description:
meningioma
QM67
203219750011_R06C01


title: HKU Meningioma 64 (methylation)

description:
meningioma
QM64
203219750011_R03C01


title: HKU Meningioma 65 (methylation)

description:
meningioma
QM65
203219750011_R04C01


title: HKU Meningioma 69 (methylation)

description:
meningioma
QM69
203219750011_R07C01


title: HKU Meningioma 63 (methylation)

description:
meningioma
QM63
204367410032_R04C01


title: HKU Meningioma 62 (methylation)

description:
meningioma
QM62
203219750011_R02C01


title: HKU Meningioma 60 (methylation)

description:
meningioma
QM60
203219750011_R01C01


title: HKU Meningioma 61 (methylation)

description:
meningioma
QM61
204367410032_R03C01


title: HKU Meningioma 6 (methylation)

description:
meningioma
QM6
203064760067_R08C01


title: HKU Meningioma 59 (methylation)

description:
meningioma
QM59
203219750010_R08C01


title: HKU Meningioma 56 (methylation)

description:
meningioma
QM56
203219750010_R06C01


title: HKU Meningioma 58 (methylation)

description:
meningioma
QM58
203219750010_R07C01


title: HKU Meningioma 55 (methylation)

description:
meningioma
QM55
204367410032_R02C01


title: HKU Meningioma 53 (methylation)

description:
meningioma
QM53
203219750010_R05C01


title: HKU Meningioma 52 (methylation)

description:
meningioma
QM52
203060700010_R08C01


title: HKU Meningioma 51 (methylation)

description:
meningioma
QM51
203060700010_R07C01


title: HKU Meningioma 50 (methylation)

description:
meningioma
QM50
203060700010_R06C01


title: HKU Meningioma 5 (methylation)

description:
meningioma
QM5
204367410003_R01C01


title: HKU Meningioma 49 (methylation)

description:
meningioma
QM49
203060700010_R05C01


title: HKU Meningioma 47 (methylation)

description:
meningioma
QM47
203060700010_R03C01


title: HKU Meningioma 45 (methylation)

description:
meningioma
QM45
204367410032_R01C01


title: HKU Meningioma 46 (methylation)

description:
meningioma
QM46
203060700010_R02C01


title: HKU Meningioma 43 (methylation)

description:
meningioma
QM43
204367410003_R07C01


title: HKU Meningioma 44 (methylation)

description:
meningioma
QM44
204367410003_R08C01


title: HKU Meningioma 420 (methylation)

description:
meningioma
QM420
204367400057_R06C01


title: HKU Meningioma 416 (methylation)

description:
meningioma
QM416
204367400057_R04C01


title: HKU Meningioma 421 (methylation)

description:
meningioma
QM421
204367400057_R07C01


title: HKU Meningioma 408 (methylation)

description:
meningioma
QM408
204365950092_R08C01


title: HKU Meningioma 42 (methylation)

description:
meningioma
QM42
203060700010_R01C01


title: HKU Meningioma 414 (methylation)

description:
meningioma
QM414
204367400057_R03C01


title: HKU Meningioma 410 (methylation)

description:
meningioma
QM410
204367400057_R01C01


title: HKU Meningioma 407 (methylation)

description:
meningioma
QM407
204365950092_R07C01


title: HKU Meningioma 405 (methylation)

description:
meningioma
QM405
204365950092_R05C01


title: HKU Meningioma 402 (methylation)

description:
meningioma
QM402
204365950092_R03C01


title: HKU Meningioma 406 (methylation)

description:
meningioma
QM406
204365950092_R06C01


title: HKU Meningioma 403 (methylation)

description:
meningioma
QM403
204365950092_R04C01


title: HKU Meningioma 401 (methylation)

description:
meningioma
QM401
204365950092_R02C01


title: HKU Meningioma 400 (methylation)

description:
meningioma
QM400
204365950092_R01C01


title: HKU Meningioma 40 (methylation)

description:
meningioma
QM40
203060700005_R08C01


title: HKU Meningioma 396 (methylation)

description:
meningioma
QM396
204365950070_R07C01


title: HKU Meningioma 393 (methylation)

description:
meningioma
QM393
204365950070_R05C01


title: HKU Meningioma 395 (methylation)

description:
meningioma
QM395
204365950070_R06C01


title: HKU Meningioma 392 (methylation)

description:
meningioma
QM392
204365950070_R04C01


title: HKU Meningioma 391 (methylation)

description:
meningioma
QM391
204365950070_R03C01


title: HKU Meningioma 390 (methylation)

description:
meningioma
QM390
204365950070_R02C01


title: HKU Meningioma 388 (methylation)

description:
meningioma
QM388
204365950033_R08C01


title: HKU Meningioma 39 (methylation)

description:
meningioma
QM39
203060700005_R07C01


title: HKU Meningioma 48 (methylation)

description:
meningioma
QM48
203060700010_R04C01


title: HKU Meningioma 389 (methylation)

description:
meningioma
QM389
204365950070_R01C01


title: HKU Meningioma 387 (methylation)

description:
meningioma
QM387
204365950033_R07C01


title: HKU Meningioma 384 (methylation)

description:
meningioma
QM384
204365950033_R05C01


title: HKU Meningioma 381 (methylation)

description:
meningioma
QM381
204365950033_R04C01


title: HKU Meningioma 380 (methylation)

description:
meningioma
QM380
204365950033_R03C01


title: HKU Meningioma 377 (methylation)

description:
meningioma
QM377
204365950033_R01C01


title: HKU Meningioma 378 (methylation)

description:
meningioma
QM378
204365950033_R02C01


title: HKU Meningioma 379 (methylation)

description:
meningioma
QM379
203220070184_R06C01


title: HKU Meningioma 418 (methylation)

description:
meningioma
QM418
204367400057_R05C01


title: HKU Meningioma 374 (methylation)

description:
meningioma
QM374
203220070184_R04C01


title: HKU Meningioma 372 (methylation)

description:
meningioma
QM372
203220070184_R03C01


title: HKU Meningioma 373 (methylation)

description:
meningioma
QM373
204365950031_R07C01


title: HKU Meningioma 376 (methylation)

description:
meningioma
QM376
204365950031_R08C01


title: HKU Meningioma 371 (methylation)

description:
meningioma
QM371
204365950031_R06C01


title: HKU Meningioma 369 (methylation)

description:
meningioma
QM369
203220070184_R02C01


title: HKU Meningioma 411 (methylation)

description:
meningioma
QM411
204367400057_R02C01


title: HKU Meningioma 37 (methylation)

description:
meningioma
QM37
204367410003_R06C01


title: HKU Meningioma 367 (methylation)

description:
meningioma
QM367
203220070184_R01C01


title: HKU Meningioma 368 (methylation)

description:
meningioma
QM368
204365950031_R04C01


title: HKU Meningioma 366 (methylation)

description:
meningioma
QM366
204365950031_R03C01


title: HKU Meningioma 397 (methylation)

description:
meningioma
QM397
204365950070_R08C01


title: HKU Meningioma 365 (methylation)

description:
meningioma
QM365
204365950031_R02C01


title: HKU Meningioma 364 (methylation)

description:
meningioma
QM364
203220070163_R08C01


title: HKU Meningioma 362 (methylation)

description:
meningioma
QM362
203220070163_R07C01


title: HKU Meningioma 361 (methylation)

description:
meningioma
QM361
204365950031_R01C01


title: HKU Meningioma 360 (methylation)

description:
meningioma
QM360
203220070163_R06C01


title: HKU Meningioma 359 (methylation)

description:
meningioma
QM359
203220070163_R05C01


title: HKU Meningioma 36 (methylation)

description:
meningioma
QM36
203060700005_R06C01


title: HKU Meningioma 358 (methylation)

description:
meningioma
QM358
203220070163_R04C01


title: HKU Meningioma 357 (methylation)

description:
meningioma
QM357
203220070163_R03C01


title: HKU Meningioma 385 (methylation)

description:
meningioma
QM385
204365950033_R06C01


title: HKU Meningioma 356 (methylation)

description:
meningioma
QM356
204365940166_R08C01


title: HKU Meningioma 355 (methylation)

description:
meningioma
QM355
203220070163_R02C01


title: HKU Meningioma 353 (methylation)

description:
meningioma
QM353
204365940166_R07C01


title: HKU Meningioma 354 (methylation)

description:
meningioma
QM354
203220070163_R01C01


title: HKU Meningioma 351 (methylation)

description:
meningioma
QM351
203220070141_R07C01


title: HKU Meningioma 352 (methylation)

description:
meningioma
QM352
203220070141_R08C01


title: HKU Meningioma 375 (methylation)

description:
meningioma
QM375
203220070184_R05C01


title: HKU Meningioma 348 (methylation)

description:
meningioma
QM348
203220070141_R05C01


title: HKU Meningioma 346 (methylation)

description:
meningioma
QM346
204365940166_R05C01


title: HKU Meningioma 35 (methylation)

description:
meningioma
QM35
204367410003_R05C01


title: HKU Meningioma 345 (methylation)

description:
meningioma
QM345
204365940166_R04C01


title: HKU Meningioma 344 (methylation)

description:
meningioma
QM344
204365940166_R03C01


title: HKU Meningioma 343 (methylation)

description:
meningioma
QM343
203220070141_R04C01


title: HKU Meningioma 341 (methylation)

description:
meningioma
QM341
203220070141_R03C01


title: HKU Meningioma 342 (methylation)

description:
meningioma
QM342
204365940166_R02C01


title: HKU Meningioma 340 (methylation)

description:
meningioma
QM340
203220070141_R02C01


title: HKU Meningioma 34 (methylation)

description:
meningioma
QM34
203060700005_R05C01


title: HKU Meningioma 370 (methylation)

description:
meningioma
QM370
204365950031_R05C01


title: HKU Meningioma 339 (methylation)

description:
meningioma
QM339
203220070141_R01C01


title: HKU Meningioma 338 (methylation)

description:
meningioma
QM338
204365940166_R01C01


title: HKU Meningioma 337 (methylation)

description:
meningioma
QM337
204367410164_R08C01


title: HKU Meningioma 336 (methylation)

description:
meningioma
QM336
204367410164_R07C01


title: HKU Meningioma 335 (methylation)

description:
meningioma
QM335
204367410164_R06C01


title: HKU Meningioma 333 (methylation)

description:
meningioma
QM333
203220070134_R08C01


title: HKU Meningioma 331 (methylation)

description:
meningioma
QM331
204367410164_R05C01


title: HKU Meningioma 330 (methylation)

description:
meningioma
QM330
203220070134_R06C01


title: HKU Meningioma 332 (methylation)

description:
meningioma
QM332
203220070134_R07C01


title: HKU Meningioma 33 (methylation)

description:
meningioma
QM33
203060700005_R04C01


title: HKU Meningioma 328 (methylation)

description:
meningioma
QM328
204367410164_R04C01


title: HKU Meningioma 326 (methylation)

description:
meningioma
QM326
203220070134_R04C01


title: HKU Meningioma 324 (methylation)

description:
meningioma
QM324
203220070134_R02C01


title: HKU Meningioma 327 (methylation)

description:
meningioma
QM327
204367410164_R03C01


title: HKU Meningioma 350 (methylation)

description:
meningioma
QM350
203220070141_R06C01


title: HKU Meningioma 323 (methylation)

description:
meningioma
QM323
204367410164_R02C01


title: HKU Meningioma 325 (methylation)

description:
meningioma
QM325
203220070134_R03C01


title: HKU Meningioma 322 (methylation)

description:
meningioma
QM322
203220070134_R01C01


title: HKU Meningioma 320 (methylation)

description:
meningioma
QM320
204367410164_R01C01


title: HKU Meningioma 321 (methylation)

description:
meningioma
QM321
203220070101_R08C01


title: HKU Meningioma 317 (methylation)

description:
meningioma
QM317
203220070101_R05C01


title: HKU Meningioma 32 (methylation)

description:
meningioma
QM32
203060700005_R03C01


title: HKU Meningioma 315 (methylation)

description:
meningioma
QM315
203220070101_R03C01


title: HKU Meningioma 314 (methylation)

description:
meningioma
QM314
204367410064_R08C01


title: HKU Meningioma 311 (methylation)

description:
meningioma
QM311
204367410064_R07C01


title: HKU Meningioma 316 (methylation)

description:
meningioma
QM316
203220070101_R04C01


title: HKU Meningioma 318 (methylation)

description:
meningioma
QM318
203220070101_R06C01


title: HKU Meningioma 313 (methylation)

description:
meningioma
QM313
203220070101_R02C01


title: HKU Meningioma 347 (methylation)

description:
meningioma
QM347
204365940166_R06C01


title: HKU Meningioma 310 (methylation)

description:
meningioma
QM310
204367410064_R06C01


title: HKU Meningioma 31 (methylation)

description:
meningioma
QM31
204367410003_R04C01


title: HKU Meningioma 308 (methylation)

description:
meningioma
QM308
204367410064_R05C01


title: HKU Meningioma 307 (methylation)

description:
meningioma
QM307
204367410064_R04C01


title: HKU Meningioma 306 (methylation)

description:
meningioma
QM306
204367410064_R03C01


title: HKU Meningioma 305 (methylation)

description:
meningioma
QM305
204367410064_R02C01


title: HKU Meningioma 304 (methylation)

description:
meningioma
QM304
203220070101_R01C01


title: HKU Meningioma 303 (methylation)

description:
meningioma
QM303
204367410064_R01C01


title: HKU Meningioma 302 (methylation)

description:
meningioma
QM302
203220070062_R08C01


title: HKU Meningioma 300 (methylation)

description:
meningioma
QM300
203220070062_R07C01


title: HKU Meningioma 301 (methylation)

description:
meningioma
QM301
204367410005_R08C01


title: HKU Meningioma 329 (methylation)

description:
meningioma
QM329
203220070134_R05C01


title: HKU Meningioma 299 (methylation)

description:
meningioma
QM299
204367410005_R07C01


title: HKU Meningioma 30 (methylation)

description:
meningioma
QM30
203060700005_R02C01


title: HKU Meningioma 3 (methylation)

description:
meningioma
QM3
203064760067_R07C01


title: HKU Meningioma 298 (methylation)

description:
meningioma
QM298
204367410005_R06C01


title: HKU Meningioma 292 (methylation)

description:
meningioma
QM292
203220070062_R05C01


title: HKU Meningioma 291 (methylation)

description:
meningioma
QM291
203220070062_R04C01


title: HKU Meningioma 290 (methylation)

description:
meningioma
QM290
203220070062_R03C01


title: HKU Meningioma 287 (methylation)

description:
meningioma
QM287
204367410005_R04C01


title: HKU Meningioma 284 (methylation)

description:
meningioma
QM284
204367410005_R03C01


title: HKU Meningioma 283 (methylation)

description:
meningioma
QM283
204367410005_R02C01


title: HKU Meningioma 282 (methylation)

description:
meningioma
QM282
203219760214_R08C01


title: HKU Meningioma 28 (methylation)

description:
meningioma
QM28
203219750010_R03C01


title: HKU Meningioma 29 (methylation)

description:
meningioma
QM29
203219750010_R04C01


title: HKU Meningioma 297 (methylation)

description:
meningioma
QM297
203220070062_R06C01


title: HKU Meningioma 289 (methylation)

description:
meningioma
QM289
204367410005_R05C01


title: HKU Meningioma 278 (methylation)

description:
meningioma
QM278
203219760214_R05C01


title: HKU Meningioma 280 (methylation)

description:
meningioma
QM280
203219760214_R06C01


title: HKU Meningioma 277 (methylation)

description:
meningioma
QM277
204367410005_R01C01


title: HKU Meningioma 276 (methylation)

description:
meningioma
QM276
204365950163_R08C01


title: HKU Meningioma 286 (methylation)

description:
meningioma
QM286
203220070062_R02C01


title: HKU Meningioma 285 (methylation)

description:
meningioma
QM285
203220070062_R01C01


title: HKU Meningioma 274 (methylation)

description:
meningioma
QM274
203219760214_R04C01


title: HKU Meningioma 272 (methylation)

description:
meningioma
QM272
203219760214_R02C01


title: HKU Meningioma 273 (methylation)

description:
meningioma
QM273
203219760214_R03C01


title: HKU Meningioma 271 (methylation)

description:
meningioma
QM271
203219760214_R01C01


title: HKU Meningioma 270 (methylation)

description:
meningioma
QM270
204365950163_R07C01


title: HKU Meningioma 268 (methylation)

description:
meningioma
QM268
204365950163_R06C01


title: HKU Meningioma 27 (methylation)

description:
meningioma
QM27
203060700005_R01C01


title: HKU Meningioma 267 (methylation)

description:
meningioma
QM267
203219760154_R07C01


title: HKU Meningioma 266 (methylation)

description:
meningioma
QM266
204365950163_R05C01


title: HKU Meningioma 263 (methylation)

description:
meningioma
QM263
204365950163_R03C01


title: HKU Meningioma 264 (methylation)

description:
meningioma
QM264
204365950163_R04C01


title: HKU Meningioma 262 (methylation)

description:
meningioma
QM262
204365950163_R02C01


title: HKU Meningioma 261 (methylation)

description:
meningioma
QM261
204365950163_R01C01


title: HKU Meningioma 260 (methylation)

description:
meningioma
QM260
203219760154_R06C01


title: HKU Meningioma 26 (methylation)

description:
meningioma
QM26
203064760113_R08C01


title: HKU Meningioma 259 (methylation)

description:
meningioma
QM259
204365950124_R08C01


title: HKU Meningioma 258 (methylation)

description:
meningioma
QM258
203219760154_R05C01


title: HKU Meningioma 255 (methylation)

description:
meningioma
QM255
204365950124_R07C01


title: HKU Meningioma 257 (methylation)

description:
meningioma
QM257
203219760154_R04C01


title: HKU Meningioma 251 (methylation)

description:
meningioma
QM251
204365950124_R04C01


title: HKU Meningioma 254 (methylation)

description:
meningioma
QM254
204365950124_R06C01


title: HKU Meningioma 256 (methylation)

description:
meningioma
QM256
203219760154_R03C01


title: HKU Meningioma 253 (methylation)

description:
meningioma
QM253
204365950124_R05C01


title: HKU Meningioma 250 (methylation)

description:
meningioma
QM250
204365950124_R03C01


title: HKU Meningioma 249 (methylation)

description:
meningioma
QM249
203219760154_R02C01


title: HKU Meningioma 25 (methylation)

description:
meningioma
QM25
203064760113_R07C01


title: HKU Meningioma 246 (methylation)

description:
meningioma
QM246
203219760071_R08C01


title: HKU Meningioma 247 (methylation)

description:
meningioma
QM247
204365950124_R02C01


title: HKU Meningioma 248 (methylation)

description:
meningioma
QM248
203219760154_R01C01


title: HKU Meningioma 245 (methylation)

description:
meningioma
QM245
203219760071_R07C01


title: HKU Meningioma 242 (methylation)

description:
meningioma
QM242
204365950124_R01C01


title: HKU Meningioma 239 (methylation)

description:
meningioma
QM239
203219760071_R06C01


title: HKU Meningioma 238 (methylation)

description:
meningioma
QM238
204365950053_R07C01


title: HKU Meningioma 237 (methylation)

description:
meningioma
QM237
203219760071_R05C01


title: HKU Meningioma 236 (methylation)

description:
meningioma
QM236
203219760071_R04C01


title: HKU Meningioma 269 (methylation)

description:
meningioma
QM269
203219760154_R08C01


title: HKU Meningioma 235 (methylation)

description:
meningioma
QM235
203219760071_R03C01


title: HKU Meningioma 234 (methylation)

description:
meningioma
QM234
204365950053_R06C01


title: HKU Meningioma 233 (methylation)

description:
meningioma
QM233
204365950053_R05C01


title: HKU Meningioma 232 (methylation)

description:
meningioma
QM232
204365950053_R04C01


title: HKU Meningioma 230 (methylation)

description:
meningioma
QM230
204365950053_R03C01


title: HKU Meningioma 231 (methylation)

description:
meningioma
QM231
203219760071_R02C01


title: HKU Meningioma 23 (methylation)

description:
meningioma
QM23
203064760113_R05C01


title: HKU Meningioma 229 (methylation)

description:
meningioma
QM229
204365950053_R02C01


title: HKU Meningioma 227 (methylation)

description:
meningioma
QM227
203219670062_R08C01


title: HKU Meningioma 226 (methylation)

description:
meningioma
QM226
203219670062_R07C01


title: HKU Meningioma 223 (methylation)

description:
meningioma
QM223
204365950038_R08C01


title: HKU Meningioma 228 (methylation)

description:
meningioma
QM228
203219760071_R01C01


title: HKU Meningioma 224 (methylation)

description:
meningioma
QM224
204365950053_R01C01


title: HKU Meningioma 225 (methylation)

description:
meningioma
QM225
203219670062_R06C01


title: HKU Meningioma 221 (methylation)

description:
meningioma
QM221
204365950038_R06C01


title: HKU Meningioma 218 (methylation)

description:
meningioma
QM218
203219670062_R04C01


title: HKU Meningioma 222 (methylation)

description:
meningioma
QM222
204365950038_R07C01


title: HKU Meningioma 215 (methylation)

description:
meningioma
QM215
204365950038_R03C01


title: HKU Meningioma 219 (methylation)

description:
meningioma
QM219
204365950038_R05C01


title: HKU Meningioma 216 (methylation)

description:
meningioma
QM216
204365950038_R04C01


title: HKU Meningioma 220 (methylation)

description:
meningioma
QM220
203219670062_R05C01


title: HKU Meningioma 240 (methylation)

description:
meningioma
QM240
204365950053_R08C01


title: HKU Meningioma 24 (methylation)

description:
meningioma
QM24
203064760113_R06C01


title: HKU Meningioma 212 (methylation)

description:
meningioma
QM212
203219760058_R08C01


title: HKU Meningioma 211 (methylation)

description:
meningioma
QM211
203219760058_R07C01


title: HKU Meningioma 209 (methylation)

description:
meningioma
QM209
204365950038_R02C01


title: HKU Meningioma 21 (methylation)

description:
meningioma
QM21
203064760113_R04C01


title: HKU Meningioma 206 (methylation)

description:
meningioma
QM206
203219760058_R05C01


title: HKU Meningioma 203 (methylation)

description:
meningioma
QM203
203219760058_R03C01


title: HKU Meningioma 205 (methylation)

description:
meningioma
QM205
203219760058_R04C01


title: HKU Meningioma 201 (methylation)

description:
meningioma
QM201
204365940154_R08C01


title: HKU Meningioma 202 (methylation)

description:
meningioma
QM202
204365950038_R01C01


title: HKU Meningioma 200 (methylation)

description:
meningioma
QM200
203219760058_R02C01


title: HKU Meningioma 20 (methylation)

description:
meningioma
QM20
203064760113_R03C01


title: HKU Meningioma 2 (methylation)

description:
meningioma
QM2
203219750010_R01C01


title: HKU Meningioma 196 (methylation)

description:
meningioma
QM196
203219760025_R07C01


title: HKU Meningioma 198 (methylation)

description:
meningioma
QM198
203219760025_R08C01


title: HKU Meningioma 199 (methylation)

description:
meningioma
QM199
203219760058_R01C01


title: HKU Meningioma 197 (methylation)

description:
meningioma
QM197
204365940154_R07C01


title: HKU Meningioma 195 (methylation)

description:
meningioma
QM195
204365940154_R06C01


title: HKU Meningioma 192 (methylation)

description:
meningioma
QM192
203219760025_R06C01


title: HKU Meningioma 184 (methylation)

description:
meningioma
QM184
203219760025_R02C01


title: HKU Meningioma 19 (methylation)

description:
meningioma
QM19
203064760113_R02C01


title: HKU Meningioma 188 (methylation)

description:
meningioma
QM188
203219760025_R04C01


title: HKU Meningioma 193 (methylation)

description:
meningioma
QM193
204365940154_R05C01


title: HKU Meningioma 217 (methylation)

description:
meningioma
QM217
203219670062_R03C01


title: HKU Meningioma 187 (methylation)

description:
meningioma
QM187
203219760025_R03C01


title: HKU Meningioma 183 (methylation)

description:
meningioma
QM183
203219760025_R01C01


title: HKU Meningioma 214 (methylation)

description:
meningioma
QM214
203219670062_R02C01


title: HKU Meningioma 182 (methylation)

description:
meningioma
QM182
204365940154_R03C01


title: HKU Meningioma 213 (methylation)

description:
meningioma
QM213
203219670062_R01C01


title: HKU Meningioma 18 (methylation)

description:
meningioma
QM18
204367410003_R03C01


title: HKU Meningioma 181 (methylation)

description:
meningioma
QM181
203219760007_R08C01


title: HKU Meningioma 180 (methylation)

description:
meningioma
QM180
204365940154_R02C01


title: HKU Meningioma 179 (methylation)

description:
meningioma
QM179
203219760007_R07C01


title: HKU Meningioma 175 (methylation)

description:
meningioma
QM175
204365940154_R01C01


title: HKU Meningioma 177 (methylation)

description:
meningioma
QM177
203219760007_R06C01


title: HKU Meningioma 207 (methylation)

description:
meningioma
QM207
203219760058_R06C01


title: HKU Meningioma 174 (methylation)

description:
meningioma
QM174
204365950096_R08C01


title: HKU Meningioma 172 (methylation)

description:
meningioma
QM172
203219760007_R05C01


title: HKU Meningioma 171 (methylation)

description:
meningioma
QM171
204365950096_R06C01


title: HKU Meningioma 170 (methylation)

description:
meningioma
QM170
204365950096_R05C01


title: HKU Meningioma 189 (methylation)

description:
meningioma
QM189
204365940154_R04C01


title: SVP 72H DYN rep4

city: Milano

first: Gaia

last: Spinetti

address: Via Fantoli 16/15

country: Italy

institute: IRCCS MultiMedica

description: 2x100 paired-end sequence reads

data_processing:
Raw sequencing reads were trimmed to remove adaptor contaminations, using Cutadapt (version 1.18) with the following parameters: cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --trim-n --pair-filter=any --minimum-length 20.
Read quality was checked for each sample using FastQC v0.11.8
Sequencing reads were, then, aligned to GENCODE’s human reference genome (GRCh38 primary assembly v31) and quantified at gene level using STAR (version 2.7.3a), with default parameters and allowing up to 3 mismatches.
Genome_build: GRCh38 v.31
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: saphenous vein

growth_protocol: Isolation of cells for in vitro experiments was performed as previously described, using two consecutive immunomagnetic selections to obtain CD31negative/CD34positive homogenous cell populations (Campagnolo P, Cesselli D, Haj Zen A Al, Beltrami AP, Kränkel N, Katare R, Angelini G, Emanueli C, & Madeddu P. Human adult vena saphena contains perivascular progenitor cells endowed with clonogenic and proangiogenic potential. Circulation 2010 121 1735–1745. (doi:10.1161/CIRCULATIONAHA.109.899252))

extract_protocol:
For RNA-Seq analysis, total RNA was extracted from 5 different donors of SVPs using TRIzol, treated with DNase I, and quantified by using NanoDrop-1000 spectrophotometer before integrity assessment with Agilent 2100 Bioanalyzer (RNA Integrity Number values >8).
RNA libraries were prepared for sequencing from 500ng purified RNA with TruSeq Stranded totalRNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: To investigate the effect of mechanical strain on cultured cells, SVPs were subjected to cyclic strain using the FlexCell Tension Plus FX-5000T system. Before cell seeding, six-well Bioflex plates were surface-coated with human fibronectin (10μg/ml) in PBS after covalent crosslinking with a crosslinking reagent (sulfosuccinimidyl 6-(4'-azido-2'-nitrophenylamino) hexanoate; Sulfo-SANPAH) at 0.2 mg/ml in Hepes 50 mM (pH 8.5), photo-activated by exposure to UV-light (365 nm). Cells were subjected to uniaxial cyclic deformation protocol (0-10% deformation, 1 Hz frequency), for 24 and 72 hours, while static controls were provided by seeding an equal amount of cells, under the same atmospheric conditions, but without mechanical stimulation.

value: cyclic uniaxial strain

tag: timepoint

value: 72 hours

value: saphenous vein progenitors


title: SVP 24H STAT rep5

description: 2x100 paired-end sequence reads

value: static culture

value: 24 hours


title: SVP 24H DYN rep5

description: 2x100 paired-end sequence reads


title: SVP 72H DYN rep5

description: 2x100 paired-end sequence reads


title: SVP 24H DYN rep4

description: 2x100 paired-end sequence reads


title: SVP 72H STAT rep3

description: 2x100 paired-end sequence reads


title: HKU Meningioma 167 (methylation)

description:
meningioma
QM167
204365950096_R03C01


title: HKU Meningioma 169 (methylation)

description:
meningioma
QM169
204365950096_R04C01


title: HKU Meningioma 166 (methylation)

description:
meningioma
QM166
204365950096_R02C01


title: HKU Meningioma 17 (methylation)

description:
meningioma
QM17
203064760113_R01C01


title: HKU Meningioma 165 (methylation)

description:
meningioma
QM165
204365950096_R01C01


title: HKU Meningioma 168 (methylation)

description:
meningioma
QM168
203219760007_R04C01


title: SVP 24H STAT rep3

description: 2x100 paired-end sequence reads


title: HKU Meningioma 163 (methylation)

description:
meningioma
QM163
203219760007_R02C01


title: SVP 24H DYN rep3

description: 2x100 paired-end sequence reads


title: SVP 72H DYN rep3

description: 2x100 paired-end sequence reads


title: SVP 72H DYN rep2

description: 2x100 paired-end sequence reads


title: SVP 24H STAT rep2

description: 2x100 paired-end sequence reads


title: SVP 24H STAT rep4

description: 2x100 paired-end sequence reads


title: SVP 72H STAT rep2

description: 2x100 paired-end sequence reads


title: SVP 72H STAT rep5

description: 2x100 paired-end sequence reads


title: HKU Meningioma 164 (methylation)

description:
meningioma
QM164
203219760007_R03C01


title: HKU Meningioma 161 (methylation)

description:
meningioma
QM161
203219750225_R08C01


title: HKU Meningioma 173 (methylation)

description:
meningioma
QM173
204365950096_R07C01