title: ZBO1910

first: David

last: Olmeda

state: Madrid

address: Melchor Fernandez Almagro 3

institute: CNIO

data_processing:
RNA-seq processing:
Eightyfive-base-pair single-end sequenced reads followed adapter and polyA tail removal as indicated by Lexogen. The resulting reads were analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.0. Reads were aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing 3 mismatches and 20 multihits. The Gencode vM20 gene annotation for GRCm38 was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, filtering out those genes where the normalized count value was lower than 2 in more than 50% of the samples.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Normalised counts obtained with DESeq2

growth_protocol: B16R2L were grown in DMEN 10% FBS media according to manufactured instructions.

extract_protocol:
Total RNA was purified using RNeasy Mini kit (Qiagen) and digested with DNase (Qiagen).
500ng of Total RNA samples were used. Sample RNA Integrity numbers were 8.6 on average (range 5.8-9.2) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation: the read1, the only read in single read format, has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}.  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols.

treatment_protocol: Mice bearing xenograft tumors of the indicated cell lines were treated with anti-PD1 antibody (clone RMP1-14, 10 mg/Kg) or the corresponding IgG2a control.

value: Melanoma tumor


title: ZBO1909

status: Public on Oct 18 2020

type: SRA

city: Madrid

department: Molecular Oncology

country: Spain

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: treatment


title: ZBO1912


title: ZBO1916


title: ZBO1907


title: 4RFPIFNb_S4_R1_001

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

description:
Ribosomal RPF
Riboseq_set2_NormalizedReadCount.txt

data_processing:
Library strategy: Ribo-seq
RNA-seq: Data, as FASTQ file, were aligned to human hg19 genome using TopHat. HTSEQ was used to count reads at exons of genes. Normalization of read counts was done using DESEQ.
Ribo-seq: Preprocessing of fastq files consisted of adapter removal using cutadapt with the parameters (--quality-base=33  -O 7 -e 0.15 -m 20 -q 5) and removal of rRNA and tRNA contaminants by means of alignment against a reference using bowtie2with parameters (--seed 42 -p1 –local). The actual alignment of pre-processed fastq files was done with tophat2  and bowtie2  against GRCh37/hg19  using parameters ( --seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25). In a subsequent step the primary aligned reads filtered for a minimum mapping quality of 10.  HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt file containing normalized read counts (DESEQ) for all comparisons

molecule: total RNA

organism: Homo sapiens

source_name: 12T cells

growth_protocol: 12T, 108T, MD55A3 Cell lines were derived from pathology-confirmed metastatic melanoma tumor resections. Cells were authenticated by Finger printing with STR profiling. 12T, 108T, MD55A3, 888-Mel and D10 cells were cultured in RPMI 1640 medium supplemented with heat-inactivated 10% fetal bovine serum 25 mM HEPES and 100 U/mL penicillin/streptomycin.

extract_protocol:
For the generation of total RNA libraries, total RNA was extracted using TRI Reagent (SIGMA), and mRNA was purified using Dynabeads mRNA DIRECT Purification Kit (Invitrogen), according to the manufactures’ protocol. For ribosome profiling in melanoma cell lines, cells were treated with Cycloheximide for 1 min (100ug/ml), lysed in lysis buffer (20mM Tris 7.5, 150mM NaCl, 15mM MgCl2, 1mM dithiothreitol) supplemented with 0.5% triton, 30 U/ml Turbo DNase (Ambion) and 100μg/ml cycloheximide. Cell lysates were loaded on sucrose cushion, followed by ultracentrifugation, and RNA was extracted from pelletsd using TRI reagent following manufacture protocol.
The construction of ribosome protected fragments (RPF) libraries were done as previously described in Ingolia NT et al, doi:10.1038/nprot.2012.086 (2012). Total RNA libraries were constructed using SENSE Total RNA-Seq Library Prep Kit for Illunima (LEXOGEN).

treatment_protocol: cell where cultured with Tryptophan-free RPMI 1640 media (custom purchased from Biological Industries)/ Tyrosine-free medium (custom purchased from Cell Culture Technologies) for 48h, IFNγ (PeproTech) was used at 250 U/mL for the indicated durations of time. IDO inhibitor, 1-Methyl-L-Tryptophan (SIGMA) was dissolved in 0.1N NaOH at a 20mM concentration, adjusted to PH=7.5, filter sterilized and used at a final concentration of 300µM for 48h.

tag: cell type

value: Melanoma  cancer cells

value: IFNg


title: ZBO1908


title: 3RFPIFNa_S3_R1_001


title: dHet-proB-Rep2 (array)

status: Public on Oct 19 2020

type: RNA

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Gene expression in dHet proB cells
dHet-proB-R2

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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ebf1+/− Pax5+/- dHet fetal liver proB cells,Replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit (One-Color) and RNA Spike-In Kit, according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: dHet leukemic cells were derived from the lymph node of Ebf1+/-Pax5+/- leukemic mice. dHet proB cells were derived by culturing the single-cell suspensions of freshly isolated c-Kit positive fetal liver cells were plated on OP9 feeder cells in OptiMEM medium, supplemented with 4% FCS, 1% PSG, 50 μM β-mercaptoethanol, 5 ng/ml interleukin 7 (IL-7), 10 ng/ml Flt3 ligand (Flt3L) and 10 ng/ml stem cell factor (SCF). wt proB (FrBC) cells were sorted from the control mice.

extract_protocol: The total RNA was prepared with the RNeasy Mini Kit following the manufacturer's recommendations.

value: Ebf1+/− Pax5+/- Rag2-/- proB fetal liver

value: dHet proB cells

tag: genotype


title: ZBO1904


title: 2RFPmIFNb_S2_R1_001

value: Control


title: MD55A_plus

description:
Ribosomal RPF
Riboseq_set1_NormalizedReadCount.txt

source_name: MD55A3 cells


title: 1RFPmIFNa_S1_R1_001


title: ZBO1901


title: MD55A_minus


title: ZBO1902


title: Mixed_exocrine_3C: Mixed exocrine fraction donor C

type: genomic

city: Heidelberg

first: Elisa

last: Espinet

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description: Submitter declares that the raw data will be deposited in the European Genome-phenome Archive (EGA) due to patient privacy concerns.

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

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol

data_processing: The data were normalised for red and green channel seperately using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Normal pancreas

label_protocol: Standard Illumina Protocol

growth_protocol: Mixed exocrine fractions were culture in vitro for 4 days as in Baldan et al. 2019. Cells were stained and separated. Dedifferentiated acinar cells were defined as CA19.9-. Ductal cells were defined as CA19.9+.

extract_protocol: DNeasy Blood & Tissue Kit (Qiagen)

value: Normal pancreas


title: Ductal_1A: Sorted Ductal donor A

growth_protocol: Mixed exocrine fractions from normal pancreatic specimens were stained with HPx1 and CD133 as in Arda et al. 2016. Acinar cells were defined as HPx1+/CD133-. Ductal cells were defined as HPx1-/CD133+.

extract_protocol: Allprep DNA/RNA/Protein Mini Kit (Qiagen)


title: ZBO1899


title: Mixed_exocrine_3E: Mixed exocrine fraction donor E


title: Ductal_2D: Sorted Ductal donor D


title: Acinar_1A: Sorted Acinar donor A


title: Dediff_Acinar_2D: Sorted dedifferentiated Acinar donor D


title: 8RFPIFNbMD55A_S9_R1_001


title: Ductal_2C: Sorted Ductal donor C


title: ZBO1900


title: Ductal_1B: Sorted Ductal donor B


title: Mixed_exocrine_3D: Mixed exocrine fraction donor D


title: PDAC17-PDX: Primary PDX from PDAC17

source_name: Primary orthotopic patient derived xenograft

growth_protocol: Patient samples grown as xenografts (PDX). Xenografts were established from surgically removed tumor specimens by transplanting pieces of 1mm3 size onto the pancreas of immune deficient mice (NSG mice, Jax laboratories). Tumors were grown to a size of >= 1cm3, typically 2-5 months. Patients with resectable pancreatic ductal adenocarcinoma were recruited at the department of surgery at the university hospital Heidelberg, Germany. To harvest the tumors, mice were sacrificed by cervical dislocation, the tumors were removed and macroscopically dissected to remove the remains of the normal pancreas. The tumor was cut in half, rapidly frozen in liquid nitrogen and stored at -80°C until DNA preparation.

value: Primary PDX Tumor


title: Dediff_Acinar_2C: Sorted dedifferentiated Acinar donor C


title: PDAC13-PDX: Primary PDX from PDAC13


title: PDAC7-PDX: Primary PDX from PDAC7

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to "Standard Illumina Scanning Protocol"

data_processing: The data were normalised for red and green channel seperately using quantile normalisation with R using function normalize.quantiles from Bioconductor package "preprocessCore"


title: Dediff_Acinar_2E: Sorted dedifferentiated Acinar donor E


title: ZBO1893


title: 7RFPIFNaMD55A_R1


title: PDAC18-PDX: Primary PDX from PDAC18


title: ZBO1890


title: ZBO1896


title: 6RFPmIFNbMD55A_S6_R1_001


title: 5RFPmIFNaMD55A_S5_R1_001


title: PDAC11-PDX: Primary PDX from PDAC11


title: ZBO1889


title: Ductal_2E: Sorted Ductal donor E


title: 108T_plus

source_name: 108T cells


title: ZBO1888


title: 108T_minus


title: PDAC14-PDX: Primary PDX from PDAC14


title: 4RFPIFNb108T_S4_R1_001


title: PDAC10-PDX: Primary PDX from PDAC10


title: PDAC15-PDX: Primary PDX from PDAC15


title: iPSC derived human liver organoids

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Sequenced reads were processed using the Cell Ranger gene expression pipelines mkfastq and count, starting with demultiplexing and conversion of barcode and read data to fastq files.
Raw reads were aligned to the Hg19 genome and filtered, creating gene-barcode matrices.
Cell and gene filtering, data integration, scaling data, clustering and visualization were performed in Seurat v3 toolkit (https://github.com/satijalab/seurat). Cells which have unique feature counts less than 1500 or mitochondrial counts more than 50% were removed. The data was normalized using default global-scaling method.
We integrated normalized liver organoid scRNA-seq data and primary human liver scRNA-seq data available in GSE115469 [Ref] and identified anchors as input into downstream analysis. Integrated dataset was scaled using a linear transformation. Then we applied a graph-based clustering to scaled dataset.
Visualization were performed by tSNE with determined cluster. The cell type of each cluster was assigned manually using known liver cell transcripts.
Genome_build: GRCh37/hg19

source_name: liver organoids

growth_protocol: hiPSCs were detached by Accutase (Thermo Fisher Scientific Inc., MA, USA) and were seeded on Laminin coated tissue culture plate with 100,000 cells/cm2. Medium was changed to RPMI 1640 medium (Life Technologies) containing 100 ng/mL Activin A (R&D Systems) and 50 ng/mL bone morphogenetic protein 4 (BMP4; R&D Systems) at day 1, 100 ng/mL Activin A and 0.2% fetal calf serum (FCS; Thermo Fisher Scientific Inc.) at day 2, and 100 ng/mL Activin A and 2% FCS at day 3. On Day4-6, cells were cultured in Advanced DMEM/F12 (Thermo Fisher Scientific Inc.) with B27 (Life Technologies) and N2 (Gibco, CA, USA) containing 500 ng/ml fibroblast growth factor (FGF4; R&D Systems) and 3 µM CHIR99021 (Stemgent, MA, USA). Cells were maintained at 37 °C in 5% CO2 with 95% air and the medium was replaced every day. The foregut cells were detached by Accutase and then frozen in Cell Banker 1(Nippon Zenyaku Kogyo Co., Ltd., Japan). The frozen foregut cells were thawed quickly and then centrifuged at 1200 rpm for 3 minutes. Cell was resuspended in Matrigel (Corning, In., NY, USA). A total of 100,000 cells were embedded in 50µl Matrigel drop on the dishes in organoid formation media 4days. After organoid formation, the media was switched to liver specification media 4days. After the liver specification step, organoids were harvested from Matrigel by scratching and pipetting. Then organoids were re-embedded in Matrigel on the Ultra-low attached plate (Corning) in liver maturation media 10 days. Cultures for HLO induction were maintained at 37 °C in 5% CO2 with 95% air and the medium was added every 2 days.

extract_protocol:
Liver organoids from five different donor-derived organoid pools were dissociated to single cells by the treatment of Trypsin-EDTA (0.05%), phenol red (Gibco) for 10 min and washed by 1xPBS at Day 30. 17,500 cells each were loaded to 96 well plate including beads loaded with adapters containing one of 750,000 different barcodes for the single cell RNA-seq library preps. 5,119 cells were recovered for liver organoids.
Single cells isolated from organoids were lysed in droplets using the 10X Chromium instrument.  Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev A
Single cell RNA sequencing

value: iPSC derived human liver organoids

tag: time


title: PDAC9-PDX: Primary PDX from PDAC9


title: 3RFPIFNa108T_S3_R1_001


title: Mut_G2M_ATAC-seq

city: Hong Kong

first: Danny

last: Leung

address: Clear Water Bay

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science & Technology

description: Yeast strain with the endogenous Orc4 expression under the regulation of the GALS promoter was generated in the W303-1a background using PCR-based approach. Plasmids for ectopic expression of Orc4-IHΔ and Orc4 under their native promoters were integrated into the corresponding GALS-ORC4 yeast strains. Tandem copies of Myc and FLAG tags were fused to the C terminus of Orc6 and Mcm7 in the relevant GALS-ORC4 strains for genomic analysis.

library_source: genomic

data_processing:
Raw sequencing reads were mapped against yeast reference genome sacCer2 (UCSC) using Bowtie2 (version 2.3.4.1) (parameters ” -t -q -p 24 -N 1 -L 25 -X 2000 --no-discordant --no-mixed --un-conc”). PCR duplicates were marked and removed using Picard tools MarkDuplicates (version 2.9.0-1-gf5b9f50-SNAPSHOT). Reads mapped to chrM were removed
For ATAC-seq peak calling, MACS2 (version 2.1.1.20160309) was used wtiht the following parameters “-g 12100000 --keep-dup all -B  --SPMR --nomodel --shift -75 --extsize 150 -p 0.01”.
.narrowPeak file contains peaks call from MACS2.
Genome_build: sacCer2

organism: Saccharomyces cerevisiae

source_name: budding yeast cells

growth_protocol: WT and mutant yeast strains were maintained in YPG medium. Shifting to YPD medium was performed before all ChIP-seq, BrdU-IP-seq, MNase-seq and ATAC-seq experiments to deplete the endogenous expression of Orc4. Strains were grown in YPD for at least 18 hours at 30ºC until OD600 of ~0.01 starter culture reached ~2. Strains were cultured in YPD medium throughout the experiment.

extract_protocol: WT and mutant yeast cell pellets were incubated on-ice for 3 min with 50 ul cold ATAC-RSB [10mM Tris HCl (pH7.4), 10mM NaCl, 3mM MgCl2, 1X ROCHE Complete Protease Inhibitor Cocktail, 0.1% IGEPAL CA-630, 0.1% Tween-20, 0.01% Digitonin]. Subsequently, 1mL of cold ATAC-RSB with 0.1% Tween-20 [10mM Tris HCl (pH7.4), 10mM NaCl, 3mM MgCl2, 1X ROCHE Complete Protease Inhibitor Cocktail, 0.1% Tween-20] was added to the mixture. Nuclei were recovered by centrifugation and resuspended in transposase mix for tagementation [1x TTBL and 2.5uL TTE Mix V50 (Vazyme TD501 TruePrep DNA Library Prep Kit V2 for Illumina®), 0.01% digitonin, 0.1% Tween-20, PBS]. The mixture was incubated at 370C for 15 minutes in a Thermomixer(1000rpm). DNA was purified using the Qiagen MinElute PCR Purification Kit. ATAC-seq libraries were amplified with the TruePrep Index Kit V2 for Illumina (Vazyme ) and KAPA HiFi HotStart ReadyMix (Roche). Purified libraries were size selected with AMPure XP beads for 150bp to 800bp fragments, according to manufacturer’s protocol. Amplified libraries were analyzed on fragment analyzer and subsequently quantified and pooled for sequencing.

treatment_protocol: Cells were arrested at G1 with alpha factor at a concentration of 10 µg/ml for ~3 hours with replenishment of alpha-factor at every 60 mins. Cells were arrested at G2/M with 20 µg/ml benomyl for ~3 hours. Cells were arrested in early S using hydroxyurea  at 200 mM for ~60 mins.

tag: cell stage

value: G2/M arrest

tag: strain

value: MATa ade2-1 ura3-1 his3-11, 15  trp1-1 leu2-3,112  can1-100  GALS-ORC4-kanMX4 ura3-1::orc4-IH_delta-URA3 ORC6-MYC-hphNT1


title: 1RFPmIFNa108T_S1_R1_001


title: 2RFPmIFNb108T_S2_R1_001


title: Mut_G1_MNase-seq

data_processing:
Raw sequencing reads were mapped against yeast reference genome sacCer2 (UCSC) using Bowtie2 (version 2.3.4.1) (parameters ” -t -q -p 24 -N 1 -L 25 -X 2000 --no-discordant --no-mixed --un-conc”). PCR duplicates were marked and removed using Picard tools MarkDuplicates (version 2.9.0-1-gf5b9f50-SNAPSHOT). Reads mapped to chrM were removed
fragments between 141bp and 190bp were extracted from the mapped reads, the middle 60 base pair of each fragment was assigned a value of 1. For each position, the sum of values is normalized by dividing by the genomic average. Genomic average was calculated as the total number of reads with fragment sizes between 141bp and 190bp, multiplied by 60 and divided by the yeast reference genome size
.bw file represent nucleosome position index.
Genome_build: sacCer2

extract_protocol:
Mononucleosomes were prepared as previously described (Belsky et al, 2015) with the following modifications. Spheroplasting of yeast cells was performed with zymolase at 25ºC for 35 minutes. Conditions for MNase digestion was first optimized with appropriate amount of the enzyme (NEB). Different dilutions of 15 units/μl MNase (NEB) were prepared to determine the best digestion conditions: 1.5-ml tubes contained 0 μl, 1 μl, 2 μl (1:4 dilution in water), 1 μl (1:4 dilution in water), 2 μl (1:16 dilution in water), and 1 μl (1:16 dilution in water) of MNase, to which 400 μl of the resuspended cells was added.
Sequencing libraries for ChIP-seq, BrdU-IP-seq and MNase-seq were prepared using Kapa Hyper Prep Kit according to manufacturer’s protocol.

tag: mnase

value: MNase (NEB, M0247S)

value: G1 arrest


title: Acinar_1B: Sorted Acinar donor B


title: riboseq_mIFN_merged


title: Mut_BrdU-IP-seq

data_processing:
Raw sequencing reads were mapped against yeast reference genome sacCer2 (UCSC) using Bowtie (version 1.2.2) (parameters “--phred33-quals -v 3 -m 1 -p 24 --best --strata”). PCR duplicates were marked and removed using Picard tools MarkDuplicates (version 2.9.0-1-gf5b9f50-SNAPSHOT). Only uniquely mapped reads were kept. Unless specifically stated, raw sequencing reads from different replicates (If any) of the same sample were merged and mapped as described above. Mapped reads were visualized using samtools (version 1.3.1) and bedtools (version 2.27.1).
RPKM for every merged sample is calculated per 100bp non-overlapping window across the genome
.bw file score represent RPKM values calculated.
Genome_build: sacCer2

extract_protocol:
For BrdU incorporation, WT and mutant (orc4-IHΔ) yeast strains bearing BrdU-Inc cassette was generated as previously described (Viggiani et al, 2006). Early S phase arrested cells with BrdU genomic DNA labelling, BrdU-labelled genomic DNA extraction, fragmentation, and immunoprecipitation were performed as described. Validation of BrdU-IP was carried out by qPCR targeting known origins using WT DNA.
Sequencing libraries for ChIP-seq, BrdU-IP-seq and MNase-seq were prepared using Kapa Hyper Prep Kit according to manufacturer’s protocol.

tag: antibody

value: anti-BrdU antibody (Invitrogen)

value: Early S phase arrested


title: PDAC6-PDX: Primary PDX from PDAC6


title: SARS-CoV-2 S-RBD lib sorted for increased binding specificity towards the engineered sACE2.v2.4 (Independent Rep 2)

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

country: USA

institute: University of Illinois

description:
v24_Hi2_ATTCCT_L001
sACE2.v2.4-specific Replicate 2
SARS-CoV-2 S-RBD library sorted for increased binding specificity towards the engineered decoy receptor sACE2.v2.4 (Independent Replicate 2)

data_processing:
Data was analyzed using python scripts in the Enrich package: http://depts.washington.edu/sfields/software/enrich/
Fuser command (Fragment A): python3 Paired_read_fuser.py --path directory_A/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq TGCCCATTTGGCGAGGTGTTCAACGCAACCCGCTTCGCCAGCGTGTACGCCTGGAATAGGAAGCGGATCAGCAACTGCGTGGCCGACTATAGCGTGCTGTACAACTCCGCCTCTTTCAGCACCTTTAAGTGCTATGGCGTGTCCCCCACAAAGCTGAATGACCTGTGCTTTACCAACGTCTACGCC --read1_overlap_start 35 --read1_overlap_end 221 --read2_overlap_start 44 --read2_overlap_end 230 --mode B
Fuser command (Fragment B): python3 Paired_read_fuser.py --path directory_B/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq GATTCTTTCGTGATCAGGGGCGACGAGGTGCGCCAGATCGCCCCCGGCCAGACAGGCAAGATCGCAGACTACAATTATAAGCTGCCAGACGATTTCACCGGCTGCGTGATCGCCTGGAACAGCAACAATCTGGATTCCAAAGTGGGCGGCAACTACAATTATCTGTACCGGCTGTTTAGAAAG --read1_overlap_start 22 --read1_overlap_end 205 --read2_overlap_start 48 --read2_overlap_end 231 --mode B
Fuser command (Fragment C): python3 Paired_read_fuser.py --path directory_C/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq AGCAATCTGAAGCCCTTCGAGAGGGACATCTCTACAGAAATCTACCAGGCCGGCAGCACCCCTTGCAATGGCGTGGAGGGCTTTAACTGTTATTTCCCACTCCAGTCCTACGGCTTCCAGCCCACAAACGGCGTGGGCTATCAGCCTTACCGCGTGGTGGTGCTGAGCTTTGAGCTG --read1_overlap_start 19 --read1_overlap_end 196 --read2_overlap_start 24 --read2_overlap_end 201 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path directory_A/ --infile sample_R1.fast_B_qc1 --referenceDNA TGCCCATTTGGCGAGGTGTTCAACGCAACCCGCTTCGCCAGCGTGTACGCCTGGAATAGGAAGCGGATCAGCAACTGCGTGGCCGACTATAGCGTGCTGTACAACTCCGCCTCTTTCAGCACCTTTAAGTGCTATGGCGTGTCCCCCACAAAGCTGAATGACCTGTGCTTTACCAACGTCTACGCC --referenceAA CPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYA --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment B): python3 Fused_read_aligner.py --path directory_B/ --infile sample_R1.fast_B_qc1 --referenceDNA GATTCTTTCGTGATCAGGGGCGACGAGGTGCGCCAGATCGCCCCCGGCCAGACAGGCAAGATCGCAGACTACAATTATAAGCTGCCAGACGATTTCACCGGCTGCGTGATCGCCTGGAACAGCAACAATCTGGATTCCAAAGTGGGCGGCAACTACAATTATCTGTACCGGCTGTTTAGAAAG --referenceAA DSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRK --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment C): python3 Fused_read_aligner.py --path directory_C/ --infile sample_R1.fast_B_qc1 --referenceDNA AGCAATCTGAAGCCCTTCGAGAGGGACATCTCTACAGAAATCTACCAGGCCGGCAGCACCCCTTGCAATGGCGTGGAGGGCTTTAACTGTTATTTCCCACTCCAGTCCTACGGCTTCCAGCCCACAAACGGCGTGGGCTATCAGCCTTACCGCGTGGTGGTGCTGAGCTTTGAGCTG --referenceAA SNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFEL --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
MapCounts command: python mapCounts.py --path directory/ --infile sample_R1.fast_B_qc1_PRO_qc2
MapRatios command Example: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts command: python mapParts.py --path directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script:  python mapUnlink.py --path directory/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size number_of_residues_in_fragment
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequencies for each mutation in the naive plasmid library.

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Synthetic coding sequences

extract_protocol:
Total RNA was extracted from FACS sorted cells using a GeneJet kit (Thermo Scientific), and cDNA was synthesized using high fidelity Accuscript (Agilent) primed from a gene-specific primer (EBV reverse, annealing to the 3’UTR). Total RNA was extracted from FACS sorted cells using a GeneJet kit (Thermo Scientific), and cDNA was synthesized using high fidelity Accuscript (Agilent) primed from a gene-specific primer (EBV reverse, annealing to the 3’UTR). The S cDNA was PCR amplified as 3 separate fragments that together fully cover the RBD.  The PCR fragments were amplified for Illumina sequencing in two rounds.  In the first round, primer overhangs added sequences for annealing to the Illumina sequencing primers. In the second round, primer overhangs added unique barcodes and Illumina adaptors.  To determine the frequencies of mutations in the naive library, the library plasmid DNA was also used as a template for PCR amplification and Illumina sequencing.
The S cDNA was PCR amplified as 3 separate fragments that together fully cover the RBD.  The PCR fragments were amplified for Illumina sequencing in two rounds.  In the first round, primer overhangs added sequences for annealing to the Illumina sequencing primers. In the second round, primer overhangs added unique barcodes and Illumina adaptors.  To determine the frequencies of mutations in the naive library, the library plasmid DNA was also used as a template for PCR amplification and Illumina sequencing.

treatment_protocol: Expi293F cells were transfected using expifectamine (ThermoFisher) with a pCEP4 episomal plasmid-based library encoding variants of myc-tagged S diluted with a 1500-fold excess of carrier DNA; these transfection conditions ensure that most cells express no more than a single S sequence variant, thereby linking genotype to phenotype.  Cells were harvested 24 h post-transfection. For the first FACS experiments, cells were incubated with 2.5 nM dimeric sACE2(WT)-8h, washed and immuno-stained with anti-myc-Alexa 647 for detection of surface expressed S and anti-his-FITC for detection of bound sACE2.  In the second set of FACS experiments, cells were co-incubated with competing 25 nM sACE2(WT)-IgG1 and 20 nM sACE2.v2.4-8h, washed and bound proteins detected by staining with anti-IgG-APC and anti-his-FITC.  For all experiments, cells were washed prior to FACS.  Gates were drawn for the main population of viable cells using forward and side scatter properties and exclusion of the fluorescent viability dye DAPI.  Gates were then drawn to collect cell populations expressing S variants with high or low sACE2(WT) binding, or in the second set of experiments, to collect cell populations expressing S variants with shifted specificity towards sACE2(WT)-IgG1 or engineered sACE2.v2.4-8h.

tag: protein

value: S

tag: sort gate

value: Top 20% of cells for bound sACE2.v2.4 relative to bound sACE2(WT)


title: PDAC12-PDX: Primary PDX from PDAC12


title: PDAC16-PDX: Primary PDX from PDAC16


title: WT_G2M_ATAC-seq

value: MATa ade2-1 ura3-1 his3-11, 15  trp1-1 leu2-3,112  can1-100  GALS-ORC4-kanMX4 ura3-1::ORC4-URA3 ORC6-MYC-hphNT1


title: Mut_MCM_ChIP-seq

data_processing:
Raw sequencing reads were mapped against yeast reference genome sacCer2 (UCSC) using Bowtie (version 1.2.2) (parameters “--phred33-quals -v 3 -m 1 -p 24 --best --strata”). PCR duplicates were marked and removed using Picard tools MarkDuplicates (version 2.9.0-1-gf5b9f50-SNAPSHOT). Only uniquely mapped reads were kept. Unless specifically stated, raw sequencing reads from different replicates (If any) of the same sample were merged and mapped as described above. Mapped reads were visualized using samtools (version 1.3.1) and bedtools (version 2.27.1).
RPKM for every merged sample is calculated per 100bp non-overlapping window across the genome
For WT and mutant ORC ChIP-seq datasets, peaks were defined with each replicate using MACS2 (version 2.1.1.20160309) (parameters “--nomodel --extsize 147 -q 0.005 -g 12.07e6”). Only those peaks that were called in both replicates of a sample and did not overlap with tRNA genes (GtRNAdb) were kept for downstream analysis.
.bed file contains peaks call from MACS2. .bw file score represent RPKM values calculated.
Genome_build: sacCer2

extract_protocol:
For ORC and MCM ChIP, WT and MUT (orc4-IHΔ) yeast strains with Myc-tagged Orc6 and FLAG-tagged Mcm7 were arrested at G2/M and G1 phase respectively. Chromatin extracts were prepared and immunoprecipitated as previously described with minor modifications. About 2x109 cells were crosslinked by adding formaldehyde (Millipore) to a final concentration of 1% and incubated at room temperature for 25 minutes with gentle shaking. Cross-linking reaction was halted by adding glycine to a final concentration of 0.125 M and incubation for additional 10 mins at room temperature. Cells   were lyzed by re-suspension in lysis buffer and subjected to bead-beating using a Mini-Beadbeater (Biospec). Chromatin fraction was collected by centrifugation and were sonicated to yield an average DNA size of 300bp using ultrasonicator (Covaris). Sonicated chromatin fractions were clarified by centrifugation and ~400 ml of clarified fraction was subjected to immunoprecipitation with 60 ml of protein G-Dynabeads (Invitrogen) conjugated to anti-Myc antibody (Roche, 9E10) for Orc6-Myc ChIP or anti-FLAG antibody (Sigma, M2) for Mcm7-FLAG ChIP at 4ºC overnight. Immunoprecipitated DNA was then recovered as previously described43. Reverse crosslinked samples were digested with RNase A (Roche) for 1 hour followed by Proteinase K (Roche) for two hours at 37ºC. DNA was purified using MinElute PCR purification column according to Qiagen protocol. Validation of the ChIP was carried out by qPCR targeting positive control loci using WT DNA.
Sequencing libraries for ChIP-seq, BrdU-IP-seq and MNase-seq were prepared using Kapa Hyper Prep Kit according to manufacturer’s protocol.

value: anti-FLAG antibody (Sigma, M2)

value: MATa ade2-1 ura3-1 his3-11, 15  trp1-1 leu2-3,112  can1-100 GALS-ORC4-kanMX4 ura3-1::orc4-IH_delta-URA3 MCM7-FLAG-hphNT1


title: riboseq_4_IFN_R1_001

value: Melanoma  cancer cells

value: IFNg


title: Mut_ORC_ChIP-seq

value: anti-Myc antibody (Roche, 9E10)


title: riboseq_IFN_merged


title: SARS-CoV-2 S-RBD library sorted for increased binding specificity towards wild type sACE2 (Independent Rep 2)

description:
WT_Hi2_ACTGAT_L001
sACE2(WT)-specific Replicate 2

value: Top 20% of cells for bound sACE2(WT) relative to bound sACE2.v2.4


title: WT_G1_MNase-seq


title: SARS-CoV-2 S-RBD library sorted for low binding to human sACE2 (wild type)

description:
ACE2_Low_CAACTA_L001
ACE2-Low

value: Bottom 20% of cells for bound sACE2(WT) relative to surface S expression


title: SARS-CoV-2 S-RBD library sorted for increased binding specificity towards wild type sACE2 (Independent Rep 1)

description:
WT_Hi1_CTTGTA_L001
sACE2(WT)-specific Replicate 1


title: PDAC4-PDX-rep2: Primary PDX from PDAC4 rep2

value: Primary PDX Tumor


title: SARS-CoV-2 S-RBD lib sorted for increased binding specificity towards the engineered sACE2.v2.4 (Independent Rep 1)

description:
v24_Hi1_ATGAGC_L001
sACE2.v2.4-specific Replicate 1
SARS-CoV-2 S-RBD library sorted for increased binding specificity towards the engineered decoy receptor sACE2.v2.4 (Independent Replicate 1)


title: riboseq_2_mIFN_R1_001

value: Control


title: SARS-CoV-2 S-RBD library sorted for high binding to human sACE2 (wild type)

description:
ACE2_High_CAAAAG_L001
ACE2-High

value: Top 20% of cells for bound sACE2(WT) relative to surface S expression


title: riboseq_1_mIFN_R1_001


title: WT_BrdU-IP-seq


title: riboseq_3_IFN_R1_001


title: 50: subject10_MNP+HA_4hr

status: Public on Oct 17 2020

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Sequenced were aligned with Casava, trimed for quality and contaminatinf adapters with TrimGalore!.
Files were aligned with Hisat2 and counts table produced with FeatureCounts from Rsubread
Date were normalised using DESeq2
Genome_build: Hg38
Supplementary_files_format_and_content: Normalised counts table as csv

source_name: Renal Cortex

extract_protocol:
RNA was extracted using Pure-link mini kit (Thermo). Contaminating genomic DNA was removed with Turbo Dnase (Thermo)
Libraries were constructed using Illumina Truseq stranded RNA library prep.

value: Renal Cortex

tag: person

value: MNP+HA

tag: timepoint


title: PACO17: hPDAC primary cell line PACO17

source_name: PDAC primary cell line

growth_protocol: Cell lines were cultured in vitro in serum free medium containing growth factors EGF, bFGF and IGF-1. The cell lines were primary pancreatic adenocarcinoma (PACO) cells derived in our laboratory from patient-derived xenografts. Cells were cultured in Primaria plates under adherent conditions and 5%CO2 at 37°C.

extract_protocol: none provided by the submitter

value: PDAC primary cell line


title: WT_ORC_ChIP-seq

value: G2/M arrest


title: WT_MCM_ChIP-seq

value: G1 arrest

value: MATa ade2-1 ura3-1 his3-11, 15  trp1-1 leu2-3,112  can1-100 GALS-ORC4-kanMX4 ura3-1::ORC4-URA3 MCM7-FLAG-hphNT1


title: 49: subject10_MNP+HA_2hr


title: PACO20: hPDAC primary cell line PACO20


title: PDAC8-PDX: Primary PDX from PDAC8


title: PDAC5-PDX: Primary PDX from PDAC5


title: 47: subject10_MNP_4hr

value: MNP


title: PACO2: hPDAC primary cell line PACO2


title: 45: subject10_MNP_0hr


title: PACO28: hPDAC primary cell line PACO28


title: 46: subject10_MNP_2hr


title: 42: subject9_MNP+HA_0hr


title: PDAC4-PDX-rep1: Primary PDX from PDAC4 rep1


title: 38: subject8_MNP+HA_4hr


title: PACO18: hPDAC primary cell line PACO18


title: 43: subject9_MNP+HA_2hr


title: 41: subject9_MNP_4hr


title: 40: subject9_MNP_2hr


title: 39: subject9_MNP_0hr


title: 37: subject8_MNP+HA_2hr


title: 36: subject8_MNP+HA_0hr


title: PACO3: hPDAC primary cell line PACO3


title: 34: subject8_MNP_2hr


title: 33: subject8_MNP_0hr


title: 32: subject7_MNP+HA_4hr


title: 35: subject8_MNP_4hr


title: 31: subject7_MNP+HA_2hr


title: 30: subject7_MNP+HA_0hr


title: 29: subject7_MNP_4hr


title: 27: subject7_MNP_0hr


title: 28: subject7_MNP_2hr


title: Naïve library of S variants

description:
S_RBD_naive_GGCTAC_L001
S-RBD_naive

value: S

tag: molecule subtype

value: plasmid DNA


title: PDAC3-PDX: Primary PDX from PDAC3


title: 25: subject6_MNP+HA_2hr


title: 48: subject10_MNP+HA_0hr


title: 26: subject6_MNP+HA_4hr


title: 22: subject6_MNP_2hr


title: 24: subject6_MNP+HA_0hr


title: 21: subject6_MNP_0hr


title: 23: subject6_MNP_4hr


title: 20: subject5_CS_2hr

value: CS


title: 18: subject5_MNP_2hr


title: 19: subject5_CS_0hr


title: 14: subject4_MNP_2hr


title: 16: subject4_CS_2hr


title: 17: subject5_MNP_0hr


title: 6X: T50-Rep-2

city: Richmond

first: Todd

last: Kitten

state: VA

address: 521 N. 11th Street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth University

data_processing:
Individual libraries were pooled equimolarly, and the final pool was sequenced on an Illumina MiSeq, with 2 x 150 bp paired end reads.  Demultiplexing was performed on the Illumina MiSeq’s on-board computer and resulting demultiplexed files uploaded to Illumina BaseSpace for data delivery.
Reads were paired in Geneious Prime and trimmed using the BBDuk Trimmer plugin with recommended settings.
Paired reads were then aligned to the reference genome and expression levels calculated for each using Geneious Prime with default settings.
Expression levels were normalized and compared, Log2 ratios generated, and adjusted p values calculated using the DESeq2 plugin in Genious.
Genome_build: NC_009009.1
Supplementary_files_format_and_content: Tab-delimited txt file containing  Locus_tag, GeneID, Gene Name, Length, Direction, Raw read count, TPM, RPKM, FPKM

organism: Streptococcus sanguinis

source_name: bacterial cells

growth_protocol: A BIOSTAT® B bioreactor (Sartorius Stedim) with a 1.5-L capacity UniVessel® glass vessel was used for growth of 800-mL cultures at 37°C. Cultures were stirred at 250 rpm and pH was maintained by the automated addition of 2 N KOH (Fisher Chemical). A 40 mL overnight pre-culture of S. sanguinis strain JFP169 was grown in BHI media and centrifuged for 10 minutes at 3,740 x g in an Allegra X-142 centrifuge at 4°C (Beckman-Coulter). The supernatant was discarded and the cells were resuspended in BHI prior to inoculation. The air flow was increased stepwise, based on the OD of the fermentor culture. At the peak OD, air flow was increased to 0.50 lpm, input flow of fresh BHI was set to 17% (~700 mL h-1) and output flow of waste was set to 34%. Cells were allowed to acclimate to the new conditions for 1 h. The T-20 sample was aseptically removed for total RNA isolation.

extract_protocol:
For each RNA sample, 2 mL of fermentor culture was added to 4 mL RNAprotect Bacteria Reagent (Qiagen) and immediately vortexed for 10 sec. The sample was then incubated at room temperature for 5-90 min. The samples were then centrifuged for 10 min at 3,740 x g at 4°C. The supernatant was discarded and the samples stored at -80°C. RNA isolation and on-column DNase treatment were completed using the RNeasy Mini Kit and RNase-Free DNase Kit, respectively (Qiagen). RNA was eluted in 50 µL RNase-Free water (Qiagen). A second DNase treatment was then performed on the samples (Invitrogen). Total RNA was quantified and purity was assessed using a Nanodrop 2000 Spectrophotometer (ThermoScientific).
Total RNA quantity and integrity were determined using an Agilent Bioanalyzer RNA Pico assay.  All samples passed quality control assessment with RNA Integrity Numbers (RIN) above 8.  Two sequential rounds of ribosomal reduction were then performed on all samples using Illumina’s Ribo-Zero rRNA Removal Kit.  The resulting depleted RNA was assessed using an Agilent Bioanalyzer RNA Pico assay to confirm efficient rRNA removal.  Stranded RNA-seq library construction was then performed on the rRNA depleted RNA using the Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following manufacturer’s specifications for library construction and multiplexing.  Final Illumina libraries were assessed for quality using an Agilent Bioanalyzer DNA High Sensitivity Assay and qPCR quantification was performed using NEBNext Library Quant kit for Illumina (New England Biolabs).

treatment_protocol: Twenty minutes later, EDTA was added to the carboy and vessel (T0) at a final concentration of 100 µM. Samples were taken for each post-EDTA time point (T10, T25, T50) 10, 25 and 50 min after EDTA addition.

value: ssaACB deletion mutant


title: 6Z: T50-Rep-4


title: 13: subject4_MNP_0hr


title: 15: subject4_CS_0hr


title: 6Y: T50-Rep-3


title: 6W: T50-Rep-1


title: 12: subject3_CS_2hr


title: Normal_bulk_4F: Normal pancreas donor F

growth_protocol: Commercial (Origene #CD564011)

value: Normal pancreas


title: 5Z: T25-Rep-4


title: 5X: T25-Rep-2


title: 10: subject3_MNP_2hr


title: 4Z: T10-Rep-4


title: 11: subject3_CS_0hr


title: 44: subject9_MNP+HA_4hr


title: Normal_bulk_4H: Normal pancreas donor H

growth_protocol: Commercial (BioChain #A712202)


title: Normal_bulk_4G: Normal pancreas donor G

growth_protocol: Commercial (Origene #CD564404)


title: 5Y: T25-Rep-3


title: HPDE2: HPDE rep2

source_name: Human pancreatic ductal normal epithelial cells

growth_protocol: HPDE cells were obtained from American Type Culture Collection (ATCC) and cultured according to the supplier’s information


title: 9: subject3_MNP_0hr


title: 4W: T10-Rep-1


title: 5W: T25-Rep-1


title: 3Y: T-20-Rep-3


title: 3Z: T-20-Rep-4


title: 4X: T10-Rep-2


title: PDAC1-PDX: Primary PDX from PDAC1


title: PACO14: hPDAC primary cell line PACO14


title: HPDE1: HPDE rep1

value: Human pancreatic ductal normal epithelial cells


title: 8: subject2_CS_2hr


title: 5: subject2_MNP_0hr


title: 3X: T-20-Rep-2


title: 7: subject2_CS_0hr


title: 4Y: T10-Rep-3


title: BRx-68

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Trimmomatic was used to crop read lengths to 50 nucleotides and to remove the TruSeq3-PE-2 Illumina adapters.
The reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu.
Reads that did not align or aligned to multiple locations were discarded.
The number of remaining reads aligning to each gene in the human transcriptome was then determined using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: counts.csv is a matrix in which rows correspond to genes and columns correspond to samples. The gene symbol is in the first column and the sample title is in the first row. Each entry in the matrix is the number of reads that aligned uniquely to the gene of that row in the sample of that column.

growth_protocol: CTCs were cultured in 4% O2 in suspension conditions using ultra-low attachment plates (Corning) in media consisting of RPMI-1640 with GlutaMAX supplemented with EGF (20ng/mL), FGF (20ng/mL), 1X B27, and 1X antibiotic/antimycotic (Life Technologies), as previously described (PMIDs 25013076, 27556950, 32029688). CTCs were checked for mycoplasma (MycoAlert, Lonza), and were authenticated by RNA-seq and DNA-seq.

extract_protocol:
Amplified cDNA was generated using 10 ng RNA from each sample using the SMART-Seq HT Kit (Takara Bio) according to manufacturer protocol. Briefly, first‐strand synthesis was performed using oligo‐dT primers followed by template switching by the reverse transcriptase, second strand synthesis and 18 cycles of amplification. Amplified cDNA was purified with 1× bead cleanup with Agencourt AMPure XP beads (Beckman Coulter).
The Nextera XT DNA Library Preparation kit (Illumina) was used for library generation with 1 ng cDNA input for enzymatic tagmentation, followed by 12 cycles of amplification and addition of unique dual‐index barcodes. PCR product was purified with 1.8X bead cleanup. After qPCR-based quantification using the KAPA Library Quantification kit (Roche), individual libraries were pooled and subsequently sequenced on a NextSeq 500 system (Illumina) using a 150 cycle V2.5 high output kit with paired end-read mode.

value: circulating tumor cells (CTCs)

tag: growth rate

value: slow


title: 3W: T-20-Rep-1


title: 4: subject1_CS_2hr


title: 3: subject1_CS_0hr


title: wn2

city: Seongnam

first: So Young

last: Kim

address: Yatapro 59

country: South Korea

institute: CHA University

description: Gene expression data from hippocampus from noise group

hyb_protocol: One hundred and nine microliters of this mixture was injected into a GeneChip Rat Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) and placed in the Affymetrix GeneChip Hybridization Oven 640 at 45°C and 60 rpm for 16 hours overnight. Stain cocktails (stain cocktail 1 and stain cocktail 2 [GeneChip Hybridization, Wash, and Stain Kit]) cocktails (stain cocktail 1 and stain cocktail 2 [GeneChip Hybridization, Wash, and Stain Kit]) were added to amplify the signal intensities. The arrays were stained and washed in an Affymetrix GeneChip Fluidics Station 450 according to the FS450_0002 fluidics protocol.

scan_protocol: All arrays were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing:
The raw analysis was performed with Transcriptome Analysis ConsoleTM (TAC) software.
Differential expression (DE) between rat exposed to noise (experimental) and unexposed rat (control) was predicted at the gene-level (probesets summarized into transcript clusters/genes).

label: biotin

organism: Rattus norvegicus

source_name: hippocampus from noise group

label_protocol: 5.5 μg of ss-cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease I (APE I) and labeled by terminal deoxynucleotidyl transferase (TDT) using the proprietary Affymetrix DNA labeling reagent.

growth_protocol: In the noise group, rats were exposed to 2–20 kHz, 115 dB SPL white noise for 4 hours/day for 3 consecutive days. The control group was not exposed to noise.

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

treatment_protocol: Immediately after the 3 days of noise exposure, all the rats were sacrificed, and the hippocampi were harvested

value: SD

value: hippocampus


title: BRx-50

value: moderate


title: BRx-42--3-10

value: fast


title: 6: subject2_MNP_2hr

value: Renal Cortex


title: wn4


title: BRx-29-p


title: 1: subject1_MNP_0hr


title: ctl6

description: Gene expression data from hippocampus from control group

source_name: hippocampus from control group


title: ZnSO4 rep1 A13

city: Banyuls-sur-mer

first: Anne-M

middle: Marie

last: GENEVIERE

address: Avenue Pierre Fabre

department: BIOM

country: France

institute: CNRS

data_processing:
Filtered FASTQ file generated by CASAVA 2.17
adapters were removed with trim_galore version 0.4.0 using standard parameters
he reads were splice-aligned on the genome using STAR (Dobinetal.,2013)(version2.4.0iusingstandardparameters) MicpuN3v2 assembly
The expression was quantified using RSEM (version 1.3.0) using the MicpuN3v2_GeneCatalog_genes_20160404.gtf transcriptome model reference file
The expected count values were cut and merge with unix command lines to create the count file
Genome_build: MicpuN3v2
Supplementary_files_format_and_content: tab-delimited text files include expected_count values for each sample

organism: Micromonas commoda

source_name: culture

growth_protocol: Micromonas commoda (Noum17/RCC299) was grown in L1 medium (Bigelow Laboratory, NCMA, USA) at 20°C under a 12/12 light/dark cycle (100 µmole photon/m2s-1).

extract_protocol:
100 ml of culture were sampled per vial 48 h later and the M. commoda cells were harvested by centrifugation at 8,000 g for 20 min at 4°C.  The pellets were flash frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted using Maxwell 16 LEV simplyRNA purification kit (Promega) in the Maxwell instrument and RNA concentration and RNA integrity (RIN) was estimated using the Bioanalyzer RNA 6000 nano (RIN>9).
RNA libraries were prepared for sequencing by GeT-PlaGe Genotoul (INRA-France-https://get.genotoul.fr/en/) using standard Illumina protocols and via poly A selection

treatment_protocol: Flasks containing 140 ml of M. commoda cell cultures in early exponential phase were prepared and ENPs or the corresponding metal ions were added 24 h later. culture were exposed for 48h to Fe2O3 (3.0 10-5M, [Fe]=2,4mg/L) and ZnO ENPs (10-5M, [Zn]=0,8mg/L) or the equivalent metal concentration of corresponding ions Fe3+ (FeCl3, 6H2O) or Zn2+ (ZnSO4, 7H2O).

tag: time in culture


title: ZnSO4 rep2 A14


title: wn3

tag: tissue


title: ZnO ENP rep3 A12


title: BRx-82


title: F3 ZnO GW14

description: GW14-Sample 18

data_processing:
adapters were removed with trim_galore version 0.4.0 using standard parameters
the reads were assembled with Drap version 1.7 to produce the contigs file
the reads were aligned on the contigs using bwa mem version 0.7.12-r1039 with standard parameters and the bam files were sorted, compressed and indexed with samtools version 1.3.1 using standard parameters
the expression was quantified using samtools idxstats and merged in the expression file using unix command lines
Genome_build: de novo reference transcriptome. FASTA file with transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

organism: Paracentrotus lividus

source_name: embryo

extract_protocol:
Embryos (about 6000) were harvested 24h p.f., briefly centrifuged and the pellet was suspended in 200 µl Thioglycerol/homogeneization solution. RNA was extracted with Maxwell 16 LEV simply RNA kit (Promega) in Maxwell 16 instrument. Purified total RNA were collected in 50 µL RNase-free water and kept afterwards at -80°C. RNA integrity (RIN>9) was estimated with a Bioanalyzer.
RNA libraries were prepared for sequencing by Genewiz LLC (www.genewiz.com) using standard Illumina protocols and via poly A selection

treatment_protocol: Sea urchin fertilized eggs were exposed for 24h to Fe2O3 (5.0 10-5M, [Fe]=4mg/L) and ZnO ENPs (10-5M, [Zn]=0,8mg/L) or the equivalent metal concentration of corresponding ions Fe3+ (FeCl3, 6H2O) or Zn2+ (ZnSO4, 7H2O).

tag: time post fertilization

value: embryo


title: 2: subject1_MNP_2hr

tag: treatment


title: BRx-07

tag: cell type


title: BRx-142--4-1


title: F3 FeCl3 GW13

description: GW13-Sample 17


title: F3 ZnSO4 GW15

description: GW15-Sample 19


title: NS130-142-shHIF1A-3

value: CTC-derived cell line

tag: knock-down


title: F3 Fe2O3 GW12

description: GW12-Sample 16


title: F3 control GW11

description: GW11-Sample 15


title: ZnSO4 rep3 A15


title: NS130-82-shHIF1A-3


title: NS130-82-shNT

value: shNT


title: NS130-142-shNT


title: F1 ZnO GW19

description: GW19-Sample 7


title: F2 FeCl3 GW8

description: GW8-Sample 12


title: ZnO ENP rep2 A11


title: F1 ZnSO4 rep2 GW20

description: GW20-Sample 9


title: F2 ZnSO4 GW10

description: GW10-Sample 14


title: F2 ZnO GW9

description: GW9-Sample 13


title: F1 Fe2O3 rep2 GW16

description: GW16-Sample 4


title: F2 control GW6

description: GW6-Sample 10


title: F2 Fe2O3 GW7

description: GW7-Sample 11


title: F1 control rep2 GW18

description: GW18-Sample 2


title: FeCl3 rep1 A7


title: Fe2O3 ENP rep3 A6


title: F1 ZnSO4 rep1 GW5

description: GW5-Sample 8


title: FeCl3 rep2 A8


title: FeCl3 rep3 A9


title: F1 FeCl3 rep2 GW17

description: GW17-Sample 6


title: F1 control rep1 GW1

description: GW1-Sample 1


title: F1 Fe2O3 rep1 GW2

description: GW2-Sample 3


title: Fe2O3 ENP rep2 A5


title: 82-brain-1

data_processing:
Trimmomatic was used to crop read lengths to 50 nucleotides and to remove the TruSeq3-PE-2 Illumina adapters.
The reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu.
Reads that did not align or aligned to multiple locations were discarded.
The reads were also aligned in the same way to the mouse genome and transcriptome version mm10. Reads that aligned to the mouse transcriptome were removed from the collection of reads that aligned to the human transcriptome.
The number of remaining reads aligning to each gene in the human transcriptome was then determined using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: counts.csv is a matrix in which rows correspond to genes and columns correspond to samples. The gene symbol is in the first column and the sample title is in the first row. Each entry in the matrix is the number of reads that aligned uniquely to the gene of that row in the sample of that column.

growth_protocol: Mice were housed in a specific pathogen–free environment in the animal facility at the Massachusetts General Hospital Cancer Center, and all experiments conformed to ethical principles and guidelines approved by the Institutional Animal Care and Use Committee of the Massachusetts General Hospital (Protocol 2010N000006). After receiving isoflurane anesthesia and buprenorphine analgesia, 6-week-old female NSG mice (NOD. Cg-Prkscsdid Il2rgtm1Wjl/SzJ) from Jackson Laboratories were stereotactically injected with 5x105 cells per mouse in the right frontal lobe of the brain or orthotopically injected with 2.5x105 cells in the right or left fourth mammary fat pad. For brain injections, the cranial burrhole was created 2.5mm to the right of the bregma on the coronal suture, and a Hamilton syringe (Hamilton) was inserted to a depth of 2.5mm below the outer table of the calvarium using a stereotactic injection system as previously described (55). A 90-day release 0.72mg estrogen pellet (Innovative Research of America) was implanted subcutaneously behind the neck of each mouse. Postoperatively, mice received buprenorphine analgesia twice daily for three days. Thereafter, mice were monitored for signs of pain or neurological dysfunction at least daily and were treated with buprenorphine for pain or sacrificed in the setting of neurologic dysfunction.

value: CTC-derived tumor

tag: tumor location

value: brain


title: ctl2


title: BRx-82-f1-cell-line

growth_protocol: Mice were housed in a specific pathogen–free environment in the animal facility at the Massachusetts General Hospital Cancer Center, and all experiments conformed to ethical principles and guidelines approved by the Institutional Animal Care and Use Committee of the Massachusetts General Hospital (Protocol 2010N000006). After receiving isoflurane anesthesia and buprenorphine analgesia, 6-week-old female NSG mice (NOD. Cg-Prkscsdid Il2rgtm1Wjl/SzJ) from Jackson Laboratories were stereotactically injected with 5x105 cells per mouse in the right frontal lobe of the brain or orthotopically injected with 2.5x105 cells in the right or left fourth mammary fat pad. For brain injections, the cranial burrhole was created 2.5mm to the right of the bregma on the coronal suture, and a Hamilton syringe (Hamilton) was inserted to a depth of 2.5mm below the outer table of the calvarium using a stereotactic injection system as previously described (55). A 90-day release 0.72mg estrogen pellet (Innovative Research of America) was implanted subcutaneously behind the neck of each mouse. Postoperatively, mice received buprenorphine analgesia twice daily for three days. Thereafter, mice were monitored for signs of pain or neurological dysfunction at least daily and were treated with buprenorphine for pain or sacrificed in the setting of neurologic dysfunction. CTCs were cultured in 4% O2 in suspension conditions using ultra-low attachment plates (Corning) in media consisting of RPMI-1640 with GlutaMAX supplemented with EGF (20ng/mL), FGF (20ng/mL), 1X B27, and 1X antibiotic/antimycotic (Life Technologies), as previously described (PMIDs 25013076, 27556950, 32029688). CTCs were checked for mycoplasma (MycoAlert, Lonza), and were authenticated by RNA-seq and DNA-seq.

tag: passage


title: 82-brain-2


title: 82-breast-1

value: breast


title: BRx-82-cell-line

value: Parental


title: BRx-50-f1-cell-line


title: ZnO ENP rep1 A10


title: BRx-50-cell-line


title: ZT8_DOX_alpha rep1 [ZT8_Doxa_160528_6]

status: Public on Oct 16 2020

city: Geneva

first: Cedric

last: Howald

state: Geneva

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: Health2030 Genome Center

data_processing:
Demultiplexing was done using bcl2fastq
Paired-end reads were mapped to the Mouse genome (GRCm38) using the STAR mapper (v2.5.3a) and the GENCODE vM16 annotation to define splice sites
The gene-level quantification and normalization (RPKM values) were performed with an in-house script using GENCODE vM16 as reference. Only reads having a mapping quality score of 150 or above, in proper orientation and having not more than 5 mismatches in both ends together were kept for quantification.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files displaying gene level read count or RPKM values

growth_protocol: α- and β-cells were separated by FACS from freshly-isolated islets around-the-clock

extract_protocol:
Total RNA was prepared from FACS-sorted α- and β-cells collected from male proGcg-Venus/RIP-Cherry/PER2::Luc/Insulin-rtTA/TET-DTA control and DOX-treated mice every 4 h around the clock in duplicates, using RNeasy® Plus Micro Kit (Qiagen).
Sequencing libraries were prepared from 300 ng of polyA+ RNA using the TruSeq RNA sample prep kit v2 (Illumina). The quality of the libraries were assessed by Bioanalyzer and TapeStation. The sequencing was performed with a Illumina HiSeq2000 and a HiSeq4000 sequencers
TruSeq mRNA sample prep kit v2

treatment_protocol: Massive β-cells ablation was induced in ProGcg-Venus/RIP-Cherry/PER2::Luc/Insulin-rtTA/TET-DTA mice by administering 300 mg of doxycycline (DOX) in the drinking water supplemented with 2% sucrose. The control group received only water supplemented with 2 % sucrose.

tag: sample group

value: Pancreatic islets

tag: cell subtype

value: alpha


title: ZT8_CTR_alpha rep1 [ZT8_Ctla_160528_6]


title: ZT8_CTR_beta rep1 [ZT8_Ctlb_160528_6]

value: beta


title: ZT4_DOX_alpha rep1 [ZT4_Doxa_160528_6]


title: F1 FeCl3 rep1 GW3

description: GW3-Sample 5


title: ZT8_DOX_beta rep1 [ZT8_Doxb_160528_5]


title: control rep3 A3


title: Control rep1 A1


title: Fe2O3 ENP rep1 A4


title: ctl1

tag: strain


title: ZT20_DOX_beta rep1 [ZT20_Doxb_160528_5]


title: control rep2 A2


title: ZT20_CTR_alpha rep1 [ZT20_Ctla_160528_5]


title: ZT4_DOX_beta rep1 [ZT4_Doxb_160528_6]


title: ZT4_CTR_beta rep1 [ZT4_Ctlb_160528_5]


title: ZT20_DOX_alpha rep1 [ZT20_Doxa_160528_5]


title: ZT4_CTR_alpha rep1 [ZT4_Ctltla_160528_6]


title: ZT12_DOX_alpha rep1 [ZT12_Doxa_160528_5]


title: ZT16_DOX_beta rep1 [ZT16_Doxb_160528_6]


title: ZT16_DOX_alpha rep1 [ZT16_Doxa_160528_5]


title: ZT20_CTR_beta rep1 [ZT20_Ctlb_160528_6]


title: ZT12_CTR_beta rep1 [ZT12_Ctlb_160528_5]


title: MLLT6 knockout with IFNG - replicate 2

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Expression levels of individual transcripts were estimated by salmon (ver. 0.13.1) using Gencode transcriptome (release 28) as a reference.
Genome_build: hg38
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by salmon. The sgRNA count files are in the tsv format, were each row represents abundance of a single sgRNA. The complete list of sgRNA IDs with respective Ensembl gene IDs, gene symbols and sgRNA sequences is provided in a separate file (sgRNA_sequences.txt.gz)

source_name: Bone

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and antibiotics streptomycin and penicillin at 37 degrees celsius and 5% CO2

extract_protocol:
Total RNA isolated from 4 million cells using Rneasy Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 1.5 ng/ml of IFNG and 20 mg/ml of BSA for 24 hours

tag: cell line

tag: tumor type

value: Osteosarcoma

tag: genotype


title: MLLT6 knockout with IFNG - replicate 3


title: MLLT6 knockout without IFNG - replicate 3


title: ZT16_CTR_alpha rep1 [ZT16_Ctla_160528_6]


title: ZT16_CTR_beta rep1 [ZT16_Ctlb_160528_6]


title: ZT12_DOX_beta rep1 [ZT12_Doxb_160528_5]


title: MLLT6 knockout without IFNG - replicate 2


title: MLLT6 knockout with IFNG - replicate 1


title: Mock cells with IFNG - replicate 2


title: Mock cells without IFNG - replicate 2


title: Mock cells without IFNG - replicate 1


title: ZT12_CTR_alpha rep1 [ZT12_Ctla_160528_5]


title: RKO PD-L1-EGFP reporter line with sgRNA library with IFNG treatment

data_processing:
Library strategy: CRISPR screen
Sequencing reads were first trimmed with cutadapt (ver. 1.12) to remove invariable 5' and 3' ends and then scanned with PatMaN (ver. 1.2) for best matches with sgRNA sequences from the library (up to 5 mismatches were allowed).
Genome_build: hg38
Supplementary_files_format_and_content: Abundance files report transcript expression levels, as reported by salmon. The sgRNA count files are in the tsv format, were each row represents abundance of a single sgRNA. The complete list of sgRNA IDs with respective Ensembl gene IDs, gene symbols and sgRNA sequences is provided in a separate file (sgRNA_sequences.txt.gz)

source_name: Colon

extract_protocol:
Extracted genomic DNA using DNA blood kit (Qiagen)
The samples were indexed for NGS sequencing in a successive PCR enrichment followed by purification and capillary electrophoresis (Fragment Analyzer, Agilent)

treatment_protocol:
Cells were infected with the custom-made pooled sgRNA library
Treated with 1.5 ng/ml of IFNG and 20 mg/ml of BSA

value: RKO

value: Colon carcinoma

value: RKO PD-L1-EGFP reporter line

tag: sorting criteria

value: EGFP (PD-L1 reporter)


title: Mock cells with IFNG - replicate 3


title: Mock cells with IFNG - replicate 1


title: RKO PD-L1-EGFP reporter line with sgRNA library (viability check) before sort

treatment_protocol: Cells were infected with the custom-made pooled sgRNA library


title: Mock cells without IFNG - replicate 3


title: RKO PD-L1-EGFP reporter line with sgRNA library without IFNG treatment


title: RKO PD-L1-EGFP reporter line with sgRNA library


title: MLLT6 knockout without IFNG - replicate 1


title: WS Minute hilum (mi) isoline (UC413_ PI547628) 50-100 mg rep 1

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

data_processing:
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 88,647  Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Genome_build: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)
Supplementary_files_format_and_content: a tab-delimited text file includes RPKM values for each of the 20 samples and also annotations of the Glyma models from Phytozome

organism: Glycine max

source_name: Whole seed coats (50-100 mg seed weight stage)

growth_protocol: Soybean plants (standard (UC7) and minute-hilum (mi) isoline (UC413) lines) were grown in the green house. Seeds of different weight ranges (10-25, 25-50 and 50-75 mg) were collected and hilum-containing seed coat regions were dissected. All tissues were lyophillized and stored at -70C till further use.

extract_protocol:
Total RNA from standard UC7 and mutant UC413 lines was extracted using standard phenol-chloroform method with lithium chloride precipitation (McCarty 1986).
Library construction with TruSeq RNA Sample Kit or Stranded TruSeq RNA Sample Kit and high-throughput sequencing was carried out using RNA-Seq technology with a Illumina HiSeq2000 at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.

treatment_protocol: optimal green house growth conditions

tag: plant introduction number

tag: repeat number

value: Repeat 1


title: WS Clark 63 (UC7_PI548532) 50-100 mg rep 1


title: WS Minute hilum (mi) isoline (UC413_ PI547628) 25-50 mg rep 1

source_name: Whole seed coats (25-50 mg seed weight stage)


title: WS Clark 63 (UC7_PI548532) 25-50 mg rep 1


title: 4211D

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

hyb_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

data_processing: Raw iDAT files were downloaded and pre-processed using ssNOOB. Outlying samples and any probes that failed detection p-value (p=0.01) were removed. Probes near SNPs at the CpG interrogation or extension were removed. Data was processed using the BMIQ function in the ChAMP R package. For analysis, probes on the X/Y chromosomes as well as probes mapping to CpG within the vicinity of SNPs with MAF > 1% in AA or EA populations, as according to 1000G were also removed.

source_name: Colon Biopsy

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

extract_protocol: Standard Illumina Protocol

tag: age

tag: pair

tag: location

value: L

tag: gender

value: M

tag: race

value: AA

tag: adenoma history

value: No

tag: sample plate


title: 4183A

scan_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

value: R

value: F

value: EA

value: Yes


title: 4694A


title: 5202D


title: WS Clark 63 (UC7_PI548532) 10-25 mg rep 1

source_name: Whole seed coats (10-25 mg seed weight stage)


title: 4712D


title: 4468D


title: 4765A


title: 4291A


title: 5458A


title: 4199A


title: 4946D


title: WS Minute hilum (mi) isoline (UC413_ PI547628) 10-25 mg rep 1


title: 4099A


title: 4309D


title: 4762D


title: 4822D


title: SC Minute hilum (mi) isoline (UC413_ PI547628) 100-200 mg rep 1

source_name: Extended hilum region of seed coats (100-200  mg seed weight stage)


title: 4811D


title: 4223A


title: 4052A


title: 4239A


title: 4364A


title: 4066D


title: SC Minute hilum (mi) isoline (UC413_ PI547628) 50-100 mg rep 1

source_name: Extended hilum region of seed coats (50-100 mg seed weight stage)


title: 4830D


title: 4954A


title: 5176D


title: SC Clark 63 (UC7_PI548532) 50-100 mg rep 1


title: 4797A


title: SC Clark 63 (UC7_PI548532) 100-200 mg rep 1


title: 4310D


title: 4310A


title: SC Minute hilum (mi) isoline (UC413_ PI547628) 25-50 mg rep 1

source_name: Extended hilum region of seed coats (25-50 mg seed weight stage)


title: SC Minute hilum (mi) isoline (UC413_ PI547628) 25-50 mg rep 2

value: Repeat 2


title: 5179A


title: SC Clark 63 (UC7_PI548532) 25-50 mg rep 2


title: SC Minute hilum (mi) isoline (UC413_ PI547628) 50-100 mg rep 2


title: 5132A


title: 4015A


title: SC Minute hilum (mi) isoline (UC413_ PI547628) 10-25 mg rep 2

source_name: Extended hilum region of seed coats (10-25 mg seed weight stage)


title: SC Clark 63 (UC7_PI548532) 25-50 mg rep 1


title: SC Clark 63 (UC7_PI548532) 50-100 mg rep 2


title: SC Minute hilum (mi) isoline (UC413_ PI547628) 10-25 mg rep 1


title: SC Clark 63 (UC7_PI548532) 10-25 mg rep 1


title: SC Clark 63 (UC7_PI548532) 10-25 mg rep 2


title: ZT8_DOX_beta rep2 [ZT8_Db_2_08-12-2017_171212_6]

tag: cell type

value: Pancreatic islets


title: ZT8_DOX_alpha rep2 [ZT8_Da_2_08-12-2017_171212_6]

tag: sample group

value: alpha


title: ZT8_CTR_beta rep2 [ZT8_Cb_2_08-12-2017_171212_6]

tag: cell subtype

value: beta


title: ZT8_CTR_alpha rep2 [ZT8_Ca_2_08-12-2017_171212_6]


title: ZT4_DOX_beta rep2 [ZT4_Db_2_08-12-2017_171212_6]


title: ZT4_DOX_alpha rep2 [ZT4_Da_2_08-12-2017_171212_6]


title: ZT4_CTR_beta rep2 [ZT4_Cb_2_08-12-2017_171212_6]


title: ZT4_CTR_alpha rep2 [ZT4_Ca_2_08-12-2017_171212_6]


title: ZT20_DOX_alpha rep2 [ZT20_Da_2_08-12-2017_171212_7]


title: ZT20_CTR_beta rep2 [ZT20_Cb_2_08-12-2017_171212_7]


title: ZT20_CTR_alpha rep2 [ZT20_Ca_2_08-12-2017_171212_7]


title: 4445D


title: 4830A


title: ZT20_DOX_beta rep2 [ZT20_Db_2_08-12-2017_171212_7]


title: ZT16_DOX_beta rep2 [ZT16_Db_2_08-12-2017_171212_7]


title: ZT16_DOX_alpha rep2 [ZT16_Da_2_08-12-2017_171212_7]


title: ZT16_CTR_beta rep2 [ZT16_Cb_2_08-12-2017_171212_7]


title: 4503D


title: 5177D


title: 4468A


title: 3897A


title: ZT16_CTR_alpha rep2 [ZT16_Ca_2_08-12-2017_171212_7]


title: 3897D


title: ZT12_DOX_beta rep2 [ZT12_Db_2_08-12-2017_171212_7]


title: 5613D


title: 4974A


title: 4312D


title: 4799D


title: ZT12_DOX_alpha rep2 [ZT12_Da_2_08-12-2017_171212_7]


title: 4900A


title: ZT12_CTR_beta rep2 [ZT12_Cb_2_08-12-2017_171212_7]


title: 3893A


title: 5334D


title: ZT12_CTR_alpha rep2 [ZT12_Ca_2_08-12-2017_171212_7]


title: 4743A


title: ZT0_DOX_beta rep2 [ZT0_Db_2_08-12-2017_171212_5]


title: 4795D


title: 4923D


title: 5202A


title: ZT0_DOX_beta rep1 [ZT0_Db_1_08-12-2017_171212_6]


title: 5625D


title: ZT0_CTR_beta rep1 [ZT0_Cb_1_08-12-2017_171212_6]


title: ZT0_CTR_beta rep2 [ZT0_Cb_2_08-12-2017_171212_5]


title: 4223D


title: ZT0_DOX_alpha rep2 [ZT0_Da_2_08-12-2017_171212_5]


title: 4965D


title: 3876D


title: ZT0_CTR_alpha rep2 [ZT0_Ca_2_08-12-2017_171212_5]


title: 4244D


title: 4707A


title: ZT0_CTR_alpha rep1 [ZT0_Ca_1_08-12-2017_171212_6]


title: ZT0_DOX_alpha rep1 [ZT0_Da_1_08-12-2017_171212_6]


title: WT_6M_M_Pde10a_17

city: Basel

first: Jonathan

last: Seguin

address: Spitalstrasse 33

institute: UKBB-DBM

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers

data_processing:
Library strategy: 4C-seq
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2)
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata
Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: Striatum

growth_protocol: mESC: J1 mouse ES cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (4.5 g/L glucose-DMEN, 15% FCS, 0.1 mM non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1 mM glutamine, 500 U/mL LIF, gentamicin), then passaged onto feeder-free 0.2% gelatin-coated plates for at least two passages to remove feeder cells. In vitro differentiation was performed by culturing for six days in medium without LIF and 10% FCS, with supplementing of 5 μM final concentration retinoic acid for the final four days.

extract_protocol:
Striatal tissue: Frozen striata from 4 mice were homogenized in ice-cold PBS supplemented with 1x Protease Inhibitors Cocktail (PIC, cOmplete EDTA free, Roche) and cross-linked in 2% formaldehyde for 15 minutes at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M and tissue was washed using ice-cold PBS. Cells were lysed then in Cell Lysis Buffer (10mM Hepes pH8; 85mM KCl; 0.5% NP-40) and nuclei were were collected after treatment with Nuclear Extraction Buffer (0.5% SDS, 10mM EDTA pH8, 50mM Tris). Nuclei were counted and aliquoted at 5 million nuclei/tube. 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then a further 1h with 2.6% Triton-X100 at 37°C. Nuclei were digested overnight with 1000 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 16°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (5 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation.
mESC: Cells were detached with trypsin, washed by centrifugation in PBS, and then fixed with 2% formaldehyde in mES culture medium for 10 min at 23°C. The fixation was quenched with cold glycine at a final concentration of 125 mM, then cells were washed with PBS and permeabilized on ice for 1 h with 10 mM Tris-HCl, pH 8, 100 mM NaCl, 0.1% NP-40 and protease inhibitors. Nuclei were resuspended in DpnII restriction buffer at 10 million nuclei/mL concentration, and 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then a further 1h with 2.6% Triton-X100 at 37°C. Nuclei were digested overnight with 1000 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 16°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (5 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation.
50 ng aliquots of 4C DNA were used as template for PCR with bait-specific primers containing Illumina adapter termini (primer sequences and optimal PCR conditions available on request). PCR reactions were pooled, primers removed by washing with 1.8x AMPure XP beads, then quantified on a Bioanalyzer (Agilent) before sequencing with a HiSeq 4000 (Illumina).

tag: tissue

value: Striatum

tag: strain

tag: replicate

value: Wild-type

value: 6 months

tag: Sex

value: males

tag: restriction enzymes

value: DpnII - Csp6I


title: WT_6M_M_Ptpn5_7

tag: cell line

tag: genotype


title: WT_6M_M_Nop14_5

tag: age


title: WT_6M_M_Msh2_17


title: 4183D

tag: pair

value: L


title: WT_6M_M_Htt_5


title: 4200A

tag: location

value: M


title: 5613A

tag: gender

value: AA


title: WT_6M_M_Gpr6_10


title: 4361D

tag: race


title: WT_6M_M_Mxd4_5


title: 5086D

tag: adenoma history

value: No


title: WT_6M_F_Ptpn5_7

value: females


title: WT_6M_M_Acox3_5


title: 4804D

tag: sample plate


title: WT_6M_F_Pde10a_17


title: 5625A

value: R


title: WT_6M_F_Mxd4_5


title: 4241D

value: EA


title: 5179D

value: F

value: Yes


title: WT_6M_F_Msh2_17


title: WT_6M_M_Lrpap1_5


title: WT_6M_F_Nop14_5


title: 5033D


title: 4309A


title: WT_6M_F_Lrpap1_5


title: 4270A


title: WT_6M_F_Htt_5


title: WT_6M_F_Gpr6_10


title: 4524D


title: WT_6M_F_Acox3_5


title: 3974A


title: 4244A


title: 4802D


title: WT_14W_Ptpn5_7

value: 14 weeks


title: 4417D


title: 5283A


title: 5289A


title: WT_14W_Pde10a_17


title: 4779D


title: 4158D


title: 5086A


title: R6_1_Pde10a_17


title: R6_1_Gpr6_10


title: 4417A


title: Q140HOM_6M_M_Ptpn5_7

value: Knock-In Q140 homozygous


title: 4822A


title: 4963A


title: Q140HOM_6M_M_Pde10a_17


title: 4277D


title: Q140HOM_6M_M_Nop14_5


title: Q140HOM_6M_M_Msh2_17


title: R61_Ptpn5_7


title: 5163D


title: WT_14W_Gpr6_10


title: Q140HOM_6M_M_Htt_5


title: 4193A


title: Q140HOM_6M_M_Gpr6_10


title: 5279A


title: 5089A


title: 4688A


title: Q140HOM_6M_M_Mxd4_5


title: Q140HOM_6M_F_Ptpn5_7


title: Q140HOM_6M_F_Pde10a_17


title: Q140HOM_6M_F_Nop14_5


title: Q140HOM_6M_M_Acox3_5


title: 4946A


title: Q140HOM_6M_F_Mxd4_5


title: 4055D


title: 4587D


title: Q140HOM_6M_F_Msh2_17


title: Q140HOM_6M_M_Lrpap1_5


title: 4099D


title: 4774A


title: 4690A


title: Q140HOM_6M_F_Gpr6_10


title: Q140HOM_6M_F_Acox3_5


title: mESC_Pde10a_17

source_name: J1 embryonic stem cells

value: mES J1


title: Q140HOM_6M_F_Lrpap1_5

value: Striatum


title: Q140HOM_6M_F_Htt_5


title: 4173D


title: H3K27ac_WT_20w_M_rep2_NeuN-

description: ChIP is performed using sorted nuclei from the striatum of HD R6/1 and control mice at 20 weeks of age. Striata from different animals are pooled. 2nd replicate

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

extract_protocol: ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with Qubit (Invitrogen). ChIP-seq libraries were prepared from 2 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode), according to manufacturer's instructions. Illumina compatible indexes were added through PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt® AMPure® XP beads (Beckman Coulter) to remove unincorporated primers and other reagents. Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). Libraries were sequenced on Illumina Hiseq 4000 sequencer as Paired-End 50 base reads following Illumina’s instructions. Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.

treatment_protocol:
Whole tissue: Frozen striata from 4 mice were pooled (sex-matched between HD and WT animals), cut into small fragments, fixed in 1% formaldehyde and incubated for 15 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then homogenized in sonication buffer, and lysates were sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (Millipore) for 1 h at 4°C. Subsequently, samples were incubated overnight at 4°C with antibodies to H3K27ac (Abcam, ab4729), H3K27me3 ()  or 7C2 RNAPII antibody. Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3 h at 4°C. Agarose beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.
NeuN sorted: Frozen striata from 4 mice were homogenized in ice-cold PBS supplemented with 1x Protease Inhibitors Cocktail (PIC, cOmplete EDTA free, Roche) and cross-linked in 1% formaldehyde for 15 minutes at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M and tissue was washed using ice-cold PBS. Cells were lysed then in Cell Lysis Buffer (10mM Hepes pH8; 85mM KCl; 0.5% NP-40) and nuclei were were collected after treatment with Nuclear Extraction Buffer (0.5% SDS, 10mM EDTA pH8, 50mM Tris). Purified nuclei were then resuspended in PBTB (PBS 1x, 5% BSA, 0.5% Tween-20) + 1x PIC, 3% Normal Horse Serum (NHS) and stained using α-NeuN antibody (1:1000, Merck Millipore). After washing, nuclei were labelled with α-Ms AF488 antibody (1:1500) and washed with ice-cold PBS. Immunostained nuclei were sorted using BD Aria Fusion flow cytometer, recovered in ice-cold 1x PBS, pelleted and stocked at -80ºC. Nuclei were resuspended in sonication buffer and sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (Millipore) for 1 h at 4°C. Subsequently, samples were incubated overnight at 4°C with antibodies to H3K27ac (Abcam, ab4729) or H3K27me3 (). Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3 h at 4°C. Agarose beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.

value: Striatum, NeuN- cells

value: Wild-type

value: 20 weeks

tag: replicats

tag: chip antibody

value: H3K27ac: ab4729, Abcam


title: input_WT_20w_M_rep2_NeuN-

value: males

value: No antibody


title: H3K27ac_WT_20w_M_rep2_NeuN+

value: Striatum, NeuN+ cells


title: 5279D

value: L

value: M

value: AA

value: No


title: 3939A

value: R


title: 4337D

value: EA


title: 4974D

value: F

value: Yes


title: 4779A


title: 4361A


title: input_WT_20w_M_rep2_NeuN+


title: 5076D


title: H3K27me3_WT_20w_M_rep2_NeuN-

value: H3K27me3:C15410195, Diagenode


title: 4437D


title: 5641D


title: H3K27me3_WT_20w_M_rep2_NeuN+


title: RNAPII_Q140_2m_M_rep1

description: ChIP is performed using the striatum of HD KI and control mice at 2 months. Striata from different animals are pooled. 3rd replicate using males

value: Striatum

value: Knock-In Q140

value: 2 months


title: 4952D


title: 5289D


title: 4804A


title: 5033A


title: 4173A


title: H3K27me3_Q140_2m_M_rep1


title: H3K27ac_Q140_2m_M_rep1


title: RNAPII_WT_2m_M_rep1

value: Wild-type


title: 4816D


title: H3K27me3_WT_2m_M_rep1


title: 5264D


title: H3K27ac_WT_2m_M_rep1

value: H3K27ac: ab4729, Abcam


title: input_Q140_2m_M_rep1

value: males


title: input_WT_2m_M_rep1

value: No antibody


title: H3K27me3_WT_20w_M_rep1_NeuN-

description: ChIP is performed using sorted nuclei from the striatum of HD R6/1 and control mice at 20 weeks of age. Striata from different animals are pooled. 1st replicate using males

value: Striatum, NeuN- cells

value: 20 weeks


title: 3876A

value: M


title: 5397A

value: AA


title: 4068A

value: No


title: H3K27me3_WT_20w_M_rep1_NeuN+

value: Striatum, NeuN+ cells


title: H3K27ac_WT_20w_M_rep1_NeuN+


title: input_WT_20w_M_rep1_NeuN-


title: 4124D

value: L


title: 4105A

value: R

value: F


title: 4202A

value: Yes


title: input_WT_20w_M_rep1_NeuN+


title: 5089D

value: EA


title: 5551A


title: RNAPII_Q140_2m_F_rep2

description: ChIP is performed using the striatum of HD KI and control mice at 2 months. Striata from different animals are pooled. 2nd replicate using females

value: Striatum

value: Knock-In Q140

value: females


title: H3K27ac_WT_20w_M_rep1_NeuN-

value: Wild-type

value: H3K27ac: ab4729, Abcam


title: H3K27ac_Q140_2m_F_rep2

value: 2 months


title: H3K27me3_Q140_2m_F_rep2

value: H3K27me3:C15410195, Diagenode


title: 4445A


title: RNAPII_WT_2m_F_rep2


title: H3K27me3_WT_2m_F_rep2


title: H3K27ac_WT_2m_F_rep2


title: 5176A


title: input_Q140_2m_F_rep2

value: No antibody


title: 4291D

value: M


title: input_WT_2m_F_rep2


title: RNAPII_Q140_6m_F_rep2

description: ChIP is performed using the striatum of HD KI and control mice at 6 months. Striata from different animals are pooled. 4th replicate using females

value: 6 months


title: 4055A

value: AA


title: 4004D

value: No


title: 4815A


title: 4503A


title: H3K27ac_Q140_6m_F_rep2


title: 3974D

value: L


title: 4500A

value: R


title: H3K27me3_Q140_6m_F_rep2


title: RNAPII_WT_6m_F_rep2


title: H3K27me3_WT_6m_F_rep2


title: 4762A

value: F


title: 4015D


title: 5161A

value: Yes


title: input_WT_6m_F_rep2


title: H3K27ac_WT_6m_F_rep2


title: 4199D

value: EA


title: H3K9me3_Q140_6m_M_rep3

description: ChIP is performed using the striatum of HD KI and control mice at 6 months. Striata from different animals are pooled. 3rd replicate using males

value: Striatum

value: males

value: H3K9me3:ab8898, Abcam


title: 4052D


title: 4784A


title: 5043A


title: H3K9me3_WT_6m_M_rep3

value: Wild-type


title: 5197A


title: input_Q140_6m_M_rep3

value: Knock-In Q140


title: 4202D


title: input_WT_6m_M_rep3


title: 3935D


title: H3K27me3_Q140_6m_M_rep1

description: ChIP is performed using the striatum of HD KI and control mice at 6 months. Striata from different animals are pooled. 1St replicate using males


title: H3K27ac_Q140_6m_M_rep1

value: H3K27ac: ab4729, Abcam


title: 4211A


title: 4360D


title: 4270D


title: 4160D


title: 4954D


title: H3K27me3_WT_6m_M_rep1

value: H3K27me3:C15410195, Diagenode


title: input_Q140_6m_F_rep2

value: females

value: No antibody


title: 4899A


title: 4856D

value: M


title: 5264A

value: AA


title: 4337A

value: No


title: RNAPII_Q140_6m_M_rep1

value: 6 months


title: input_Q140_6m_M_rep1


title: H3K27ac_WT_6m_M_rep1


title: input_WT_6m_M_rep1


title: 4500D

value: L


title: 5076A

value: R

value: F


title: RNAPII_WT_6m_M_rep1


title: 4321D


title: 5103A

value: EA


title: 4688D


title: 4245D


title: 4312A


title: 5177A


title: 4811A


title: 4846A


title: 4765D


title: 4459D

value: Yes


title: 4437A


title: 3935A


title: 4364D


title: 4200D


title: 4288D


title: 4473D


title: 4160A


title: 4923A


title: 5339D


title: 4727A


title: 4004A1


title: PtenCS/+ basal_4 [30_4400CS_B_S12]

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
RNA-seq data was converted to a per-gene read-count matrix using RNAsik pipeline v1.5.3 as implemented in Laxy.
Reads were mapped to the mouse genome (GRCm38) using STAR
duplicates were marked using Picard Markduplicates
reads were assigned to gene models (exonic only) from the GRCm38 annotation using featureCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: counts tsv format

source_name: PtenCS/+ basal

extract_protocol:
Total RNA were isolated from FACS sorted cells using TRI Reagent and Direct-zol RNA Microprep kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: PtenCS/+

value: female

value: 12-14 weeks old

tag: cell type

value: mammary epithelial cells


title: 4504A


title: 4743D


title: 4695A


title: 4899D


title: PtenCS/+ luminal_4 [29_4400CS_L_S11]

source_name: PtenCS/+ luminal


title: PtenCS/+ basal_3 [28_4401CS_B_S10]


title: 4796D


title: 4504D


title: PtenCS/+ luminal_3 [27_4401CS_L_S9]


title: PtenGE/+ basal_4 [26_4409GE_B_S4]

source_name: PtenGE/+ basal

value: PtenGE/+


title: 5132D


title: 4605A


title: 5163A


title: 4146D


title: 4605D


title: 5339A


title: PtenGE/+ luminal_4 [25_4409GE_L_S3]

source_name: PtenGE/+ luminal


title: PtenGE/+ luminal_3 [21_4393GE_L_S1]


title: 4799A


title: PtenGE/+ basal_3 [22_4393GE_B_S2]


title: Pten+/+ basal_4 [20_4392WT_B_S8]

source_name: Pten+/+ basal

value: Pten+/+


title: 5395D


title: 5641A


title: 4816A


title: 4587A


title: 4125D


title: 4278D


title: 5551D


title: 3893D


title: 4826A


title: 4784D


title: 4690D


title: 4239D


title: Pten+/+ luminal_4 [19_4392WT_L_S7]

source_name: Pten+/+ luminal


title: 4208D


title: 4695D


title: 4815D


title: 4825D


title: 5458D


title: 4369D


title: PtenCS/+ luminal_1 [15_4366CS_L_S5]


title: PtenCS/+ luminal_2 [17_4379CS_L_S7]


title: 4796A


title: 5397D


title: PtenCS/+ basal_2 [18_4379CS_B_S8]


title: 4288A


title: 4774D


title: PtenGE/+ basal_2 [12_4381GE_B_S12]


title: PtenGE/+ basal_1 [10_4348GE_B_S10]


title: 4048D


title: 4245A


title: PtenGE/+ luminal_1 [9_4348GE_L_S9]


title: PtenCS/+ basal_1 [16_4366CS_B_S6]


title: 3952A


title: 4360A


title: Pten+/+ basal_3 [8_4345WT_B_S6]


title: 4124A


title: 4614A


title: 5103D


title: 4825A


title: 4614D


title: Pten+/+ basal_2 [6_4338WT_B_S4]


title: PtenGE/+ luminal_2 [11_4381GE_L_S11]


title: Pten+/+ luminal_2 [5_4338WT_L_S3]


title: Pten+/+ basal_1 [4_4382WT_B_S2]


title: 4158A


title: Pten+/+ luminal_1 [3_4382WT_L_S1]


title: Pten+/+ luminal_3 [7_4345WT_L_S5]


title: 3939D


title: 4105D


title: 4759D


title: 4193D


title: 4066A


title: Grm1-S458A_4

city: San Francisco

first: Zenghua

last: Fan

state: CA

address: 1550 4th Street

institute: University of California, San Francisco

data_processing:
Paired-end reads were mapped to mouse reference genome (mm10) by Hisat2 (v2.1.0).
Curated genes annotations from RefSeq were used to quantify gene expression as reads count by HTseq (v0.9.1)
Aggregation of raw reads count, preprocessing, normalization and differential expression analysis were performed by DESeq2 package in R environment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files for raw reads count for every gene by HTseq for each sample

source_name: Hippocampus

growth_protocol: Grm1b-R889W and Grm1-S458A knock-in mice were generated by CRISPR/Cas9. Male mice were used for all experiments.

extract_protocol:
Hippocampus tissues were isolated and flash frozen at ZT20, and then stored at -80 degree.
Paried-end RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: All experimental animals were singly housed on a LD 12:12 cycle and given ad libitum access to food and water.

tag: strain

value: 5 months


title: 4846D


title: Grm1-S458A_2


title: 4241A


title: Grm1-S458A_3


title: 4278A


title: 4727D


title: 4321A


title: 4277A


title: 4802A


title: 5043D


title: 4759A


title: Grm1b-R889W_4


title: Grm1-S458A_1


title: 4856A


title: 5197D


title: 4020A


title: Grm1b-R889W_3


title: Grm1b-R889W_2


title: 4020D


title: Grm1b-R889W_1


title: 4346D


title: 4146A


title: WT_4

value: wild type


title: 4952A


title: 4473A

value: M


title: tyrR-rep4

city: Fredericton

first: Cheryl

middle: L.

last: Patten

state: New Brunswick

address: 10 Bailey Drive

department: Biology

country: Canada

institute: University of New Brunswick

data_processing:
Sequence data was inspected for overall quality using FastQC v0.11.2 (S. Andrews, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low-quality reads and contaminating Illumina TruSeq adapter sequences were removed using Trimmomatic v0.3 with a sliding window size of 4 bp, cutting sequences when the average Phred score dropped below 15. Surviving paired reads were mapped to the E. cloacae UW5 reference genome (GenBank Accession number CP011798) using bwa (v0.7.9-r789) as single fragments with a maximum mismatch of 1%. Read alignments were sorted, indexed and converted to BAM format with SAMtools v0.1.19-44428cd. Sample read alignments were visualised using the Integrative Genomics Viewer v2.3.32 to ensure correct mapping of reads to genomic features. The number of reads that mapped to each genomic feature was calculated using the default parameters of HTSeq-count v 0.6.1.p1. Genes with significantly different levels of expression between wild-type and tyrR mutant strains were called using DESeq2 v1.12.4. Genes were considered to be differentially expressed when there was at least a four-fold change (i.e., |log2-fold change| > 2) in expression with a false discovery rate (FDR) threshold adjusted p-value (padj) of ≤ 0.001 as determined by the Benjamini-Hochberg correction method.
Genome_build: CP011798
Supplementary_files_format_and_content: Differential expression of all E. cloacae UW5 genes in the tyrR mutant vs. the wild-type provided in an Excel file

organism: Enterobacter ludwigii

source_name: Rhizobacterium

growth_protocol: Overnight cultures from single colonies of wild-type and tyrR mutant E. cloacae were inoculated 1:100 into 3 ml fresh LB in quadruplicate and incubated at 30℃ and 250 rpm for ~2.5 hrs until reaching mid logarithmic phase of growth (OD600 = 0.6-0.9).

extract_protocol:
A total of 0.5 ml of cell culture were transferred to a 2 ml tube containing 1 ml RNAprotect Bacteria Reagent (Qiagen), incubated 5 minutes at room temperature, and then pelleted by centrifugation. Cell pellets were resuspended with 15 mg/ml lysozyme and 15 mg/ml Proteinase K in 200 µl TE buffer to lyse cells for 10 min at 4°C. Total RNA was extracted using the RNeasy Mini Kit (Qiagen). Contaminating genomic DNA was removed by treating 5 µg total RNA in a 50 µl reaction containing 5 units Amplification Grade DNase I (Invitrogen, CA, USA) and 5 µl 10x DNase I digestion buffer and incubating at 37°C for 60 minutes. The reaction was terminated with 1 mM EDTA and heating at 70°C for 10 minutes. The DNase-treated RNA was purified using the Qiagen MinElute Cleanup Kit (Qiagen, Hilden, Germany) and eluted into 30 µl RNase-free water. DNA removal was verified by PCR. The final quality and quantity of RNA samples were measured on an Agilent Bioanalyzer-RNA 6000 Pico chip (Agilent Technologies, CA, USA).
Construction of RNA-Seq libraries and sequencing were performed by the Genome Quebec Innovation Centre (McGill, Montreal, Quebec). Ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Illumina, CA, USA). The resulting enriched mRNA was used to construct a 100 bp paired-end stranded Illumina library using the TruSeq RNA Library Prep Kit v2 (Illumina). The libraries were individually barcoded and sequenced together on a single Illumina HiSeq 2000 lane.

value: TyrR deletion mutant

value: Strain J126


title: tyrR-rep3


title: tyrR-rep2


title: Gox621H_L-arabinose_vs_control_I

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Gluconobacter oxydans 621H

source_name: G. oxydans treated with L-arabinose

label_protocol: Synthesis of fluorescently labelled cDNA were performed as described previously (Kranz et al., Global mRNA Decay and 23S rRNA Fragmentation in Gluconobacter oxydans 621H, BMC Genomics 2018 Oct 16;19(1):753;  doi: 10.1186/s12864-018-5111-1).

growth_protocol: For comparison of the transcriptomes, G. oxydans 621H were cultivated in complex medium with 4% (w/v) D-mannitol.  In the mid-exponential growth phase, 1% (w/v) L-arabinose was supplemented to G. oxydans 621H cells cultured in 4% (w/v) mannitol medium and the same volume of water in another 621H culture as a control. After 30 min of cultivation, each cell suspension was harvested by centrifugation (4500 g, 5 min, 4°C). The resulting pellets were directly frozen in liquid nitrogen and stored at -80°C until RNA preparation.

extract_protocol: The preparation of total RNA samples were performed as described previously (Kranz et al., Global mRNA Decay and 23S rRNA Fragmentation in Gluconobacter oxydans 621H, BMC Genomics 2018 Oct 16;19(1):753;  doi: 10.1186/s12864-018-5111-1).

tag: treatment

value: 4% D-mannitol + 1% L-arabinose

tag: growth phase

value: exponential

source_name: non-treated  G.oxydans

value: 4% D-mannitol only


title: tyrR-rep1


title: WT- rep4

value: Wild-type

value: Strain UW5


title: WT_1


title: 4797D

source_name: Colon Biopsy

value: L

value: F

value: AA

value: No


title: WT_2


title: WT- rep2


title: 3952D

value: Yes