title: EpithelialSample4, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts


title: EpithelialSample1, EpithelialKrasG12DOncogene, p53flfl Fibroblasts

status: Public on May 01 2022

type: RNA

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathon Lucas Street

department: Biochemistry & Molecular Biology

country: USA

institute: Medical University of South Carolina

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing:
Raw signal intensity preprocessing from .CEL files was done using RMA. This consisted of background adjustment, quantile normalization, and median polish. R was used to form class comparisons to determine differentially expressed genes at P < 0.05 with the Student's t-test. For heat map construction, geometric means after RMA normalization from control samples was set as the reference, with the color (blue or red) corresponding to the ratio between the gene expression in mutant and reference samples. Functional gene annotation was done with DAVID.
MoEx-1_0-st-v1, Mm9
MoEx-1_0-st-v1 Annotations, Probeset, Mm9

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mammary epithelia

label_protocol: Samples were fragmented and  labeled using the GeneChip™ WT Terminal Labeling Kit

growth_protocol: Isolated mammary epithelia and fibroblasts grown in vitro

extract_protocol: Total RNA extraction using Trizol (Invitrogen) followed by purification with RNeasy (Qiagen)

treatment_protocol: None other than described genetic modification. Mice were treated with doxycycline for 9 weeks prior to epithelial and fibroblast isolation and cells maintained in doxycycline in vitro

tag: cell type

value: Mammary epithelia

tag: epithelia status

value: KrasG12D mutation

tag: fibroblast status

value: Wild-type p53


title: monocytes sorted from spleen, high_GS_treated1

type: SRA

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software used for basecalling.
Raw reads were aligned to the reference genome (mm10) using Tophat2 or STAR aligner (for myeloid cells). Number of reads aligned to the exonic region of each gene were counted using the Rsamtools Bioconductor package based on the genome annotation from UCSC ‘ensGene’ table. Genes on the sex chromosomes were excluded from the following analysis.
Only genes that achieved at least two read count per million reads (CPM) in at least three samples were kept. Read counts were further normalized using the conditional quantile normalization (cqn) method accounting for gene length and GC content.
This generated normalized log2 RPKM values for each filtered gene across all samples. Differential expression analysis was performed using LIMMA, with the array quality weights function applied
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 transformed RPKM values for each sample

source_name: monocytes sorted from spleen

extract_protocol:
Whole tumours were frozen in RNAlater and RNA was extracted using Qiagen RNeasy mini kit. The RNA library was prepared using TruSeq Stranded Total RNA library preparation with Ribozero Gold and quality measured on Agilent BioAnalyzer. The NGS was performed on HiSeq 2000 TM using V3 flow cells on one lane at 100bp paired-end. whole RNA was extracted from pellets of sorted myeloid cells using Qiagen RNeasy mini kit and stored in -80 until analysis. Libraries were made by using either IlluminaTrue Seq kits or Nugen Library Construction kits. Samples were multiplexed in 4 lanes and sequenced via the Illumina HiSeq2000 platform. 100 base-pair, paired-end data sequence data were then generated and subsequently analysed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: KPC

tag: tissue

value: myeloid cell

tag: treatment

value: GS9820 treated

tag: days after treatment

value: 14 days


title: blood feeding with 2 μM hsa-miR-150-5p antagomir (RNA-seq)

city: Beijing

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

country: China

institute: Tsinghua University

description:
blood feeding
Sample name: B

data_processing:
HCS 2.012 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes Aegypti genome using SOAPaligner/SOAP2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
NOIseq method coming from Sonia Tarazona et al., Genome Research, 2011., was applied to screen differentially expressed genes between two groups
Genome_build: AaegL5.0
Supplementary_files_format_and_content: BvsA_deg_up.txt includes RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample

organism: Aedes aegypti

source_name: whole body

growth_protocol: Aedes Aegypti was reared at 28℃ and 80% humidity.

extract_protocol:
The total mosquito 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 days old mosquitos were fed a blood meal, then cultured after 3 days

value: Rockefeller

value: whole body

value: hsa-miR-150-5p antagomir

tag: time

value: 3 days


title: EpithelialSample4, EpithelialKrasG12DOncogene, p53flfl Fibroblasts


title: D8.B6.B6.FO.4

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Assembly: mm10
Supplementary files format and content: Notch_lymphopenia.normExp.txt.gz: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary files format and content: Notch_lymphopenia.rawTPM.txt.gz: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol

source_name: Splenic B cell

growth_protocol: C57BL6, Rag2-/- and B6.SJL.C20 mice were bred and maintained in UPENN SPF facilities.

extract_protocol:
Spleens were harvested at time of saccrifice and lypmhocytes were stained and double FACS sorted directly into TRIZOL reagent as follows:  follicular B cell: live, singlet, CD19+, CD93-, CD23+, CD21/35int.  marginal zone B cell: live, singlet, CD19+, CD93-, CD23-, CD21/35high. intermediate B cell: live, singlet, CD19+, CD93-, CD23int/+, CD21/35int/+
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech SMART-Seq HT kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.

treatment_protocol: adoptive transfer protocol: B6.SJL.C20 spleens were harvested at time of sacrifice and mature follicular B cells were celltrace violet labeled and FACS-sort purified gate: live, singlet, CD19+, CD93-, CD23+, CD21/35int . Resulting cells were adoptively transferred at 2x10^6 cells per mouse i.v. into either Rag2-/- or C57BL6 hosts.

value: Spleen

tag: age

value: 12 weeks

tag: adoptive transfer host

tag: congenic marker

value: CD45.2+ follicular B cell


title: EpithelialSample3, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts

value: p53 deletion


title: D8.B6.B6.FO.3


title: D8.B6.B6.FO.2


title: FFPE prostate_cancer_primary_159

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

organism: Homo sapiens

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

treatment_protocol: Not Applicable

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: race

value: African descendant

tag: randomization arm

value: Treatment

tag: ecog3805 id


title: EpithelialSample2, EpithelialKrasG12DOncogene, p53flfl Fibroblasts

tag: cell type

value: Mammary epithelia


title: blood feeding with antagomir mock (RNA-seq)

description:
blood feeding
Sample name: A

value: antagomir mock


title: EpithelialSample2, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts

tag: epithelia status

value: KrasG12D mutation


title: D8.B6.B6.FO.1


title: FFPE prostate_cancer_primary_158

value: Caucasian


title: FFPE prostate_cancer_primary_157


title: C5

city: yinchuan

first: yufei

last: zhang

state: ningxia

address: ningxia medicine university

institute: ningxia medicine university

description: Control group5

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.   After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slices are scanned immediately after washing on an Agilent DNA microarray scanner (G2505C) using a color scan setting of 1x44K array slices (scan area 61x21.6 mm, scan resolution 10um, dye channel set to green, green PMT set to 100%)

data_processing: Feature extraction software 9.1 (Agilent) is used to analyze the scanned images with default parameters, and the signal strength after background subtraction and spatial de-trending is obtained.  Exclude features marked as feature non-uniform outliers in feature extraction.

source_name: Control group5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).   Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Quick Amp Labeling Kit, one-color (Agilent P/N 5190-0442), as recommended by manufacturers.  Use GLOBINclear (Ambion Inc., Austin, TX) to further reduce globin information, specifically removing a- and B-globin.  The RNA was quantified using a nanodrop-1000 spectrophotometer and the quality was monitored using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood of the experimental group and the control group was collected on an empty stomach and stored in AN EDTA anticoagulant tube. All the EDTA anticoagulant blood samples were centrifuged by a high-speed centrifuge within 30 minutes (3000rpm, 10min). After that, the upper plasma was collected and placed in a cryopreserved tube and frozen at -80 ℃ for use. Frozen plasma was frozen and crushed with liquid nitrogen using a biological grinder, and specimens were homogenized by adding TRIzol to a bead-mill tissue grinder.

tag: disease state

value: control

value: whole blood

tag: Sex

value: female


title: FFPE prostate_cancer_primary_160


title: EpithelialSample1, EpithelialKrasG12DOncogene, FspCrep53flfl Fibroblasts

tag: fibroblast status


title: D8.B6.B6.MZ.4

tag: strain

tag: tissue

value: CD45.2+ marginal zone B cell


title: FFPE prostate_cancer_primary_153

value: Placebo


title: C3

description: Control group3

source_name: Control group3


title: micu_mcu_rep3

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1, Gebaeude 99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

data_processing:
Base call files were converted to fastq format and demultiplexed using bcl2fastq v2.20.
The 75 bp single-end reads were aligned to Caenorhabditis elegans reference transcriptome WBcel235 by kallisto using default parameters.
Genome_build: WBcel235
Supplementary_files_format_and_content: est_counts,  tpm

organism: Caenorhabditis elegans

source_name: whole worm tissue

growth_protocol: Nematodes were grown and maintained at 20 ºC on NGM plats following standard culture methods.

extract_protocol:
Adult nematodes were dissolved in 1mL Trizol and total RNA was isolated via the RNeasy Micro kit. RNA concentration ad integrity were determined by High Sensitivity RNA assay on a TapeStation 4200 system. cDNA libraries were prepared from 5ng total RNA using the SMART-seq2 protocol and tagmented with the Nextera XT kit. Libraries were sequenced SR 75 cycles on a NextSeq500 system (illumina) using High Output v2 chemistry.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 days

tag: stain

tag: genotype

value: micu1; mcu-1 mutant


title: FFPE prostate_cancer_primary_154

tag: age


title: FFPE prostate_cancer_primary_151


title: FFPE prostate_cancer_primary_152


title: EpithelialSample4, NoEpithelialOncogene, p53flfl Fibroblasts

value: Wild-type

value: Wild-type p53


title: FFPE prostate_cancer_primary_156


title: FFPE prostate_cancer_primary_155


title: D8.B6.B6.MZ.3

value: Spleen

value: 12 weeks

tag: adoptive transfer host

tag: congenic marker


title: micu_mcu_re2


title: EpithelialSample2, NoEpithelialOncogene, p53flfl Fibroblasts


title: FFPE prostate_cancer_primary_150

tag: primary gleason

tag: secondary gleason


title: EpithelialSample1, NoEpithelialOncogene, p53flfl Fibroblasts


title: micu_rep3

value: BAN362 micu-1(bon20)IV/nT1[qIs51](IV;V)

value: micu-1 mutant


title: D8.B6.B6.MZ.2


title: FFPE prostate_cancer_primary_149

tag: pre-treatment psa (ng/ml)

tag: race

value: Treatment


title: micu_mcu_rep1


title: D8.SJL.B6.FO.3

value: CD45.1+ follicular B cell


title: FFPE prostate_cancer_primary_148

tag: randomization arm

tag: ecog3805 id


title: D8.B6.B6.MZ.1

tag: cell type


title: FFPE prostate_cancer_primary_147


title: micu_rep1


title: EpithelialSample4, NoEpithelialOncogene, FspCrep53flfl Fibroblasts

value: Mammary epithelia

tag: epithelia status

value: p53 deletion


title: D8.SJL.B6.FO.4


title: WT_rep2

value: 5 days

value: N2 (Bristol)

value: WT


title: FFPE prostate_cancer_primary_146

value: Caucasian


title: FFPE prostate_cancer_primary_145


title: micu_rep2


title: EpithelialSample3, NoEpithelialOncogene, FspCrep53flfl Fibroblasts


title: D8.SJL.B6.MZ.4

value: CD45.1+ marginal zone B cell


title: EpithelialSample1, NoEpithelialOncogene, FspCre;p53flfl Fibroblasts


title: FFPE prostate_cancer_primary_143

value: Placebo


title: FFPE prostate_cancer_primary_144


title: D8.SJL.B6.FO.2


title: EpithelialSample2, NoEpithelialOncogene, FspCrep53flfl Fibroblasts


title: WT_rep1


title: WT_rep3


title: D8.SJL.B6.FO.1


title: FFPE prostate_cancer_primary_142


title: D8.SJL.B6.MZ.3


title: FFPE prostate_cancer_primary_141


title: AOM/DSS tumor, distal, T/T, rep1

city: Nashville

first: Christopher

last: Williams

state: Tennessee

address: 1075 MRBIV/Light Hall, 22 Garland Ave.

department: Medicine/Gastroenterology

institute: Vanderbilt University Medical Center

description:
5698-RB-2
AOMDSS_Dist_tumor_P209Thomo_vs_WT.csv

data_processing:
Raw reads in FASTQ format were trimmed with fastp (v0.20.0) with default parameters.
Quantification was performed using Salmon (v1.3.0) against a decoy transcriptome generated from Mus musculus GENCODE (v21).
Quantification files were imported with tximeta (v1.4.5) in R (v3.6.3). Genes with counts ≤1 across all samples were omitted.
Differential expression analysis was performed on raw transcript counts using DESeq2 (v1.26.0) and annotated with AnnotationDbi (v1.46.1) .
Assembly: mm10
Supplementary files format and content: Comma-delimited files with differential expression analysis, including normalized counts for each sample, by DESeq2.

source_name: Colon tumor

growth_protocol: Mtg16-null mice (C57/BL6 background) and homozygous P209T (T/T) mice (C57/BL6 background) were bred using heterozygous x heterozygous breeding schemes in independent colonies. All mice were at least 8 weeks old. WT and Mtg16-null or WT and T/T mice were appropriately littermate-matched in each analysis.

extract_protocol:
For baseline and DSS injury-repair analyses, murine colon was harvested and splayed longitudinally. The proximal (5 cm from cecum) and/or distal (5 cm from anus) colons were washed in PBS without calcium or magnesium and minced. Tissue fragments were incubated in chelation buffer (2 mM EDTA in PBS without calcium or magnesium) with nutation for 90 min at 4 °C and washed with PBS followed by 2-min cycles of gentle shaking in shaking buffer (43.3 mM sucrose and 54.9 mM sorbitol in PBS without calcium or magnesium) to free colon crypts. Intact crypts were collected by centrifugation at 150 x g, 4 °C for 12 min. Samples were homogenized in TRIzol Reagent (#15596018, Invitrogen) by 5x shearing through a 25G needle. For AOM/DSS analyses, murine colons were harvested and splayed longitudinally. Tumors (identified by vascular, non-dimpled appearance) were dissected, incubated in RNAlater (#R0901, Sigma-Aldrich) at 4°C for 24 h, and stored at -80°C. Tumors were mechanically homogenized in TRIzol using an electronic homogenizer. All samples were centrifuged for 10 min at 16,200 x g, 4 °C to remove insoluble material. Cleared homogenate was chloroform-extracted. RNA was isolated from the aqueous layer using the RNeasy Mini Kit (#74106, Qiagen) with on-column DNase treatment (#79254, Qiagen).
NEBNext® Poly(A) mRNA Magnetic Isolation (#E7490, NEB) followed by NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (#E7645, NEB)

treatment_protocol: For DSS injury-repair: Bedding was mixed between cages to normalize microbiome 2 weeks prior to experiments. Water deprivation caps were placed to accustom mice to drinking from water bottles 1 week prior to experiments. Water bottles were filled with 2% (w/v) DSS (#DS1004, Gojira Fine Chemicals) for 5 days and then replaced with water for 4 days of recovery prior to sacrifice and colon crypt isolation. For AOM/DSS: mice were injected with 10 mg/kg AOM (#A5486, Sigma-Aldrich) followed by 3 cycles of 3% (w/v) DSS (#DB001, TdB Labs) administered in the drinking water (4 days DSS, 16 days water per cycle).

value: Colon tumor

tag: location

value: Distal colon

tag: treatment

value: AOM/DSS

value: P209Thomozygous (T/T)


title: AOM/DSS tumor, distal, T/T, rep3

description:
5698-RB-6
AOMDSS_Dist_tumor_P209Thomo_vs_WT.csv

tag: strain


title: AOM/DSS tumor, distal, T/T, rep2

description:
5698-RB-3
AOMDSS_Dist_tumor_P209Thomo_vs_WT.csv

tag: tissue


title: AOM/DSS tumor, distal, WT matched to T/T, rep3

description:
5698-RB-5
AOMDSS_Dist_tumor_P209Thomo_vs_WT.csv

value: WT littermate-matched to P209T


title: D8.SJL.RAG.FO.4

value: Spleen

value: 12 weeks


title: RBE_2AG_2wk_rep2

city: Guangzhou

first: Li

last: Huang

state: Guangdong

address: Zhongshan NO.2 Road

department: Pancreatobiliary surgery

institute: The first affiliated hospital, Sun Yat-sen University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.    a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first          denatured for 2 min at 95°C, incubated on ice for 2 min    b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization          System - Nimblegen Systems, Inc., Madison, WI, USA)      c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.
Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value.

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:    a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture          was incubated for 30 min at 37°C.      b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of          fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling          reaction was incubated for 1 h at 16°C    c, Terminated by incubation for 15 min at 65°C.

growth_protocol: DMEM with 10%FBS

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: RBE were treated with 2-AG(10μM) or DMSO respectively for 14 days and reagents were replaced every 48 hours

tag: cell line

value: RBE

tag: agent

tag: time point

tag: disease

value: intrahepatic cholangiocarcinoma


title: RBE_2AG_2wk_rep3


title: D8.SJL.RAG.FO.2

tag: age

tag: adoptive transfer host

tag: congenic marker

value: CD45.1+ follicular B cell


title: sgRNA_plasmid_library

city: Kanazawa

first: Yusuke

last: Miyanari

address: Kakuma

department: NanoLSI

country: Japan

institute: Kanazawa University

description: lentivirus plasmid

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Adaptor sequences were trimmed by using cutadapt
Bowtie2 with the parameter “-N 1 -X 2000 --no-mixed --no-discordant” mapped ATAC-seq reads to the hybrid reference genome (hg38 and dm6).
MAGeCK-RRA in MAGeCK-VISPR v0.5.3 [Li 2015 Genome Biology] was used to analyze the data
Supplementary_files_format_and_content: MAGeCK-VISPR output

molecule: genomic DNA

organism: synthetic construct

source_name: CRISPR lentivirus sgRNA library (Brunello)

growth_protocol: eHAP cells (Horizon Discovery) (Essletzbichler et al., 2014) grown in Iscove’s Modified Dulbecco’s Medium (IMDM, Wako) supplemented with 10% FBS (Sigma) and penicillin/streptomycin (Wako).

extract_protocol:
In one batch of screen, a series of these processes was repeated five times to collect ~ 2.2 x 106 cells in total for each population. Three batches of screen was independently performed to collect three biological replicates. Genomic DNA was extracted from the sorted cells by phenol chloroform extraction
Integrated lentivirus genome encoding sgRNA was sequenced with illumina HiSeq2500 as described previously (Doench et al., 2016)[Doench, 2016 Nat Biotech]

treatment_protocol: Cas9 expressing eHAP cells were transduced with human sgRNA lentivirus library (Doench, 2016 Nature biotech, Addgene, #73178). The cells were selected with 1 µg/ml of puromycin for 2 days, and then used for ATAC-see at 5 and 7 days post-transduction, respectively. Cells in the G2 phase were specifically gated to sort th 5% of the cells with the highest and lowest ATAC-see signal intensity(“high” or “low” population) . The sgRNA enrichment in each population was analysed by high-throughput sequencing and computationally compared by using the MAGeCK program (Li et al., Genome Biology 2014).


title: RBE_2AG_2wk_rep1


title: FFPE prostate_cancer_primary_138

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

value: Treatment


title: RBE_DMSO_2wk_rep3

value: DMSO


title: D8.SJL.B6.MZ.2


title: D8.SJL.B6.MZ.1


title: FFPE prostate_cancer_primary_140

tag: race

tag: randomization arm

tag: ecog3805 id


title: EpithelialSample3, NoEpithelialOncogene, p53flfl Fibroblasts

tag: cell type

value: Mammary epithelia

tag: epithelia status

value: Wild-type

tag: fibroblast status

value: Wild-type p53


title: AOM/DSS tumor, distal, WT matched to T/T, rep1

description:
5698-RB-1
AOMDSS_Dist_tumor_P209Thomo_vs_WT.csv

tag: strain

tag: tissue

tag: location

tag: treatment

tag: genotype


title: FFPE prostate_cancer_primary_135

tag: age

value: Caucasian


title: AOM/DSS tumor, distal, WT matched to T/T, rep2

description:
5698-RB-4
AOMDSS_Dist_tumor_P209Thomo_vs_WT.csv


title: Colon epithelial isolate, DSS Injury-repair, distal, T/T, rep2

description:
5740-RB-4
DSS_Dist_P209Thomo_vs_WT.csv

source_name: Colon crypts

value: Colon crypts

value: DSS injury-repair


title: D8.SJL.RAG.FO.3

tag: adoptive transfer host


title: FFPE prostate_cancer_primary_136

value: African descendant

value: Placebo


title: RBE_DMSO_2wk_rep1

tag: cell line

tag: agent

tag: time point

tag: disease


title: Colon epithelial isolate, DSS Injury-repair, distal, T/T, rep3

description:
5740-RB-6
DSS_Dist_P209Thomo_vs_WT.csv

value: Distal colon

value: P209Thomozygous (T/T)


title: FFPE prostate_cancer_primary_133

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: race


title: FFPE prostate_cancer_primary_139

tag: randomization arm

tag: ecog3805 id


title: RBE_DMSO_2wk_rep2


title: D8.SJL.RAG.MZ.2

tag: strain

value: Spleen

tag: congenic marker

tag: cell type

value: CD45.1+ marginal zone B cell


title: Colon epithelial isolate, DSS Injury-repair, distal, WT matched to T/T, rep2

description:
5740-RB-2
DSS_Dist_P209Thomo_vs_WT.csv
WT_Dist_DSS_vs_Baseline.csv

tag: tissue

tag: location

tag: treatment

value: WT littermate-matched to P209T


title: D8.SJL.RAG.FO.1

tag: age

value: 12 weeks

tag: adoptive transfer host


title: FFPE prostate_cancer_primary_132


title: 0-2 Hr pre-MZT MTD-GAL4>CLAMPRNAi

city: Providence

first: Erica

last: Larschan

state: RI

address: 164 Angell St

institute: Brown University

description: MLE males CLAMP RNAi 0-2 hrs

data_processing:
Library strategy: Cut&Run
Sequenced reads were run through FASTQC (Andrews 2010)(fastqc replicate_R1_001.fastq.gz replicate_R2_001.fastq.gz) with default parameters to check the quality of raw sequence data filter out any sequences flagged for poor quality.
Sequences were trimmed for quality using TrimGalore (https://github.com/FelixKrueger/TrimGalore/issues/25, https://github.com/FelixKrueger/TrimGalore).
Sequences were reassessed using FASTQC (Andrews 2010).
All Illumina lanes of the same flow cell .fastq files were merged
Sequenced reads were then mapped using BWA (Li and Durbin 2009) to release 6 Drosophila melanogaster genome (dm6).
Next, we performed conversion to bam and sorting (e.g. using: bowtie2 -x dm6_genome -1 replicate_R1_001.fastq.gz -2 replicate_R2_001.fastq.gz -S out.sam > stout.txt 2> alignment_info.txt; samtools view -bS out.sam > out.bam; rm -rf out.sam; samtools sort out.bam -o out.sorted.bam).
We removed reads (using samtools) with a MAPQ less than 30 and any reads with PCR duplicate reads (identified using MarkDuplicates Picard -2.20.2).
Peaks identified using MACS2 (Zhang et al. 2008)(macs2 callpeak -t out.sorted.bam -B -f BAM --nomodel --SPMR -- keep-dup all -g dm --trackline -n outname --cutoff-analysis --call-summits -p 0.01 --outdir outdir) and keep duplicates separate.
To calculate fold-enrichment macs2 is run again (macs2 bdgcmp -t $treat -c $control -o $out.sorted.bam_FE.bdg -m FE 2> $ out.sorted.bam_FE.log; macs2 bdgcmp -t $treat -c $control -o $out.sorted.bam_logLR.bdg -m logLR -p 0.00001 2)
Genome_build: dm6
Supplementary_files_format_and_content: mac2 output narrowPeak files show called peaks ofMLE binding in presence or absence of CLAMP
Supplementary_files_format_and_content: macs2 output bedgraph files show continuous-valued binding information of MLE in presence or absence of CLAMP

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Drosophila melanogaster fly stocks were maintained at 24℃ on standard corn flour sucrose media. Fly strains used: MTD-GAL4 (Bloomington, #31777), UAS-CLAMPRNAi[val22] (Bloomington, #57008), Meiotic drive fly stocks +; SD72/CyO and 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO (Bloomington, #64332). These were crossed to obtained male embryo of desired genotypes according to Rieder et al 2017.

extract_protocol:
The embryos were dechorionated in 6% bleaching solution, washed in cold 1XPBS and permeabilised using 0.05% Digitonin. pAMNase (700ng/ml) allowed to bind to antibody bound to MLE protein on chromatin. MNAse activity initiated by adding CaCl2 at 0℃ and after 30 minutes incubation allowed to stop by adding 2X RSTOP Buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/ml RNase, 40ug/ml glycogen, 10pg/ml yeast spike-in DNA). DNA fragment extracted and purified using Phenol:Chloroform extraction and 1ng of DNA used for making libraries.
Library prepared using Kapa hyper prep kit using manufacturer's protocol

value: Whole embryo

value: 0-2 Hr old

tag: antibody

value: rat anti-MLE (1:50, 6E11)

tag: genotype of mother


title: D4.SJL.RAG.INT.4

value: CD45.1+ intermediate B cell


title: FFPE prostate_cancer_primary_134


title: 0-2 Hr pre-MZT MTD-GAL4>GFPRNAi

description: MLE males control 0-2 hrs


title: Colon epithelial isolate, DSS Injury-repair, distal, T/T, rep1

description:
5740-RB-3
DSS_Dist_P209Thomo_vs_WT.csv

tag: genotype


title: Sample_F3T3 Generation 4 Control

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

description:
Generation 4 Control
Control

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Mapping with  STAR v020201 against  WormBase235 C elegans reference genome and Ensembl v91 exon-exon junctions
Quantification and normalization with Deseq2 v1.22.2
Genome_build: WormBase235
Supplementary_files_format_and_content: Trimed reads in fastq
Supplementary_files_format_and_content: Read count files from RNAstar

source_name: Entire young adult

growth_protocol: C. elegans was cultured by standard techniques at 19°C, 80% humidity, on petri dishes with NGM (nematod Growth Medium) and seeded E. Coli OP50 as food source. Embryos are synchronized by bleaching technique.

extract_protocol:
Total RNA was extracted using FastPrep with Direct-zol Reagent and purified with RNEasy Mini Kit
cDNA synthesis and sequencing library were obtained using Strand-specific TruSeq RNA-Seq pair-end libraries with 350bp fragment size
Libraries were sequenced using Illumina HiSeq 3000 as paired-end 150 base reads with high quality score

treatment_protocol: Synchronized embryos are exposed to chronic exposure to gamma radiation (50mGy/h) or placed in control environment, from embryos to L4 young adult stage (65 hours)

tag: genetic background

tag: developemental stage

tag: generation

tag: dose rate

value: Control


title: FFPE prostate_cancer_primary_130

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: race

tag: randomization arm

value: Treatment


title: FFPE prostate_cancer_primary_137

value: Caucasian

tag: ecog3805 id


title: D8.SJL.RAG.MZ.3

tag: strain

tag: tissue

tag: congenic marker

tag: cell type


title: D8.SJL.RAG.MZ.1

tag: age

tag: adoptive transfer host


title: Colon epithelial isolate, DSS Injury-repair, distal, Mtg16-null, rep3

description:
6217-RB-6
DSS_Dist_Mtg16null_vs_WT.csv

value: Colon crypts

tag: location

tag: treatment

tag: genotype


title: D8.SJL.RAG.MZ.4


title: Colon epithelial isolate, DSS Injury-repair, distal, Mtg16-null, rep2

description:
6217-RB-4
DSS_Dist_Mtg16null_vs_WT.csv

value: DSS injury-repair


title: 2-4 Hr pre-MZT MTD-GAL4>GFPRNAi

description: MLE males control 2-4 hrs

value: 2-4 Hr old

tag: antibody

tag: genotype of mother


title: Sample_F3R3 Generation 4 Recovery

description:
Generation 4 Recovery
Exposed at F0 and then put in control condition for 3 generations

tag: genetic background

tag: developemental stage

tag: generation

tag: dose rate

value: Recovery


title: Colon epithelial isolate, DSS Injury-repair, distal, Mtg16-null, rep1

description:
6217-RB-3
DSS_Dist_Mtg16null_vs_WT.csv

value: Distal colon


title: FFPE prostate_cancer_primary_131

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: race

tag: randomization arm

value: Placebo


title: FFPE prostate_cancer_primary_129

tag: ecog3805 id


title: 2-4 Hr pre-MZT MTD-GAL4>CLAMPRNAi

description: MLE males CLAMP RNAi 2-4 hrs

tag: tissue

tag: age


title: Colon epithelial isolate, DSS Injury-repair, distal, Mtg16-null, rep4

description:
6217-RB-7
DSS_Dist_Mtg16null_vs_WT.csv

tag: strain

tag: location


title: FFPE prostate_cancer_primary_125


title: CDAHFD_D7_cMaf_WT#4

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: polyA RNA

source_name: Whole liver

extract_protocol: For MuSC samples, cells were isolated by enzymatic digestion of the indicated tissue and cells were purified by fluoresence activated cell sorting. 1000 cells were sorted in TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing. For whole muscle and liver samples, tissue was homogenized in Trizol, and then RNA was isolated per the manufacterure protocol. 2ng of purified RNA were added to TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing.

tag: genotype

value: Maf-wt

value: CDAHFD feeding for 7 days


title: Colon epithelial isolate, DSS Injury-repair, distal, WT matched to T/T, rep3

description:
5740-RB-5
DSS_Dist_P209Thomo_vs_WT.csv
WT_Dist_DSS_vs_Baseline.csv

tag: treatment

value: WT littermate-matched to P209T


title: Sample_F3E3 Generation 4 Exposed

description:
Generation 4 Exposed
Exposed chronicaly to ionizing radiations over 4 generations


title: CDAHFD_D7_cMaf_KO#2

value: MafdeltaTreg


title: D4.SJL.RAG.INT.3

value: Spleen

value: 12 weeks

tag: adoptive transfer host

tag: congenic marker

tag: cell type


title: Sample_F3T1 Generation 4 Control

description:
Generation 4 Control
Control

tag: genetic background

tag: developemental stage

tag: generation


title: FFPE prostate_cancer_primary_128

tag: primary gleason

tag: secondary gleason


title: D4.SJL.RAG.INT.1


title: FFPE prostate_cancer_primary_126

tag: pre-treatment psa (ng/ml)

tag: race


title: FFPE prostate_cancer_primary_127

tag: randomization arm

tag: ecog3805 id


title: Sample_F3T2 Generation 4 Control

description:
Generation 4 Control
Control

tag: dose rate


title: FFPE prostate_cancer_primary_122

tag: age


title: Sample_F3R2 Generation 4 Recovery


title: FFPE prostate_cancer_primary_123


title: Colon epithelial isolate, DSS Injury-repair, distal, WT matched to Mtg16-null, rep3

description:
6217-RB-5
DSS_Dist_Mtg16null_vs_WT.csv

tag: strain

tag: tissue

tag: location

value: WT littermate-matched to Mtg16-null


title: Colon epithelial isolate, DSS Injury-repair, distal, WT matched to T/T, rep1

description:
5740-RB-1
DSS_Dist_P209Thomo_vs_WT.csv
WT_Dist_DSS_vs_Baseline.csv

tag: treatment

tag: genotype


title: CDAHFD_D7_cMaf_KO#4


title: CDAHFD_D7_cMaf_KO#3


title: Colon epithelial isolate, DSS Injury-repair, distal, WT matched to Mtg16-null, rep2

description:
6217-RB-2
DSS_Dist_Mtg16null_vs_WT.csv


title: Sample_F3E1 Generation 4 Exposed


title: Sample_F3R1 Generation 4 Recovery


title: Whole_muscle_D7_cMaf_KO#2

source_name: Tibialis anterior muscle

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: Colon epithelial isolate, baseline, distal, T/T, rep3

description:
5094-RB-5
Baseline_Dist_P209Thomo_vs_WT.csv

value: Baseline

value: P209Thomozygous (T/T)


title: Colon epithelial isolate, DSS Injury-repair, distal, WT matched to Mtg16-null, rep1

description:
6217-RB-1
DSS_Dist_Mtg16null_vs_WT.csv


title: CDAHFD_D7_cMaf_WT#3


title: FFPE prostate_cancer_primary_124

value: Caucasian


title: Sample_F3E2 Generation 4 Exposed


title: Colon epithelial isolate, baseline, distal, T/T, rep4

description:
5094-RB-12
Baseline_Dist_P209Thomo_vs_WT.csv

value: Colon crypts


title: Sample_F2R3 Generation 3 Recovery

description:
Generation 3 Recovery
Exposed at F0 and then put in control condition for 2 generations


title: Colon epithelial isolate, baseline, distal, WT matched to T/T, rep3

description:
5094-RB-11
Baseline_Dist_P209Thomo_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv
WT_Dist_DSS_vs_Baseline.csv


title: FFPE prostate_cancer_primary_119

value: Treatment


title: CDAHFD_D7_cMaf_WT#2


title: FFPE prostate_cancer_primary_121


title: Sample_F2R2 Generation 3 Recovery


title: Sample_F2T3 Generation 3 Control

description:
Generation 3 Control
Control

value: Control


title: Whole_muscle_D7_cMaf_KO#3


title: Sample_F2T2 Generation 3 Control

description:
Generation 3 Control
Control


title: Colon epithelial isolate, baseline, distal, T/T, rep1

description:
5094-RB-1
Baseline_Dist_P209Thomo_vs_WT.csv


title: Whole_muscle_D7_cMaf_KO#1


title: Whole_muscle_D7_cMaf_WT#2


title: Whole_muscle_D7_cMaf_WT#3


title: Sample_F2E3 Generation 3 Exposed

description:
Generation 3 Exposed
Exposed chronicaly to ionizing radiations over 3 generations


title: Sample_F2E2 Generation 3 Exposed


title: Whole_muscle_D7_cMaf_WT#1


title: Colon epithelial isolate, baseline, proximal, WT matched to T/T, rep2

description:
5582-RB-3
Baseline_Prox_P209Thomo_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv

value: Proximal colon


title: Colon epithelial isolate, baseline, distal, WT matched to T/T, rep2

description:
5094-RB-3
Baseline_Dist_P209Thomo_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv
WT_Dist_DSS_vs_Baseline.csv

value: Distal colon


title: MuSCs_D3_rIL-17a#1

source_name: MuSCs isolated from cardiotoxin-injured skeletal muscle

value: wild-type

value: i.p and i.m. rIL-17A


title: Colon epithelial isolate, baseline, distal, T/T, rep2

description:
5094-RB-4
Baseline_Dist_P209Thomo_vs_WT.csv


title: Sample_F2E1 Generation 3 Exposed


title: Colon epithelial isolate, baseline, distal, WT matched to T/T, rep1

description:
5094-RB-2
Baseline_Dist_P209Thomo_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv
WT_Dist_DSS_vs_Baseline.csv


title: Colon epithelial isolate, baseline, proximal, T/T, rep2

description:
5582-RB-4
Baseline_Prox_P209Thomo_vs_WT.csv


title: MuSCs_D3_rIL-17a#3


title: Sample_F2R1 Generation 3 Recovery

value: Recovery


title: Colon epithelial isolate, baseline, proximal, WT matched to T/T, rep1

description:
5582-RB-1
Baseline_Prox_P209Thomo_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv

value: WT littermate-matched to P209T


title: MuSCs_D3_rIL-17a#2


title: FFPE prostate_cancer_primary_113


title: Colon epithelial isolate, baseline, proximal, T/T, rep1

description:
5582-RB-2
Baseline_Prox_P209Thomo_vs_WT.csv


title: Sample_F1T3 Generation 2 Control

description:
Generation 2 Control
Control


title: FFPE prostate_cancer_primary_118

value: African descendant

value: Placebo


title: FFPE prostate_cancer_primary_116


title: MuSCs_D3_PBS#3

value: i.p and i.m. PBS


title: FFPE prostate_cancer_primary_120


title: Sample_F1T2 Generation 2 Control

description:
Generation 2 Control
Control


title: MuSCs_D3_PBS#2


title: FFPE prostate_cancer_primary_115


title: FFPE prostate_cancer_primary_114


title: FFPE prostate_cancer_primary_111


title: Colon epithelial isolate, baseline, distal, Mtg16-null, rep4

description:
4149-RB-10
Baseline_Dist_Mtg16null_vs_WT.csv


title: Sample_F1T1 Generation 2 Control

description:
Generation 2 Control
Control


title: MuSCs_D1_rIL-17a#4


title: FFPE prostate_cancer_primary_117


title: Colon epithelial isolate, baseline, distal, Mtg16-null, rep3

description:
4149-RB-4
Baseline_Dist_Mtg16null_vs_WT.csv


title: FFPE prostate_cancer_primary_110


title: MuSCs_D3_PBS#1


title: Colon epithelial isolate, baseline, distal, Mtg16-null, rep2

description:
5094-RB-9
Baseline_Dist_Mtg16null_vs_WT.csv


title: FFPE prostate_cancer_primary_112


title: FFPE prostate_cancer_primary_109


title: Sample_F1R3 Generation 2 Recovery

description:
Generation 2 Recovery
Exposed at F0 and then put in control condition for 1 generation


title: Sample_F1R2 Generation 2 Recovery


title: MuSCs_D1_rIL-17a#3


title: MuSCs_D1_rIL-17a#1


title: Colon epithelial isolate, baseline, distal, WT matched to Mtg16-null, rep4

description:
4149-RB-12
Baseline_Dist_Mtg16null_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv

value: WT littermate-matched to Mtg16-null


title: Sample_F1R1 Generation 2 Recovery


title: FFPE prostate_cancer_primary_106


title: Colon epithelial isolate, baseline, distal, WT matched to Mtg16-null, rep3

description:
4149-RB-2
Baseline_Dist_Mtg16null_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv


title: Sample_F1E3 Generation 2 Exposed

description:
Generation 2 Exposed
Exposed chronicaly to ionizing radiations over 2 generations


title: MuSCs_D1_PBS#4

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: FFPE prostate_cancer_primary_107


title: Colon epithelial isolate, baseline, distal, Mtg16-null, rep1

description:
5094-RB-8
Baseline_Dist_Mtg16null_vs_WT.csv

value: Baseline


title: Colon epithelial isolate, baseline, distal, WT matched to Mtg16-null, rep2

description:
5094-RB-10
Baseline_Dist_Mtg16null_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv


title: Colon epithelial isolate, baseline, distal, WT matched to Mtg16-null, rep1

description:
5094-RB-7
Baseline_Dist_Mtg16null_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv


title: MuSCs_D0#3

source_name: MuSCs isolated from uninjured skeletal muscle


title: Sample_F0T3 Generation 1 Control

description:
Generation 1 Control
Control


title: MuSCs_D0#2


title: Sample_F1E1 Generation 2 Exposed


title: Colon epithelial isolate, baseline, proximal, Mtg16-null, rep2

description:
4149-RB-9
Baseline_Prox_Mtg16null_vs_WT.csv


title: MuSCs_D1_PBS#1


title: Sample_F0T2 Generation 1 Control

description:
Generation 1 Control
Control


title: Sample_F2T1 Generation 3 Control

description:
Generation 3 Control
Control


title: MuSCs_D1_PBS#3


title: Colon epithelial isolate, baseline, proximal, WT matched to Mtg16-null, rep2

description:
4149-RB-11
Baseline_Prox_Mtg16null_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv


title: FFPE prostate_cancer_primary_104


title: FFPE prostate_cancer_primary_101


title: FFPE prostate_cancer_primary_105


title: MuSCs_D0#1


title: Sample_F0E3 Generation 1 Exposed

description:
Generation 1 Exposed
Exposed chronicaly to ionizing radiations


title: FFPE prostate_cancer_primary_100


title: YT330_RPMI_OCT11_2_S5

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing reads were first trimmed and filtered with Trimmomatic (0.39-Java-11) with minimal read length 50 using default settings for ChIP-Seq. For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using Hisat2 2.1.0 with default  setting.
For ChIP-Seq, Reads that passed the quality control were then mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting and 2 mismatches are allowed
For ChIP-Seq, Bam files are then  sorted with Samtools 1.11 with default settings. PCR duplicates were removed with Picard  2.21.6 with default settings and indexed with Samtools. Peaks were called with Macs2 2.2.7.1 with  input as negative control with default settings and a 5% FDR as cutoff.
Bedtools 2.30.0 was used to intersect as well as merge peaks from different experiments to generate high-confidence peaks or all C11orf53-OCT11 occupying sites (54, 55). Homer v4.11 makeTagDirectory and makeUCSCfile were used to generate bigwigs files for visualizing ChIP-Seq tracks on UCSC genome browser. The annotatePeaks was used to annotate peak features for C11orf53-OCT11 occupying peaks as well as  calculating tag counts on C11orf53/OCT11 intensity on all C11orf53-OCT11 binding sites with +/- 250  bp around peak center. MEME SUIT 5.4.1 MEME was used to discover motifs enriched on defined peak  regions.
For scRNA-seq, the Cell Ranger  pipeline (v5.0.0, 10X Genomics) was used to align FASTQ reads to the mouse reference genome (gexmm10-  2020-A, 10X Genomics) and produce digital gene-cell counts matrices. The resulting genebarcode  matrices were fed into Scanpy 1.8.1 for secondary analysis.
For RNA-seq, differentially expressed genes were analyzed using counts from HTSeq-count 0.13.5. Genes  with TPM >= 2 in at least one condition were then fed into DESeq2 with masking structural RNAs and  non-coding RNA for calculating fold change. TPM was quantified with Salmon 1.0.0 with  default settings.
Genome_build: hg38
Supplementary_files_format_and_content: TPM or htseq-count matrix for RNA-Seq, h5ad and h5 files for scRNA-seq. Trimmed fastq file, bigwig, bam/bai and peak files for ChIP-Seq.

source_name: Notch high small cell lung cancer

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin.streptomycin except NCIH1048, which was cultured in DMEM:F12 supplemented with 0.005 mg/mL insulin, 0.01 mg/mL transferrin, 30 nM sodium  selenite, 10 nM hydrocortisone, 10 nM β-estradiol, 4.5 mM L-glutamine and 5% FBS.

extract_protocol:
Total RNA was extracted using TRIzol following the standard protocol; cells were fixed with 1% formaldehyde for 10 minutes and quenched with glycine following standard protocol (see method in paper) for ChIP-Seq.
polyA RNA was selected and fragmented with NEBNext Poly (A) mRNA Magnetic isolation  module (NEB #E7350) and the library was prepared with NEBNext Ultra II RNA Library Prep kit for  Illumina (NEB #E7770) with 2 ug RNA according to the manufacturer's protocol. For single cell RNA-seq, cell suspensions were stained for viability with Sytox blue (ThermoFisher S34857) and sorted on a Sony  SH800S (Sony Biotechnology Inc, San Jose, CA) using a 100 μm chip (Catalog #LE-C3110) in “Ultra  Purity” mode. Sorted cells were washed and resuspended in PBS containing 0.04% BSA. An aliquot  was stained with ViaStain AOPI (Nexcelom #CS2-0106-5mL) and counted using a Countess FL II  automated cell. Up to 12,000 cells were loaded per lane on 10X Chromium microfluidic chips. Single  cell capture, barcoding, and library preparation were performed using the 10X Chromium chemistry,  using the NextGEM Single-Cell 3’ Library Kit v3.1 (1000121; 10X Genomics). ChIP-seq library was prepared using the NEBNext Ultra II DNA Library Prep Kit  for Illumina (E7645) following manufacturer's protocol with AMPure XP beads (Beckman, A63881)  with no size selection.

treatment_protocol: see above

tag: cell line

value: OCT11 overexpression


title: FFPE prostate_cancer_primary_103


title: Sample_F1E2 Generation 2 Exposed

tag: genetic background


title: Colon epithelial isolate, baseline, proximal, Mtg16-null, rep1

description:
4149-RB-3
Baseline_Prox_Mtg16null_vs_WT.csv


title: Sample_F0E2 Generation 1 Exposed

tag: developemental stage


title: Colon epithelial isolate, baseline, proximal, WT matched to Mtg16-null, rep1

description:
4149-RB-1
Baseline_Prox_Mtg16null_vs_WT.csv
Baseline_WT_Dist_vs_Prox.csv


title: YT330_RPMI_OCA-T_2_S4

value: C11orf53 overexpression


title: Sample_F0E1 Generation 1 Exposed

tag: generation


title: YT330_RPMI_GFP_2_S3

value: GFP overexpression


title: FFPE prostate_cancer_primary_98

tag: primary gleason

value: Caucasian

value: Treatment


title: YT330_RPMI_OCA-T_OCT11_2_S6

value: C11orf53 and OCT11 overexpression


title: Sample_F0T1 Generation 1 Control

description:
Generation 1 Control
Control

value: Control


title: sham3 ip

city: zhengzhou

first: Weidong

last: Li

address: kexuedadao zhengzhou

institute: Zhengzhou University

data_processing:
Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads.
Assembly: mm10

source_name: heart tissue; sham; 4w

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: heart

value: sham


title: TAC3 ip

source_name: heart tissue; TAC; 4w

value: transverse aortic constriction (TAC)


title: C27F2.4-3_RiboSeq

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description:
ribosome footprint
Ribo-seq

data_processing:
To remove illumina adapter from Ribo-seq libraries run "cutadapt -u 1 -m 23 -a AGATCGGAAGAGCACACGTCT --discard-untrimmed -o output.fastq input.fastq"
refer to the publication for details
analytical pipeline is also available here https://github.com/germaximus/Greer_2021
Genome_build: W279
Supplementary_files_format_and_content: read counts contain raw read count of individual genes

source_name: young adult

extract_protocol: DNA adapter (rApp-AGATCGGAAGAGCACACGTCT- ddC) was ligated to the 3' end of RNA footprint. Illumina flanking sequences were added through reverse transcription and consequent Circligation technique.

tag: knockdown


title: TAC1 ip


title: FFPE prostate_cancer_primary_96

source_name: FFPE prostate cancer

tag: secondary gleason

tag: pre-treatment psa (ng/ml)


title: FFPE prostate_cancer_primary_99

tag: race

tag: randomization arm


title: C27F2.4-2_RiboSeq

description:
ribosome footprint
Ribo-seq


title: C27F2.4-4_RiboSeq

description:
ribosome footprint
Ribo-seq


title: FFPE prostate_cancer_primary_97

tag: ecog3805 id


title: FFPE prostate_cancer_primary_102

tag: age


title: E02H1.1-4_RiboSeq

description:
ribosome footprint
Ribo-seq


title: sham2 ip


title: FFPE prostate_cancer_primary_94


title: TAC2 ip


title: YT330_OCT11_HA_OCA-T_S13


title: YT330_OCT11_S21


title: sham1 ip


title: TAC2 input


title: FFPE prostate_cancer_primary_95


title: TAC3 input


title: YT330_OCA-T_OCA-T_S15


title: YT330_OCT11_OCA-T_S20


title: FFPE prostate_cancer_primary_91


title: FFPE prostate_cancer_primary_93


title: E02H1.1-2_RiboSeq

description:
ribosome footprint
Ribo-seq


title: sham3 input


title: FFPE prostate_cancer_primary_92


title: YT330_HITES_OCA-T_S10


title: YT330_HITES_OCT11_S11


title: sham2 input


title: YT330_HITES_OCA-T_OCT11_S12


title: YT330_HITES_OCA-T_OCT11_2_S16


title: Empty_vector-3_RiboSeq

description:
ribosome footprint
Ribo-seq


title: FFPE prostate_cancer_primary_87


title: Empty_vector-1_RiboSeq

description:
ribosome footprint
Ribo-seq


title: YT330_HITES_GFP_S9


title: C27F2.4-1_RiboSeq

description:
ribosome footprint
Ribo-seq


title: sham1 input


title: Empty_vector-2_RiboSeq

description:
ribosome footprint
Ribo-seq


title: TAC1 input


title: E02H1.1-3_RiboSeq

description:
ribosome footprint
Ribo-seq


title: FFPE prostate_cancer_primary_85


title: FFPE prostate_cancer_primary_108


title: YT330_HITES_OCT11_2_S15


title: FFPE prostate_cancer_primary_82


title: FFPE prostate_cancer_primary_86


title: Starved-4_RiboSeq

description:
ribosome footprint
Ribo-seq

value: Starved


title: Empty_vector-4_RiboSeq

description:
ribosome footprint
Ribo-seq


title: FFPE prostate_cancer_primary_89


title: FFPE prostate_cancer_primary_88


title: FFPE prostate_cancer_primary_90


title: YT330_GFP_S11


title: FFPE prostate_cancer_primary_83


title: KOCKD+RNLS_2

city: shanghai

first: YI

last: WANG

address: Yishan Road No.600

institute: Shanghai Sixth People’s Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) were processed using Trimmomatic. The reads containing poly-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq2 R package functions estimateSizeFactors and nbinomTest.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Heart

extract_protocol:
Total RNA was extracted using the mirVana microRNA isolation kit (Ambion, Austin, TX, USA), and RNA integrity was evaluated by the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: time point

value: 18 weeks post-surgery

value: rnls-/-


title: KOCKD+RNLS_1

tag: tissue


title: YT330_HITES_GFP_2_S13

tag: treatment


title: Starved-2_RiboSeq

description:
ribosome footprint
Ribo-seq


title: scRNA-seq_small_intestine_WT_rep2

description:
Rep2_filtered_feature_bc_matrix.h5
Rep2.h5ad

source_name: C11orf53 wild type, small intestine

value: small intestine

value: wild type


title: Starved-3_RiboSeq

description:
ribosome footprint
Ribo-seq


title: KOCKD+RNLS_3

tag: genotype


title: FFPE prostate_cancer_primary_79

value: Placebo


title: YT330_HA-OCA-T_S12

tag: cell line


title: KOCKD_3

value: vector


title: scRNA-seq_small_intestine_KO_rep1

description:
Rep1_filtered_feature_bc_matrix.h5
Rep1.h5ad

source_name: C11orf53 knockout, small intestine

value: C11orf53 knockout


title: Fed-5_RiboSeq

description:
ribosome footprint
Ribo-seq

value: Fed


title: FFPE prostate_cancer_primary_80


title: scRNA-seq_small_intestine_KO_rep2


title: Starved-1_RiboSeq

description:
ribosome footprint
Ribo-seq


title: Fed-6_RiboSeq

description:
ribosome footprint
Ribo-seq


title: Fed-4_RiboSeq

description:
ribosome footprint
Ribo-seq


title: FFPE prostate_cancer_primary_81


title: KOCKD_2


title: KO_H3K27ac_input_2

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

data_processing:
Trimgalore version 0.4.1 was used to remove adaptor sequences and to remove reads shorter than 35bp or with phred quality scores less than 20.
Trimmed reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.4.2.
Qualified (MAPQ quality score>30) mappable reads were retained using Samtools version 1.8.
Peak calling was performed using MACS version 2.1.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak files in bigwig format.

source_name: Adipocyte

growth_protocol: Minced white inguinal fat depots from Control or Zfp423-iAKO mice were incubated for 1 hour in digestion buffer (1×Hank’s Balanced Salted Solution, 1.5% bovine serum albumin and 1 mg/ml Collagenase D [Roche, #11088882001]) at 37°C within a shaking water bath. The digested mixture was then filtered through a 100 μm cell strainer and then a 40 μm cell strainer. Freshly isolated inguinal WAT SVF cells were cultured in DMEM/F12 plus 10% FBS, Pen/Strep, and gentamicin (growth media). For in vitro differentiation, iWAT SVF cells were cultured in 10% CO2 at 37°C until confluency. Confluent cultures were stimulated with adipogenic induction media (growth media supplemented with 5 ug ml-1 insulin, 1 uM dexamethasone, 0.5 mM isobutylmethyxanthine and 1 uM rosiglitazone) for 48 hours. Subsequently, cells were maintained in growth media supplemented with 5 ug ml-1 insulin (maintenance media) for another 8 days until used for the following ChIP experiments.

extract_protocol:
Treated differentiated adipocytes were cross-linked with 1% formaldehyde in PBS for 10 minutes at 37 °C and quenched in 125 mM glycine in PBS for 5 minutes at 4 °C. DPP4+ cells were then lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]) to obtain nuclear material. Crude nuclear pellets were collected by centrifugation and then lysed by incubation in lysis buffer containing 5 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]. Chromatin fragmentation (200-500 bp length) was performed at 4 °C by Bioruptor 300 using the setting of 10 cycles of 30 seconds on and 60 seconds off. Soluble chromatin was diluted 1:10 with dilution buffer (20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]) and pre-cleared using Protein G Sepharose 4 Fast Flow (GE Healthcare Bio-sciences, #17-0618-01) for 1 hour at 4 °C. Pre-cleared samples were incubated with the indicated antibodies at 4 °C overnight. Antibody-protein-DNA complexes were captured by incubation with Protein G Sepharose 4 Fast Flow (GE Healthcare Bio-sciences, #17-0618-01) at 4 °C for 2 hours. Immunoprecipitated material was consecutively washed with low salt wash buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, and Protease inhibitor cocktail [Sigma, #P8340]), high salt wash buffer (20 mM Tris-HCl pH 7.9, 2mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, and Protease inhibitor cocktail [Sigma, #P8340]), LiCl wash buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, and Protease inhibitor cocktail [Sigma, #P8340]), and 1x Tris-EDTA (TE). After elution (100 mM NaHCO3, 1% SDS), the immunoprecipitated material was digested with RNase (Roche, #11119915001) and proteinase K (ThermoFisher Scientific, #EO0491) prior to the purification and concentration of the immunoprecipitated genomic DNA by ChIP DNA Clean & Concentrator kit (Zymo Research, #D5201). 50ng immunoprecipitated DNA of each sample was used for the construction of sequencing libraries.
DNA libraries were prepared for sequencing using NEBNext NGS DNA Library Preparation for Illumina Kit following manufacturer's instructions.

treatment_protocol: Differentiated Control and Zfp423-iAKO adipocytes were treated with 5 uM DOX for 12 hr to inactivate Zfp423. 48 hr after DOX treatment, cells were harvested for ChIP seq analysis.

value: Zfp423-iAKO (Zfp423 knockout)

tag: cell type

value: Adipocyte

tag: chip antibody


title: KO_H3K27ac_input_1


title: KOCKD_1


title: FFPE prostate_cancer_primary_77

value: Caucasian

value: Treatment


title: FFPE prostate_cancer_primary_78


title: FFPE prostate_cancer_primary_76


title: FFPE prostate_cancer_primary_75


title: Control_H3K27ac_input_2

value: Control (wild type)


title: WTCKD+RNLS_3

value: heart


title: FFPE prostate_cancer_primary_74


title: Fed-3_RiboSeq

description:
ribosome footprint
Ribo-seq


title: Control_H3K27ac_input_1


title: Fed-2_RiboSeq

description:
ribosome footprint
Ribo-seq


title: C27F2.4-3_mRNAseq

description:
polyA RNA
mRNA-seq

extract_protocol: none provided by the submitter


title: WTCKD+RNLS_1


title: FFPE prostate_cancer_primary_73


title: WTCKD+RNLS_2


title: C27F2.4-4_mRNAseq

description:
polyA RNA
mRNA-seq


title: Control_H3K27ac_IP_2


title: WTCKD_3


title: KO_H3K27ac_IP_2


title: KO_H3K27ac_IP_1


title: Fed-1_RiboSeq

description:
ribosome footprint
Ribo-seq


title: KO_BRG1_CHD4_common_input_2

description:
KO_BRG1_peaks.bigwig
Control_CHD4_peaks.bigwig


title: WTCKD_2


title: FFPE prostate_cancer_primary_71


title: FFPE prostate_cancer_primary_72


title: Control_H3K27ac_IP_1


title: C27F2.4-2_mRNAseq

description:
polyA RNA
mRNA-seq


title: KO_BRG1_CHD4_common_input_1


title: WTCKD_1


title: E02H1.1-1_RiboSeq

description:
ribosome footprint
Ribo-seq


title: FFPE prostate_cancer_primary_70


title: Starved-5_RiboSeq

description:
ribosome footprint
Ribo-seq


title: WTsham_3

value: sham


title: FFPE prostate_cancer_primary_68


title: FFPE prostate_cancer_primary_69


title: C27F2.4-1_mRNAseq

description:
polyA RNA
mRNA-seq


title: YT330_HITES_OCA-T_2_S14

value: C11orf53 overexpression


title: E02H1.1-4_mRNAseq

description:
polyA RNA
mRNA-seq


title: WTsham_2


title: Control_BRG1_CHD4_common_input_1

description:
Control_BRG1_peaks.bigwig
Control_CHD4_peaks.bigwig


title: Control_BRG1_CHD4_common_input_2


title: E02H1.1-3_mRNAseq

description:
polyA RNA
mRNA-seq


title: FFPE prostate_cancer_primary_67


title: Empty_vector-4_mRNAseq

description:
polyA RNA
mRNA-seq


title: E02H1.1-2_mRNAseq

description:
polyA RNA
mRNA-seq


title: Mutant InhPos polysomalRNA_rep2

first: Danielle

last: Minichino

address: 3400 civic center blv

department: Pediatric Rheumatology

institute: Children's Hospital of Philadelphia

data_processing:
Library strategy: RIBO-seq
illumina used for basecalling
used Salmon to count mRNA and polysome data against the transcriptome defined in Gencode vM27
annotated and summarized transcriptome count data to the gene level with tximeta and biomaRt, filtered on protein coding genes
normalized data using DESeq2 (rlog)
used Anota2seq under defult parameters to contrast WT  to LCH (no V600E inhibitor) and WT to LCH (with V600E inhibitor). FDR cutoff=15%
Genome_build: mm9
Supplementary_files_format_and_content: raw and normalized counts

source_name: BMDC

growth_protocol: BMDCs were routinely generated by plating bulk bone marrow in GMCSF-rich IF10 media for 7 days.

extract_protocol:
For polysome fractions, 500uL of fractions with >2 polysomes were pooled per sample and dispensed into 50-mL conical tubes with 2-parts Trizol LS.  After a 5-minute incubation at room temperature, the Direct-Zol RNA Miniprep Kit was used as per the manufacturers protocol.  Total RNA was extracted from an aliquot of cells using the Direct-Zol RNA Miniprep Kit as per the manufacturers protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were pre-treated with or without the BRAF-V600E inhibitor for 1 hour. All cells were stimulated with LPS (100ug/mL) for 3 hours followed by a cycloheximide pulse (100ug/mL). An aluqot of cells were aside for total RNA analysis. The remainig cells were subject to polysome profiling before RNA was harvested.

value: LCH

tag: biological replicate

tag: inhibitor status

value: positive

tag: molecule subtype

value: polysome RNA


title: FFPE prostate_cancer_primary_66

tag: primary gleason

tag: secondary gleason

value: African descendant


title: Mutant InhPos polysomalRNA_rep3


title: Mutant InhPos polysomalRNA_rep1


title: WTsham_1

value: 18 weeks post-surgery

value: wild type


title: KO_CHD4_IP_2


title: Control_CHD4_IP_2


title: Empty_vector-3_mRNAseq

description:
polyA RNA
mRNA-seq

tag: knockdown


title: KO_CHD4_IP_1


title: E02H1.1-1_mRNAseq

description:
polyA RNA
mRNA-seq


title: Control_CHD4_IP_1


title: Empty_vector-2_mRNAseq

description:
polyA RNA
mRNA-seq


title: Starved-6_RiboSeq

description:
ribosome footprint
Ribo-seq

value: Starved


title: KO_BRG1_IP_2


title: Empty_vector-1_mRNAseq

description:
polyA RNA
mRNA-seq


title: FFPE prostate_cancer_primary_65

tag: pre-treatment psa (ng/ml)

tag: race

tag: randomization arm

value: Placebo


title: WT InhPos polysomalRNA_rep1

value: WT


title: WT InhPos polysomalRNA_rep2


title: KO_BRG1_IP_1

tag: strain

value: Zfp423-iAKO (Zfp423 knockout)


title: FFPE prostate_cancer_primary_84

tag: age

tag: ecog3805 id


title: FFPE prostate_cancer_primary_63


title: FFPE prostate_cancer_primary_61


title: FFPE prostate_cancer_primary_60


title: Mutant IngNeg polysomalRNA_rep3

value: negative


title: FFPE prostate_cancer_primary_64

value: Caucasian


title: WT InhPos polysomalRNA_rep3


title: Control_BRG1_IP_1

value: Adipocyte


title: scRNA-seq_small_intestine_WT_rep1

tag: tissue

value: small intestine

tag: treatment


title: Control_BRG1_IP_2

tag: genotype

value: Control (wild type)


title: FFPE prostate_cancer_primary_62


title: FFPE prostate_cancer_primary_59

value: Treatment


title: FFPE prostate_cancer_primary_58


title: WT IngNeg polysomalRNA_rep2


title: Starved-3_mRNAseq

description:
polyA RNA
mRNA-seq


title: Starved-5_mRNAseq

description:
polyA RNA
mRNA-seq


title: WT IngNeg polysomalRNA_rep3


title: Starved-1_mRNAseq

description:
polyA RNA
mRNA-seq


title: Mutant IngNeg polysomalRNA_rep2


title: Starved-6_mRNAseq

description:
polyA RNA
mRNA-seq


title: Starved-4_mRNAseq

description:
polyA RNA
mRNA-seq


title: KO_PPARg_input_2

tag: cell type


title: Control_PPARg_input_2

tag: chip antibody


title: FFPE prostate_cancer_primary_57


title: Control_PPARg_input_1


title: Starved-2_mRNAseq

description:
polyA RNA
mRNA-seq


title: Fed-6_mRNAseq

description:
polyA RNA
mRNA-seq

value: Fed


title: KO_PPARg_input_1


title: FFPE prostate_cancer_primary_55


title: Mutant IngNeg polysomalRNA_rep1

value: LCH

tag: biological replicate


title: FFPE prostate_cancer_primary_56


title: WT IngNeg polysomalRNA_rep1

tag: inhibitor status


title: KO_PPARg_IP_1

value: PPARg


title: Fed-4_mRNAseq

description:
polyA RNA
mRNA-seq


title: Mutant InhPos totalRNA_rep1

data_processing:
illumina used for basecalling
used Salmon to count mRNA and polysome data against the transcriptome defined in Gencode vM27
annotated and summarized transcriptome count data to the gene level with tximeta and biomaRt, filtered on protein coding genes
normalized data using DESeq2 (rlog)
used Anota2seq under defult parameters to contrast WT  to LCH (no V600E inhibitor) and WT to LCH (with V600E inhibitor). FDR cutoff=15%
Genome_build: mm9
Supplementary_files_format_and_content: raw and normalized counts

value: positive

tag: molecule subtype

value: total RNA


title: Mutant InhPos totalRNA_rep3


title: Fed-2_mRNAseq

description:
polyA RNA
mRNA-seq


title: FFPE prostate_cancer_primary_54

tag: primary gleason

value: African descendant


title: Control_PPARg_IP_1


title: Fed-5_mRNAseq

description:
polyA RNA
mRNA-seq


title: KO_PPARg_IP_2


title: KO_EBF2_input_2


title: WT InhPos totalRNA_rep2


title: FFPE prostate_cancer_primary_53

tag: secondary gleason


title: Fed-1_mRNAseq

description:
polyA RNA
mRNA-seq


title: FFPE prostate_cancer_primary_52


title: Mutant InhPos totalRNA_rep2


title: Mutant IngNeg totalRNA_rep3


title: KO_EBF2_input_1


title: Control_EBF2_input_2


title: WT InhPos totalRNA_rep1


title: Fed-3_mRNAseq

description:
polyA RNA
mRNA-seq


title: FFPE prostate_cancer_primary_51


title: Control_PPARg_IP_2


title: FFPE prostate_cancer_primary_48


title: FFPE prostate_cancer_primary_50


title: Control_EBF2_input_1


title: FFPE prostate_cancer_primary_49


title: WT InhPos totalRNA_rep3


title: FFPE prostate_cancer_primary_47


title: RNAseq.stg16.YAPd 2

city: Heidelberg

first: Javier

last: Vázquez-Marín

state: Baden-Württemberg

address: Im Neuenheimer Feld 230, 5th floor

department: Centre for Organismal Studies (COS)

institute: Heidelberg University

data_processing:
Raw reads were pre-processed using Trimmomatic (HEADCROP:12 MINLEN:50 AVGQUAL:20)
Potential rRNA contaminating sequences were removed using Sortmerna.
Reads were mapped against the latest medaka genome assembly (ASM223467) using Hisat2.
Reads with low quality scores (-q 60) were filtered out using samtools.
Reads per gene were count using Htseq-count (GTF file from Ensembl version 99).
Subsequent analysis was performed using DEBrowser v1.14.2 (RowMeans < 10). Data was normalized using the RLE method and batch effects were removed using ComBat. Differential gene expression was carried out using DESeq2).
Assembly: ASM223467 (Oryzias latipes)
Supplementary files format and content: Tab-limited TXT files showing unnormalized counts for each gene, genotype and replicate. BW files containing read coordinated for each sample and replicate (mapped against the OryLat2 genome build)

organism: Oryzias latipes

source_name: Whole embryos

growth_protocol: Medaka embryos were raised in E3 medium at 28ºC.

extract_protocol:
RNA and gDNA fractions from stage 16 medaka embryos were extracted using TRIzol (Ambion). Possible DNA contamination was eliminated treating the RNA samples with TURBO DNAse-free (Ambion). Each embryo was genotyped using its DNA fraction following a previously published approach (Vázquez-Marín et al., 2019). RNA from embryos with the same genotype were pooled together in up to four replicates and sent to sequence (Illumina Hiseq 2500).
cDNA libraries were prepared for sequencing using standard Illumina protocols.

tag: developmental stage

value: Stg 16

tag: tag

value: yap-/- yap1b-/-

value: whole embryos


title: RNAseq.stg16.YAPd 3


title: KO_EBF2_IP_1


title: RNAseq.stg16.YAPs 3

value: yap-/-


title: RNAseq.stg16.YAPs 1


title: Mutant IngNeg totalRNA_rep2


title: FFPE prostate_cancer_primary_46

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: pre-treatment psa (ng/ml)

tag: race


title: WT IngNeg totalRNA_rep3

value: WT


title: FFPE prostate_cancer_primary_45

tag: randomization arm

value: Placebo


title: Control_EBF2_IP_1

tag: strain


title: WT IngNeg totalRNA_rep1

value: negative


title: ZFP423H1285N-Avi_input_2

growth_protocol: Minced white inguinal fat depots from Control (Cre negative), Adipo-Zfp423WT-Avi or Adipo-Zfp423H1285N-Avi mice were incubated for 1 hour in digestion buffer (1×Hank’s Balanced Salted Solution, 1.5% bovine serum albumin and 1 mg/ml Collagenase D [Roche, #11088882001]) at 37°C within a shaking water bath. The digested mixture was then filtered through a 100 μm cell strainer and then a 40 μm cell strainer. Freshly isolated inguinal WAT SVF cells were cultured in DMEM/F12 plus 10% FBS, Pen/Strep, and gentamicin (growth media). For in vitro differentiation, iWAT SVF cells were cultured in 10% CO2 at 37°C until confluency. Confluent cultures were stimulated with adipogenic induction media (growth media supplemented with 5 ug ml-1 insulin, 1 uM dexamethasone, 0.5 mM isobutylmethyxanthine and 1 uM rosiglitazone) for 48 hours. Subsequently, cells were maintained in growth media supplemented with 5 ug ml-1 insulin (maintenance media) for another 8 days until used for the following ChIP experiments.

extract_protocol:
iWAT SVF isolated from Control (Cre negative), Adipo-Zfp423WT-Avi or Adipo-Zfp423H1285N-Avi mice were induced to differentiate in vitro. Differentiated adipocytes were treated with 5 uM DOX for 12 hr to induce BirA expression and biotinylation of ZFP423 proteins. 48 hr after DOX treatment, cells were cross-linked with 1% formaldehyde in PBS for 10 minutes at 37 °C and quenched in 125 mM glycine in PBS for 5 minutes at 4 °C. Fixed cells were then lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]) to obtain nuclear material. Crude nuclear pellets were collected by centrifugation and then lysed by incubation in lysis buffer containing 5 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]. Chromatin fragmentation (200-500 bp length) was performed at 4 °C by Bioruptor 300 using the setting of 10 cycles of 30 seconds on and 60 seconds off. Soluble chromatin was diluted 1:10 with dilution buffer (20 mM Tris-HCl pH 7.9, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, and Protease inhibitor cocktail [Sigma, #P8340]) and pre-cleared using Streptavidin Sepharose High Performance beads (GE Healthcare Bio-sciences, #17-5113-01) for 1 hour at 4 °C. Pre-cleared samples were incubated with the streptavidin sepharose beads at 4 °C for 2 hours. Affinity purified material was consecutively washed with SDS wash buffer (2% SDS in 50 mM Tris-HCl pH 7.9 and Protease inhibitor cocktail [Sigma, #P8340]) twice, high salt wash buffer (50 mM Tris-HCl pH 7.9, 1mM EDTA, 500 mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100, and Protease inhibitor cocktail [Sigma, #P8340]), LiCl wash buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, and Protease inhibitor cocktail [Sigma, #P8340]), and 1x Tris-EDTA (TE). After elution at SDS elution buffer (50 mM Tris-Hcl pH 7.9, 1% SDS, and 10mM EDTA) at 70°C overnight, the affinity purified material was digested with RNase (Roche, #11119915001) and proteinase K (ThermoFisher Scientific, #EO0491) prior to the purification and concentration of the affinity purified genomic DNA by ChIP DNA Clean & Concentrator kit (Zymo Research, #D5201). ChAP-isolated DNA was subjected to library production (ChAP-seq) using NEBnext NGS DNA Library Preparation for Illumina kit (New England BioLabs, #E7645). Sequencing was performed with Illumina NextSeq 500 Mid Output (130M) by the UT Southwestern McDermott Center Next Generation Sequencing Core.
DNA libraries were prepared for sequencing using NEBNext NGS DNA Library Preparation for Illumina Kit following manufacturer's instructions.

treatment_protocol: Differentiated Control (Cre negative), Adipo-Zfp423WT-Avi or Adipo-Zfp423H1285N-Avi adipocytes were treated with 5 uM DOX for 12 hr to induce BirA expression and subsequent biotinylation of genetically modified ZFP423 proteins. 48 hr after DOX treatment, cells were harvested for ChAP seq analysis.

value: Adipocyte

tag: purification

value: Input


title: RNAseq.stg16.YAPs 2

tag: tissue


title: FFPE prostate_cancer_primary_42

tag: age

tag: ecog3805 id


title: Control_EBF2_IP_2

tag: genotype

value: Control (wild type)

tag: cell type


title: RNAseq.stg16.WT 2

value: wild type


title: RNA-seq_H1KO_rep1

first: Yu

last: Juan

address: 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
RNA-seq: the pair-end RNA-seq reads were mapped to the Mus musculus mm9 gene annotation model using Subread (Liao et al., 2013) with the default parameters, and the only uniquely mapped reads were used for further analysis. The differential expression between samples was performed with featureCounts (Liao et al., 2014) and R package DESeq2
Genome_build: mm9, dm6
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bedgraph
Supplementary_files_format_and_content: normalized counts

source_name: mouse embryonic stem cells

growth_protocol: Hela cells were cultured in medium with 90% DMEM, 10%FBS, 1% Pen/Strep in standard incubator with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instruction.
For RNA-seq, libraries(sample 22-25)  were prepared according to the Illumina TruSeq protocol.

value: mouse embryonic stem cells

tag: chip antibody

value: no


title: Mutant IngNeg totalRNA_rep1

value: LCH

tag: biological replicate

tag: inhibitor status


title: RNAseq.stg16.WT 3


title: ZFP423H1285N-Avi_IP_2

value: ChAP


title: RNAseq.stg16.WT 4


title: KO_EBF2_IP_2

value: Zfp423-iAKO (Zfp423 knockout)


title: RNA-seq_WT_rep2

value: Wild type


title: FFPE prostate_cancer_primary_44

first: Elai

last: Davicioni

address: 9725 Lusk Blvd

institute: Veracyte, Inc

tag: primary gleason

value: Caucasian


title: ZFP423H1285N-Avi_input_1


title: RNA-seq_WT_rep1


title: ZFP423H1285N-Avi_IP_1


title: RNA-seq_H1KO_rep2


title: FFPE prostate_cancer_primary_43

tag: secondary gleason

value: Treatment


title: RNAseq.stg16.WT 1

tag: developmental stage

value: Stg 16

value: whole embryos


title: ChOR-seq_H1KO_T6_rep2

data_processing:
Library strategy: ChOR-seq
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
RNA-seq: the pair-end RNA-seq reads were mapped to the Mus musculus mm9 gene annotation model using Subread (Liao et al., 2013) with the default parameters, and the only uniquely mapped reads were used for further analysis. The differential expression between samples was performed with featureCounts (Liao et al., 2014) and R package DESeq2
Genome_build: mm9, dm6
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bedgraph
Supplementary_files_format_and_content: normalized counts

growth_protocol: mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol:
Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
H3K27me3,V5-H1e Libraries(sample 6-21) were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.


title: FFPE prostate_cancer_primary_41


title: ChOR-seq_H1KO_T4_rep2


title: FFPE prostate_cancer_primary_37


title: RNAseq.stg16.YAPd 1

tag: tag

value: yap-/- yap1b-/-


title: ZFP423WT-Avi_input_2


title: FFPE prostate_cancer_primary_38

tag: pre-treatment psa (ng/ml)

value: Placebo


title: FFPE prostate_cancer_primary_36

tag: race


title: WT IngNeg totalRNA_rep2

value: WT

value: negative

tag: molecule subtype

value: total RNA


title: FFPE prostate_cancer_primary_39

tag: randomization arm


title: ChOR-seq_H1KO_T6_rep1

tag: strain


title: ZFP423WT-Avi_input_1

value: Adipocyte

tag: purification

value: Input


title: FFPE prostate_cancer_primary_40

tag: age

value: Other


title: ZFP423WT-Avi_IP_1


title: ChOR-seq_H1KO_T4_rep1

value: mouse embryonic stem cells


title: ZFP423WT-Avi_IP_2


title: ChOR-seq_H1KO_T2_rep2


title: FFPE prostate_cancer_primary_35

tag: ecog3805 id


title: Control_input_1

tag: genotype

value: Control (Cre negative)


title: Control_input_2

tag: cell type


title: Control_IP_2

value: ChAP


title: ChOR-seq_H1KO_T2_rep1

tag: chip antibody


title: FFPE prostate_cancer_primary_34


title: ChOR-seq_H1KO_T0_rep2


title: Control_IP_1


title: FFPE prostate_cancer_primary_33


title: FFPE prostate_cancer_primary_31

value: African descendant


title: FFPE prostate_cancer_primary_32


title: ChOR-seq_WT_T6_rep2

value: Wild type


title: ChOR-seq_WT_T4_rep2


title: Lymph Treg - Burn - CD44low - 2

first: James

last: Lederer

address: 20 Shattuck Street

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: lymph node

extract_protocol:
Injury-site draining lymph nodes (axillary, brachial, and inguinal) were harvested and immediately placed in ice-cold culture medium, lymph nodes were mechanically minced through sterile 70- μm cell strainers. Cell preparations were washed twice in culture medium and then strained to remove debris, RNA was purified from 50,000 cells from each sample using the RNeasy Micro Kit (Qiagen, CA)
cDNA was synthesized using Takara SmartSeq v4 reagents from 1ng of total RNA. cDNA was fragmented by Covaris AFA to ~150bp and adapters ligated using Swift 2S library prep kit from 2ng of cDNA according to manufacturer's protocol.

value: Lymph node CD4+CD44lowFoxP3-GFP+

tag: group

value: 7 Days after Injury

tag: cd44 staining

value: CD44 low

value: Foxp3DTR (stock #01695.8)


title: ChOR-seq_WT_T4_rep1


title: Lymph Treg - Burn - CD44low - 5


title: Lymph Treg - Burn - CD44low - 4_2


title: Lymph Treg - Burn - CD44low - 1_2


title: ACL-201118-T-10XSC3

city: Qingdao City

first: Haibo

last: Zhao

address: No. 16, Jiangsu Road, Shinan District

institute: Qingdao University Hospital

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10XGenomics was used to demultiplex cellular barcodes,map reads to the human reference genome GRch38.
Assembly: hg19
Supplementary files format and content: filtered_feature_bc_matrix; Matrix table with raw gene counts for every gene and every cell

source_name: Tendon

extract_protocol:
Single cells were resuspended in 200 μL of 1×PBS solution containing 0.04% BSA.Cell viability was ≥ 85% and cell concentration and total volume were ≥ 1×106 cell/mL. The cells were labeled using the 10x Genomics ChromiumTM system. Gel Beads containing Barcode information were mixed with cells, enzymes, and separated oil beads, and formed GEMs.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol

tag: tissue

value: Tendon

tag: disease state

value: injured 6 months later


title: ChOR-seq_WT_T6_rep1

city: Beijing


title: ChOR-seq_WT_T2_rep2


title: Lymph Treg - Burn - CD44low - 5_2


title: ACL-T-201116-10XSC3

value: injured one week later


title: ChOR-seq_WT_T2_rep1


title: FFPE prostate_cancer_primary_30

tag: primary gleason

tag: secondary gleason

value: Caucasian

value: Placebo


title: Lymph Treg - Burn - CD44low - 1


title: Lymph Treg - Burn - CD44high - 5

value: Lymph node CD4+CD44highFoxP3-GFP+

value: CD44 high


title: ChOR-seq_WT_T0_rep2


title: ACL-201120-T

value: injured 2 week later


title: ACL-201120

value: healthy


title: ChOR-seq_WT_T0_rep1

value: mouse embryonic stem cells


title: ACL-201112-R


title: ChIP-seq_WT_H1

extract_protocol:
Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
H3K27me3,V5-H1e Libraries(sample 1-4, 5) were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.

value: V5 tag (Gene-Protein Link,P01L075)


title: Lymph Treg - Burn - CD44high - 2


title: Lymph Treg - Burn - CD44high - 4


title: Lymph Treg - Burn - CD44high - 3


title: CB1376T

city: Stanford

first: Ravindra

last: Majeti

state: CA

address: 875 Blake Wilbur Dr Clinic F

institute: Stanford University

description:
RNA sequencing
CB1376 TET2 in HSC Expansion media

data_processing:
For RNA-seq, FASTQ sequencing reads were quantified using kallisto pseudoalignment to the reference human genome hg38. The kallisto output was imported to DEseq2 for differential analysis where a paired differential test was performed to control for differences between cords. The R package tximport was used to derive TPM values from the kallisto output for subsequent analyses.
Assembly: hg19
Supplementary files format and content: Raw reads in peaks or reads in gene bodies data across all samples, RNA kallisto output normalized counts matrix

source_name: Human Cord Blood HSPCs

growth_protocol:
Healthy hematopoietic cells were sorted and enriched
Cord blood cells were CD34 enriched, edited, and subjected to engraftment or other assays.

extract_protocol: Total RNA was extracted from CRISPR/Cas9 edited samples using the QIAGEN RNeasy micro kit following the manufacturer’s protocol. Purified RNA was submitted to the Novogene commercial sequencing facility for Bioanalyzer quality control analysis, Illumina Next Generation Sequencing, and data quality control analysis.

treatment_protocol: For TET2 edited and control samples, cells were grown in steady state or drug treated conditions before being assayed using the 5hmC sequencing protocol. See sample descriptioins for specific treatment conditions.

tag: source

value: Human Cord Blood HSPCs


title: CB1369T

description:
RNA sequencing
CB1369 TET2 in HSC Expansion media


title: FFPE prostate_cancer_primary_29

city: San Diego

tag: pre-treatment psa (ng/ml)

tag: race

value: Treatment


title: CB1376A

description:
RNA sequencing
CB1376 AAVS1 in HSC Expansion media


title: Lymph Treg - Sham - CD44low - 4

value: Lymph node CD4+CD44lowFoxP3-GFP+

value: Uninjured


title: ChIP-seq_WT_H3K27me3_rep2

value: Wild type


title: Lymph Treg - Sham - CD44low - 3

value: CD44 low

value: Foxp3DTR (stock #01695.8)


title: FFPE prostate_cancer_primary_28

tag: randomization arm


title: FFPE prostate_cancer_primary_26


title: FFPE prostate_cancer_primary_27


title: FFPE prostate_cancer_primary_25

value: African descendant


title: CB1369A

description:
RNA sequencing
CB1369 AAVS1 in HSC Expansion media


title: FFPE prostate_cancer_primary_23


title: FFPE prostate_cancer_primary_24


title: ACL-201112-L

value: Tendon


title: Retina Elovl2C234W rep2

city: Irvine

first: Dorota

last: Skowronska-Krawczyk

address: 837 Health Sciences Rd

department: Physiology & Biophysics

institute: University of California, Irvine

data_processing:
All clean-reads were mapped to Mus musculus reference genome mm10 by STAR v2.7.8a. Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For mRNA quantification, mm10 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
Differentially regulated RNA expression features were found via the homer tool - getDiffExpression.pl with the differential Expression Calculation program DESeq2. The significance cutoffs were log2fold>1, FDR<0.05 for up-regulated genes and log2fold<-1, FDR<0.05 for down-regulated genes.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Retina

extract_protocol:
Fresh bulk mouse retina tissue were collected and homogenized thoroughly in TRIzol Reagent (15596026, Invitrogen) followed by RNA isolation.. 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 poly-adenylated (poly-A) transcripts from the isolated total RNA sample were enriched and performed strand specific mRNA-Seq TruSeq libraries preparation for sequencing using standard Illumina protocols

value: Retina

tag: strain

value: 4 month


title: FFPE prostate_cancer_primary_19

value: Caucasian


title: Lymph Treg - Sham - CD44low - 5


title: FFPE prostate_cancer_primary_21


title: Lymph Treg - Sham - CD44low - 2


title: FFPE prostate_cancer_primary_20


title: FFPE prostate_cancer_primary_22

value: Placebo


title: CB1362A

description:
RNA sequencing
CB1362 AAVS1 in HSC Expansion media


title: Lymph Treg - Sham - CD44low - 1


title: Retina WT rep3

value: wild type


title: Retina WT rep2


title: Retina Elovl2C234W rep3


title: Lymph Treg - Sham - CD44high - 5

value: Lymph node CD4+CD44highFoxP3-GFP+

value: CD44 high


title: FFPE prostate_cancer_primary_18


title: CB1357T

description:
RNA sequencing
CB1357 TET2 in HSC Expansion media


title: FFPE prostate_cancer_primary_17


title: FFPE prostate_cancer_primary_15


title: Lymph Treg - Sham - CD44high - 4


title: CB1357A

description:
RNA sequencing
CB1357 AAVS1 in HSC Expansion media


title: CB1362T

description:
RNA sequencing
CB1362 TET2 in HSC Expansion media


title: Lymph Treg - Sham - CD44high - 3


title: CD4+CD25+ Tregs, KO3

city: Xi'an

first: baojun

last: zhang

state: --- Select One ---

address: No.76, West Yanta Rd

institute: xi'an jiaotong university

data_processing:
Illumina NovaSeq 6000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina NovaSeq 6000 sequencer (Illumina NovaSeq 6000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Firstly, the bulk RNA-seq data were filtered by using SAOPnuke (version 1.5.6) with parameters “-l 15 -q 0.2 -n 0.05 -Q 2”. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10) by using HISAT2 with parameters “-k 1 -p 4 -q --no-unal --dta --un-conc-gz”. Then the expression levels of each gene were calculated by the transcripts per kilobase of exon model per million mapped reads (TPM) by using StringTie3 with parameters “-t -C -e -B -A -p 1”.
The final TPM matrix of all samples was used for subsequent analysis. A 1.5-fold variance in expression levels, a P value less than 0.05, and an adjusted P value less than 0.1 were used as cutoffs to define differentially expressed genes. The P value and adjusted P value were calculated using R software (DESeq2)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen, Tregs

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD4+CD25+ Tregs were sorted from the spleens of ERCre+Zfp335f/f mice and wild-type littermates

value: Spleen

value: Tregs

value: Zfp335 deficient


title: HaCat_50mJ_3

city: Changsha

last: Min

state: Hunan

address: Nor.139 of Furong street

department: Second Xiangya Hospital

institute: Central South University

data_processing:
Illumina Novaseq was used for basecalling
The raw data were firstly processed through in-house perl scripts
The RNA-seq data were then mapped to the human reference genome hg38 with Hisat2 v2.0.5
The HERVs were obtained from RepeatMasker for expression analyses by stringtie
The differential analysis was performed using DESeq
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HaCat cells

growth_protocol: HaCat cells were seeded in 60 mm culture dishes at a density of 2×106 cells/well for overnight.

extract_protocol:
RNA was harvested using Trizol reagent.RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Cat#FC-122-1001) was used to 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were irradiated with UVB light source and cultured for 24 h

tag: cell line

value: HaCat


title: Lymph Treg - Sham - CD44high - 2

value: Uninjured


title: Retina Elovl2C234W rep1

tag: age


title: CD4+CD25+ Tregs, KO2


title: HaCat_50mJ_2


title: FFPE prostate_cancer_primary_16

tag: ecog3805 id


title: CD4+CD25+ Tregs, KO1

tag: genotype


title: HaCat_50mJ_1


title: FFPE prostate_cancer_primary_12

value: Treatment


title: Retina WT rep1


title: HaCat_control_3


title: FFPE prostate_cancer_primary_14


title: HaCat_control_2


title: CD4+CD25+ Tregs, WT2

tag: cell type

value: WT


title: HaCat_control_1


title: FFPE prostate_cancer_primary_11


title: CD4+CD25+ Tregs, WT1


title: FFPE prostate_cancer_primary_10


title: CD45(-) cells from pancreatic cancer, run 5 [GEX_45_MM]

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
raw base call files were demultiplexed with cellranger (v 3.1.0) pipeline
reads were aligned to the GRCh38-3.0.0 genome assembly using cellranger (v. 3.1.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix output from cellranger (v 3.1.0)

source_name: CD45(-) cells from pancreatic cancer

growth_protocol: Non-immune cells were sorted from single-cell suspensions obtained from pancreatic cancer tumor tissues by ARIA sorter

extract_protocol:
RNA was extracted from cells using 10x chromium single cell 5' V1.1 (Next GEM)
Chromium Next GEM Single Cell 5’ library v1.1 (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions
Single index kit T set A from 10x chromium single cell 5' V1.1 (Next GEM)

treatment_protocol: Untreated

value: pancreas

value: CD45(-) cells

tag: tissue type

value: pancreatic cancer tumor tissue


title: FFPE prostate_cancer_primary_13

growth_protocol: Not Applicable


title: CD45(-) cells from pancreatic cancer, run 4 [5_GEX_9]


title: CD4+CD25+ Tregs, WT3