title: NPSC after complement n=3

city: Lubbock

first: Jannette

last: Dufour

state: TX

department: Cell Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

data_processing:
Sequencing was performed on the Illumina® NovaSeqTM or HiSeq® platforms with the following conditions 2x150 base pairs configuration, 20-30 million read depth, and a guaranteed data quality of ≥80% bases with at least Q30.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Sus scrofa 10.2 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: Sus scrofa 10.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: raw data in fastq format: sample_R1_001.fastq.gz sample_R2_001.fastq.gz

source_name: Testis

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

extract_protocol:
Cells were washed, then placed in 1mL Trizol at -80C until shipping to GENEWIZ from Azenta Life Sciences in dry ice for RNA sequencing service.
The RNA sequencing service prepared the library for standard and strand-specific RNA, small RNA, and ultra-low input RNA.

treatment_protocol: Complement samples were incubated for 90 min in 1:1 human serum with complement preserved and DMEM+10% FBS in humidified atmosphere with 5% CO2 at 37C.

value: Testis

value: Sertoli cells

tag: genotype

value: WT

value: 1:1 human serum containing complement and media


title: AK58_DAP9_ATAC-seq_rep1

status: Public on Feb 15 2023

type: SRA

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

country: China

institute: Institute of Crop Sciences

library_source: genomic

data_processing:
Raw reads were trimmed with Trimmomatic v0.36, clean sequencing reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using Bowtie2. Peak calling was performed using MACS2. A black list was first generated by using the control samples as input.The raw peaks were first called with MACS2 with the following parameter “--keep-dup all --nomodel --extsizes 150 --shift -75”; then split into 150bp bins with 50bp overlapping; bins passed filtering by a Tn5 integration site density cutoff were selected and merged with bedtools with “-d 150”; peaks overlapped with the blacklist peaks, or homologous to plant orgenella DNA (NCBI) were discard  and the rest  were considered as high-quality ACRs.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: peak files

molecule: genomic DNA

organism: Triticum aestivum

source_name: Triticum aestivum endosperm at nine days after fertilization

growth_protocol: 16h light  22°C, 8h dark 19°C

extract_protocol: ATAC-seq libraries were prepared following the ATAC-seq protocol as previously described in (Lu et al. 2016)

treatment_protocol: Wheat endosperm was excised by removing the seed embryo at 5 and 9 days after fertilization. Wheat seed was collected at 15 and 20 days after fertilization.

tag: tissue

value: Endosperm

tag: cultivar


title: NPSC after complement n=2

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Sus scrofa

tag: cell type

tag: treatment


title: AK58_DAP5_RNA-seq_rep2

data_processing:
Raw reads were trimmed with Trimmomatic v0.334 with default parameters. The remaining reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using HISAT2 v2.0.5. Gene expression values were computed using StringTie v1.3.3b.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: TPM values for each sample

source_name: Triticum aestivum endosperm at five days after fertilization

extract_protocol:
total RNA
For each sample, total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit (Illumina, San Diego, CA) following the manufacturer’s instructions.

treatment_protocol: The three tissues of wheat, including leaves, roots and shoot apices, were obtained after 2 weeks of growth. The 2-week-old seeding were vernalized at 4°C under 16h light/8h dark conditions for 30 days and 1.0 - 2.0 cm axillary buds were obtained from these vernalized seedings.

tag: time point

value: at five days after fertilization


title: 23003

type: RNA

city: Berlin

first: Arndt

last: Stahler

address: Chariteplatz 1

department: Medical Department of Hematology, Oncology and Cancer Immunology

country: Germany

institute: Charite Universitaetsmedizin Berlin

description: RNA derived from FFPE tissue sample which was obtained prior to treatment start

hyb_protocol: 130 ng of RNA (controlled for quality and quantity by spectrophotometry and bioanalyzer) were hybridized with reporter and capture probes for 16 to 48 h

scan_protocol: The Nanostring nCounter SPRINT Profiler platform was used for scanning according to manual.

data_processing: Normalization and log2 transformation of .RCC data was performed using the Nanostring nSolver Analysis software.

label: fluorescent barcode

molecule: polyA RNA

organism: Homo sapiens

source_name: metastatic colorectal cancer

extract_protocol: mRNA was isolated from tumor slides following the instructions of the RNeasy FFPE tissue kit (Qiagen, Hilden, Germany)

value: metastatic colorectal cancer

tag: Stage

value: IV

tag: age

tag: Sex

value: male


title: NPSC after complement n=1


title: NPSC baseline n=3

value: Media


title: AK58_DAP5_ATAC-seq_rep2


title: NPSC baseline n=2


title: 23001


title: 23002

value: female


title: NPSC baseline n=1


title: 22006


title: MGP234_NMS_rep2

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

description: growth in NMS medium

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol.

data_processing:
Probe-level expression intensity was estiimated from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009) .
An aggregated expression value was computed for each defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
A quantile-normalization transformation was estimated on 3,195 genes selected belonging to the conserved gene set of the six strains (MS, MGP181, MGP192, MGP229, MGP254, and MGP234) and after excluding the most variable genes (with standard deviation across hybridizations twice higher than the median standard deviation). This quantile-normalizing transformation was then applied to all expression values.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: Cells were cultivated in NMS medium with shaking at 37°C and harvested at an OD600nm of 0.3

extract_protocol: Total RNA was isolated from cells using an acid phenol method as described in Nicolas et al. 2012. RNA concentration and quality were checked using a Spectrophotometer Nanodrop ND-1000 (Thermo scientific, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).


title: 22005


title: MGP254_NMS_rep1

description: growth in NMS medium


title: MGP254_NMS_rep2

description: growth in NMS medium


title: MGP229_NMS_rep2

description: growth in NMS medium


title: S5-T, eyelid sebaceous gland carcinoma tissue (RNA-seq)

city: Tianjin

first: Yuchuan

last: Wang

address: Gansu Road

institute: Tianjin Eye hospital

data_processing:
For sequencing data, FASTQ files were generated by CASAVA 2.0. The human reference file that was used is GRCh37/hg19.Duplicates were removed using Picard. The base quality scores were recalibrated using BaseRecalibrator (GATK). Single nucleotide variations (SNVs) were identified using MuTect. Somatic indels of tumor–normal pairs were called using GATK Somatic Indel Detector. Variants annotations were obtained using the software tool ANNOVAR.
The full-length sequenced transcriptome was used as a reference for sequence alignment and subsequent analysis, and minimap2 was used to align the clean reads with the reference transcriptome to obtain the corresponding information of the transcript and the reference transcriptome.
Assembly: mm10
Supplementary files format and content: WES: tab-delimited text files include indel and snp
Supplementary files format and content: RNA-seq: tab-delimited text files include RPKM values for each Sample

source_name: eyelid sebaceous gland carcinoma tissue

extract_protocol:
Frozen tissues were extracted using the QIAamp Fast DNA Tissue Kit (Qiagen) for DNA.The experimental process was performed according to the standard protocol provided by Oxford Nanopore Technologies (ONT), including sample quality detection, library construction, library quality detection and library sequencing.
DNA-seq libraries were captured to exome regions using Roche NimbleGen SeqCap EZ Exome V3/Agilent SureSelect Human All Exon V6. RNA was subjected to library preparation using ONT Direct RNA Sequencing Kit. Libraries were sequenced on PromethION.

value: eyelid sebaceous gland carcinoma tissue

tag: pair id


title: 22004


title: S5-N, adjacent normal tissues (RNA-seq)

source_name: adjacent normal tissues

value: adjacent normal tissues


title: 22003


title: MGP192_NMS_rep2

description: growth in NMS medium


title: MGP229_NMS_rep1

description: growth in NMS medium


title: EGCG 2

city: Fukuoka

first: Yuki

last: Marugame

address: 744 Motooka, Nishi-ku

country: Japan

institute: Kyushu university

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The blank value (average of the C1 blank) was subtracted from the sample measurements and set to null if the value was less than 0.

source_name: EVs derived from HUVECs, EGCG (+)

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: HUVECs were maintained with EGM-2 containing 10%FBS.

extract_protocol: RNA samples were extracted from EVs using miRNesy mini kit (Qiagen).

treatment_protocol: HUVECs were preincubated in 10% FBS/EGM2 for 24 h and then incubated in 1%BSA/M199. After 2 h, HUVECs were treated with 5 mM EGCG. After a 24-h incubation with M199, EVs were isolated.

tag: cell

value: HUVECs


title: S4-T, eyelid sebaceous gland carcinoma tissue (RNA-seq)


title: AK58_DAP5_ATAC-seq_rep1


title: EGCG 3


title: MGP234_NMS_rep1

description: growth in NMS medium


title: Control 3

source_name: EVs derived from HUVECs, EGCG (-)


title: S4-N, adjacent normal tissues (RNA-seq)


title: EGCG 1


title: MGP192_NMS_rep1

description: growth in NMS medium


title: 15018


title: Control 2


title: S3-T, eyelid sebaceous gland carcinoma tissue (RNA-seq)


title: MGP181_NMS_rep2

description: growth in NMS medium


title: Control 1


title: 15017


title: S2-T, eyelid sebaceous gland carcinoma tissue (RNA-seq)


title: MGP181_NMS_rep1

description: growth in NMS medium


title: PNA-10b+21-2

city: Storrs

first: Shipra

last: Malik

state: CT

address: 69 North Eagleville Road, Unit 3092

department: Pharmaceutical Sciences

institute: University of Connecticut

data_processing:
Read trimming: Sickle, -l 45, q 25
Mapping: hisat2/2.1.0, Index=hg38
File format conversion: samtools/1.7
Feature count: htseq/0.11.0, htseq-count -s no -r pos -t exon -i gene_id -f bam,
Assembly: hg38
Supplementary files format and content: tabdelimited-text file inlcude raw counts for each sample

source_name: Brain

growth_protocol: U87 cells were grown in DMEM medium (Invitrogen) supplemented with 10% fetal FBS, 1% Pen-Strep and cultured at 37 °C with 5% CO2 in a humidified chamber.

extract_protocol:
Total RNA from each sample was extracted using the mirVana miRNA Isolation Kit.
Illumina TruSeq Stranded mRNA library preparation

treatment_protocol: U87 cells were seeded in 24-well plates at a density of 50,000 cells/well and cultured overnight before use. sgPNA-21/BNP (150 nM sgPNA-21), sgPNA-10b/BNP (150 nM sgPNA-10b), sgPNA/BNP (150 nM sgPNA-21, 150 nM sgPNA-10b) were added to cells and incubated for 72 h.

value: Brain

tag: cell line

value: Glioblastoma

value: miR-10b+miR-21 knockdown


title: S2-N, adjacent normal tissues (RNA-seq)


title: 15015


title: PNA-10b+21-1


title: S1-T, eyelid sebaceous gland carcinoma tissue (RNA-seq)


title: PNA-21-3

value: miR-21 koockdown


title: MS_NMS_rep1

description: growth in NMS medium

value: MS


title: 22002


title: PNA-21-2


title: S1-N, adjacent normal tissues (RNA-seq)


title: PNA-21-1


title: hTERT-RPE1-TOShOFD1 cells, shOFD1, 72 hours, rep3

city: SHANGHAI

first: xiaoxiao

last: zou

state: SHANGHAI

address: 280 SOUTHEAST CHONGQING ROAD

department: Department of Pathophysiology

institute: shanghaijiaotong university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38, version 94 whole genome using hisat2 v2.0.5.
Summarized by StringTie as fragments per kilobase transcript per million mapped reads (FPKM)
Assembly: GRCh38, version 94
Supplementary files format and content: tab-delimited text file include FPKM values for all Samples

source_name: Retina

growth_protocol: hTERT-RPE1-TOShOFD1 cells were cultured inDMEM/F12 (1:1 mixture) supplemented with 10% FBS (Sigma Aldrich) and 100U/ml Penicillin-Streptomycin (GIBCO, 15140122).

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The RNA-seq libraries were prepared with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina according to the manufacturer's instructions.

treatment_protocol: hTERT-RPE1-TOShOFD1 cells treated with 200 ng/mL Doxycycline for 72 hours or not.

value: Retina

value: epithelial cells

value: OFD1 knockdown

value: 200 ng/mL Doxycycline


title: hTERT-RPE1-TOShOFD1 cells, shOFD1, 72 hours, rep1


title: hTERT-RPE1-TOShOFD1 cells, Control, 72 hours, rep3

value: WT

value: control


title: 15014

value: metastatic colorectal cancer

value: IV

value: male


title: S3-N, adjacent normal tissues (RNA-seq)


title: TY5837_IGG_CHIP

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

data_processing:
After barcode removal, reads were aligned uniquely to the C. briggsae CB4 genome using the default settings in Bowtie 2 version 2.3.4.3. To account for read depth, ChIP signal was normalized to the total number of reads that uniquely aligned to the genome. BigWig files were created via samtools and bamCoverage with bin size 50 bp.
Assembly: cb4
Supplementary files format and content: bw

organism: Caenorhabditis briggsae

source_name: mixed-stage animals

growth_protocol: Mixed-stage animals were grown on MYOB agar plates with concentrated HB101 bacteria at 20C.

extract_protocol:
Animals were cross-linked with 2% formaldehyde for 10 min and quenched with 100 mM Tris-HCl, pH 7.5. Cross-linked animals were resuspended in 1 mL of FA Buffer (150 mM NaCl, 50 mM HEPES-KOH, pH 7.6, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM DTT, and protease inhibitor cocktail [Calbiochem, #539134]) for every 1 gram of animals. This mixture was frozen on liquid nitrogen and then ground under liquid nitrogen by mortar and pestle for 3 minutes. Once thawed, the mixture was then homogenized with 50 strokes in a Dounce homogenizer. The chromatin was sheared using the Covaris S2 (20% duty factor, power level 8, 200 cycles per burst) for a total of 30 min processing time (60 sec ON, 45 sec OFF, 30 cycles). The concentration of protein in each extract was quantified using the BCA assay (Thermo Fisher, #23228).
C. briggsae ChIP Reactions.  To perform the ChIP reactions, a 50 µL bed volume of protein A Dynabeads (Thermo Fisher, #10001D) was re-suspened in 1 mL of FA Buffer (150 mM NaCl, 50 mM HEPES-KOH, pH 7.6, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM DTT, and protease inhibitor cocktail [Calbiochem, #539134]). The beads were incubated in a microcentrifuge tube with 5 µg of anti-FLAG antibodies (Sigma-Aldrich, #F1804) and 5 µg of rabbit anti-mouse IgG antibodies (Jackson ImmunoResearch, #315-005-003), or 5 µg of mouse IgG (Sigma-Aldrich, #I5381) and 5 µg of rabbit anti-mouse IgG antibodies (Jackson ImmunoResearch, #315-005-003), for 90 minutes at room temperature. Tubes with incubated beads were placed on a magnetic rack, and the liquid was discarded. Extracts containing 2 mg of protein ChIPs were increased in volume to 1 mL with FA buffer and then added to each tube of Dynabeads for a for 90-min incubation.  The Dynabead-extract mixture was washed at room temperature twice with FA Buffer (150 mM NaCl), once with FA Buffer (1 M NaCl), once with FA Buffer (500 mM NaCl), once with TEL buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1% IGEPAL CA-630 [Sigma-Aldrich, #I3021], 1% sodium deoxycholate, 1 mM EDTA), and twice with TE Buffer (10 mM Tris, pH 8.0, 1 mM EDTA). Protein and DNA were eluted with 250 µL of buffer (1% SDS, 250 mM NaCl, 1mM EDTA) at 65C for 20 min. After elution, sequencing libraries were prepared as published (Zhong et al., 2010) with minor changes: sequencing adapters were obtained from Bioo (NEXTflex) and adapters were ligated using NEB Quick Ligation Kit (M2200). Libraries were sequenced on the Illumina HiSeq4000 platforms.

value: mixed-stage animals


title: PNA-10b-3

value: miR-10b koockdown


title: PNA-10b+21-3


title: 15013

value: female


title: MS_NMS_rep2

description: growth in NMS medium


title: 15012


title: hTERT-RPE1-TOShOFD1 cells, shOFD1, 72 hours, rep2


title: PNA-10b-2

value: Brain


title: 15011


title: 15010


title: hTERT-RPE1-TOShOFD1 cells, Control, 72 hours, rep2


title: PNA-10b-1

value: Glioblastoma


title: Control-3


title: 15009


title: TY5836_IGG_CHIP


title: TY5836_DPY27_CHIP


title: TY5837_DPY27_CHIP


title: Control-2


title: TY5774_IGG_CHIP


title: Control-1


title: 15007


title: 11.5_Trailing_2

city: Boston

first: Rhian

last: Stavely

state: MA

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

data_processing:
Samples were sequenced using a 2x50 Paired End (PE) configuration on an Illumina MiSeq instrument according to manufacturer’s instructions.
Raw sequence data (.bcl files) generated from Illumina MiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Samples raw reads were aligned using the STAR alignment tool version 2.5.2b and the Genome Reference Consortium Mouse Build 38 (GRCm38/mm10).
Alignment and quality control was performed with FastQC Version 0.11.9. Expression levels were quantified using featureCounts.
The normalized counts and differential expression analysis was performed on Galaxy using the DeSeq2 package
Assembly: mm10
Supplementary files format and content: Processed data contains count output in CPM and DEGs

organism: Mus musculus

source_name: Embryonic gut

extract_protocol:
Tissues from the gut of Wnt1-tdT mice were collected that contain enteric neural crest-derived cells at the invasive wavefront  and enteric neural crest-derived cells trailing 1-1.5mm behind the wavefront at 11.5 days post coitum. Tissues were enzymatically dissociated in collagenase-dispase solution to generate primary single-cell suspensions. Neural crest-derived cells were purified by FACS of Wnt1-tdT expressing cells before RNA isolation with Trizol as of manufacturer’s instructions.
Illumina Nextera XT library was used for sequencing library preparation as of manufacturers instructions.

tag: developmental stage

tag: location

value: Trailing

value: enteric neural crest-derived cells


title: TY5775_IGG_CHIP_rep2


title: 15005


title: 15004


title: TY5775_SDC2_CHIP_rep2


title: 11.5_Trailing_1


title: hTERT-RPE1-TOShOFD1 cells, Control, 72 hours, rep1


title: 15006


title: A549, SP 24 Hours, R2 (RNA-seq)

city: Odense

first: Paolo

last: Ceppi

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
SP_24H_R2
Raw_Count_Table_2

data_processing:
Quality control analysis of Fastq files were done using FastQC package.
Reads were then aligned to human reference genome with GRCh38 build (release 105) with the respective Ensembl GTF annotation file using STAR v2.7.9a aligner in a two-pass mode.
Read counts were measured with featureCounts function in Rsubread package using R 4.2.1
Differential gene expression analysis was performed using DESeq2 v1.36.0 pipeline.
Assembly: hg38; GRCh38 (release 105)
Supplementary files format and content: tab-delimited text file includes Raw count values from featureCounts for all samples

growth_protocol: A549 cell line was maintained in DMEM high glucose medium (Gibco) with 10% fetal bovine serum (FBS) and maintained at 37oC with 5% CO2 in a humidified incubator

extract_protocol:
Total RNA was isolated using miRNeasy kit (Qiagen) as per manufacturer's protocol. 1 µg of Total RNA was used for the library construction.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol (NEB).

treatment_protocol: A549 cell line was treated with sodium propionate (SP) at 5 mM for 3 hours, 24 hours, 3 days and 12 days

value: NSCLC cell line

value: SP 5 mM

tag: time

value: 24 Hours


title: A549, SP 3 Hours, R3 (RNA-seq)

description:
SP_3H_R3
Raw_Count_Table_2

value: 3 Hours


title: TY5774_DPY27_CHIP


title: A549, SP 3 Hours, R1 (RNA-seq)

description:
SP_3H_R1
Raw_Count_Table_2


title: A549, SP 24 Hours, R1 (RNA-seq)

description:
SP_24H_R1
Raw_Count_Table_2


title: A549, SP 24 Hours, R3 (RNA-seq)

description:
SP_24H_R3
Raw_Count_Table_2


title: TY5775_IGG_CHIP_rep1


title: A549, SP 3 Hours, R2 (RNA-seq)

description:
SP_3H_R2
Raw_Count_Table_2


title: 11.5_WF_2

value: Wavefront


title: A549, Control 24 Hours, R3 (RNA-seq)

description:
Control_24H_R3
Raw_Count_Table_2

value: WT

value: No treatment


title: TY5775_SDC2_CHIP_rep1


title: 15008

value: metastatic colorectal cancer


title: 15003

value: IV


title: 11.5_WF_1


title: LNCaP_R1881_Enzalutamide_22h_rep5

first: Andreas

last: Schlicker

address: Muellerstr 178

department: Translational Sciences Oncology Computational Biology

institute: Bayer AG

description: 84_1nM_R1881_high_Enzalutamide_22h_S46_R1_001

data_processing:
Illumina bcl2fastq v2.17 was used to convert bcl to fastqs.
RNA-seq reads were aligned to GRCh38 using STAR aligner.
featureCounts from subread package was used to quantify reads in genes
Counts per Million (CPM) were calculated per gene and sample by dividing raw counts by the overall sum of counts for the given sample and multiplying by 1 million
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts per million (cpm) for all genes and samples

source_name: prostate cancer

growth_protocol: Cells were routinely grown in the recommended medium in the presence of 10% (v/v) fetal bovine serum (Life Technologies, Carlsbad, CA) at 37°C and 5% CO2. Authentication was performed by the DSMZ using short tandem repeat DNA typing analysis.

extract_protocol:
Cells were lyzed and RNA was isolated using RNeasy columns with on-column DNA digestion, as described by the manufacturer (Qiagen, Hilden, Germany). RNA integrity was measured and samples with values above 8 were further processed.
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit and sequenced on Illumina HiSeq2500 HTv4 (single-end, dual-indexing, 50 Cycles).

treatment_protocol: Cells were stimulated with the synthetic androgen R1881 at a concentration of 1 nM after two days of starvation in medium supplemented with 10% charcoal-stripped fetal calf serum (cFCS). Enzalutamide was added at a final concentration of 2 µM, and the cells were harvested 22 h post-treatment.

value: prostate cancer

value: LNCaP

value: prostate cancer cell

value: R1881 1nM + Enzalutamide 2uM


title: LNCaP_R1881_DMSO_22h_rep10


title: A549, Control 24 Hours, R1 (RNA-seq)

description:
Control_24H_R1
Raw_Count_Table_2


title: 15002

value: female


title: A549, SP 12 Days, R3 (RNA-seq)

description:
SP_12D_R3
Raw_Count_Table_1

value: Day 12


title: 19184R-01-03

city: Houston

first: David

last: Piwnica-Worms

address: 1881 East Road, Unit 1907

department: Cancer Systems Imaging

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Raw data QA and preprocessing (FastQC v0.11.8)
Sequence alignment and secondary QA (STAR 2.7.1a)
Data exploration and QA on gene expression (featureCounts 1.6.0)
Quantification of differential expression and exploratory analysis (DEseq2 1.22.2)
Downstream functional analysis (R 3.6)
Assembly: Mm10
Supplementary files format and content: tab-delimited cvs files include p values

growth_protocol: Myeloid cells were isolated from the spleens and bone marrow of adult C57BL/6 mice using a CD3e depletion kit. 1 x 10^6 B16F10 cells or YUMM3.3 were seeded in a 100 mm cell culture plate for 4 days.

extract_protocol:
RNA was isolated from themyeloid cells and melanoma cells using a RNeasy Mini Kit
RNA sequencing and analysis was performed by Admera Health conducted by Genohub using standard Illumina protocols

treatment_protocol: Isolated myeloid cells and melanoma cells were processed for RNA Seq

tag: strain

tag: disease state

value: melanoma

value: cell line


title: 19184R-01-02


title: LNCaP_R1881_DMSO_22h_rep9


title: 19184R-02-12


title: LNCaP_R1881_Enzalutamide_22h_rep4

description: 85_1nM_R1881_high_Enzalutamide_22h_S78_R1_001


title: 13003

value: male


title: A549, SP 12 Days, R2 (RNA-seq)

description:
SP_12D_R2
Raw_Count_Table_1

value: NSCLC cell line

tag: genotype

value: SP 5 mM


title: 15001

tag: tissue


title: A549, SP, 3 Days, R3 (RNA-seq)

description:
SP_3D_R3
Raw_Count_Table_1

value: Day 3


title: LNCaP_R1881_Enzalutamide_22h_rep3

description: 81_1nM_R1881_high_Enzalutamide_22h_S50_R1_001


title: A549, SP 12 Days, R1 (RNA-seq)

description:
SP_12D_R1
Raw_Count_Table_1


title: 13001


title: 19184R-02-11


title: 10002


title: 10001


title: LNCaP_R1881_DMSO_22h_rep8


title: 19184R-02-10


title: LNCaP_R1881_Enzalutamide_22h_rep2

description: 83_1nM_R1881_high_Enzalutamide_22h_S25_R1_001


title: 5003


title: A549, SP, 3 Days, R2 (RNA-seq)

description:
SP_3D_R2
Raw_Count_Table_1


title: A549, Control 24 Hours, R2 (RNA-seq)

description:
Control_24H_R2
Raw_Count_Table_2

value: 24 Hours


title: 19184R-03-18

value: myeloid cell

value: YUMM3.3 tumor-bearing animal

value: spleen


title: LNCaP_R1881_DMSO_22h_rep7


title: 5002

value: metastatic colorectal cancer

value: IV


title: 19184R-01-01


title: LNCaP_R1881_Enzalutamide_22h_rep1

description: 82_1nM_R1881_high_Enzalutamide_22h_S72_R1_001

value: prostate cancer

value: LNCaP


title: 19184R-03-16


title: A549, SP, 3 Days, R1 (RNA-seq)

description:
SP_3D_R1
Raw_Count_Table_1

value: WT


title: 5001


title: 19184R-03-14

value: bone marrow


title: A549, Control, 3 Days, R2 (RNA-seq)

description:
Control_3D_R2
Raw_Count_Table_1

value: No treatment


title: LNCaP_R1881_DMSO_22h_rep6

value: prostate cancer cell


title: 4006


title: 19184R-03-13


title: LNCaP_R1881_DMSO_22h_rep5


title: A549, Control, 3 Days, R1 (RNA-seq)

description:
Control_3D_R1
Raw_Count_Table_1


title: LNCaP_R1881_DMSO_22h_rep4


title: 19184R-03-11

value: B16F10 tumor-bearing animal


title: A549, Control 3 Hours, Input (ChIP-seq)

description: Input Control

data_processing:
Duplicated reads from PCR amplification were removed using samtools
Peaks were called with the default setting in MACS2
Peaks called within all replicates were considered as consensus peaks
Homer was used for counting normalised tag counts within promoter regions
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were double-crosslinked in 2 mM DSG and 1% Formaldehyde. After fixation, cells pellet was sonicated until fragment size ranges between 200 bp and 500 bp. Sonicated chromatin was then immunoprecipitated overnight using Dynabeads protein A (Dynabeads, 10002D) coated with the antibody of interest. Beads were washed, and the DNA was decrosslinked and purified using standard phenol-chloroform purification.
Sequencing libraries was constructed with the purified DNA using NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E765), and sequenced with NovaSeq 6000 (Illumina) platform.

treatment_protocol: A549 cell line was treated with sodium propionate (SP) at 5 mM for 3 hours.

value: 3 hr

tag: chip antibody


title: 19184R-03-09

tag: cell type


title: A549, SP 3 Hours, R3 (ChIP-seq)

value: NSCLC cell line

tag: treatment


title: 4005

value: female


title: 4004

value: male


title: 19184R-03-10


title: 4003


title: 19184R-03-08


title: A549, SP 3 Hours, R2 (ChIP-seq)

value: SP 5 mM


title: A549, Control, 3 Days, R3 (RNA-seq)

description:
Control_3D_R3
Raw_Count_Table_1

value: Day 3


title: LNCaP_R1881_DMSO_22h_rep2


title: 4002


title: 4001


title: 19184R-03-07

value: myeloid cell


title: 1002


title: 19184R-03-06

value: Healthy animal

value: spleen


title: A549, SP 3 Hours, Input (ChIP-seq)

description: Input SP


title: 1001

value: metastatic colorectal cancer

value: IV


title: LNCaP_R1881_DMSO_22h_rep3

value: prostate cancer

value: LNCaP


title: 19184R-03-04


title: Foxp1 transgenic

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

library_source: transcriptomic single cell

data_processing:
Aligned reads to a reference genome that included the mm10 genome, GFP, and Cre, then generated feature-barcode matrices using cellranger count 3.1.0 with expected-cells set to 5000.
Filtered feature matrices from cellranger were further filtered with the aid of Seurat v4.0.3. High quality cells were identified by a mitochondrial percentage < 7.5 and a high number of freatures. The minimum feature cut off was 1000 for Foxp1 control and 1050 for Foxp1 cTG. Each sample was run, individually, through Seurat’s SCTransform pipeline, regressing out mitochondrial percentage, to generate unsupervised cell clusters.
Foxp1 cTG single cell samples were combined with Seurat's merge function. Clusters were manually annotated using expression of known cell markers: Vsx2, Lhx2, and Pax6 for RPCs, Neurog2 and Olig2 for neurogenic cells, Crx for photoreceptor precursors, Thrb for cones, Nrl for rods, Rbpms for retinal ganglion cells, Tfap2a for amacrine cells, and Lhx1 for horizontal cells.
Assembly: mm10
Supplementary files format and content: matrix.mtx, barcodes.tsv, featrures.tsv: Filtered feature count matrix, generated by cellranger, stored as a sparse numeric matrix and tab separated values for row and column names.
Supplementary files format and content: foxp1_cTG_counts_normalized.tsv: scaled gene expression
Supplementary files format and content: foxp1_cTG_meta_data.tsv: meta data for all cells including cell type and UMAP coordintes.

source_name: retina

extract_protocol:
Cells for single cell sequencing were obtained from two P0 female littermates with the genotypes Foxp1 tg/+; Six3-Cre (Foxp1 cTG) and Foxp1 tg/+ (control). Two freshly dissected retinas from one individual animal were pooled for each sample and dissociated in PBS, 50 mM HEPES, 0.05 mg/ml DNase I and 0.025 mg/ml Liberase for 35 min with intermediate trituration. Cells were passed through a 40 μm nylon cell strainer, washed with washing buffer (1X PBS, 2% BSA, 0.1% sodium azide, 0.05% EDTA), and red blood cells were lysed in RBC lysis buffer. Cell counts were determined using a Countess. 1x 10e6 cells was resuspended in 1mL DPBS and provided to the High Throughput Genomics Core for library prep.
Single cell libraries were generated with Next GEM Single Cell 3’ Gene Expression Library prep v3.1 according to manufacturer’s protocol (10X Genomics PN-1000128). Sequencing libraries were applied to a NovaSeq flow cell using XP chemistry workflow v1.5 (Illumina 20043131) and a 150 x 150 cycle paired end sequence run was performed using an Illumina NovaSeq 6000 instrument and S4 reagent Kit v1.5 (20028312). Libraries were sequenced to > 200 million reads per sample.

value: retina

tag: genetic background

value: postnatal day 0

value: Foxp1 tg/+; Six3-Cre


title: LCA1.D150.NoTreat.3

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: human retinal organoids at age D150 from LCA-1 donors and treated with DMSO, replicate no 3

data_processing:
Unprocessed fastq files from the sequencer were quality checked, trimmed and aligned to the Mus musculus Ensembl annotation.
Transcript level quantitation was performed using Kallisto v0.42.4 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl v105 ftp site.
Gene level quantification was generated by summarization of the transcript level quantitation using tximport v0.99.9 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.32.1.
Assembly: GRCh38.p13, Ensembl v105 annotation
Supplementary files format and content: Tab-delimited text files containing transcript level counts, gene level counts, or normalized gene level counts-per-million results.

source_name: human retinal organoids

growth_protocol: Human retinal organoid differentiation was performed as previously described (Regent et al., 2020).

extract_protocol:
Total RNA was purified from homogenized retinal organoids using TriPure isolation reagent (Roche). Quality of isolated RNAs was assessed using Bioanalyzer RNA 6000 nano assays (Agilent) and high-quality total RNA (RNA integrity number ≥7.5) were used for construction of mRNA sequencing library. 100ng total RNA were used to construct the strand-specific libraries using TruSeq RNA Sample Prep Kit-v2 (Illumina).
RNAseq data were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Drug treated and untreated retinal organoids were harvested at D150.

tag: donor

tag: drug

value: DMSO

value: NoTreat

tag: replicate


title: Foxp1 control

value: Foxp1 tg/+


title: Control.D150.B05_30.3

description: human retinal organoids at age D150 from Control donors and treated with B05, replicate no 3

value: Control

tag: age


title: 19184R-03-03

value: bone marrow


title: Control.D150.NoTreat.3

description: human retinal organoids at age D150 from Control donors and treated with DMSO, replicate no 3


title: control IgG rep 3

data_processing:
All CUT&RUN samples were aligned to mouse genome build mm10 with Novoalign (v4.02.02) using standard Illumina TruSeq adapters. Samtools fixmate (v1.10) removed unmapped reads and added mate scores, then bam files were sorted and indexed. Unique Molecular Indexes (UMIs) were sequenced to identify PCR duplicates, and the UMIs were handled by scripts written by the Huntsman Cancer Institute Bioinformatics Core. PCR and optical duplicates were removed with optical distance threshold at 2500.
H3K27me3 broad peak calling was done with a Macs2-based pipeline, MultiRepMacsChIPSeq (v14) developed by the Bioinformatics Shared Resource. Briefly, multirep_macs2_pipeline.pl was run with the following parameters: q-value threshold for peak calling set to 2, minimum peak size of 600, maximum gap size of 300, minimum mapping quality of 10, q-value cutoff of 0.1, maximum link size of 1500 and mappable genome size 2.5x10e9. The output of this pipeline includes counts per million (CPM) normalized fragment tracks, log2 fold enrichment of H3K27me3 relative to IgG, identification of called peaks, annotation with Ensembl release 102, and counts of fragments in each peak. Difference calling between control and Jarid2 cKO was done with DESeq2 (v1.38.1), controlling for batch effect.
Assembly: mm10
Supplementary files format and content: fragment.bw files show normalized aligned reads for each sample
Supplementary files format and content: peaks.txt is a tsv containing all identified H3K27me3 peaks with annotation, sample counts, and DESeq2 results
Supplementary files format and content: log2FE.bw files show H3K27me3 enrichment compared to IgG control for each genotype
Library strategy: CUT&RUN

extract_protocol:
For each biological sample, two freshly dissected retinas from one individual animal were pooled for and dissociated in PBS, 50 mM HEPES, 0.05 mg/ml DNase I and 0.025 mg/ml Liberase for 35 min with intermediate trituration. Cells were passed through a 40 μm nylon cell strainer, washed with washing buffer (1X PBS, 2% BSA, 0.1% sodium azide, 0.05% EDTA), and red blood cells were lysed in RBC lysis buffer. CUT&RUN was performed using a CUT&RUN Assay Kit (Cell Signaling 86652) according to manufacturer’s protocol. 300K single cells were used for each reaction. 2 µl rabbit anti-H3K27me3 antibody (Millipore 07-449) was used for H3K27me3 immunoprecipitation. This antibody has been validated for specificity by ENCODE. 5 µl Rabbit I (DA1E) mAb IgG XP Isotype Control provided by the kit was used as a negative control. DNA fragments were purified on spin columns, eluted with 50 µl buffer (Cell Signaling 14209) and provided to University of Utah High Throughput Genomics Core for library generation.
DNA quality was confirmed by PCR, libraries were created with the NEBNext UItra II DNA Library Prep Kit (New England Biolabs E7645S), and 150 bp paired-end sequencing was performed on a NovaSeq 6000 using the XP chemistry workflow (20021664) and S4 reagent Kit v1.5 (20028312).

treatment_protocol:
Cre activity was induced by intraperitoneal injection of 75 μg Tamoxifen per gram of body weight to pregnant females at E10.5.
H3K27me3 CUT&RUN was performed in two separate batches. In batch I, two biological replicates were used for control (Jarid2 fl/fl) and conditional knockout ( Jarid2 fl/fl; Rax-CreERT2), all from a single litter. Batch II consisted of all male littermates: three biological replicates, each with two technical duplicates, for a total of 12 samples.

value: embryonic day 18.5

value: Jarid2 fl/fl

tag: biological replicate

tag: technical replicate

tag: batch

tag: Sex

value: male

tag: antibody

value: IgG


title: A549, Control 3 Hours, R2 (ChIP-seq)

tag: cell line

value: NSCLC cell line

value: No treatment

tag: time

value: 3 hr


title: A549, Control 3 Hours, R1 (ChIP-seq)


title: 19184R-03-01

value: myeloid cell

tag: strain

tag: disease state

value: Healthy animal


title: LCA1.D150.NoTreat.2

description: human retinal organoids at age D150 from LCA-1 donors and treated with DMSO, replicate no 2


title: Jarid2 cKO IgG rep 3

tag: tissue

value: retina

tag: developmental stage

tag: genotype

value: Jarid2 fl/fl; Rx-cre


title: LCA1.D150.B05_30.3

description: human retinal organoids at age D150 from LCA-1 donors and treated with B05, replicate no 3

tag: treatment


title: A549, SP 3 Hours, R1 (ChIP-seq)

tag: cell type

value: SP 5 mM

tag: chip antibody


title: LCA1.D150.B05_30.2

description: human retinal organoids at age D150 from LCA-1 donors and treated with B05, replicate no 2

tag: donor

tag: drug

tag: replicate


title: Jarid2 cKO rep 5b

tag: genetic background

tag: biological replicate

tag: technical replicate


title: JINB8_TSP1_H6

first: Thomas

middle: Joshua

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Reads were trimmed for adapters and low-quality bases using the Cutadapt v1.18.
Reads were aligned to the hg38 reference genome (GRCh38) and transcripts using STAR v2.4.2a in 2-pass mode.
Gene and isoform expression was quantified using RSEM v1.3.3 with GENCODE annotation version 36.
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by differential expression of genes analysis.
Assembly: hg38
Supplementary files format and content: Both processed data files are comma-separated values (CSV) files.

source_name: cell line

growth_protocol: Jurkat T cells and the CD47-deficient Jurkat somatic mutant JinB8 were routinely cultured in RPMI 1640 medium supplemented with 10% FBS (or Gemini BioProducts), penicillin/streptomycin, and glutamine (Thermo Scientific). For RNA sequencing studies, Jurkat cells were grown in serum-free medium containing 90% Ham's F-12, 10% RPMI 1640 medium, 5 mm HEPES, 2 mm glutamine, 0.1% BSA, 5 μg/ml insulin, 5 ng/ml sodium selenite, 5 μg/ml transferrin and 200 nm hydrocortisone.

extract_protocol:
Cell pellets from each treatment were washed with PBS, and total RNA was extracted using TriPURE. The concentration of RNA and RNA quality was measured via Nanodrop.
All samples were processed with the TruSeq mRNA kit using 40M PE125 reads per sample

treatment_protocol: For T cell activation assay, 10 cm plates (BD, Biosciences) were coated with 2mg/ml anti-CD3 and 4 μg/ml of anti-CD28 in PBS at 4°C overnight.  Approximately 5x106 cells in 5 ml were plated for 1 h, 3 h and 6 h for each treatment using HITES medium.}, and 1 μg/ml of TSP1 was added either alone or in combination with anti-CD3 and an-ti-CD28.

value: cell line

value: Cancer cell line


title: Cal-33 cells, sip53

city: New York

first: Wei

last: Gu

state: NY

address: 1130 St. Nicholas Ave.

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: Cal-33 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Control, p53, or BACH1 siRNA  was trasnfected into Cal-33 cells, and incubated for 72h.

value: tongue squamous cell carcinoma cells

value: WT

value: p53 siRNA transfection


title: A549, Control 3 Hours, R3 (ChIP-seq)


title: Cal-33 cells, siBACH1

value: BACH1 siRNA transfection


title: Control.D150.B05_30.2

description: human retinal organoids at age D150 from Control donors and treated with B05, replicate no 2

value: Control

tag: age


title: JINB8_CD3_CD28_TSP1_H6

tag: cell line


title: Jarid2 cKO rep 5a

value: embryonic day 18.5

tag: batch

tag: Sex

value: male

tag: antibody


title: control rep 5b

tag: tissue

value: Jarid2 fl/+


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.5μM, Day 4 [Pac0.5muMR2]

city: Montreal

first: Georgios

last: Mitsis

state: Quebec

address: McConnell Engineering Building, 3480 University Street, Room 350

department: Bioengineering

country: Canada

institute: McGill University

data_processing:
The quality of the raw reads was evaluated using FASTQC (v.0.11.9). Adapter sequences and low quality bases were removed with Trimmomatic (v.0.39).
Trimmed reads were aligned to the hg reference genome (GRCh37) with STAR (v.2.7.5), and only uniquely mapped reads were kept.
The gene expession levels were calculated by quantifying the uniquely mapped reads to exonic regions using Rsubread (v.2.4.2).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

growth_protocol: A cell-Matrigel (Corning) suspension was created using 2 mL of Matrigel (4oC) and 5X10^4 MDA-MB-231/GFP cells. Droplets of 5μL cell-Matrigel mixture were manually deposited onto a high performance #1.5 glass bottom 6-well plate.

extract_protocol:
The RNeasy Plus Universal Mini Kit (QIAGEN) was used for the extraction of the total RNA from on the instrument QIA cube Connect, according to instructions from the manufacturer.
Library preparation construction and sequencing were carried out at Génome Québec using Illumina NovaSeq 6000 platform and produced paired-end reads (PE100).

treatment_protocol: The treated datasets were administered Paclitaxel on the 2nd day of the experiment. The examined dose were 0.0005μΜ, 0.005μΜ, 0.05μΜ and 0.5μM.

value: Triple Negative Breast Cancer

value: 0.5μM Paclitaxel


title: JINB8_CD3_CD28_H6


title: 19184R-03-02

value: myeloid cell

tag: strain

tag: disease state

value: bone marrow


title: Control.D150.NoTreat.2

description: human retinal organoids at age D150 from Control donors and treated with DMSO, replicate no 2

value: DMSO

tag: treatment

value: NoTreat


title: LCA1.D150.B05_30.1

description: human retinal organoids at age D150 from LCA-1 donors and treated with B05, replicate no 1


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.5μM, Day 4 [Pac0.5muMR1]

tag: cell type

tag: genotype


title: LCA1.D150.NoTreat.1

description: human retinal organoids at age D150 from LCA-1 donors and treated with DMSO, replicate no 1

tag: donor


title: Jurkat_TSP1_H6

value: Jurkat


title: control rep 4b

value: retina

tag: developmental stage


title: Jurkat_CD3_CD28_TSP1_H6

value: cell line

value: Cancer cell line


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.05μM, Day 4 [Pac0.05muMR1]

value: WT

value: 0.05μM Paclitaxel


title: Jurkat_CD3_CD28_H6


title: Control.D150.B05_30.1

description: human retinal organoids at age D150 from Control donors and treated with B05, replicate no 1

tag: drug

tag: replicate


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.005μM, Day 4 [Pac0.005muMR2]

value: 0.005μM Paclitaxel


title: Control.D150.NoTreat.1

description: human retinal organoids at age D150 from Control donors and treated with DMSO, replicate no 1

value: Control


title: Cal-33 cells, siControl

value: tongue squamous cell carcinoma cells

value: Control siRNA transfection

tag: time


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.005μM, Day 4 [Pac0.005muMR1]


title: PR

city: Hefei

first: Ting

address: Huangshan

institute: University of Science and Technology of China

data_processing:
As to RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean reads were aligned to the reference genome using TopHat2 v2.1.0.
Cuffdiff v2.2.1 was used to count the reads numbers mapped to each gene.
Assembly: hg19 and dm6
Supplementary files format and content: fastq for RNA-seq data

source_name: no

growth_protocol: Human PLC cells were cultured in DMEM containing 25mM glucose, 4mM L-glutamine and 1mM pyruvate (Gibco, 12800). THLE3 cells were cultured in BEGM (LONZA, CC3170). The medium was supplemented with 1% penicillin-streptomycin and 10% FBS. For serum starvation, cells were washed twice with PBS and cultured in the medium without FBS.

extract_protocol:
As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: no

value: PLC

value: Liver cancer cells

value: PRSS35 over-expression


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.0005μM, Day 4 [Pac0.0005muMR2]

value: Triple Negative Breast Cancer

value: 0.0005μM Paclitaxel


title: control rep 3a

tag: genetic background

value: embryonic day 18.5

value: Jarid2 fl/fl

tag: biological replicate

tag: technical replicate

value: male


title: JINB8_CD3_CD28_TSP1_H3

value: cell line

tag: cell line


title: EV


title: JINB8_TSP1_H3

value: Cancer cell line


title: control rep 3b

value: retina

tag: batch

tag: Sex


title: control rep 5a

tag: tissue

value: Jarid2 fl/+

tag: antibody


title: JINB8_CD3_CD28_H3


title: control rep 4a


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.0005μM, Day 4 [Pac0.0005muMR1]

value: WT


title: TNBC cells from MDA-MB-231 cell line, treated with Paclitaxel, dose: 0.05μM, Day 4 [Pac0.05muMR2]

value: 0.05μM Paclitaxel


title: Aminus6

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene (ensembl release 92, curated to remove contigs, unknown and alternate chromsomes ) using RNAsik pipeline (version 1.4.7). A matching custom GTF annotation file was generated as well
The RNAsik pipeline was run with the following parameters: ‘-align star -paired -all’ and used the combined fasta file and gtf file as input for the ‘-fastaRef’ and ‘-gtfFile’ parameters.
The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes.
The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM.
Using multiple t-tests, Z+ was tested against the 3 other groups, as well as p > 0.05 between the A- and Z- groups to ensure no difference in gene expression in non-transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p-values do not exceed 0.01.
Assembly: Ensembl GRCz11 (modified to include the AAT transgene)
Supplementary files format and content: comma separated file containing raw counts for each sample

organism: Danio rerio

source_name: Liver

growth_protocol: Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle

extract_protocol:
Total RNA was isolated from fish liver using Trizol lysis reagent (Sigma Aldrich) followed by isopropanol precipitation and the RNA pellet washed with 70% (v/v) ethanol.
PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.

value: Liver

tag: strain

value: Non-transgenic sibling

value: 2 month post fertilisation


title: Jarid2 cKO rep 4a

value: Jarid2 fl/fl; Rx-cre


title: Jurkat_TSP1_H3

value: Jurkat

tag: treatment


title: LNCaP_R1881_DMSO_22h_rep1

value: prostate cancer

value: LNCaP

tag: cell type

value: prostate cancer cell


title: Jarid2 cKO rep 4b

value: embryonic day 18.5

tag: genotype


title: Aminus5


title: Jarid2 cKO rep 3b


title: Jurkat_CD3_CD28_TSP1_H3


title: Jurkat_CD3_CD28_H3


title: Aminus3


title: control IgG rep 2

value: female

value: IgG


title: Jarid2 cKO rep 3a

value: male


title: TNBC cells from MDA-MB-231 cell line, no treatment, Day 2 [C1R2]

value: Triple Negative Breast Cancer

value: no treatment


title: TNBC cells from MDA-MB-231 cell line, no treatment, Day 2 [C1R1]


title: JINB8_TSP1_H1

value: cell line

value: Cancer cell line


title: Aminus2


title: 15016

first: Arndt

address: Chariteplatz 1

institute: Charite Universitaetsmedizin Berlin

description: RNA derived from FFPE tissue sample which was obtained prior to treatment start

data_processing: Normalization and log2 transformation of .RCC data was performed using the Nanostring nSolver Analysis software.

extract_protocol: mRNA was isolated from tumor slides following the instructions of the RNeasy FFPE tissue kit (Qiagen, Hilden, Germany)

value: metastatic colorectal cancer

tag: Stage

value: IV

tag: age


title: Jarid2 cKO IgG rep 2

value: retina

tag: developmental stage


title: JINB8_CD3_CD28_TSP1_H1


title: TNBC cells from MDA-MB-231 cell line, no treatment, Day 4 [C2R2]

value: WT


title: JINB8_CD3_CD28_H1


title: Jarid2 cKO IgG rep 1

value: Jarid2 fl/fl; Rx-cre


title: Aplus6

value: Liver

value: 2 month post fertilisation


title: TNBC cells from MDA-MB-231 cell line, no treatment, Day 4 [C2R1]


title: control IgG rep 1

value: Jarid2 fl/+; Rx-cre


title: control rep 2

value: Jarid2 fl/+


title: Jurkat_TSP1_H1

value: Jurkat


title: Aminus4

value: Non-transgenic sibling


title: Aplus5


title: Con-5

city: beijing

first: yuanshu

last: peng

state: 北京

address: 8 Beijing Workers stadium South Road, Chaoyang District, Beijing

department: heart center, beijing chaoyang hospital

institute: Beijing Chaoyang Hospital, Capital Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.8.4)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: hg19
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: heart

extract_protocol:
RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: Epicardial adipose tissue

value: heart

tag: subject status

value: control


title: JINB8_UT_H1

value: UT


title: Con-3


title: Aplus4


title: Con-1


title: Aplus3


title: Jurkat_CD3_CD28_TSP1_H1

value: cell line


title: Con-2


title: Jarid2 cKO rep 2

value: embryonic day 18.5

value: male


title: AF-5

value: patient with new-onset postoperative atrial fibrillation after coronary artery bypass grafting


title: Jarid2 cKO rep 1

value: retina

value: female


title: Con-4


title: Aminus1


title: Jurkat_CD3_CD28_H1

value: Cancer cell line

value: WT


title: Jurkat_UT_H1


title: Aplus2

value: Liver

value: 2 month post fertilisation


title: control rep 1

value: Jarid2 fl/+; Rx-cre


title: AF-4


title: MDA-MB-231 cells, biological replicate 2

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

description: nascent RNA

data_processing:
Library strategy: GRO-seq
cutadapt (v1.18) was used to remove linkers, quality trim, and remove reads shorter than 18nt.
bowtie2 (v2.3.5) was used to align reads to human transcriptome (GRC38.96)
Logistic regression was used to compare sense and antisense mapping across the transcriptome at every interval and report logASR (log fold-change in antisense to sense ratio)

source_name: MDA-MB-231 cells

growth_protocol: Cells were cultured in a humidified incubator at 37degC, 5%CO2 in high glucose DMEM supplemented with 10% FBS, penicillin (100units/mL), streptomycin (100ug/mL) and amphotericin (1ug/mL0. 1x10^7 cells were used per replicate.

extract_protocol:
Extraction of nascent RNA was performed as described in Core et al 2008 and Wang et al 2011, with some adaptations: For each sample, nuclei from 1x107 MDA-MB-231 cells was used. All steps were done on ice. Cells were harvested by scraping and then resuspended in swelling buffer (10mM Tris-HCl pH 7.5, 2mM MgCl2, 3mM CaCl2) for 5 minutes on ice, then spun at 500 x g 5 minutes at 4°C. Swelling buffer was aspirated, and 10mL lysis buffer (10mM Tris-HCl pH 7.5, 2mM MgCl2, 3mM CaCl2, 0.5% IGEPAL CA-630, 10% glycerol) was added. The nuclei were then pelleted at 1000 x g for 5 minutes at 4°C. Lysis buffer was aspirated and nuclei resuspended in 1mL freezing buffer (50mM Tris-HCl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). Nuclei were then pelleted at 1000 x g 5 minutes 4°C. Freezing buffer was aspirated and nuclei resuspended in 100ul of freezing buffer and stored at -80°C. For the run-on assay, the frozen nuclei were thawed on ice and mixed with 100ul reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 0.2units/ul SuperaseIN, 1% sarkosyl, 500uM each ATP, GTP, and Br-UTP, 2uM CTP), then incubated at 30°C for 5 minutes. Reaction was stopped by adding 600ul Trizol LS (Invitrogen), and RNA was isolated per the manufacturer’s protocol.
Libraries were constructed by first fractionating the RNA (in 20ul H2O) by adding 5ul 1M NaOH and incubating on ice for 40 minutes. Reaction was stopped by adding 25ul 1M Tris-HCl pH 6.8. This solution was run through micro biospin P-30 columns (BioRad), then DNase-treated by adding 10ul RQ1 DNase (Promega), 6.7ul 10X DNase reaction buffer, 1ul SuperaseIN and incubating at 37°C 10 minutes. This was run through a micro biospin P-30 column (BioRad). The RNA was dephosphorylated by adding 5ul Antarctic phosphatase (NEB), 8.5ul 10X phosphatase buffer, 1ul superaseIN, and incubated at 37°C for 1 hour. Labeled RNA was isolated with anti-BrdU agarose beads (Santa Cruz Biotech) that were prepared by incubating in blocking buffer (0.5X SSPE, 1mM EDTA, 0.05% tween-20, 0.1% PVP, 1mg/mL BSA) for 1 hour at 4°C, then resuspended in 500ul binding buffer (0.5X SSPE, 1mM EDTA, 0.05% tween-20). The RNA was added to the prepared beads after the RNA was heated at 65°C for 5 minutes, then placed on ice. The RNA was incubated with the beads with end-over-end rotation for 1 hour at 4°C. The beads were then washed 1X with low salt buffer (0.2X SSPE, 1mM EDTA, 0.05% tween-20), 2X with high salt buffer (0.5X SSPE, 1mM EDTA, 0.05% tween-20, 150mM NaCl), and 2X TET buffer (TE pH 7.4, 0.05% tween-20). RNA was eluted by adding 125ul elution buffer (5mM Tris-HCl pH 7.5, 300mM NaCl, 1mM EDTA, 0.1% SDS, 20mM DTT) and rotating end-over-end at room temp. Elution by repeated for a total of four times. RNA was isolated from the eluate by acid phenol chloroform extraction and precipitation. The RNA pellet was resuspended in 45ul H2O, and then phosphorylated by adding 5.2ul T4 PNK buffer, 1ul superaseIN, 1ul T4 PNK (NEB) and incubating at 37°C for 1 hour. RNA was isolated from the reaction by acid phenol chloroform extraction and precipitation. The RNA was polyA tailed by adding 0.8ul 10X polyA polymerase buffer, 1ul 1mM ATP, 0.5ul SuperaseIN, 0.75ul polyA polymerase (NEB), and incubating at 37°C for 30 minutes. RNA was then reverse transcribed by first adding 1ul 10mM dNTPs, 2.5ul 12.5uM oNTI223 primer, incubating at 75°C 3 minutes, then on ice 1 minute, then adding 2ul 10X superscript III buffer, 2ul 25mM MgCl2, 3ul 0.1M DTT, 0.5ul superaseIN, 1ul superscript III (Invitrogen), and incubating at 48°C for 20 minutes. Excess primer was digested by adding 4ul exonuclease I and incubating at 37°C for 1 hour. RNA was hydrolyzed by adding 1.8ul 1M NaOH and incubating at 98°C for 20 minutes, then adding 1.8ul 1M HCl to neutralize. The resulting cDNA was run on a 10% polyacrylamide TBEurea gel (Invitrogen) and the region from 110-405nt was excised and the DNA recovered by the crush soak method. The precipitated DNA was resuspended in 7.5ul H2O and circularized by adding 1ul CircLigase buffer, 0.5ul 1mM ATP, 0.5mM MnCl2, 0.5ul CircLigase (Lucigen) and incubated at 60°C for 1 hour, then 80°C for 20 minutes. Linearization was then performed by adding 3.8ul of 100mM KCl, 2mm DTT and 1.5ul APE1 (NEB), and then incubating at 37°C for 1 hour. The cDNA was run on a 10% polyacrylamide TBE-urea gel (Invitrogen) and the region from 125-305nt was excised and the DNA recovered by the crush soak method. The precipitated cDNA was resuspended in 20ul H2O. PCR was then performed by combining 10ul of the cDNA with 4ul 5X phusion HF buffer, 0.4ul 10mM dNTPs, 2ul each 5uM oNTI200 and oNT1201, 1.4ul H2O, 0.2ul phusion HF DNA polymerase (NEB) and running the following cycle: 98°C 30s, then repeat X13 98°C 10s, 60°C 15s, 72°C 15s. PCR product was run on an 8% polyacrylamide TBE gel, and the region from 150-230bp was excised. DNA was extracted by the crush soak method, and the library was sequenced.

value: triple negative breast cancer cell line


title: Aplus1


title: AF-3


title: Zminus6

value: Non-transgenic sibling


title: MDA-MB-231 cells, biological replicate 1

description: nascent RNA


title: AF-2

value: Epicardial adipose tissue


title: Zminus5


title: AF-1

value: heart


title: Dura fibroblast with IL-1β stimulation (1ng/mL), Day 2

city: Seoul

first: Min-Ho

last: Hwang

address: 8, Gamasan-ro 20-gil, Guro-gu

department: Biomedical Sciences

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Brain

value: HDuF

value: Fibroblast

value: pro-inflammatory cytokine IL-1β, inflammatory response


title: NSPC, NTG, rep3

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

institute: University of Ottawa

data_processing:
MultiQC was run to aggregate results
hisat2 was used to align them to the mouse genome (mm10).
Samtools was used to index the BAM files.
DESeq2 was used to establish differential gene expression between NTG and 3xTg.
Significantly different genes meet two criteria: 1) adjusted p-value < 0.05, and 2) log2 fold change > 0.5 or < -0.5.
Assembly: mm10
Supplementary files format and content: 3xTG_SGZ_RNA-seq_normalized_abundance.xlsx (FPKM Value)

source_name: subgranular zone

extract_protocol:
A tamoxifen (TAM)-inducible Nestin-CreERT2;ROSA26-EYFP reporter mouse line  was cross-bred with NTG or 3xTG-AD mice to label NSPC upon TAM administration. YFP-positive NSPCs were sorted through FACS (Fluorescence-Activated Cell Sorting) 10 days after TAM from NTG; Nestin-CreERT2;ROSA26-EYFP and 3xTg-AD;Nestin-CreERT2;ROSA26-EYFP mice. Subgranular zone (SGZ) was removed and digested. YFP-positive cells were sorted through FACS. RNA was extracted with RNeasy Micro Kit.
cDNA library was estalished using Takara  SMART-Seq V4 cDNA synthesis / Nextera XT library prep.

value: NSPC

value: subgranular zone

value: post natal day 35

value: wild type

tag: sorting

value: FACS-sorted


title: NSPC, NTG, rep2


title: NSPC, 3xTg, rep1


title: Zminus3


title: Dura fibroblast without IL-1β stimulation, Day 2

value: WT

value: none (control)


title: center_neg_4

first: Natasha

last: Frank

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
RNA-seq counts were generated by Salmon (Patro et al., 2017)
Assembly: hg19
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample

source_name: FACS sorted MUC16-negative cells

extract_protocol:
Human donor whole globes were obtained from eye banks. Cornea was dissected from the other parts of the eyes, the central cornea was separated by an 8mm disposable biopsy punch and the corneal endothelium was removed mechanically. After 1 h incubation with PluriSTEM Dispase II Solution at 37 °C, limbal epithelial cells and central corneal epithelial cells were scraped and incubated with TrypLE Express Enzyme at 37 °C for 30 min to dissociate. (1) Dissociated limbal epithelial cells were cultured and treated with siRNAs (Control, TET2 knockdown #1 and TET2 knockdown #2). siRNAs were transfected on day 0, 2 and 4 and the cells were harvested on day 7 for RNA extraction. (2) Dissociated central corneal epithelial cells were stained with fluorescence conjugated antibodies for 30 min on ice (mouse anti-MUC16 monoclonal antibody (mAb) conjugated with Alexa Fluor 647 and  0.125μg/ml PE-conjugated anti-CD45 mAb. The cells were incubated with 30nM SYTOX Green Dead Cell Stain to exclude nonviable cells. Cell sorting was performed using FACSAria II cell sorter (BD Biosciences, San Jose, CA) using a 100 mm nozzle. RNA was extracted from sorted MUC16-positive cells and MUC-negatibe cells.
mRNA libraries were generated by SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech, Mountain View, CA) and sequencing was carried out by the Illumina NextSeq 500 Platform (Single-end 75 bp) (Illumina, San Diego, CA) at the Molecular Biology Core Facility (MBCF) of Dana-Farber Cancer Institute.

value: FACS sorted MUC16-negative cells

value: In vivo human corneal epithelial cells

value: Sample 7, MUC16-negative cells


title: Zminus1

value: Liver

value: Non-transgenic sibling

value: 2 month post fertilisation


title: Zminus2


title: NSPC, 3xTg, rep2


title: Zminus4


title: NSPC, 3xTg, rep3


title: center_pog_3

source_name: FACS sorted MUC16-positive cells

value: FACS sorted MUC16-positive cells

value: Sample 6, MUC16-positive cells


title: Twist1 sgRNA_5377

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

description: Primary tumor vascular endothelial cells treated with Twist1 CRISPR/sgRNA

data_processing:
Kallisto quantification was performed for the RNA-Seq data using Kallisto version 0.46.1 obtained from github. Kallisto index was built with reference transcriptome GRCh38.
In R (version 4.0.5), transcripts were collapsed to genes using package tximport (version 1.22.0), and then normalized and filtered by edgeR (version 3.36.0) to generate a count matrix.
Assembly: GRCh38
Supplementary files format and content: CPM (Counts per million mapped reads) in .csv file

source_name: GBM patient #5377

extract_protocol:
2E6 ECs were lysed in 1 ml TRIzol (Thermo Fisher Scientific), followed by RNA extraction according to the manufacturer’s instructions. The isolated RNA was purified with RNeasy Plus Mini Kit (Qiagen).
After a quality control step using RNA Nano assay chips with a 2100 Bioanalyzer (Agilent), a library was constructed using a Ribo-Zero protocol with TapeStation (Agilent) and subjected to deep sequencing (approximately 20 MB reads for each sample, Illumina NovaSeq sequencer) at the Children’s Hospital of Philadelphia High Throughput Sequencing Core.

treatment_protocol: ECs were lentivirally transduced to express CRISPR/sgRNA targeting control sequence or Twist1.

value: Brain tumor

tag: transduced with

value: Twist1 sgRNA


title: Control sgRNA_5441

description: Primary tumor vascular endothelial cells treated with control CRISPR/sgRNA

source_name: GBM patient #5441

value: control sgRNA


title: Lens epithelial explants, 5 day in differentiation  media after D0 D5_DM_C

city: OXFORD

first: Anil

last: Upreti

state: OH

address: 501 E High St, Oxford, OH 45056

department: Biology

institute: Miami University

data_processing:
Raw reads were quality-analyzed using FastQC and MultiQC .
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cut adapt and trim galore with paramaters  -q 20 --phred33 --length 20.
Trimmed sequence reads were mapped to GrCM39 using Hisat2 incorporating splice juncation from genecode GTF .
Gene counts were generated using Stringtie2.1.5
Differential expression testing was performed with DESeq2.
Assembly: GRCm39 v.M27
Supplementary files format and content: Normalized gene count matrix from DESeq2

source_name: Lens Epithelium

growth_protocol: Lens epitheliall explants were maintained in 35mm culture dish with either pre-calibrated M-199 media supplemented with 1% antibiotic-antimycotic solution  and 0.1% bovine serum albumin  henceforth referred to as “culture medium (CM)” or cultured in vitreous, diluted by CM to 50% concentration, henceforth referred to as “differentiation medium (DM)”, for 1 day or 5 days at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using the RNEasy Mini Kit (Qiagen cat. 74104) following the manufacturer’s instructions.
RNA libraries were constructed by DNA Link (Los Angeles, CA, USA) using a TruSeq (Illumina) library prep kit.

value: Lens Epithelium

value: FVB/N

value: D5 DM


title: Twist1 sgRNA_5391

source_name: GBM patient #5391

value: Primary tumor vascular endothelial cells


title: Zplus6


title: Twist1 sgRNA_5441


title: Lens epithelial explants, 5 day in differentiation  media after D0 D5_DM_B


title: NSPC, NTG, rep1

value: NSPC

value: subgranular zone

value: post natal day 35

value: wild type

value: FACS-sorted


title: center_neg_3

value: FACS sorted MUC16-negative cells

value: In vivo human corneal epithelial cells

value: Sample 6, MUC16-negative cells


title: Zplus5

value: Liver

value: 2 month post fertilisation


title: center_pog_4

value: FACS sorted MUC16-positive cells

value: Sample 7, MUC16-positive cells


title: center_pog_2

value: Sample 5, MUC16-positive cells


title: Lens epithelial explants, 5 day in differentiation  media after D0 D5_DM_A

value: Lens Epithelium


title: Control sgRNA_5377

value: Brain tumor

value: control sgRNA


title: Lens epithelial explants, 5 day in culture media after D0 D5_CM_C

value: FVB/N

value: D5 CM


title: Zplus4


title: S5-T, eyelid sebaceous gland carcinoma tissue (WES)

city: Tianjin

first: Yuchuan

last: Wang

address: Gansu Road

institute: Tianjin Eye hospital

description:
S5-T.vs.S5-N.indel.hg19_multianno.GO_KEGG.txt
S5-T.vs.S5-N.SNP.hg19_multianno.GO_KEGG.txt

data_processing:
For sequencing data, FASTQ files were generated by CASAVA 2.0. The human reference file that was used is GRCh37/hg19.Duplicates were removed using Picard. The base quality scores were recalibrated using BaseRecalibrator (GATK). Single nucleotide variations (SNVs) were identified using MuTect. Somatic indels of tumor–normal pairs were called using GATK Somatic Indel Detector. Variants annotations were obtained using the software tool ANNOVAR.
The full-length sequenced transcriptome was used as a reference for sequence alignment and subsequent analysis, and minimap2 was used to align the clean reads with the reference transcriptome to obtain the corresponding information of the transcript and the reference transcriptome.
Assembly: mm10
Supplementary files format and content: WES: tab-delimited text files include indel and snp
Supplementary files format and content: RNA-seq: tab-delimited text files include RPKM values for each Sample

source_name: eyelid sebaceous gland carcinoma tissue

extract_protocol:
Frozen tissues were extracted using the QIAamp Fast DNA Tissue Kit (Qiagen) for DNA.The experimental process was performed according to the standard protocol provided by Oxford Nanopore Technologies (ONT), including sample quality detection, library construction, library quality detection and library sequencing.
DNA-seq libraries were captured to exome regions using Roche NimbleGen SeqCap EZ Exome V3/Agilent SureSelect Human All Exon V6. RNA was subjected to library preparation using ONT Direct RNA Sequencing Kit. Libraries were sequenced on PromethION.

value: eyelid sebaceous gland carcinoma tissue

tag: pair id


title: center_pog_1

value: Sample 4, MUC16-positive cells


title: Zplus2


title: center_neg_2

value: Sample 5, MUC16-negative cells


title: Lens epithelial explants, 5 day in culture media after D0 D5_CM_B


title: Zplus3


title: S5-N, adjacent normal tissues (WES)

source_name: adjacent normal tissues

value: adjacent normal tissues


title: S3_siRNA2

source_name: Cultured corneal epithelial cells

value: Cultured corneal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 3, TET2 knockdown #2


title: Lens epithelial explants, 5 day in culture media after D0 D5_CM_A


title: Lens epithelial explants, 1 day in differentiation  media after D0 D1_DM_B

value: D1 DM


title: Zplus1

value: Liver

value: 2 month post fertilisation


title: Lens epithelial explants, 1 day in differentiation  media after D0 D1_DM_C


title: S3_control

value: Sample 3, Control for TET2 knockdown


title: Lens epithelial explants, 1 day in differentiation  media after D0 D1_DM_A


title: S3-N, adjacent normal tissues (WES)

description:
S3-T.vs.S3-N.indel.hg19_multianno.GO_KEGG.txt
S3-T.vs.S3-N.SNP.hg19_multianno.GO_KEGG.txt


title: Amygdala, young, HFD, rep3

city: Columbus

first: Michael

last: Butler

address: 460 Medical Center Drive

institute: Ohio State University

data_processing:
FASTQ files were aligned to the rat Rnor 7.1 reference genome using the STAR (spliced transcripts to a reference) aligner.
Data were normalized and differential expression was determined using DESeq2 in R.
Assembly: Rnor 7.1

organism: Rattus norvegicus

source_name: Brain - Amygdala

extract_protocol:
RNA extraction was performed with Trizol and molecular biology grade isopropanol
NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L); NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490); NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #6444S/L); Library input amount 200ng total RNA (quantified using Qubit Fluorometer); Fragmentation: 10 minutes; Libraries were sequenced with Novaseq SP Paired-End 150bp format

value: Brain - Amygdala

tag: gender

value: male

value: F344 X BN

value: Young, High Fat Diet


title: Amygdala, aged, chow, rep2

value: Aged, Chow


title: Control sgRNA_5391

value: Brain tumor

value: Primary tumor vascular endothelial cells

value: control sgRNA


title: Amygdala, aged, chow, rep3


title: S4-T, eyelid sebaceous gland carcinoma tissue (WES)

description:
S4-T.vs.S4-N.indel.hg19_multianno.GO_KEGG.txt
S4-T.vs.S4-N.SNP.hg19_multianno.GO_KEGG.txt

value: eyelid sebaceous gland carcinoma tissue


title: S2-T, eyelid sebaceous gland carcinoma tissue (WES)

description:
S2-T.vs.S2-N.indel.hg19_multianno.GO_KEGG.txt
S2-T.vs.S2-N.SNP.hg19_multianno.GO_KEGG.txt


title: center_neg_1

city: Boston

value: FACS sorted MUC16-negative cells

value: In vivo human corneal epithelial cells

value: Sample 4, MUC16-negative cells


title: S4-N, adjacent normal tissues (WES)

value: adjacent normal tissues


title: S2_siRNA2

value: Cultured corneal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 2, TET2 knockdown #2


title: S3-T, eyelid sebaceous gland carcinoma tissue (WES)


title: Amygdala, aged, chow, rep1


title: Lens epithelial explants, 1 day in culture media after D0 D1_CM_C

value: Lens Epithelium

value: FVB/N

value: D1 CM


title: Lens epithelial explants, 1 day in culture media after D0 D1_CM_B


title: S2-N, adjacent normal tissues (WES)


title: S3_siRNA1

value: Sample 3, TET2 knockdown #1


title: Lens epithelial explants, 1 day in culture media after D0 D1_CM_A


title: Amygdala, aged, HFD, rep3

value: Brain - Amygdala

value: male

value: F344 X BN

value: Aged, High Fat Diet


title: Amygdala, aged, HFD, rep2


title: Lens epithelial explants, 24 hrs in Culture media D0_C

value: 24 hrs in media


title: S2_control

value: Sample 2, Control for TET2 knockdown


title: S1-T, eyelid sebaceous gland carcinoma tissue (WES)

description:
S1-T.vs.S1-N.indel.hg19_multianno.GO_KEGG.txt
S1-T.vs.S1-N.SNP.hg19_multianno.GO_KEGG.txt

value: eyelid sebaceous gland carcinoma tissue


title: S1_siRNA2

value: Sample 1, TET2 knockdown #2


title: S1-N, adjacent normal tissues (WES)


title: Amygdala, aged, HFD, rep1


title: Lens epithelial explants, 24 hrs in Culture media D0_B


title: S1_siRNA1

value: Sample 1, TET2 knockdown #1


title: Lens epithelial explants, 24 hrs in Culture media D0_A


title: scRNA-seq of patient 8 post NMP

city: Innsbruck

first: Stefan

last: Salcher

address: Anichstraße 35

department: Internal Medicine V

country: Austria

institute: Medical University of Innsbruck

description: Liver P8_T1

data_processing:
scRNA-seq: FASTQ files were processed with Seven Bridges Genomics cloud server with the BD Rhapsody WTA Analysis Pipeline
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: CSV files containing molecules per gene per cell from Seven Bridges Genomics cloud server using the BD Rhapsody WTA Analysis Pipeline

source_name: liver tissue

extract_protocol:
Liver biopsies taken pre (T0) and at the end (T1) of NMP as well as after reperfusion (T2) (n=8 livers) were immediately minced into small pieces (<1 mm) on ice and subsequently digested enzymatically for 10 minutes at 37°C with agitation using the BD TuDoR™ dissociation reagent (BD Biosciences). The single-cell suspension was filtered through a 100 µM cell strainer and red blood cells were removed with the BD Pharm Lyse™ (BD Biosciences) lysing solution according to the manufacturer´s protocol. Cell viability was measured with the BD Rhapsody™ scRNASeq platform (BD Biosciences) using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
The freshly isolated single-cell suspension was immediately processed (<30 minutes from tissue dissociation to cell lysis) and whole transcriptome amplification (WTA) sequencing libraries were generated according to the BD Rhapsody™ single-cell WTA protocol. The quality of the obtained sequencing libraries was verified with the 4200 TapeStation system (Agilent) and the Qubit dsDNA HS (High Sensitivity) assay kit (Thermo Fisher Scientific). Sequencing was performed on the NovaSeq 6000 System platform (Illumina) with the S1 Reagent Kit v1.5 (200 cycles, 68 bp index read 1; Illumina) at a calculated sequencing depth of 50.000 reads/cell.

value: liver tissue

tag: disease state

value: benign

tag: condition

value: post normothermic machine perfusion (NMP)


title: Amygdala, young, HFD, rep1

value: Young, High Fat Diet


title: S1_control

value: Cultured corneal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 1, Control for TET2 knockdown


title: uninduced MCF10A YAP5SA cells p63

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

institute: University of Wuerzburg

data_processing:
Base calling was performed with Illumina’s CASAVA software or FASTQ Generation software v1.0.0 and overall sequencing quality was tested using the FastQC script.
Galaxy was used to analyze NGS data (https://usegalaxy.org). Reads were mapped to the human genome (hg19 assembly) using Bowtie2 for Cut&Run-seq and ChIP-seq samples. Differential peak analysis was performed within Galaxy with Limma-voom (Liu et al., 2015).
To create heat maps and density profiles of ATACseq, ChIPseq and CUT&RUN data, DeepTools 2 was used (Ram.rez et al., 2016).
Normalized bigWig files were created using bamcoverage with a bin size of 10 and normalizing to counts per million (CPM). BigWig files were used to compute reads centered on ATAC-seq peak summits (called with Genrich), YAP peak summits or on the TSS of MMB-target genes (Fischer et al., 2016) using computeMatrix.
Heatmaps and profiles were created with the plotHeatmap and plotProfile tools. Metagene plots of PolII enrichment across MMB target genes were created with plotProfiles. ChIPseq data were visualized with the Integrated Genome Viewer (Robinson et al., 2011).
Assembly: hg19
Supplementary files format and content: For Cut&Run-seq and ChIP-seq, the provided processed files are bigWig files for data display in a genome browser.

growth_protocol: MCF10A stably expressing doxycycline inducible YAP5SA were grown and cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.

extract_protocol:
For ChIP-seq, cells were cross-linked with 1% formaldehyde (Sigma) for 10 min at room temperature. The reaction was stopped by adding 125 mM glycine (Sigma). After cells were lysed for 10 minutes on ice [5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40, 1 mM PMSF, protease inhibitor cocktail (Sigma)], nuclei were resuspended in RIPA buffer [50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM PMSF, protease inhibitor cocktail (Sigma)].
Chromatin was fragmented to an approximate length of 150 to 300 bp using a Branson sonifier. Antibodies (9 µg) were coupled to protein G dynabeads (Thermo Fisher Scientific) for 6 hours at 4°C and then incubated with fragmented chromatin over night at 4°C. Beads were washed in total twelve times with wash buffer I (50mM Tris-HCl pH8, 0.15M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer II (50mM Tris-HCl pH8, 0.5M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer III (50mM Tris-HCl pH8, 0.5M LiCl2, 1mM EDTA, 1% Nonidet P-40, 0.7% sodium deoxycholate) and wash buffer IV (10mM Tris-HCl pH8, 1mM EDTA).
1mM PMSF and protease inhibitor cocktail (Sigma ) was added freshly to all buffers. Chromatin was eluted in (10mM Tris-HCl pH8, 0.3M NaCl, 5mM EDTA, 0.5% SDS, 10µg/ml RNaseA) and crosslink was reversed at 65°C over night. Proteins were digested by adding 200 µg/ml proteinase K at 55°C for 2 hours. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN) and eluted in 50 µl EB buffer.
For ChIPseq, DNA libraries were generated using 10ng purified ChIP-DNA and the NEBNext®Ultra II DNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s instructions. DNA library was amplified by 15-18 PCR cycles and quality was analyzed using the Fragment Analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq 500 platform (Illumina).

treatment_protocol:
ATAC-seq and ChIP-seq: YAP5SA was induced with 0.5µg/ml doxycycline for 48 hours.
RNA-seq: Cells were induced with 0.5 µg/ml doxycycline for 45 hours and with 1µM OHT for 14h.

tag: dox-treatment (yap5sa)

value: uninduced

tag: chip antibody

value: p63-alpha (D2K8X) (Cell Signalling, #13109)

tag: cell line


title: induced MCF10A YAP5SA cells p63

value: induced


title: Amygdala, young, HFD, rep2

tag: tissue

value: Brain - Amygdala

value: male

value: F344 X BN


title: Lens epithelial explants, Immediate collection IMD_B

value: Lens Epithelium

value: FVB/N

tag: treatment

value: Immediate Collection


title: Lens epithelial explants, Immediate collection IMD_C


title: Amygdala, young, chow, rep2

value: Young, Chow


title: scRNA-seq of patient 8 pre NMP

description: Liver P8_T0

value: liver tissue

value: pre normothermic machine perfusion (NMP)


title: scRNA-seq of patient 7 after reperfusion

description: Liver P7_T2

value: benign

value: after reperfusion


title: S2_siRNA1

value: Cultured corneal epithelial cells

tag: cell type

value: Sample 2, TET2 knockdown #1


title: Lens epithelial explants, Immediate collection IMD_A

tag: genotype


title: scRNA-seq of patient 7 post NMP

description: Liver P7_T1

value: post normothermic machine perfusion (NMP)


title: Amygdala, young, chow, rep1


title: withDox withOHT replicate 3

data_processing:
Galaxy was used to analyze NGS data (https://usegalaxy.org).
Reads were mapped to the human genome (hg19 assembly) using Bowtie2 (for ChIP-seq and ATAC-seq) and HISAT2 (for RNA-seq) with default parameters (Langmead and Salzberg, 2012).
For ATAC-seq, ATAC-peaks were called using Genrich (https://github.com/jsh58/Genrich).
Differential peak analysis and RNA-seq analysis was performed within Galaxy with Limma-voom (Liu et al., 2015).
Nucleosome calling was carried out with NucleoATAC (Schep et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: For ATAC-seq and ChIP-seq, the provided processed files are bigWig files for data display in a genome browser. For RNA-seq, a normalized count-matrix and a differential expression analysis file are provided, both in text-format (*.txt).

growth_protocol: MCF10A stably expressing doxycycline inducible YAP5SA or ER-YAP2SA and MY-COMP were grown in were cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.

extract_protocol:
For RNA-seq, cells were harvested according to the protocol of the Quiagen RNAeasy Mini Kit. Total RNA was isolated by using the RNeasy Mini Kit (Qiagen). 1 µg of total RNA was used to isolate mRNA by using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
For RNA-seq, cDNA libraries were generated with purified mRNA by using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). The quality of the cDNA library was determined with the Fragment Analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq500 platform (Illumina).

tag: 4-oht treatment (er-yap2sa)

tag: dox treatment (my-comp)


title: Hippocampus, aged, chow, rep3

source_name: Brain - Hippocampus

value: Brain - Hippocampus

value: Aged, Chow


title: KOMI_72H

city: Bern

first: Mey

last: Boukenna

address: Bühlstrasse 28

country: Switzerland

institute: IBMM University of Berne

description: NCM pooled from 4 mice, scRNAseq

data_processing:
Fastq files were processed with cell ranger count with default settings (cellranger-6.0.0) on the mouse genome reference refdata-gex-mm10-2020-A.
Assembly: mouse genome reference refdata-gex-mm10-2020-A.
Supplementary files format and content: The processed data files are in the format _cr_outs.tar.gz and for each sample each file includes one .tsv file containing the barcode, one .tsv file containing the features (genes) and one .mtx file containing the matrix

source_name: Heart

extract_protocol:
Each mouse was euthanized via neck dislocation and the heart was explanted and rinsed with ice-cold HBSS. Subsequently, the ventricles were cut in pieces and incubated at 37°C for 30 minutes for enzymatic digestion (using thermolysin and papain). After 30 minutes the tissue pieces were resuspended several times to dissociate cells from fibrous tissue. The suspension was filtered via 300um mesh to get rid of big fibrous tissues and then 40um mesh to filter out cardiomyocytes. The resulting non-cardiomyocytes (NCM) suspension was then incubated with Calcein-AM and DAPI and live cells were sorted using FACS (fluorescence activated cell sorting). The live NCM from 4 different mice hearts were pooled for each sample before performing single-cell RNAseq.
10x 3-RNA-seq

treatment_protocol: All mice underwent surgery: Either SHAM intervention as a control or LAD ligation to induce myocardial infarction.

value: Non-cardiomyocytes

value: Heart

tag: strain

tag: age

value: 8-12 weeks old

value: 72h after LAD Ligation

tag: Sex


title: withDox withOHT replicate 1

value: induced


title: WTMI_72H

description: NCM pooled from 4 mice, scRNAseq

value: male


title: withDox withOHT replicate 2


title: Hippocampus, young, HFD, rep3

value: F344 X BN

value: Young, High Fat Diet


title: scRNA-seq of patient 7 pre NMP

description: Liver P7_T0

value: liver tissue


title: Amygdala, young, chow, rep3

value: Brain - Amygdala

value: Young, Chow


title: KOMI_24H

description: NCM pooled from 4 mice, scRNAseq

value: 24h after LAD Ligation


title: Hippocampus, aged, chow, rep2


title: withDox noOHT replicate 2

value: non induced


title: scRNA-seq of patient 6 pre NMP

description: Liver P6_T0

value: benign

value: pre normothermic machine perfusion (NMP)


title: WTMI_24H

description: NCM pooled from 4 mice, scRNAseq


title: Hippocampus, aged, chow, rep1

value: Brain - Hippocampus


title: withDox noOHT replicate 1


title: scRNA-seq of patient 5 pre NMP

description: Liver P5_T0


title: KOSHAM_24H

description: NCM pooled from 4 mice, scRNAseq

value: 24h after SHAM intervention


title: noDox withOHT replicate 3


title: Hippocampus, aged, HFD, rep3

value: Aged, High Fat Diet


title: scRNA-seq of patient 4 after reperfusion

description: Liver P4_T2

value: after reperfusion


title: Hippocampus, aged, HFD, rep2


title: scRNA-seq of patient 6 after reperfusion

description: Liver P6_T2


title: noDox withOHT replicate 2


title: mIMCD3 cells,hypertonic,6h [HYPER_4]

city: Dalian

first: Chunxiu

last: Du

address: Lushunkou District

institute: Dalian medical university

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp（0.12.2）
Trimmed sequence reads were mapped to GrCM38/mm10 using hisat2（2.0.5）
Read count extraction and normalization were performed using featureCounts（1.5.0-p3）
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA)

value: Kidney collecting duct cell line


title: scRNA-seq of patient 6 post NMP

description: Liver P6_T1

value: post normothermic machine perfusion (NMP)


title: mIMCD3 cells,hypertonic,6h [HYPER_3]


title: scRNA-seq of patient 4 post NMP

description: Liver P4_T1


title: withDox noOHT replicate 3

value: induced


title: mIMCD3 cells,hypertonic,6h [HYPER_2]


title: noDox withOHT replicate 1


title: Hippocampus, aged, HFD, rep1

value: male


title: Hippocampus, young, HFD, rep2

value: F344 X BN


title: noDox noOHT replicate 3


title: scRNA-seq of patient 4 pre NMP

description: Liver P4_T0


title: noDox noOHT replicate 2


title: mIMCD3 cells,hypertonic,6h [HYPER_1]


title: Hippocampus, young, HFD, rep1

value: Young, High Fat Diet


title: scRNA-seq of patient 5 post NMP

description: Liver P5_T1

value: liver tissue


title: WTSHAM_24H

description: NCM pooled from 4 mice, scRNAseq

value: Non-cardiomyocytes

value: Heart

value: 8-12 weeks old


title: scRNA-seq of patient 3 after reperfusion

description: Liver P3_T2


title: mIMCD3 cells,Isotonic,6h [ISO_4]


title: scRNA-seq of patient 3 post NMP

description: Liver P3_T1


title: Hippocampus, young, chow, rep3

value: Young, Chow


title: noDox noOHT replicate 1

value: non induced


title: Hippocampus, young, chow, rep2


title: induced MCF10A YAP5SA cells Input to unphosphorylated Pol II

extract_protocol:
For ChIP-seq, cells were cross-linked with 1% formaldehyde (Sigma) for 10 min at room temperature. The reaction was stopped by adding 125 mM glycine (Sigma). After cells were lysed for 10 minutes on ice [5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40, 1 mM PMSF, protease inhibitor cocktail (Sigma)], nuclei were resuspended in RIPA buffer [50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM PMSF, protease inhibitor cocktail (Sigma)].
Chromatin was fragmented to an approximate length of 150 to 300 bp using a Branson sonifier. Antibodies (9 µg) were coupled to protein G dynabeads (Thermo Fisher Scientific) for 6 hours at 4°C and then incubated with fragmented chromatin over night at 4°C. Beads were washed in total twelve times with wash buffer I (50mM Tris-HCl pH8, 0.15M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer II (50mM Tris-HCl pH8, 0.5M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer III (50mM Tris-HCl pH8, 0.5M LiCl2, 1mM EDTA, 1% Nonidet P-40, 0.7% sodium deoxycholate) and wash buffer IV (10mM Tris-HCl pH8, 1mM EDTA).
1mM PMSF and protease inhibitor cocktail (Sigma ) was added freshly to all buffers. Chromatin was eluted in (10mM Tris-HCl pH8, 0.3M NaCl, 5mM EDTA, 0.5% SDS, 10µg/ml RNAseA) and crosslink was reversed at 65°C over night. Proteins were digested by adding 200 µg/ml proteinase K at 55°C for 2 hours. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN) and eluted in 50 µl EB buffer.
For ChIPseq, DNA libraries were generated using 10ng purified ChIP-DNA and the NEBNext®Ultra II DNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s instructions. DNA library was amplified by 15-18 PCR cycles and quality was analyzed using the Fragment Analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq 500 platform (Illumina).


title: scRNA-seq of patient 3 pre NMP

description: Liver P3_T0

value: benign

value: pre normothermic machine perfusion (NMP)


title: scRNA-seq of patient 2 after reperfusion

description: Liver P2_T2


title: mIMCD3 cells,Isotonic,6h [ISO_2]


title: scRNA-seq of patient 2 post NMP

description: Liver P2_T1


title: Twist1 antibody_5785

data_processing:
CUT&RUN data were processed using the nf-core/ cutandrun pipeline. Specifically, reads were trimmed to 50 bases with barcodes removed, followed by alignment using Bowtie2. Duplicates were removed using Picard. Peak calling was performed by MACS2 and visualized by R package ChipSeeker and Gviz
Assembly: GRCh38
Supplementary files format and content: MACS2 .narrowPeak file
Library strategy: CUT&RUN

source_name: GBM patient #5785

extract_protocol:
5E5 EC cells per reaction were collected, washed, and mixed with activated ConA beads using a CUTANA kit (Version 3, EpiCypher), following by incubation with 0.5 μg of IgG or anti-TWIST1 antibody (20 μg, Abcam, ab50887). K-MetStat Panel was spiked-in before addition of antibody. Cells were incubated with PAGmicrococcal nuclease, and the reaction was terminated by stop buffer with E. coli Spike-in DNA.Solubilized chromatin fragments were released and purified.
Isolated DNA was enriched for library preparation and sequenced by Illumina NextSeq (Center for Applied Genomics, Children’s Hospital of Philadelphia)

value: Brain tumor

value: Primary tumor vascular endothelial cells


title: uninduced MCF10A YAP5SA cells Input to unphosphorylated Pol II

value: uninduced


title: mIMCD3 cells,Isotonic,6h [ISO_1]

value: Kidney collecting duct cell line


title: Twist1 antibody_5441


title: scRNA-seq of patient 2 pre NMP

description: Liver P2_T0


title: induced MCF10A YAP5SA cells unphosphorylated Pol II

value: Pol II (8WG16) (Santa Cruz, sc-56767 )


title: scRNA-seq of patient 1 pre NMP

description: Liver P1_T0


title: scRNA-seq of patient 1 after reperfusion

description: Liver P1_T2

value: after reperfusion


title: Twist1 antibody_5391


title: Control IgG_5785

value: IgG


title: Control IgG_5441


title: scRNA-seq of patient 1 post NMP

description: Liver P1_T1

value: post normothermic machine perfusion (NMP)


title: mIMCD3 cells,Isotonic,6h [ISO_3]


title: Control IgG_5391


title: induced MCF10A YAP5SA cells pSer2 Pol II

value: induced

value: p-S2 RNA Pol II (Abcam, ab5095)