title: pool.10_tumor.1431R

description: pool-10-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.10_tumor.1430R

status: Public on Mar 26 2020

type: SRA

city: Dallas

first: Ping

last: Mu

state: TX

address: 6000 Harry Hines Blvd., NA6.308A

department: Human Oncology and Pathogenesis

country: USA

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
Transform files from Fastq to Fasta (galaxy)
Clip sequences at TACATC (galaxy)
Filter sequences by length (22bp, galaxy)
Reverse-complement (galaxy)
Collapse sequences to number of reads (galaxy)
Align with shRNA guide sequences (use join from Galaxy)
Genome_build: shRNA sequences
Supplementary_files_format_and_content:
Fasta to tabular (galaxy).  For each shRNA and condition, the number of matching reads was normalized to the total number of library-specific reads per lane (10 million total reads per pool) and used for further analysis, which were reported in the processed data column as normalized count.
prostate_cancer_human_deletome.txt: A tab-delimted file containing a pooled shRNA library targeting genes most frequently deleted in primary or metastatic prostate cancer, annotated from a survey of six prostate cancer genomic datasets. (Barbieri et al., 2012; Grasso et al., 2013; Holcomb et al., 2009; Kim et al., 2007; Network, 2015; Taylor et al., 2010).
RIGER data matrix of tumor sequencing results: As requested by reviewers, a probabilistic ranking algorithm (used for in vitro screens (RIGER) to our in vivo screen) was adapted to identify true hits. However, because in vivo library screening is noisier than in vitro library screening and there are clearly stochastic effects, tumors were collected on week 16 before control tumors arise, resulting in the collection of very different numbers of resistant tumors from each pool. Thus, this data was not directly used as a probabilistic matrix, which would require the same number of repeats an in vitro library. To use a probabilistic ranking algorithm such as RIGER, the hairpin reads (in the tumors which did not score by week 16) was records as "0" because they failed to enriched quicker than the stochastic enriched hairpins, in order to have a working matrix for a probabilistic statistic model. This file is the data matrix of tumor reads ready to use by RIGER-E, which has 14 data columns including 13 (reads in tumors, maxi tumor number is 13) + 1 (reads in plasmid).

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: LNCaP/AR cell line was generated and maintained as previously described (Chen et al 2003). Cells were cultured at 37° C (5% CO2) in high-glucose RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% HEPES, 1% Sodium Pyruvate, 1% penicillin-streptomycin and 1% L-Glutamine. In vivo xenograft experiments were done by subcutaneous injection of 2 × 106 LNCaP/AR cells (100 μl in 50% Matrigel [BD Biosciences, San Jose, CA] and 50% growth media) into the flanks of castrated male SCID mice.

extract_protocol:
Resistant LNCaP/AR xenograft tumors were harvested and the genomic DNA was isolated by two rounds of phenol extraction using PhaseLock tubes (5prime) followed by isopropanol precipitation.
All genomic DNAs from tumors, plasmid or pregraft cells were PCR amplified using a protocol previously described (Zuber NBT 2011). Libraries were analyzed on an Illumina HiSeq 2500 and 18 nucleotides of the guide strand were sequenced using a custom primer as previously described (Zuber Nature 2011).

treatment_protocol: Daily gavage treatment with 10mg/kg enzalutamide was initiated on the day of injection. Once tumors were palpable, tumor size was measured weekly by tumor measuring system Peira TM900 (Peira bvba, Belgium).

tag: sample type

value: tumor extracted from right side

tag: cell line

value: LNCaP/AR cells

tag: treatment

value: enzalutamide


title: pool.12_tumor.1435L

description: pool-12-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)

value: tumor extracted from left side


title: pool.12_tumor.1435R


title: pool.10_tumor.1430L


title: pool.10_tumor.1428R


title: pool.10_tumor.1429L


title: pool.11_tumor.1437L

description: pool-11-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.10_tumor.1429R


title: pool.10_tumor.1428L


title: pool.10_tumor.1427L


title: pool.11_tumor.1441L


title: pool.10_tumor.1427R


title: pool.1_tumor.7864L

description: pool-1-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.1_tumor.7864R


title: pool.1_tumor.7862R


title: pool.1_tumor.7863L


title: pool.1_tumor.7862L


title: pool.1_tumor.7861R


title: Pool_43_pregraft

value: pregraft


title: Pool_41_pregraft


title: pool.10_tumor.1431L


title: Pool_7_pregraft


title: pool.1_tumor.7861L


title: Pool_4_pregraft


title: Pool_34_pregraft


title: Pool_33_pregraft


title: Pool_37_pregraft


title: Pool_35_pregraft


title: Pool_31_pregraft


title: Pool_3_pregraft


title: Pool_24_pregraft


title: pool.1_tumor.7865

value: only one tumor extracted from this animal


title: Pool_25_pregraft


title: Pool_26_pregraft


title: Pool_23_pregraft


title: Pool_22_pregraft


title: Pool_27_pregraft


title: Pool_20_pregraft


title: Pool_2_pregraft


title: Pool_21_pregraft


title: pool.1_tumor.7863R


title: Pool_13_pregraft


title: shCHD1-XE-1_2_2 (RNA-seq)

library_source: transcriptomic

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCh38 (hg38) using the HiSAT2 (v 2.0.1) (Pertea et al., 2016) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015).
Aligned reads were quantified using featurecount (v1.4.6) (Liao et al., 2014) per gene ID against Gencode version 10 (Mudge and Harrow, 2015).
Differential gene expression analysis was done using the R package DEseq2 (v 1.6.3).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and logCPM values for all samples.

molecule: total RNA

growth_protocol: LNCaP/AR cell line was generated and maintained as previously described (Chen et al 2003). Cells were cultured at 37° C (5% CO2) in high-glucose RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% HEPES, 1% Sodium Pyruvate, 1% penicillin-streptomycin and 1% L-Glutamine. All cells were passaged every 3 days. LNCaP/AR cells were cultured in same RPMI medium supplemented with full serum.

extract_protocol:
Total RNA from cells or homogenized tissues was extracted using Trizol (Ambion, Cat 15596018) following manufacturer’s instructions. RNA-Seq library construction and sequencing was performed at the integrated genomics operation (IGO) Core at MSKCC according to standard protocols.
Approximately 10 million 50bp paired-end reads were acquired per replicate condition for sequencing and Poly-A selection was performed.

treatment_protocol: LNCaP/AR cells were transduced with different shRNA against CHD1 gene, as described in the manuscript.

tag: transduction

tag: genotype

value: deletion of CHD1 genes


title: shCHD1-XE-1_2_1 (RNA-seq)


title: shCHD1-XE-1_3_1 (RNA-seq)


title: Pool_1_pregraft


title: shCHD1-XE-1_1_2 (RNA-seq)


title: shCHD1-XE-1_1_1 (RNA-seq)


title: shCHD1-XE-2_3_1 (RNA-seq)


title: shCHD1-XE-2_1_2 (RNA-seq)


title: shCHD1-XE-2_3_2 (RNA-seq)


title: shCHD1-XE-2_2_2 (RNA-seq)


title: shCHD1-XE-2_1_1 (RNA-seq)


title: shNT_2_2 (RNA-seq)

value: shNT

value: control


title: shNT_3_2 (RNA-seq)


title: shNT_1_2 (RNA-seq)


title: shCHD1-1_3_2 (RNA-seq)


title: shNT_1_1 (RNA-seq)


title: shCHD1-1_2_1 (RNA-seq)


title: shCHD1-1_3_1 (RNA-seq)


title: shCHD1-2_3_2 (RNA-seq)


title: shCHD1-XE-1_3_2 (RNA-seq)


title: shNT_2_1 (RNA-seq)


title: shNT_3_1 (RNA-seq)


title: shCHD1-1_1_1 (RNA-seq)


title: shCHD1-2_3_1 (RNA-seq)


title: shCHD1-1_2_2 (RNA-seq)


title: shCHD1-1_1_2 (RNA-seq)


title: shCHD1-2_2_2 (RNA-seq)


title: shCHD1-2_1_1 (RNA-seq)


title: TtnKO3

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Paired-end FASTQ files were aligned to mm9 using Tophat2. Read count per gene was calculated using htseq-count.
Genome_build: mm9
Supplementary_files_format_and_content: raw gene count (htseq-count)

organism: Mus musculus

source_name: Mouse LV Tissue

extract_protocol:
RNA was harvested using Trizol reagent.
1 ug of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.1 ug of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.

treatment_protocol: Control shRNA and Ttn shRNA viruses were injected via insulin syringe into thoracic cavity at postnatal date 10. Heart tissues were collected after 3 weeks.

tag: strain

tag: genotype/variation

value: Ttn-KO

tag: tissue

value: left ventricular (LV)


title: TtnKO2


title: TtnKO4


title: shCHD1-2_1_2 (RNA-seq)


title: shCHD1-XE-2_2_1 (RNA-seq)


title: shCHD1-2_2_1 (RNA-seq)


title: TtnKO1


title: Lacz1

value: LacZ


title: Lacz3


title: Lacz2


title: WTCHG_513493_224192

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

data_processing:
Fastq quality was evaluated using FastQC (0.11.2) and contamination by other organisms was excluded using FastQ Screen (0.4.4). Files were not trimmed.
Transcripts per million (TPM) and counts tables were obtained using Salmon (0.8.2 [40]) with kmer size option 31 and index option fmd. Salmon results were imported into R using tximport (1.10.0 [41]).
Genome_build: hg38
Supplementary_files_format_and_content: TPM tables from salmon

source_name: iPSC-derived motor neurons

growth_protocol: iPSCs were grown on Matrigel until confluency, then neural induction was started using DMEM/F12:Neurobasal 1:1, N2, B27,  ascorbic acid (0.5 mM), 2-mercaptoethanol, compound C (3 µM) and Chir99021 (3 µM). After 4 days in culture, RA (1 µM) and SAG (500 nM) were added to the medium. On the next day, Chir99021 and compound C were removed from the medium, and the cells were cultured for another 4–5 days. After that, cells were split 1:3 on approximately day 10. Subsequently, the medium was supplemented with growth factors BDNF (10 ng/ mL), GDNF (10 ng/mL), N-[N-(3,5-Difluorophenacetyl)-L-ala- nyl]-S-phenylglycine t-butyl ester (DAPT) (10 mM), and laminin (0.5 mg/mL). After 7 days, DAPT and laminin were removed from the medium, and the neurons were allowed to mature until day 25-30.

extract_protocol:
RNA was extracted from whole iPSMN cultures at day 30.
Library preparation was carried out using the Illumina TruSeq RNA Sample Prep Kit v2 by the Oxford Centre for Human Genomics. RNA sequencing was performed on the Illumina HiSeq4500 platform over 75 cycles. Sequences were paired-end. Fastq files were generated from the sequencing platform using the manufacturer’s proprietary software.

tag: clone

value: TARDBP M337V

tag: disease state

value: ALS

tag: age

tag: cell type

value: iPSC-derived motor neurons


title: WTCHG_513493_226121


title: WTCHG_513493_212143

value: wildtype

value: healthy control


title: WTCHG_513493_225109


title: WTCHG_513493_221156


title: WTCHG_513493_209107


title: C4P14MY

city: Montpellier

first: Albertina

last: DE SARIO

address: 641, av du doyen Gaston Giraud

department: PhyMedExp

country: France

institute: INSERM 1046-CNRS 9214-Univ Montpellier

data_processing:
Total RNA sequencing libraries were prepared with the TruSeq Stranded Total RNA kit (Illumina®) and ribosomal RNA was depleted using the Ribo-Zero Gold rRNA removal kit. Libraries were sequenced in paired-end 75 nucleotides mode with a HiSeq4000 Illumina. The quality of raw sequenced reads was assessed using the FASTQC quality control tool and reads were mapped to the reference genome with Tophat 2 (Kim et al., 2013).
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: raw count

source_name: cystic fibrosis patient

extract_protocol:
RNA was extracted from whole blood samples using the PAXgene Blood RNA kit (#762124, PreAnalytix)
Total RNA sequencing libraries were prepared with the TruSeq Stranded Total RNA kit (Illumina®) and ribosomal RNA was depleted using the Ribo-Zero Gold rRNA

tag: patient diagnosis

value: cystic fibrosis

value: whole blood

tag: gender

value: M


title: WTCHG_513493_211131


title: C4P12LJ

value: F


title: C4P13ML


title: C4P15DG


title: WTCHG_513493_210119


title: WTCHG_513493_222168


title: C4P09PA


title: C4P03PD


title: C4P02TR


title: C4P08JS


title: C3P03BE


title: C3P04PB


title: C4P11AJ


title: C3P06VQ


title: C1P21TA


title: C1P19PF


title: C3P02OJ


title: C1P18CS


title: WTCHG_513493_223180


title: C1P20PJ


title: C4P10LF


title: C5P01GA


title: C1P17CG


title: C1P02NN


title: C1P11BL


title: C1P12DA


title: C1P04SD


title: C4P04VF


title: C1P07CJ


title: C1P05MA


title: C5T03DT

source_name: healthy controls


title: C1P01RD


title: C1P14HS


title: C1P03MX


title: C1P15PA


title: C1P16AB


title: C1P08MA


title: C5T02DS


title: ZH11N_3

city: Wuhan

first: Ye

last: Ren

state: Hubei

address: NO.1, Shizishan

department: College of Life Science and Technology

country: China

institute: Huazhong Agriculture University

data_processing:
Illumina CASAVA 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and the raw reads were filtered for adaptors and low-quality reads. Clean reads were mapped to the reference genome of rice (RGAP v. 7.0) using HISAT2 (v.2.0.5).
DESeq2 in R was used to select the differentially expressed genes (DEGs). DEGs were defined as those with an expression change > 2-fold and corrected P value < 0.05
Genome_build: RGAP v. 7.0
Supplementary_files_format_and_content: Excel files include baseMean values for each sample.

organism: Oryza sativa Japonica Group

source_name: Caryopsis

growth_protocol: The plants were cultivated in paddy fields under natural long-day conditions (approximately 14 h light/10 h dark) during May to October 2018.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The ambient temperature above 35 ℃ was about 6 h a day and the highest temperature was about 40 ℃ during almost the whole growth period of the natural heat stressed plants, the ambient temperature above 35 ℃ was only 3 days and the mean daytime temperature was about 30 ℃ during the growth period of the normal cultivation condition plants.

tag: condition

value: Normal cultivation condition

value: Rice caryopsis

tag: development stage

value: 7 days after pollination


title: ZH11N_2


title: C4T03FP


title: ZH11N_1


title: P6_TNFa

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Sequence reads were filtered and mapped against the main chromosomes of the hg38 reference genome by the HiCUP pipeline, which also removes duplicate reads and filters out experimental artefacts
The aligned reads were processed by diffHic using standard parameters
Enhancers were defined as regions that contained a consensus peak of both H3K27ac and H3K4me1, as defined in the ChIP-seq part of this experiment. All enhancers were widened to 10kb and interactions between a promoter and a histone mark were extracted
Only interactions with an average mean of 5 counts per million and, with a signal at least two-fold above the expected were kept. These criteria and cut-offs were as described in the package manual
Genome_build: hg38
Supplementary_files_format_and_content: csv file with 12 columns: chromosome, start, end and widt for the two ends as well as number of supporting reads for the different samples.

source_name: hSMCs

extract_protocol:
Cells were fixated in 1% formaldehyde to be used for promoter capture Hi-C as previously described (Creyghton, M.P., et al., Proc Natl Acad Sci U S A, 2010; Rada-Iglesias, A., et al., Nature, 2011.)
Promoter capture was performed by using 37,608 biotin-labeled RNA baits (each 120 nucleotides) covering 21,841 human promoters (approximately two baits per promoter targeting each end of a HindIII fragment were designed). Baits were synthesized by Agilent Technologies and hybridization was performed using the Sure Select Target Enrichment kit ILM (Agilent Technologies) and SureSelect XT library prep kit ILM (Agilent Technologies) according to manufacturer’s instructions. DNA libraries were sequenced on a HiSeq2000 by 75‐bp paired‐end sequencing at the National High‐Throughput Sequencing Centre (University of Copenhagen, Denmark).

treatment_protocol: Two 15 cm plates of myotubes differentiated in vitro (n=3, different passages of cells) were treated with palmitate or TNF-a

value: Primary Human Skeletal Muscle cells (hSMCs)

tag: passage

value: TNFa


title: C4T02AA


title: P8_Palm

value: palmitate


title: P8_Ctrl

value: control (Ctrl)


title: P8_TNFa


title: ZH11H_3

value: Natural heat stress


title: C3T05PJ


title: ZH11H_2


title: P6_Palm


title: C3T04PM


title: C3T02BG


title: P6_Ctrl


title: CR-ONAC127N_2

value: ONAC127 mutant


title: CR-ONAC129N_2

value: ONAC129 mutant


title: ZH11H_1


title: CR-ONAC127N_3


title: CR-ONAC129H_2


title: CR-ONAC127N_1


title: CR-ONAC129N_3


title: C1T11LT


title: CR-ONAC129H_3


title: CR-ONAC129N_1


title: CR-ONAC129H_1


title: P6 TNFa Rep1 K4me1

description:
processed data file:
TNFa_K4me1.bw
K4me1_consensus.bed.gz
K4me1_counts.csv.gz

data_processing:
Reads were aligned using the Subread aligner, against a full index of the main chromosomes of the hg38 reference genome, as genomic DNA and keeping only uniquely mapped reads (-t 1 and -u flags set)
Duplicate reads were removed using Picard tools
Peaks were called using MACS2 with input control and a p-value cutoff of 0.05, this was purely to assess the homogeneity of the samples and highlight poor samples (less than 200.000 peaks, or failure to estimate fragment length), no samples were discarded
For each histone modification, a consensus peak set was generated by pooling all samples, the pooled reads were shuffled and split in two (pseudo replicates).
Peaks were called as above on each of these three samples (pool and two pseudo replicates)
a consensus peak list was generated using the irreproducible discovery rate software with the pseudo replicate peak lists as input and the pooled peak list as oracle peak list. A lenient threshold of 0.05 was used.
For each sample, reads were summarized into consensus peaks using featureCounts
Differentially bound peaks were detected in edgeR as described by (Lun, A.T. and G.K. Smyth. Nucleic Acids Res, 2014), using reads along the entire peak and model of the form ~ Condition + Passage
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of ChIP signals, bed files with consensus peaks as defined by the IDR software, csv files with counts of reads within peaks for each sample.

source_name: hSMCs_P6 TNFa K4me1

extract_protocol:
Cells were fixated in 1% formaldehyde in PBS for 10 min at room temperature followed by quenching with glycine (final concentration of 0.125M) to stop the crosslinking reaction. Fixated cells were washed with PBS and harvested in 1 ml SDS Buffer (50mM Tris-HCl (pH 8), 100mM NaCl, 5mM EDTA (pH 8.0), 0.2% NaN3, 0.5% SDS, 0.5 mM phenylmethylsulfonyl fluoride) and centrifuged for 6 min at 250g. The pelleted nuclei were lysed in 1.5 ml ice-cold IP Buffer (67mM Tris-HCl (pH 8), 100mM NaCl, 5mM EDTA (pH 8.0), 0.2% NaN3, 0.33% SDS, 1,67% Triton X-100, 0.5 mM phenylmethylsulfonyl fluoride) and sonicated (Diagenode, Biorupter) to an average length of 200-500 bp (between 15 and 20 cycles, high intensity). For preparation of chromatin from human skeletal muscle biopsies, frozen biopsies (20-40 mg) were thawed on ice and chopped into small pieces (between 1-3 mm3). The tissue was fixated in 0.5% formaldehyde in PBS for 7.5 min at room temperature followed by quenching with glycine (0.125M). The fixated tissue was washed with PBS before resuspension in 1 ml of IP buffer and homogenization by douncing until the tissue was completely disassociated. The chromatin was sonicated (Diagenode, Biorupter) to an average length of 200-500 bp (between 20 and 30 cycles, high intensity). Before starting the ChIP experiment, chromatin was cleared by centrifugation for 30 min at 20,000g. For each ChIP, 2-10 ug DNA was combined with 2.5 ug antibody and incubated with rotation at 40C for 16 hours. The following antibodies were used for ChIP: H3K27ac (Ab4729), H3K4me1 (Ab8895), H3K4me3 (CST-9751S), H3 (Ab1791). Immunoprecipitation was performed by incubation with Protein G Sepharose beads (GE healthcare) for 4 hrs followed by three washes with low-salt buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA (pH 8.0), 1% Triton X-100, 0.1% SDS, 150 mM NaCl) and two washes with high-salt buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA (pH 8.0), 1% Triton X-100, 0.1% SDS, 500 mM NaCl). Chromatin was de-cross-linked in 120 ul 1%SDS and 0.1M NaHCO3 for 6h at 650C, and DNA was subsequently purified using Qiagen MinElute PCR purification kit
For library preparation and sequencing, 3-10 ng of immunoprecipitated DNA was used to generate adaptor-ligated DNA libraries using the NEBNext® Ultra DNA library kit for Illumina (New England Biolabs, E7370L) and indexed multiplex primers for Illumina sequencing (New England Biolabs E7335). DNA libraries were sequenced on a Illumina HiSeq 2000 by 50‐bp single‐end sequencing at the National High‐Throughput Sequencing Centre (University of Copenhagen, Denmark)

treatment_protocol: differentiated hSMCs treated with palmitate or TNF-a (n=4, cells from two different passages were used)

tag: chip antibody

value: H3K4me1 (Abcam, Ab8895)

tag: replicate


title: C4T05CS


title: C1T10LA


title: CR-ONAC127H_3


title: P6 TNFa Rep1 K27ac

description:
processed data file:
TNFa_K27ac.bw
K27ac_consensus.bed.gz
K27ac_counts.csv.gz

source_name: hSMCs_P6 TNFa K27ac

value: H3K27ac (Abcam, Ab4729)


title: CR-ONAC127H_2


title: C1T07GV

value: healthy control


title: P6 TNFa Rep2 K27ac


title: CR-ONAC127H_1


title: P6 Palm Rep2 K4me1

description:
processed data file:
Palm_K4me1.bw
K4me1_consensus.bed.gz
K4me1_counts.csv.gz

source_name: hSMCs_P6 Palm K4me1


title: OX-ONAC129N_3

value: ONAC129 over expressed


title: C1T05TY

value: whole blood


title: C3T01CL


title: P6 TNFa Rep2 K4me1


title: P6 Palm Rep2 K27ac

description:
processed data file:
Palm_K27ac.bw
K27ac_consensus.bed.gz
K27ac_counts.csv.gz

source_name: hSMCs_P6 Palm K27ac


title: OX-ONAC129N_1


title: C1T04HM

value: M


title: OX-ONAC127N_3

value: ONAC127 over expressed


title: OX-ONAC127N_2

value: Normal cultivation condition


title: OX-ONAC129H_3

value: Rice caryopsis


title: OX-ONAC127N_1

value: 7 days after pollination


title: C1T01ZR


title: C1T03BE

value: F


title: P6 Palm Rep1 K27ac

value: Primary Human Skeletal Muscle cells (hSMCs)


title: OX-ONAC129H_2


title: P6 Palm Rep1 K4me1


title: OX-ONAC129H_1


title: OX-ONAC127H_2


title: OX-ONAC127H_3


title: P6 Ctrl Rep2 K4me1

description:
processed data file:
Ctrl_K4me1.bw
K4me1_consensus.bed.gz
K4me1_counts.csv.gz

source_name: hSMCs_P6 Ctrl K4me1


title: P6 Ctrl Rep2 K27ac

description:
processed data file:
Ctrl_K27ac.bw
K27ac_consensus.bed.gz
K27ac_counts.csv.gz

source_name: hSMCs_P6 Ctrl K27ac


title: ONAC129N-Input

data_processing:
Raw fastq data were trimmed using SolexaQA v2.5 program with Q20 (Phred score) and L18 (Length).
Cleaned data were then mapped to the rice reference genome (RGAP v. 7.0) using BWA with default parameters and allowing unique reads only.
Peak calling was generated by MACS2  (v2.1.0) (band width = 300；model fold = [5, 50]; qvalue cutoff = 0.05)
Genome_build: RGAP 7.0
Supplementary_files_format_and_content: bigwig files include information of genome-wide signal.

extract_protocol:
Caryopses at 7 DAP were harvested and immediately crosslinked in 1% formaldehyde under vacuum for 30 min and 2 g tissues for each sample were used for chromatin isolation. Chromatin was fragmented to 150-500 bp by sonication. ONAC127-DNA complexes and ONAC129-DNA complexes were isolated with FLAG magnetic beads, and the precipitated DNA was purified and then dissolved in ddH2O.
The eluted DNA was uesd to generate Illumina sequencing libraries following the manufacture's protocol.

tag: antibody


title: ONAC129H-Input


title: OX-ONAC129N_2


title: ONAC127N-Input


title: P6 Ctrl Rep1 K4me1


title: OX-ONAC127H_1


title: P6 Ctrl Rep1 K27ac


title: ONAC127H-Input


title: ONAC129N-ChIP

value: ANTI-FLAG M2 Magnetic Beads (Sigma-Aldrich, M8823)


title: ONAC127N-ChIP


title: P5 TNFa Rep2 K4me1

source_name: hSMCs_P5 TNFa K4me1


title: hepg2_ctrl_d3_rep2

city: Quebec

first: Gary

last: Kobinger

state: Quebec

address: 2705 blvd Laurier

country: Canada

institute: Universite de Laval

data_processing:
Basecalls performed by Illumina CASAVA
Raw reads were trimmed using Trimmomatic requiring a minimum read length of 30 bp, a minimum Phred score of 20 over a 5 bp sliding window, and trimmed trailing base pairs with a Phred score of 19 or less
Raw reads were aligned to the GRCh38 release of the human genome [33] using HISAT2 v.2.1. [34] with the ‘–dta’ option enabled
Quality of the alignment was evaluated using the RSeQC v2.6.4
StringTie v.1.3.3b was used to assemble the transcriptome in a two-step process. Following primary assembly for each sample, all assemblies were merged into an experiment-level reference assembly and the abundances of all transcripts were then re-estimated based on the experiment-level reference
Differential expression analysis was performed using the DESeq2 v1.18.1 package for R
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited GTF files

molecule: polyA RNA

source_name: liver

growth_protocol: Cells were maintained in Dulbecco’s modified eagle media, supplemented with 10% fetal bovine serum, 2mM L-glutamine, and penicillin (100 IU/ml)/streptomycin (100μg/ml)

extract_protocol:
Infected and uninfected cells were harvested at 1- and 3-days post-infection. Total RNA was isolated from cells using the Qiagen RNeasy kit according to manufacturer’s instructions.
Libraries were prepared using Illumina’s TruSeq stranded mRNA kit (Cat#20020594) following the manufacturer’s recommendation for low sample protocol. A total of 500ng of RNA was end repaired, A-tailed and ligation controls were added to all samples.  Libraries were amplified using 15 PCR cycles and cleaned up using PCR Clean DX beads. Library sizes (~260bp) were confirmed on the Bioanalyzer using the DNA High Sensitivity kit.  Samples were multiplexed 12 per flow cell and performing 100PE reads. Libraries were sequenced on the HiSEq 4000 (Illumina).

treatment_protocol: All infected samples used Crimean Congo Hemorrhagic Fever virus (CCHFV) IbAr 10200 (accession numbers AY389508, AF467768, and CHU88410)

tag: cell line

tag: cell origin

value: hepatocellular carcinoma derived liver cells

tag: infection

value: control

tag: time


title: hepg2_infected_d3_rep1

value: CCHFV


title: hepg2_ctrl_d3_rep3


title: P5 TNFa Rep2 K27ac

source_name: hSMCs_P5 TNFa K27ac


title: hepg2_infected_d3_rep3


title: GFC-3

city: Shanghai

first: Hailing

last: Zi

address: Chenhua road3888

institute: Shanghai center for plant stress biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Cucumber genome sequence (http://cucumber.genomics.org.cn, v2i) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (readss per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 2 Samples .

organism: Cucumis sativus

source_name: fruit

growth_protocol: Near-isogenic lines 32X and GFC,  northern China type cucumbers with short and light green fruits , were used in this study. The cucumber seeds were germinated in 28℃ in dark, and  then the seedlings were transferred to a greenhouse under standard conditions in the experimental field of China Agricultural University in Beijing. Water management and pest control were performed according to standard protocols.

extract_protocol:
Fruits at anthesis of 32X and GFC cucumber plants were collected for RNA-seq analysis. Total RNAs were extracted using the RNA extraction kit (Huayueyang, Beijing, China). Three biological replicates were performed for each tissue sample. RNA-seq library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) according to the manufacturer’s instructions and four index codes were added to attribute sequences to different samples(Wang et al., 2009).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: fruit

tag: genotype

value: inbred line 1461


title: ONAC129H-ChIP

value: Natural heat stress


title: P5 TNFa Rep1 K4me1

value: H3K4me1 (Abcam, Ab8895)


title: ONAC127H-ChIP


title: hepg2_ctrl_d3_rep1


title: hepg2_infected_d1_rep3


title: hepg2_infected_d3_rep2


title: GFC-1


title: GFC-2


title: P5 TNFa Rep1 K27ac

value: H3K27ac (Abcam, Ab4729)


title: 32X-2


title: 32X-3


title: hepg2_infected_d1_rep2


title: hepg2_infected_d1_rep1


title: 32X-1


title: P5 Palm Rep2 K4me1

source_name: hSMCs_P5 Palm K4me1


title: P5 Palm Rep2 K27ac

source_name: hSMCs_P5 Palm K27ac


title: hepg2_ctrl_d1_rep3


title: P5 Palm Rep1 K4me1


title: hepg2_ctrl_d1_rep2


title: P5 Palm Rep1 K27ac


title: rST ATAC rep 1

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

data_processing:
paired reads were iteratively mapped to the Mus musculus mm10 genome via bowtie2 (v 2.2.5) (Langmead and Salzberg, 2012); the unmapped reads contain the MboI ligation sites were then trimmed and aligned back to the mm10 genome again. After combing the two-round mapping results, uniquely aligned paired reads were kept and assigned to Mboi restriction fragments. The paired reads with dangling ends and or predicted self-circle structures pairs were excluded from valid pairs.
We merged replicates and sampled all valid pairs of each sample to the same 172,252,595 reads
Matrix binning and balancing was performed with the cooler software package
ChIP-seq raw data were trimmed and quality controlled using NGmerge and bbduk. Reads were aligned to mm10 using bowtie with the parameter of -m 1 --best. Duplicated reads were removed using samblaster --removeDups, and each bam file were down sampled to the same reads number using sambamba view.
Rpkm in bw files were counted by the number of reads falling into 100bp bin in the genome
All ATAC-Seq sequencing data were mapped to the mm10 reference genome using bowtie2 (v 2.2.5). Samtools was then used to further sorted and index the aligned reads.
Genome_build: mm10
Supplementary_files_format_and_content: .mcool files were generate using cooler software package; they store the Hi-C interaction matrix.

source_name: testes

growth_protocol: Testes were removed and minced by scissors until a semiliquid state had been achieved, followed by incubation in 10 ml DMEM (Gibco, 11995-081) containing 1 mg/ml collagenase IV (Sigma, C5138-1G) and 1 unit/ml DNase I (Sigma, AMPD1-1KT) in a shaking water bath at 37 °C for 5 min. To stop the digestion, 20 ml of fresh DMEM containing 10% FBS was added to samples. The seminiferous tubules were collected by centrifugation at 500 g for 2 min.

extract_protocol: About 5 x 10^5 to 5 x 10^6 cells were crosslinked using formaldehyde (a final 1% (v/v); Sigma, F8775-500ML), followed by quenching with a Glycine (final 125 mM; Sigma, G8898-1KG), mixed well and incubated for another 10 min. Cells were pelleted and washed once with ice-cold 1x PBS. After removing the supernatant, the cell pellets were stored at -80°C or directly used for the following Hi-C experiments.  For ATAC-seq, First, 5 × 10^4 cells were spun at 500 g for 5 min, 4 °C, which was followed by a wash using 50 μl of cold 1× PBS and centrifugation at 500 g for 5 min, 4 °C. Cells were resuspended in 50 μl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% (v/v) Igepal CA-630) and centrifugation at 500 g for 10 min, 4 °C. Second, the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina, FC-121-1030) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Then, the samples were purified by using a Qiagen MinElute PCR Puriﬁcation Kit (Qiagen, 28004) and amplified by PCR. After size selected by VAHTS DNA Clean Beads, the samples were sequenced by HiSeq X Ten at Novogene. ChIP-seq sequencing libraries were generated by Tn5 transposase and then PCR amplification and size selected by VAHTS DNA Clean Beads. Libraries were sent for high throughput sequencing with the HiSeq X Ten at Novogene.

value: round spermatids

tag: days postpartum

value: adult

tag: strain


title: SG-A ATAC rep 3

tag: cell type

value: type A spermatogonia


title: pacSC ATAC rep2

value: pachytene spermatocytes


title: SG-A ATAC rep 2


title: hepg2_ctrl_d1_rep1


title: P5 Ctrl Rep2 K4me1

source_name: hSMCs_P5 Ctrl K4me1


title: SG-A ATAC rep 1


title: huh7_infected_d3_rep2


title: PriSG-A ATAC rep 2

value: Primitive type A spermatogonia


title: P5 Ctrl Rep2 K27ac

source_name: hSMCs_P5 Ctrl K27ac


title: huh7_infected_d3_rep3


title: PriSG-A ATAC rep 3


title: rST Rad21 rep 2

value: Rad21 (Abcam, ab992)


title: P5 Ctrl Rep1 K4me1


title: huh7_ctrl_d3_rep3


title: rST ATAC rep 2


title: rST Rad21 rep 1


title: pacSC Rad21 rep 1


title: hSMCs_Input

value: Pool of samples


title: P5 Ctrl Rep1 K27ac

value: Primary Human Skeletal Muscle cells (hSMCs)


title: huh7_ctrl_d3_rep2


title: pacSC Rad21 rep 2


title: rST Input rep 2


title: rST Input rep 1


title: pacSC ATAC rep1


title: rST CTCF rep 2

value: CTCF (Santa Cruz Biotechnology, sc-271514/sc-28198/sc-15914)


title: huh7_ctrl_d3_rep1

value: hepatocellular carcinoma derived liver cells


title: rST CTCF rep 1


title: GHT2_34

city: SAO PAULO

first: Robson

middle: José de

last: Almeida

state: SAO PAULO

address: RUA VERGUEIRO 235 249

department: Pós Graduação Stricto Sensu em Medicina

country: Brazil

institute: Universidade Nove de Julho

data_processing:
counts
Genome_build: RefSeq GRch37

source_name: whole blood

extract_protocol:
The venous blood was collected in PAXgene Blood RNA tube and extracted with the PAXgene Blood RNA Kit.
AmpliSeq

tag: age

tag: gestational age

tag: tsh


title: huh7_infected_d1_rep3


title: pacSC Input rep 2


title: GHT1_33


title: PriSG-A ATAC rep 1


title: pacSC Input rep 1


title: pacSC CTCF rep 2


title: huh7_infected_d3_rep1


title: pacSC CTCF rep 1


title: HTP2_43


title: huh7_ctrl_d1_rep3

value: control


title: HTP1_42


title: pacSC Hi-C rep 1

description: pacSC.mcool

tag: restriction enzyme

value: MboI


title: rST Hi-C rep 2

description: rST.mcool


title: huh7_infected_d1_rep2

value: CCHFV


title: rST Hi-C rep 1

description: rST.mcool


title: pacSC Hi-C rep 2

description: pacSC.mcool


title: huh7_infected_d1_rep1


title: SG-A Hi-C rep 1

description: SGA.mcool


title: SG-A Hi-C rep 2

description: SGA.mcool


title: huh7_ctrl_d1_rep2


title: GHT3_36


title: huh7_ctrl_d1_rep1


title: PriSG-A Hi-C rep 1

description: PriSG.mcool


title: shCHD1-XE-1_3 (ATAC-seq)

data_processing:
The raw reads were aligned to the human reference genome (GRCh38/hg38) using default parameters in BWA v0.7.12 (Li and Durbin, 2009).
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 (Li et al., 2009) and Sambamba version 0.6.6 (Tarasov et al., 2015).
Library complexity was measured using BEDTools version 2.26.0 (Quinlan and Hall, 2010) and meets ENCODE data quality standards (Landt et al., 2012).
Relaxed peaks were called using MACS version 2.1.0 (Feng et al., 2012) with a p-value of 1x10e-2 for H2K27ac and SPP version 1.4 (Kharchenko et al., 2008) with an IDR = 0.01 for each replicate and pseudoreplicates. For H3K27ac peak calls that are either observed in both pseudoreplicates were used for subsequent analysis.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: ATAC-seq BigWig files were generated using MACS version 2.1.0; Scores represent the ATAC-seq fold change over control

extract_protocol:
DNA and ATAC-seq samples were generated as previously described protocol (Buenrostro et al 2016).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LNCaP/AR cells

tag: transduction

value: deletion of CHD1 genes


title: HTP3_39


title: prostate cancer case with archival biopsy tissue 715

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
the quality of sequence reads from the RNAseq data were assessed and low quality reads were filtered using the FastQC tool (Babraham Bioinformatics, Cambridge, UK) and ShortRead (v. 1.30.0) package from R bioconductor (version 3.3).
Quantification of gene level expression from preprocessed RNA-seq results were performed with the UCSC hg19 build of the Homo Sapiens genome, through the use of the Subread aligner and the featureCounts software
To reduce systemic bias between samples, the Trimmed Mean Method (TMM) was applied to gene level expression counts
Genome_build: hg19

source_name: prostate tissue

extract_protocol:
Diagnostic hematoxylin and eosin (H&E) PNBX slides were reviewed by a genitourinary pathologist, and high-grade tumor areas (Gleason grade 4, 5, or neuroendocrine/small cell) were encircled.  Transfer of annotated areas to the paraffin-embedded tissue blocks was performed and 1-2mm sterile circular biopsy punches enabled manual procurement of formalin-fixed tissue from the block. A minimum of 2 (1mm) cancer cores were used from each high-grade tumor area for RNA and/or DNA preparation. Total RNA was extracted from tissue cores using the Ambion Recover All Total Nucleic Acid Isolation Kit for FFPE (ThermoFisher). Samples were eluted with H20 and quantitated with nanodrop and bioanalyzer.
Approximately 40-100ng of RNA was used to generate the libraries using the TruSeq RNA Access Library Prep Kit (Illumina) according to manufacturer’s instructions.

tag: disease stage

value: M1 poly

tag: metastasis

value: Metastasis


title: NPG1_26


title: shCHD1-XE-1_2 (ATAC-seq)


title: prostate cancer case with archival biopsy tissue 5


title: prostate cancer case with archival biopsy tissue 658


title: prostate cancer case with archival biopsy tissue 593


title: shCHD1-XE-1_1 (ATAC-seq)


title: prostate cancer case with archival biopsy tissue 557


title: prostate cancer case with archival biopsy tissue 473


title: KO DMM 4w

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

data_processing:
The read quality of RANseq raw fastq files were checked using FastQC (v0.11.8) and the adapter sequences in reads and low-quality reads were eliminated using BBduk (BBMap v38.50b).
Trimmed fastq files were aligned to GRCh38 genome using STAR aligner(v2.6.0a). Gene level TPM and FPKM were acquired using RSEM (v1.2.17) with Gencode v22 annotation GTF (https://www.gencodegenes.org/human/release_22.html).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene id, transcript id, gene length, effective length, expected count, TPM, and FPKM values for each gene.

source_name: Knee joint

growth_protocol: We used C57BL/6J (WT) male mice and OSCAR-deficient mice (Oscar-/-, C57BL/6) for experimental OA studies. We purchased 8-to 10-week-old C57BL/6 male mice from Japan SLC, Inc. (Hamamatsu, Japan);

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Sequencing libraries were prepared according to the manufacturer’s instructions (TruSeq Stranded mRNA Library Prep Kit; Illumina, San Diego, CA, USA).

treatment_protocol: C57BL/6 Oscar-/- mice have been described before. Experimental OA was performed at 8-to 10-week-old male mice or DMM surgery in 10-to 12-week-old male mice; mice injected with phosphate-buffered saline (PBS) or sham-operated mice were used as controls.

value: AC (Articular Cartilage)

value: 10 weeks old

tag: genotype/variation

value: KO


title: KO Sham 4w


title: NPG3_32


title: PriSG-A Hi-C rep 2

description: PriSG.mcool


title: prostate cancer case with archival biopsy tissue 415


title: shCHD1-XE-2_3 (ATAC-seq)

tag: cell line


title: WT DMM 4w

value: WT


title: prostate cancer case with archival biopsy tissue 384


title: prostate cancer case with archival biopsy tissue 353


title: NPG2_34


title: prostate cancer case with archival biopsy tissue 395


title: shCHD1-XE-2_2 (ATAC-seq)


title: shNT_3 (ATAC-seq)

value: shNT


title: shCHD1-XE-2_1 (ATAC-seq)


title: prostate cancer case with archival biopsy tissue 409


title: KO DMM 2w


title: WT Sham 4w


title: prostate cancer case with archival biopsy tissue 701


title: shNT_2 (ATAC-seq)


title: prostate cancer case with archival biopsy tissue 334


title: prostate cancer case with archival biopsy tissue 226


title: prostate cancer case with archival biopsy tissue 262


title: KO Sham 2w


title: WT DMM 2w


title: prostate cancer case with archival biopsy tissue 420


title: prostate cancer case with archival biopsy tissue 216


title: shNT_1 (ATAC-seq)


title: prostate cancer case with archival biopsy tissue 206


title: shCHD1-1_3 (ATAC-seq)


title: prostate cancer case with archival biopsy tissue 103


title: prostate cancer case with archival biopsy tissue 167


title: shCHD1-1_2 (ATAC-seq)


title: 11_ZT18_2_ST_S6

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

description: Ribosome-protected mRNA fragments

data_processing:
Footprint sequences were trimmed for adapters using fastx_clipper (fastx_toolkit) with parameters –Q33 –a TGGAATTCTCGGGTGCCAAGG -l 11. Fastqs files were parsed and duplicated sequences (UMIs and inserts) were removed. UMIs (4 nucleotides on both sides) were trimmed for each read.
The genome index was built using STAR software with Ensembl transcript annotations and the mm10 mouse genome. Fastq files were aligned against the genome using STAR software with options --seedSearchStartLmax 15 . The subsequence BAM files were sorted and indexed with samtools.
A custom Perl script was used to quantify reads. For each Ensembl gene, all the exons of the respective annotated protein-coding transcripts were considered. Reads with zero mismatch and size between 25 nts and 40 nts were quantified for each gene considering read orientation. Uniquely mapping reads were reported. Genes were selected accordingly to the ones used for the ribosome dwell times and flux modeling in the related study. Samples ZT12_ST_CHX and ZT04_ST_NOCHX were removed of the analysis in the related study.
Genome_build: mm10
Supplementary_files_format_and_content: Quantified read counts. Tab-delimited file.

source_name: Liver

extract_protocol:
Ribosome unprotected-mRNAs were digested with RNAse I (350 U/mg of protein, Invitrogen) and resulting footprints were isolated (sucrose gradients, monosome peaks) and extracted with classical methods using guanidium  thiocyanate lysis buffer.
Eluted RNA was heat denatured 3 min at 65°C. The 3’-terminal cyclophosphate resulting from the RNAse I digestion was removed in a 50 L reaction with 10 U of T4 PNK (New England Biolabs) in the absence of ATP. After 60 min incubation at 37°C, ATP is supplemented to a final concentration of 1 mM together with an addition of 10 U T4 PNK and reaction is further incubated 60 min at 37°C. Libraries were generated using NEXTflex™ Small RNA Sequencing Kit 3. For both methods, manufacturer's recommendations were stricly followed.

treatment_protocol: Immediately after the organ collection, livers were homogenized in lysis buffer containing 20 mM HEPES (pH 7.6), 250 mM NaCl, 10 mM MgCl2, 10 mM DTT, 20 µg/ml cycloheximide (CHX conditions) or no cycloheximide (NOCHX conditions), 10 U/µl RNase inhibitor (New England Biolabs), and a protease inhibitor cocktail containing 0.5 mM PMSF, 10 µg/ml Aprotinin, 0.7 µg/ml Pepstatin A, and 0.7 µg/ml Leupeptin.

value: Liver

tag: feeding

value: Fasted

tag: lysis buffer drugs

value: CHX-


title: prostate cancer case with archival biopsy tissue 640-SC


title: shCHD1-1_1 (ATAC-seq)


title: shCHD1-2_3 (ATAC-seq)


title: 10_ZT18_1_ST_S4

description: Ribosome-protected mRNA fragments

tag: time

value: CHX+


title: prostate cancer case with archival biopsy tissue 211-5A


title: prostate cancer case with archival biopsy tissue 270-5-NE


title: prostate cancer case with archival biopsy tissue 546-5a


title: prostate cancer case with archival biopsy tissue 750-4a


title: 09_ZT18_2_AL_S2

description: Ribosome-protected mRNA fragments

tag: tissue

value: Ad Libitum


title: prostate cancer case with archival biopsy tissue 22


title: prostate cancer case with archival biopsy tissue 734-5a


title: prostate cancer case with archival biopsy tissue 732-4a


title: prostate cancer case with archival biopsy tissue 637-4a


title: shCHD1-2_1 (ATAC-seq)

tag: genotype


title: 07_ZT12_2_ST_S10

description: Ribosome-protected mRNA fragments


title: 06_ZT12_1_ST_S9

description: Ribosome-protected mRNA fragments


title: prostate cancer case with archival biopsy tissue 619-5a


title: WT Sham 2w


title: prostate cancer case with archival biopsy tissue 612-3a


title: pool_9_plasmid

data_processing:
Transform files from Fastq to Fasta (galaxy)
Clip sequences at TACATC (galaxy)
Filter sequences by length (22bp, galaxy)
Reverse-complement (galaxy)
Collapse sequences to number of reads (galaxy)
Align with shRNA guide sequences (use join from Galaxy)
Genome_build: shRNA sequences
Supplementary_files_format_and_content:
Fasta to tabular (galaxy).  For each shRNA and condition, the number of matching reads was normalized to the total number of library-specific reads per lane (10 million total reads per pool) and used for further analysis, which were reported in the processed data column as normalized count.
prostate_cancer_human_deletome.txt: A tab-delimted file containing a pooled shRNA library targeting genes most frequently deleted in primary or metastatic prostate cancer, annotated from a survey of six prostate cancer genomic datasets. (Barbieri et al., 2012; Grasso et al., 2013; Holcomb et al., 2009; Kim et al., 2007; Network, 2015; Taylor et al., 2010).
RIGER data matrix of tumor sequencing results: As requested by reviewers, a probabilistic ranking algorithm (used for in vitro screens (RIGER) to our in vivo screen) was adapted to identify true hits. However, because in vivo library screening is noisier than in vitro library screening and there are clearly stochastic effects, tumors were collected on week 16 before control tumors arise, resulting in the collection of very different numbers of resistant tumors from each pool. Thus, this data was not directly used as a probabilistic matrix, which would require the same number of repeats an in vitro library. To use a probabilistic ranking algorithm such as RIGER, the hairpin reads (in the tumors which did not score by week 16) was records as "0" because they failed to enriched quicker than the stochastic enriched hairpins, in order to have a working matrix for a probabilistic statistic model. This file is the data matrix of tumor reads ready to use by RIGER-E, which has 14 data columns including 13 (reads in tumors, maxi tumor number is 13) + 1 (reads in plasmid).

organism: synthetic construct

extract_protocol:
Resistant LNCaP/AR xenograft tumors were harvested and the genomic DNA was isolated by two rounds of phenol extraction using PhaseLock tubes (5prime) followed by isopropanol precipitation.
All genomic DNAs from tumors, plasmid or pregraft cells were PCR amplified using a protocol previously described (Zuber NBT 2011). Libraries were analyzed on an Illumina HiSeq 2500 and 18 nucleotides of the guide strand were sequenced using a custom primer as previously described (Zuber Nature 2011).

tag: sample type

value: plasmid

tag: treatment

value: enzalutamide


title: prostate cancer case with archival biopsy tissue 482-4a


title: prostate cancer case with archival biopsy tissue 450-5a


title: 05_ZT12_2_AL_S8

description: Ribosome-protected mRNA fragments

tag: strain


title: 08_ZT18_1_AL_S11

description: Ribosome-protected mRNA fragments


title: 04_ZT12_1_AL_S7

description: Ribosome-protected mRNA fragments


title: prostate cancer case with archival biopsy tissue 416-4a


title: prostate cancer case with archival biopsy tissue 2249-5a


title: shCHD1-2_2 (ATAC-seq)


title: pool_7_plasmid


title: pool_8_plasmid


title: prostate cancer case with archival biopsy tissue 414-5a


title: pool_6_plasmid


title: prostate cancer case with archival biopsy tissue 321-5a


title: 02_ZT4_1_ST_S3

description: Ribosome-protected mRNA fragments


title: prostate cancer case with archival biopsy tissue 401-5a


title: prostate cancer case with archival biopsy tissue 410-5a


title: pool_5_plasmid


title: prostate cancer case with archival biopsy tissue 319-5a


title: 01_ZT4_2_AL_S1

description: Ribosome-protected mRNA fragments


title: prostate cancer case with archival biopsy tissue 296-5a


title: pool_43_plasmid


title: ZT18_ST_2_Periodate

description: tRNAs pull-down through DNA probes hybridization and ligation. Sequencing of ligated left and right DNA probes.

data_processing:
To assess the fidelity of left/right probe ligation and efficiency of hybridization, a fasta file with all the possible combinations between left and right probes was created. In case two tRNA genes share the same left/right probes, they were grouped and annotated accordingly. Genome index was generated with STAR with options --runMode genomeGenerate --genomeSAindexNbases 3. Fastq files were trimmed for adapters. Sequencing reads were aligned against the index with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outSAMunmapped Within --winAnchorMultimapNmax 1000 --outFilterMismatchNmax 5 --clip3pNbases 6 --clip5pNbases 6 --outFilterMultimapNmax 50 --outSAMattributes NM nM NH NM --alignIntronMax 1 --alignEndsType EndToEnd --seedSearchStartLmax 20 --seedMultimapNmax 100000.
For each combination, the number of counts were computed and corrected for PCR duplicates using both unique molecular identifiers sequences. Reads larger than 60 nucleotides with less than 3 mismatches and less than 5 insertions compared to the reference were retained. Combinations with less than 10 reads were discarded.
Reads mapping to combinations of probes coming from different codons were reassigned in function of the newly ligated sequence. tRNA read count for the same codon were summed up.
Genome_build: mm10 (GtRNAdb)
Supplementary_files_format_and_content: Quantified read counts. Tab-delimited file.

extract_protocol:
RNAs were extracted from mouse liver using phenol/chloroform and miRNeasy Kit (Qiagen) under cold and acidic conditions (pH4.9). Samples were either treated with NaCl (control) or NaI04 (periodate) for 3’-oxidation. Purified tRNAs were deacylated and 3’-end biotinylated. DNA probes designed to target annotated mouse tRNAs (GtRNAdb), mixed at an equimolar ratio, were hybridized. Dynabeads MyOne Streptavidin C1 (Thermo Fisher) beads were incubated with the resulting RNA-DNA hybridization reaction and magnetized. Bead purified DNA-RNA hybrids were ligated at the anticodon nick by a combination of SplintR and T4 DNA ligases (NEB). RNase H and A (NEB) were added and digestion was performed. DNA probes were purified.
DNA ligated-probes was assessed by quantitative PCR and amplified by PCR (13-17 cycles). The PCR was designed following Illumina’s recommendation taking advantage of the indexed oligos from the TruSeq small RNA kit.  Amplified libraries were quantified with Picogreen. An equimolar library pool was prepared from the individual libraries based on the concentrations calculated from Picogreen data. Pools were denaturated with NaOH and neutralized with HT1 buffer (Illumina) to reach a final concentration of 20pM. Pools were spiked with 10% PhiX and clustered (loading equivalent to 12 samples per lane) onto a rapid single-end flow cell v2 at a final concentration of 7pM. Sequencing was performed on a HiSeq 2500 (Illumina) in rapid mode for 130 cycles.

tag: rna treatment


title: prostate cancer case with archival biopsy tissue 292-5a-B


title: prostate cancer case with archival biopsy tissue 212-4a-B


title: pool_42_plasmid


title: prostate cancer case with archival biopsy tissue 122-4a


title: prostate cancer case with archival biopsy tissue 747-4plus5a


title: pool_41_plasmid


title: ZT12_ST_2_Periodate


title: prostate cancer case with archival biopsy tissue 735-5a


title: 03_ZT4_2_ST_S5

description: Ribosome-protected mRNA fragments


title: pool_40_plasmid


title: ZT04_ST_2_Periodate


title: prostate cancer case with archival biopsy tissue 608-5a


title: pool_4_plasmid


title: pool_39_plasmid


title: prostate cancer case with archival biopsy tissue 719-5a


title: ZT04_AL_2_Periodate


title: ZT18_ST_2_NaCl

value: NaCl


title: prostate cancer case with archival biopsy tissue 294-5a


title: prostate cancer case with archival biopsy tissue 552-4a


title: pool_38_plasmid

value: LNCaP/AR cells


title: pool_37_plasmid


title: LID Rat Striatal Microarray 11

type: RNA

city: Omaha

first: SHETTY RAVI

last: DYAVAR

state: NE

address: 4040 EMILE ST

department: Pharmacy Practice and Science

institute: University of Nebraska Medical Center

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: In microarray data, per gene normalization to median was performed and then, we performed probe set summarization.

label: biotin

organism: Rattus norvegicus

source_name: Striatum

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted with QIAGEN Rneasy Lipid Tissue mini kit in accordance with the prescribed protocol provided by the manufacturer. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Chronic Levodopa (L-DOPA) treatment (L-Dopa methyl ester plus benserazide were given at 25 mg/kg and 6.25 mg/kg dose) was performed in Parkinsonian Disease model of rat and kept Parkinsonian Rats as controls.

value: Striatum

tag: parkinsonian disease

value: YES

tag: chronic levodopa treatment


title: LID Rat Striatal Microarray 12

description: replicate 6


title: prostate cancer case with archival biopsy tissue 227-5a

value: M1 poly

value: Metastasis


title: pool_36_plasmid


title: prostate cancer case with archival biopsy tissue 214-5a


title: prostate cancer case with archival biopsy tissue 4

value: M1 oligo


title: pool_35_plasmid


title: ZT12_ST_2_NaCl


title: LID Rat Striatal Microarray 9

description: replicate 3


title: ZT18_AL_2_NaCl


title: ZT04_ST_2_NaCl


title: ZT18_AL_2_Periodate


title: ZT12_AL_2_Periodate


title: pool_34_plasmid


title: LID Rat Striatal Microarray 8

description: replicate 2


title: prostate cancer case with archival biopsy tissue 159


title: ZT12_AL_2_NaCl


title: prostate cancer case with archival biopsy tissue 217


title: pool_33_plasmid


title: prostate cancer case with archival biopsy tissue 683-5a


title: LID Rat Striatal Microarray 10

description: replicate 4


title: PD Control Rat Striatal Microarray 6

description: replicate 6

value: NO


title: pool_32_plasmid


title: ZT04_AL_2_NaCl


title: ZT18_ST_1_Periodate


title: prostate cancer case with archival biopsy tissue 67-4a


title: PD Control Rat Striatal Microarray 5

description: replicate 5


title: PD Control Rat Striatal Microarray 4

description: replicate 4


title: LID Rat Striatal Microarray 7

description: replicate 1


title: pool_31_plasmid


title: pool_30_plasmid


title: pool_29_plasmid


title: pool_3_plasmid


title: prostate cancer case with archival biopsy tissue 224-4a


title: prostate cancer case with archival biopsy tissue 505-4a


title: prostate cancer case with archival biopsy tissue 2248-5a


title: ZT18_AL_1_Periodate


title: ZT04_ST_1_Periodate


title: pool_28_plasmid


title: prostate cancer case with archival biopsy tissue 702-5b


title: ZT04_AL_1_Periodate


title: ZT12_AL_1_Periodate


title: PD Control Rat Striatal Microarray 3

description: replicate 3


title: prostate cancer case with archival biopsy tissue 562-5a


title: pool_27_plasmid


title: PD Control Rat Striatal Microarray 2

description: replicate 2


title: ZT12_ST_1_NaCl


title: ZT12_ST_1_Periodate


title: prostate cancer case with archival biopsy tissue 708-5s

value: M0 poly

value: No metastasis


title: MeDIP-seq KO Tumor rep 2

city: Barcelona

first: Lorenzo

last: Rinaldi

state: Spain

address: Carrer Reixac Baldiri 10

department: Oncology

country: Spain

institute: IRB

data_processing:
MeDIP-seq datasets were aligned to the mouse genome build mm10 using BowTie (version 1.0.1) (Langmead et al. 2009); the parameters used were –k 1, –m 1, and –n 2. UCSC browser tracks (Kent et al. 2002) were created from the mapped bam file after converting it to bedGraph (normalized to 10 million reads) and subsequently bigWig format. Peaks of the methylation and hydroxymethylation datasets were determined MACS version 1.4.1. MeDIP-seq peaks were annotated using the annotatePeaks.pl script of the HOMER suite (version 4.6).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Deseq2 for the differential methylated regions.

source_name: DNA methylation profile of Dnmt3a KO Itga6+ tumor cells

growth_protocol: Inbred male or female Dnmt3a flox/flox (C57/Bl6) backcrossed to Krt14-CRE-YFP (C57/Bl6) for 6-9 generations were used for all animal experiments.

extract_protocol:
Tumor cells (YFPbright/lineageneg cells), pre-cancerous epidermis of interfollicular epidermis (YFPpos/CD49fhigh/CD34neg cells), and bulge hair follicle stem cells (YFPbright/CD49fhigh/CD34pos cells) were FACS-sorted using a BD FACSAria Fusion flow cytometer (BD Biosciences). Approximately 3-20x10^4 cells were sorted and lysed in 1 ml of TRIzol for RNA and DNA isolation. After adding 200 µl chloroform, samples were vortexed for 30 second and then centrifuged at 12,000 g to separate the RNA-containing supernatant from the organic phase. RNA was precipitated with 1´ volume of isopropanol, washed twice with 70% ethanol, and then used for library preparation. The interphase of the TRIzol solution (after removal of the supernatant) was precipitated adding 1´ volume of isopropanol, centrifuged for 1 h at 4°C at 13,000 g, washed twice with ethanol, and digested overnight at 55°C with proteinase K (10 mg/ml) in TE 1´ buffer. The following day, digested material was incubated 1 h at 37°C with RNase A and purified using a conventional phenol/chloroform separation. The DNA pellet was quantified, and DNA was used for library preparation for MeDIP-seq and hMeDIP-seq experiments.
Purified genomic DNA (250 ng) from tumor cells was sonicated to obtain fragments of 300-700 bp. Adaptors from the NEBNext Ultra DNA Library Prep Kit for Illumina were added to the fragmented DNA. DNA was denatured for 10 min at 99°C and cooled to avoid re-annealing. Fragmented DNA was incubated overnight with 1 mg of antibodies (5-methylcytosine, Abcam cat. # ab10805; 5-hydroxymethylcytosine, Active Motif, cat. # 39769) previously cross-linked with 15 ml of Dynabeads Protein A (Life Technologies). Immunocomplexes were recovered using 8 ml for 2 h. The following morning, DNA was washed three times for 10 min each, and purified DNA was extracted using QIAquick MinElute (Qiagen). Amplified libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following the manufacturer's instructions.

treatment_protocol: Chemically-induced skin carcinogenesis was performed as previously described (Nassar et al. 2015; Abel et al. 2009), with a slight modification to yield high-frequency SCCs in the C57/Bl6 genetic background. Briefly, the back skin of 8-week-old mice -- at which time hair follicles are in their resting phase (telogen) -- was shaved and treated with the mutagen 7,12-dimethylbenz[a]anthracene (DMBA; 200 µl of 0.25 mg/ml solution in acetone) and the pro-inflammatory and pro-proliferation agent 12-O-tetradecanoyl phorbol-13-acetate (TPA; 200 µl of 0.02 mg/ml solution in acetone) once weekly for 6 weeks. Specifically, DMBA was given on Monday and TPA always on the Friday of the same week.

value: Itga6+ tumor cells

tag: genetic background

value: CU Black Six

value: Dnmt3a Flox/Flox Krt14-CRE (Dnmt3a Krt14 KO)

tag: age

value: 6 months

tag: gender

value: Female

tag: medip antibody

value: 5-methylcytosine (Abcam 10805, clone 33D3)


title: prostate cancer case with archival biopsy tissue 344

tag: disease stage

tag: metastasis


title: MeDIP-seq KO Tumor rep 1

tag: genotype/variation


title: MeDIP-seq WT Tumor rep 2

source_name: DNA methylation profile of WT Itga6+ tumor cells

value: Wild-Type


title: pool_26_plasmid

value: plasmid

tag: cell line

value: enzalutamide


title: ZT18_AL_1_NaCl

value: Liver

tag: time

tag: feeding

value: Ad Libitum

value: NaCl


title: pool_24_plasmid

value: LNCaP/AR cells


title: prostate cancer case with archival biopsy tissue 601-4a


title: ZT04_ST_1_NaCl

tag: tissue

value: Fasted


title: pool_23_plasmid

tag: sample type


title: pool_25_plasmid

tag: treatment


title: prostate cancer case with archival biopsy tissue 430-5a


title: MeDIP-seq WT Tumor rep 1


title: PD Control Rat Striatal Microarray 1

description: replicate 1

value: Striatum

value: YES

value: NO


title: ZT12_AL_1_NaCl

tag: strain


title: ZT04_AL_1_NaCl

tag: rna treatment


title: pool_21_plasmid


title: pool_22_plasmid


title: ZT18_ST_1_NaCl


title: M2630

city: Aachen

first: Emiel

last: van der Vorst

address: Pauwelstraße 30

country: Germany

institute: IMCAR/IZKF

data_processing:
base calling and quality score was performed with Illumina sequencing Q scores
alignment was performed with STAR
Reads per feauture per genes were calculated using FeuturesCounts funtion from Subread software
The data were filtered, normalized and the differential gene expression was computed using the packages limma (https://bioconductor.org/packages/release/bioc/html/limma.html) and edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) on R
Genome_build: mm10 and GCRh38
Supplementary_files_format_and_content: tab-delimited text files include Readcounts and CPM values for each Sample

source_name: Mouse naïve

extract_protocol:
Total RNA from the cells was extracted with the Trizol protocol followed by Qiagen RNeasy Mini Kit
Libraries were prepared according to Illumina trueseq specifications

tag: cell type

value: mouse aortas endothelial cells

tag: genotype

value: naive

tag: straub


title: M2629


title: M2631


title: pool_20_plasmid


title: prostate cancer case with archival biopsy tissue 295-4a

value: M0 poly

value: No metastasis


title: prostate cancer case with archival biopsy tissue 149-5s


title: M2628

source_name: Mouse KO miRNA26B

value: KO miRNA26B


title: HEK_rep1

city: Waltham

first: WEIJIN

last: XU

state: MASSACHUSETTS

address: 415 SOUTH STREET

institute: Brandeis University/HHMI

data_processing:
RNA sequencing data were analyzed as described in (Rodriguez et al., 2012; McMahon et al., 2016), with minor modifications.
Scripts available on GitHub (https://github.com/rosbashlab/TRIBE).
Alignment to respective genomes was done with STAR with referenence annotation in gtf format. Multimapped reads are removed.
PCR duplicate is removed with UMIs by samtools for HEK cell and rat cortical neuron samples.  PCR duplicate is removed with Picard v2.8.2 for N2A sample.
Genome_build: hg38, rn6, mm10
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format, (Chromosome, co-ordinate, co-ordinate, edit %, edit%_number of total reads)

source_name: HEK293 Cells

extract_protocol:
RNA from transfected cells are extracted by TRIZOL
HEK293 cell and rat cortical neuron samples were prepared using NEXTFLEX Rapid Directional qRNA-Seq Kit. N2A cells were prepared by SMART-Seq2 protocol and Illumina Nextera libarary kit.

treatment_protocol: HEK cell transfection was done by calcium phosphate transfection, rat cortical neurons were tranduced by recombinant lentivirus and N2A cells were transfected by lipofectamine

tag: selection method

value: control sample


title: hADARcd_HEK_rep2

value: Transient tranfection


title: pool_2_plasmid

city: Dallas

first: Ping

last: Mu

address: 6000 Harry Hines Blvd., NA6.308A

institute: UT Southwestern Medical Center

value: plasmid


title: HEK_rep2


title: M2627


title: prostate cancer case with archival biopsy tissue 501-5a


title: prostate cancer case with archival biopsy tissue 677

value: M0 oligo


title: pool_19_plasmid

value: enzalutamide


title: prostate cancer case with archival biopsy tissue 61


title: hADARcd_HEK_rep1


title: M2626


title: pool_18_plasmid


title: prostate cancer case with archival biopsy tissue 493


title: TDP43_5FL_TRIBE_HEK_rep1


title: pool_17_plasmid


title: HNEC 5

city: BREST

first: Stéphanie

last: MOISAN

address: 22 avenue Camille Desmoulins

department: Functional Genetics

institute: INSERM UMR 1078

data_processing:
Library strategy: 5C-seq
5C Reference Maker - This tool accepts as input a file containing the primers and sequences used in the 5C experiment. They must be in the following, tab delimited, format. The final output of this program, is a fasta file containing all possible combinations of these primers as possible 5C products. This is to be used in conjunction with tmap to map 5C Sequence data.
Map FASTQ with TMAP - This program will map any FASTQ file from the Ion Torrent Server to the specified reference file. Output is in SAM format.
5C Sequence Counter - This program takes as an input a SAM file with header from a 5C Seq experiment and generates an IF file. Basic filtering is also done on mapping quality, presence of the restriction cut site, and location of the mapped read on the reference strand. Output is in tabular format.
Convert - This tool takes a 5C interaction frequency (IF) list and converts it into a heatmap format readable by my5C. By default, this is a symmetrical heatmap, with every interaction appearing once on either side of the diagonal axis. Output is in tabular format.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files

source_name: Human nasal epithelial cells

growth_protocol: Human nasal epithelial cells (HNEC) from healthy control individuals were harvested using a sterile cytology brush (Gyneas, cat. no. 02-106). HNECs were collected by brushing the middle turbinate with backward-forward and rotatory movements and were placed in a collecting medium (Ham’s F12 (Lonza) containing 1% Ultroser G (Pall, cat. no. 15950-17), and 1% antibiotic (PAA, cat. no. P11-002). Survival of the cells in this medium was tested until 96 hours at room temperature. HNECs were detached from the brush by vortexing and were washed three times with Dulbecco's modified eagle medium (DMEM; Lonza) supplemented with decreasing antibiotic concentrations and a final wash with 1X phosphate buffered saline (PBS). Cell suspensions were centrifuged 5 min at 2,200 g at 4°C. The cell pellets were resuspended in a selected and optimized cell culture media of human airway epithelial cells (Airway Epithelial Cell Growth Medium; PromoCell) and cells were cultured following the manufacturer’s instructions.

extract_protocol:
5C libraries were generated by incubating an individual 3C library with a pool of 5C primers to a final volume of 10ul of annealing buffer and to final individual primer concentrations of 2nM. 5C primers were annealed to 3C templates overnight at 50ºC, and ligated the following day by adding 20ul of ligation buffer containing 10 units of Taq DNA ligase for 1h at 50ºC. The reactions were terminated by a 10 minute incubation at 65ºC.
5C libraries were quantified on agarose gel and diluted to 0.048 ng/ml. One microliter of diluted 5C library was used for sequencing with an Ion PGM™ sequencer. Samples were sequenced onto Ion 316™ Chips v2 following the Ion PGM Hi-Q Chef kit and Ion PGM™ Hi-Q Sequencing Kit protocols as recommended by the manufacturer’s instructions (Thermo Fisher Scientific).

tag: disease status

value: Healthy

value: Middle turbinate nasal mucosa

value: Nasal epithelial cells


title: HNEC 4


title: pool_16_plasmid

value: LNCaP/AR cells


title: prostate cancer case with archival biopsy tissue 441


title: TDP43_TRIBE_HEK_rep2


title: HNEC 3


title: TDP43_TRIBE_HEK_rep1


title: prostate cancer case with archival biopsy tissue 68


title: prostate cancer case with archival biopsy tissue 104


title: pool_14_plasmid


title: pool_15_plasmid


title: HNEC 2


title: prostate cancer case with archival biopsy tissue 417


title: SU540

city: Palo Alto

first: Ritika

last: Dutta

address: 265 Campus Drive

institute: Stanford School of Medicine

data_processing:
cDNA libraries were sequenced on the Illumina Nextseq platform to obtain 80-bp single-end reads. The reads were trimmed, 2 nt on each end, to remove low quality parts, and improve mapping to the genome. The 78 nt reads that resulted were compressed by removing duplicates, but keeping track of how many times each sequence occurred in each sample in a database. (Performed by Girihlet)
The unique reads were then mapped to the human genome, using exact matches. Each mapped read was then assigned annotations from the underlying genome. In case of multiple annotations (e.g. a miRNA occurring in the intron of a gene), a hierarchy based on heuristics was used to give a unique identity to each read. This was then used to identify the reads belonging to each transcript and coverage over each position on the transcript was established. (Performed by Girihlet)
We used the median of this coverage as an estimate of the gene's expression value. In order to compare the expression in different samples, quantile normalization was used. (Performed by Girihlet)
The ratios of expression levels were then calculated to estimate the log (base 2) of the fold-change. In order to prevent low-expressed genes from dominating the list of genes with a large fold change, we added a regularizer (5) to each value, ensuring that genes with expression around or below 5 would appear to have low fold-change.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with normalized read counts

source_name: AML Patient Sample

extract_protocol:
Qiagen RNAeasy Kit
cDNA libraries were prepared using 500ng of total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina) - performed by Girihlet

value: sorted blasts

tag: markers sorted on

value: PI-, Annexin V-, CD45 mid, CD3-, CD33 mid blast gate after thawing and culture in Myelocult (+TPO, SCF, Flt3L, IL3, IL6, GMCSF, GCSF) for 24 hrs

tag: time in culture

value: After sorting, cultured for 72 hours in StemSpan + TPO, SCF, Flt3L


title: pool_13_plasmid


title: SU575

growth_protocol: cultured for 72 hours in StemSpan + TPO, SCF, Flt3L


title: HNEC 1


title: prostate cancer case with archival biopsy tissue 746-5a-B

tag: disease stage

tag: metastasis


title: SU209


title: prostate cancer case with archival biopsy tissue 753-5s


title: pool_12_plasmid

tag: cell line


title: TDP43_5FL_TRIBE_HEK_rep2


title: pool_11_plasmid


title: OSCA-40

city: VIENNA

first: Angelos

middle: Theodoros

last: Athanasiou

address: Veterinärplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Primary analysis and de-multiplexing using Illumina's CASAVA 1.8.2
Mapping to the dog genome (CanFam3.73) with Tophat and the help of Cufflinks packages using default parameters
Filtering of uniquely mapped reads using samtools
Normalization using DEXSeq
Genome_build: CanFam3.73
Supplementary_files_format_and_content: tab-delimited text file including DEXSeq normalized counts

organism: Canis lupus familiaris

source_name: bone tumor

extract_protocol:
RNeasy Mini Kit (Qiagen)
Illumina's TruSeq RNA library preparation kit v2 (Illumina, San Diego, CA, USA)

value: bone tumor

tag: tumor type

value: cell line

tag: diagnosis

value: Osteosarcoma

tag: histopath

value: Osteoblastic osteosarcoma

tag: breed

value: Saint Bernard

tag: gender

value: F

tag: sample origin

value: R. distal femur

tag: age at dx in y/m/d

value: AMP


title: OSCA-32

tag: tissue

value: Fibroblastic

value: Great Pyrenees

value: L. distal radius

tag: treatment

value: SOC


title: OSCA-30

value: German Shepherd

value: M


title: SU353

tag: cell type

value: sorted blasts


title: pool_10_plasmid

tag: sample type

value: plasmid

value: LNCaP/AR cells

value: enzalutamide


title: SU351

value: PI-, Annexin V-, CD45 mid, CD3-, CD33 mid blast gate after thawing and culture in Myelocult (+TPO, SCF, Flt3L, IL3, IL6, GMCSF, GCSF) for 24 hrs

value: After sorting, cultured for 72 hours in StemSpan + TPO, SCF, Flt3L


title: prostate cancer case with archival biopsy tissue 604-4a

value: No metastasis


title: DOS-71

extract_protocol:
TRIzol (Thermo Fisher Scientific)
Illumina's TruSeq RNA library preparation kit v2 (Illumina, San Diego, CA, USA)

value: bone tumor

value: tumor

value: Osteosarcoma

value: Osteoblastic osteosarcoma

value: Golden Retriever

value: unknown


title: SU369


title: pool_1_plasmid


title: DOS-127

value: English Mastiff

value: F

value: front leg

value: PALL


title: DOS-126

value: Unknown

value: Great Dane

value: M

value: L. distal radius

value: SOC


title: SU555

value: sorted blasts

value: PI-, Annexin V-, CD45 mid, CD3-, CD33 mid blast gate after thawing and culture in Myelocult (+TPO, SCF, Flt3L, IL3, IL6, GMCSF, GCSF) for 24 hrs

value: After sorting, cultured for 72 hours in StemSpan + TPO, SCF, Flt3L


title: prostate cancer case with archival biopsy tissue 553-5a

value: No metastasis


title: CD34_4

source_name: Umbilical cord blood

value: sorted CD34+ cells

value: DAPI-, CD3-, CD34+ after Ficoll + MACS CD34 enrichment


title: jac1 UV-treated rep2

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

data_processing:
Reads were aligned to the Arabidopsis genome by STAR (v2.5.2b) (Dobin et al., 2013) using the Araport11 annotation (Cheng et al. 2017).
The number of reads per gene was quantified with the featureCounts function as implemented in the Subread package v1.6.2 (Liao et al., 2014).
Genome_build: Araport11
Supplementary_files_format_and_content: Tab-delimited text files include gene counts by featureCounts function

organism: Arabidopsis thaliana

source_name: Plant rosette

growth_protocol: Four-week-old Arabidopsis thaliana Columbia-0 gl1 (Col-0 gl1) wild-type plants and jac1 mutant in the Col-0 gl1 background, were used in this study. Plants were grown in Jiffy pots in standard laboratory conditions (8 h photoperiod, PPFD: 80 mol m ̄² s ̄¹, 50% relative air humidity and temperature day/night: 22/18 °C).

extract_protocol:
Whole rosettes were harvested from non-treated plants and 30 min after UV-C treatment. The RNA was isolated from three biological replicates, each consisting of at least four rosettes. Total RNA isolation was performed using a GeneMATRIX Universal RNA Purification Kit (EURX, Gdańsk, Poland) with the additional step of on-column DNase I digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Precise amount of UV-C radiation (100 mJ cm ̄²) was applied using 500 Crosslinker (Hoefer Pharmacia Biotech, San Francisco, CA, USA), equipped with lamps emitting light in the wavelength ranging from 250 to 258 nm (type G8T5, 8W; Sankyo Denki, Hiratsuka, Japan).

value: whole rosette

tag: genotype

value: jac1 mutant

tag: background ecotype

value: Col-0 gl1

value: UV-C radiation (100 mJ cm-2)

tag: age

value: Four weeks


title: jac1 UV-treated rep3


title: DOS-119

value: bone tumor

value: tumor

value: Osteosarcoma

value: Osteoblastic osteosarcoma

value: Great Pyrenees

value: F

value: R. distal radius

value: EUTH at Dx


title: prostate cancer case with archival biopsy tissue 510-4a

tag: disease stage


title: 0320

extract_protocol:
RNeasy Fibrous Tissue Mini Kit (Qiagen)
Illumina's TruSeq RNA library preparation kit v2 (Illumina, San Diego, CA, USA)

value: Osteochondrosarcoma

value: Mixed

value: distal femur/proximal tibia


title: CD34_3

value: sorted CD34+ cells

tag: markers sorted on

value: DAPI-, CD3-, CD34+ after Ficoll + MACS CD34 enrichment

tag: time in culture

value: After sorting, cultured for 72 hours in StemSpan + TPO, SCF, Flt3L


title: jac1 UV-treated rep1

value: whole rosette

value: jac1 mutant

value: Col-0 gl1


title: jac1 non-treated rep3

value: Non-treated control

value: Four weeks


title: 0460

value: bone tumor

tag: tumor type

value: tumor

value: Osteosarcoma

value: Landseer

value: distal tibia

value: CARBO


title: jac1 non-treated rep2


title: prostate cancer case with archival biopsy tissue 478-5s-B

tag: metastasis

value: No metastasis


title: CD34_2


title: prostate cancer case with archival biopsy tissue 656-5a


title: CD34_1


title: 1091

tag: diagnosis

tag: histopath

value: Osteoblastic osteosarcoma

value: Leonberger

value: F

value: AMP


title: prostate cancer case with archival biopsy tissue 45-4a


title: 1033

value: Lung metastasis of an osteosarcoma

tag: breed

value: Boxer

tag: gender


title: jac1 non-treated rep1

value: whole rosette

value: jac1 mutant


title: wildtype UV-treated rep3

value: Wild-type

value: Col-0 gl1

value: UV-C radiation (100 mJ cm-2)


title: prostate cancer case with archival biopsy tissue 578-5a


title: hSMCs_P6 TNFa Rep2 [RNA-seq]

city: Copenhagen

first: Lars

last: Ingerslev

address: Blegdamsvej 3B

institute: Copenhagen University

data_processing:
Reads were aligned to the hg38 GENCODE Comprehensive gene annotations (Harrow et al., 2012) version 27 using STAR (Dobin et al., 2013).
Read summation onto genes was performed by featureCounts (Liao et al., 2014).
Differential expression testing was performed with edgeR (Lun and Smyth, 2014) using a model of the form ~ 0 + group + block, where group was a factor containing information on both passage and treatment, and block encoded the two replicates.
Gene ontology enrichments were performed using the camera function (Wu and Smyth, 2012) which is part of the edgeR package.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file with expression of GENCOVE v28 genes

source_name: hSMCs_P6 TNFa

extract_protocol:
Total RNA was purified from hSMCs cells differentiated into myotubes (control, palmitate or TNFα treated) using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
1 mg of total RNA was depleted of rRNA and subsequently used to generate libraries using the TruSeq standard total RNA with Ribo-Zero Gold kit (Illumina). The PCR cycle number for each library amplification was optimized by running 10% of the library DNA in a real-time PCR reaction using Brilliant III Ultra-fast SYBR Green QPCR Master Mix (AH Diagnostic) and a C1000 Thermal cycler (Bio-Rad) (Table S7). Libraries were sequencing on a Illumina NextSeq 500 system (Illumina) using the NextSeq 500/550 High Output v2 kit (75 cycles).

value: Primary Human Skeletal Muscle cells (hSMCs)

tag: passage

tag: replicate

value: TNFa


title: hSMCs_P6 TNFa Rep1 [RNA-seq]

tag: treatment


title: NEURON_rep2

source_name: rat cortical neurons

tag: selection method

value: control sample


title: prostate cancer case with archival biopsy tissue 403-5a


title: wildtype UV-treated rep2

tag: tissue

value: Four weeks


title: hSMCs_P6 Palm Rep2 [RNA-seq]

source_name: hSMCs_P6 Palm

tag: cell type

value: palmitate


title: NEURON_rep1


title: prostate cancer case with archival biopsy tissue 492-5a

source_name: prostate tissue

value: No metastasis


title: hSMCs_P6 Palm Rep1 [RNA-seq]


title: prostate cancer case with archival biopsy tissue 490-5m-B


title: wildtype UV-treated rep1

tag: genotype

tag: background ecotype


title: prostate cancer case with archival biopsy tissue 326-4a

tag: disease stage


title: wildtype non-treated rep3

value: Non-treated control

tag: age


title: hSMCs_P6 Ctrl Rep2 [RNA-seq]

source_name: hSMCs_P6 Ctrl

value: control (Ctrl)


title: hADARcd_NEURON_rep2

value: Lentiviral transduction


title: hADARcd_NEURON_rep1


title: wildtype non-treated rep2


title: wildtype non-treated rep1


title: prostate cancer case with archival biopsy tissue 249-5a


title: prostate cancer case with archival biopsy tissue 238-4a


title: hSMCs_P6 Ctrl Rep1 [RNA-seq]


title: TDP43_TRIBE_NEURON_rep2


title: phot1/phot2 UV-treated rep3

growth_protocol: Four-week-old Arabidopsis thaliana Columbia-0 gl1 (Col-0 gl1) wild-type plants and three mutant lines, phot1, phot2 and phot1/phot2, all in the Col-0 gl1 background, were used in this study. Plants were grown in Jiffy pots in standard laboratory conditions (8 h photoperiod, PPFD: 80 mol m ̄² s ̄¹, 50% relative air humidity and temperature day/night: 22/18 °C).

value: phot1/phot2 mutant


title: prostate cancer case with archival biopsy tissue 221-5a


title: phot1/phot2 UV-treated rep2


title: prostate cancer case with archival biopsy tissue 42-5a


title: hSMCs_P5 Palm Rep2 [RNA-seq]

source_name: hSMCs_P5 Palm


title: hSMCs_P5 TNFa Rep1 [RNA-seq]

source_name: hSMCs_P5 TNFa


title: prostate cancer case with archival biopsy tissue 716-4a


title: prostate cancer case with archival biopsy tissue 138-5a-B


title: TDP43_TRIBE_NEURON_rep1


title: phot1/phot2 UV-treated rep1


title: hSMCs_P5 Palm Rep1 [RNA-seq]


title: phot1/phot2 non-treated rep3


title: prostate cancer case with archival biopsy tissue 574-5a


title: hSMCs_P5 Ctrl Rep2 [RNA-seq]

source_name: hSMCs_P5 Ctrl


title: A1-2 cells, Dex18hr, single-cell RNAseq

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

description:
scRNAseq_rawCounts.txt
scRNAseq_seuratV3_normalized.txt

data_processing:
For bulk RNAseq, adapter sequences were trimmed from RNA-seq reads using Cutadapt (Martin, 2011) and low quality reads were removed from analysis using Sickle (Joshi NA et al., 2011). Alignment was performed using STAR (Dobin et al., 2013) to generate coverage tracks and using Salmon (Patro et al., 2017) and to obtain gene counts for differential expression analysis using limma-voom (Law et al., 2014) with cutoffs of Fold Change > 1.5, p-value<0.01, and False Discovery Rate < 0.05
For single-cell RNAseq, read 1 was technical and read 2 was biological. Barcode and UMI sequence positions are not fixed, so Bio-Rad ddSEQ reads were parsed for cell barcode and UMI information. Reads were filtered out according to the following constraints: no 6nt barcode segment is more than a Hamming distance of 1 from a valid barcode block; all linker segments are within 1nt length of the expected value; the UMI has a length of 8nt; and only 1 mismatch is allowed within the ACG-GAC segments flanking the UMI. Reads with cell barcode information passing these filters were then aligned to the hg19 reference genome using STAR v2.5.2b (Dobin et al., 2013) and annotated with the Gencode comprehensive v28lift37. Uniquely-mapped reads were subsequently assigned to genes using featureCounts v1.5.3 (Liao et al., 2013). PCR duplicates were removed using umi_tools (Smith et al., 2017) in per-gene mode. The knee-calling algorithm from umi_tools was used to identify an appropriate total transcript count cut-off for cells in each sample, yielding a total of 4001 cells. Cells with mitochondrial gene percentage greater than 5% were removed. Biological replicates of 4hr and 8hr treatments were combined and cell counts were balanced between all time points by randomly sub-setting each time point to 400 cells. Cyclone from the scran package (Lun et al., 2016; Scialdone et al., 2015) was used to determine cell-cycle scores for all cells, and Seurat v3 (Stuart et al., 2019) was then use to normalize and scale the data such that the impacts of transcript counts, mitochondrial percent, and cell-cycle scores were regressed-out.
Genome_build: hg19
Supplementary_files_format_and_content: raw Counts and normalized Counts
bigwigs were generated from STAR coverage files using bedGraphToBigWig.

source_name: A1-2 breast cancer cells

growth_protocol: Cells were cultured in modified Eagle medium (MEM) containing 10% fetal bovine serum, 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131).

extract_protocol:
For bulk RNAseq, Qiagen RNeasy kits with on-column DNase treatment were used to isolate total RNA. For single-cell RNAseq, cells were dissociated using 0.25% Trypsin-EDTA (Gibco 25200) into single cell suspension and the BioRad ddSeq Single-Cell Isolator was used to create single cell emulsions
Bulk RNAseq libraries were generated using Ribo-Zero Gold and the Illumina TruSeq RNA Stranded kit. Single-cell RNAseq libraries were generated using the Illumina SureCell WTA 3’ Library Prep kit

treatment_protocol: For Dexamethasone treatments, cells were initially cultured for 24 hours in reduced-serum, hormone-stripped media (Phenol-red free MEM (Gibco 51200) with 5% Charcoal/Dextran treated FBS (Atlanta S11650), 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131)). Subsequently, Dexamethasone (Sigma D4902) was added to the media at 100 nM for all treatments timepoints and 9.5 x 10e-4% ethanol was used as vehicle control. For both RNAseq experiments, control cells were treated with ethanol for 18 hours.

value: A1-2 breast cancer cells

value: 18hr Dex


title: phot1/phot2 non-treated rep2

value: whole rosette


title: phot1/phot2 non-treated rep1


title: hSMCs_P5 Ctrl Rep1 [RNA-seq]


title: phot2 UV-treated rep3

value: phot2 mutant


title: prostate cancer case with archival biopsy tissue 35-5a

extract_protocol:
Diagnostic hematoxylin and eosin (H&E) PNBX slides were reviewed by a genitourinary pathologist, and high-grade tumor areas (Gleason grade 4, 5, or neuroendocrine/small cell) were encircled.  Transfer of annotated areas to the paraffin-embedded tissue blocks was performed and 1-2mm sterile circular biopsy punches enabled manual procurement of formalin-fixed tissue from the block. A minimum of 2 (1mm) cancer cores were used from each high-grade tumor area for RNA and/or DNA preparation. Total RNA was extracted from tissue cores using the Ambion Recover All Total Nucleic Acid Isolation Kit for FFPE (ThermoFisher). Samples were eluted with H20 and quantitated with nanodrop and bioanalyzer.
Approximately 40-100ng of RNA was used to generate the libraries using the TruSeq RNA Access Library Prep Kit (Illumina) according to manufacturer’s instructions.


title: hSMCs_P5 TNFa Rep2 [RNA-seq]


title: A1-2 cells, Dex8hr_rep2, single-cell RNAseq

value: 8hr Dex


title: prostate cancer case with archival biopsy tissue 146-4a


title: A1-2 cells, Dex4hr_rep2, single-cell RNAseq

value: 4hr Dex


title: TDP43_CTL_N2A_rep1

source_name: N2A Cells


title: phot2 UV-treated rep2

value: Col-0 gl1

value: UV-C radiation (100 mJ cm-2)


title: TDP43_KD_N2A_rep2

value: Transient tranfection


title: A1-2 cells, Dex4hr_rep1, single-cell RNAseq


title: SM-AYS2Y

type: genomic

hyb_protocol: Approximately 80ng of gDNA was used in the Affymetrix OncoScan FFPE Assay kit (Affymetrix) according to manufacturer’s instructions.

scan_protocol: The arrays were washed and stained using GeneChip Fluidics Station 450 (Affymetrix, Inc.) and scanned in GeneChip Scanner 3000 7G (Affymetrix, Inc.). The fluorescence of clusters was measured to generate a DAT file. Cluster intensity values were automatically calculated using a built-in algorithm from DAT files using GeneChip Command Console software (Affymetrix, Inc.), and a CEL file was generated.

data_processing:
data was processed with Affymetrix Chromosome Analysis Suite 3.1 (ChAS 3.1) to generate probe level and gene level log2-ratio using normalized data.
Primary data description: Output (probe level) of OncoScan profiles using ChAS: Log2Ratio, WeightedLog2Ratio, AllelicDifference, NormalDiploid, BAF (B allele frequency)

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Primary tumor tissues

extract_protocol: DNA was extracted from 1mm FFPE cores with AnaPrep 12 Automated Nucleic Acid Preparation Instrument (Biochain) and quantitated with Qubit (Life technology).

treatment_protocol: No treatment

tag: tissue/sample type

value: prostate needle biopsy (PNBx)


title: TDP43_KD_N2A_rep1


title: SM-AYS2X


title: prostate cancer case with archival biopsy tissue 381-5a


title: SM-AYS32


title: A1-2 cells, Dex2hr, single-cell RNAseq

value: 2hr Dex


title: TDP43_OE_N2A_rep2


title: SM-AYS21


title: SM-AYS1J


title: TDP43_CTL_N2A_rep2

value: control sample


title: A1-2 cells, Dex1hr, single-cell RNAseq

value: 1hr Dex


title: phot2 UV-treated rep1

value: Four weeks


title: A1-2 cells, Dex8hr_rep1, single-cell RNAseq


title: phot2 non-treated rep2

value: Non-treated control


title: TDP43_OE_N2A_rep1


title: SM-AYS2G


title: A1-2 cells, D18hr_rep3, Bulk RNAseq


title: phot1 UV-treated rep3

value: phot1 mutant


title: SM-AYS31


title: A1-2 cells, D18hr_rep2, Bulk RNAseq


title: phot1 UV-treated rep2


title: gfppos_dc1_3

city: NEW YORK

first: Miriam

last: Merad

state: New York

address: 1470 Madison Ave, Room 5-301

department: Oncological Sciences

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

description: bulk RNAseq

data_processing:
For CITEseq GEX libraries: Read 1 is technical: Cell barcode is bp 1-16; UMI is bp 17-26. Read 2 is biological.
For CITEseq ADT libraries: Read 1 is technical: Cell barcode is bp 1-16; UMI is bp 17-26. Read 2 is biological: bp 1-7 identify a CITEseq antibody (as indicated in ADT_TAGS.CSV).
After library demultiplexing, gene expression libraries were aligned to the mm10 or GRCh38 reference transcriptomes and count matrices were generated using the default Cell Ranger 2.1 workflow, using the “raw” matrix output. CITEseq library reads were directly queried for antibody barcodes (listed in ADT_TAGS.CSV) and cell barcodes in the appropriate read positions, including antibody sequences within a Hamming distance of 1 from the reference sequence.
single_cell_metadata.csv.gz represents the results of QC filtering and transcriptome-based clustering on CITEseq data.
For RNAseq: Fastqs were aligned to the mm10 reference genome, reads were dereplicated for PCR duplicates, and gene counts were generated using STAR v2.5 using –quantMode GeneCounts.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts

source_name: lung conventional type-1 dendritic cells (CD45+ Siglec F- Ly6G- MHCIIhi CD11c+ CD24hi CD11b- CD103+) positive for GFP in mice bearing GFP-expressing tumors

extract_protocol:
10e4 DC were sorted as described above into 700 mL Trizol. RNA was isolated using RNeasy Micro Kits (Qiagen). 0.5-1 ng of RNA was synthesized into cDNA using the Smart-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio). Sequencing libraries were prepared using the Low Input Library Prep Kit (Takara Bio).
Single cell suspensions were obtained from lung and LN by digestion with collagenase IV 0.25mg/ml (Sigma) at 37C for 30min (lung) or 25min (LN) followed by passing through a 70um cell strainer and RBC lysis (RBC lysis buffer, BioLegend) for 2min at room temperature. For flow cytometry or FACS cells were stained in FACS buffer (PBS supplemented with 2% BSA and 5mM EDTA) with mAbs specific to CD45 (clone 30-F11, BioLegend), Siglec F (clone E50-2440, BD Pharmingen), CD11c (clone N418, Invitrogen), CD24 (clone M1/69, Invitrogen), CD103 (clone 2E7, BioLegend), I-A/I-E (clone M5/114.15.2, eBioscience), CD11b (clone M1/70, eBioscience)

treatment_protocol: 8-week-old mice were injected intravenously with 5x10e5 KP-GFP cells. Lungs were analyzed on day 28.

tag: strain

value: lung


title: SM-AYS3K


title: VA337


title: phot2 non-treated rep3


title: VA333


title: A1-2 cells, D18hr_rep1, Bulk RNAseq

value: A1-2 breast cancer cells


title: A1-2 cells, EtOH, single-cell RNAseq

value: 18hr EtOH


title: A1-2 cells, D8hr_rep3, Bulk RNAseq


title: phot2 non-treated rep1

value: whole rosette


title: VA330


title: phot1 non-treated rep2


title: phot1 UV-treated rep1


title: A1-2 cells, D8hr_rep2, Bulk RNAseq


title: phot1 non-treated rep3


title: A1-2 cells, D8hr_rep1, Bulk RNAseq


title: gfpneg_dc1_1

description: bulk RNAseq

source_name: lung conventional type-1 dendritic cells (CD45+ Siglec F- Ly6G- MHCIIhi CD11c+ CD24hi CD11b- CD103+) negative for GFP in mice bearing GFP-expressing tumors


title: gfppos_dc1_1

description: bulk RNAseq


title: beadpos_dc1_3

description: bulk RNAseq

source_name: lung conventional type-1 dendritic cells (CD45+ Siglec F- Ly6G- MHCIIhi CD11c+ CD24hi CD11b- CD103+) positive for beads in mice treated with fluorescent beads intranasally

treatment_protocol: 50ml Polybead Dyed Blue 1.0 Micron Microspheres (Polysciences Inc) were coated while rotating for 20h at 4°C with ovalbumin (Worthington Ovalbumin, Low EndoTM, purified; 50mg/ml in PBS), washed twice with PBS, and intranasally applied into mouse lungs. Lungs were analyzed 5h after beads application.


title: gfpneg_dc1_2

description: bulk RNAseq


title: phot1 non-treated rep1


title: VA329


title: A1-2 cells, D4hr_rep3, Bulk RNAseq


title: Wild-type UV-treated rep3

value: Wild-type


title: beadpos_dc1_2

description: bulk RNAseq


title: VA326


title: A1-2 cells, D4hr_rep2, Bulk RNAseq


title: beadpos_dc1_1

description: bulk RNAseq


title: SM-AYS2W


title: HCT116 sh LIG1

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

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

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: openSesame from SeSAMe R package

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: 37ºC, 5% CO2, McCoy's 5A media with 10% FBS and 1% penicillin-streptomycin

extract_protocol: 3x extraction: phenol, phenol/chlorofom/isoamyl alcohol (25:24:1), chloroform/isoamyl alcohol (24:1); precipitation; RNase treatment; precipitation

tag: cell line

tag: shRNA


title: A1-2 cells, D4hr_rep1, Bulk RNAseq


title: beadneg_dc1_3

description: bulk RNAseq

source_name: lung conventional type-1 dendritic cells (CD45+ Siglec F- Ly6G- MHCIIhi CD11c+ CD24hi CD11b- CD103+) negative for beads in mice treated with fluorescent beads intranasally


title: SM-AYS2Q (VA324)


title: A1-2 cells, D2hr_rep3, Bulk RNAseq


title: A1-2 cells, D2hr_rep1, Bulk RNAseq


title: SM-AYS1O


title: A1-2 cells, D2hr_rep2, Bulk RNAseq


title: Wild-type non-treated rep3


title: SM-AYS1Q


title: beadneg_dc1_2

description: bulk RNAseq


title: Wild-type non-treated rep2


title: Wild-type UV-treated rep1