title: J06_FFPE_028

type: RNA

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

hyb_protocol: FF tissues. Hybridization on U133 Plus 2.0 arrays overnight (17 h) according to the manufacturer's protocol.  FFPE tissues. Hybridization on U133 Plus 2.0 arrays overnight (17‑20 h) according to the manufacturer's protocol.

scan_protocol: FF tissues. The hybridized DNA microarray was fluorescently stained with GeneChip Fluidics Station 450, and scanned using a GeneChip Scanner 3000.   FFPE tissues. The hybridized DNA microarray was fluorescently stained using GeneChip Fluidics Station 450, and scanned using a GeneChip Scanner 3000 (both Affymetrix; Thermo Fisher Scientific, Inc.).

data_processing: Probe intensities were normalized with MAS5.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE tumor

label_protocol: FF tissues. Approximately 100 ng RNA (RNA integrity number >7) was used to generate second‑strand cDNA, and cRNA was amplified using the oligodeoxynucleotide ribosylthymine primers, then biotinylated and fragmented using the Gene Profiling Reagent kit (Affymetrix; Thermo Fisher Scientific, Inc.).  FFPE tissues. Second‑strand cDNA was generated using 70‑100 ng of RNA, and cDNA was amplified using the oligodeoxynucleotide ribosylthymine and random primers using an Ovation FFPE whole‑transcriptome amplification system (NuGEN Technologies, Inc.) according to the manufacturer's protocol. The cDNA was then biotinylated and fragmented using the Encore Biotin Module (NuGEN Technologies, Inc.).

extract_protocol: FF tissues. RNA was extracted from FF tumor tissues using Qiagen RNeasy Lipid Tissue Mini kits (Qiagen GmbH).   FFPE tissues. RNA was extracted from four consecutive sections (10 μm) of each FFPE tissue using RNeasy FFPE kits (Qiagen GmbH).

treatment_protocol: The patients agreed to have their research specimens cryopreserved for future use after undergoing radical breast cancer surgery. Adjuvant treatments are unknown.

tag: assay

value: FFPE

value: Yes

tag: pair

value: pair 028

tag: tissue

value: FFPE tumor

tag: disease state

value: breast cancer


title: J06_FFPE_026

status: Public on Jul 11 2023

value: No

value: pair 026


title: J06_FFPE_031

value: pair 031


title: J06_FFPE_027

value: pair 027


title: J06_FFPE_025

value: pair 025


title: J06_FFPE_029

value: pair 029


title: J06_FFPE_030

value: pair 030


title: J06_FFPE_021

value: pair 021


title: J06_FFPE_017

value: pair 017


title: J06_FFPE_024

value: pair 024


title: J06_FFPE_018

value: pair 018


title: 7C_M_129

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 7C_M_1289


title: J06_FFPE_019

value: pair 019


title: 7C_M_1291


title: J06_FFPE_020

value: FFPE

value: pair 020


title: J06_FFPE_016

value: pair 016


title: J06_FFPE_023

value: pair 023

value: FFPE tumor


title: J06_FFPE_022

value: No

value: pair 022

value: breast cancer


title: 7C_M_1288


title: J06_FFPE_014

value: pair 014


title: JVPep112_2

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

country: Germany

institute: University of Würzburg

library_source: transcriptomic

data_processing:
Raw RNA-Seq reads were trimmed, filtered and mapped to the SL1344 genome.
Then, BBduk was used to trim nucleobases with Phred quality scores below 10 and to remove adapter sequences.
Next, Reads were mapped against the SL1344 genome using BBMap
resulting alignments were assigned to both coding sequences and sRNAs using the featureCounts methods of the Subread package.
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 , Taxonomy ID: 216597
Supplementary files format and content: counttable.tsv: Count table in tab seperated format

growth_protocol: Bacterial overnight cultures were diluted 1:100 in fresh MHB and grown to OD600 0.5. The obtained cultures were diluted to ∼106 cfu/ml in non-cation-adjusted MHB.

extract_protocol:
Total RNA was purified from bacterial pellets using the miRNeasy Mini kit (Qiagen) according to the protocol #3 described in Popella etal.(30) Briefly, cells were resuspended in 0.5 mg/ml lysozyme (Roth) in TE buffer (pH 8.0) and incubated for 5min. Afterwards, RLT buffer supplemented with β-mercaptoethanol, and ethanol were added according to the manufacturer's instructions. After sample loading, column wash-steps were performed according to the manual. RNA concentration was measured with a NanoDrop spectrophotometer.
Briefly, samples were treated with DNase (XXX) and quality was checked on a bioanalyzer (RNA chip XXX). Then, RNA was subjected to cDNA library preparation using the Corall kit (Lexogen) and including the depletion of ribosomal RNA (RiboCop-META kit, Lexogen) according to the manufacturer’s instructions. Afterwards, library samples were pooled in equimolar amounts and quality was verified using a bioanalyzer (DNA chip XXX). The cDNA pools were sequenced using the NextSeq 500 system (HighOutput flow cell, 400 M, 1x 75 cycle single-end; Illumina).

treatment_protocol: Afterward, the bacterial solution was transferred into low-binding 5 ml tubes (LABsolute) along with the 20×PNA, peptide or PPNA solution. The final concentrations were 5 μM for all test compounds. As a negative control, cells were treated with the respective volume of sterile nuclease-free water, which was used as solvent for the test compounds. After incubating the samples for 15min at 37°C, RNAprotect Bacteria (Qiagen) was added according to the manufacturer's instructions. Following a 10-min incubation, cells were pelleted at 4°C and 21,100 ×g for 20min. The supernatant was discarded and pellets were either directly used or stored at –20°C (<1 day) for subsequent bacterial RNA isolation.

tag: treatment

value: 15 min exposure to KFF


title: 7C_M_1287


title: KFFN3_2

organism: Salmonella enterica subsp. enterica serovar Typhimurium

value: 15 min exposure to KFFN3


title: 7C_M_1286


title: 7C_M_1285


title: 7C_M_1284


title: PNA_21_2

value: 15 min exposure to PNA


title: PMO_2

value: 15 min exposure to PMO


title: DNA_PTO_2

value: 15 min exposure to DNA_PTO


title: 7C_M_1455


title: J06_FFPE_011

value: pair 011


title: J06_FFPE_009

value: pair 009


title: 7C_M_1282


title: J06_FFPE_010

value: pair 010


title: J06_FFPE_005

value: FFPE

value: pair 005


title: J06_FFPE_012

value: pair 012


title: J06_FFPE_004

value: Yes

value: pair 004


title: J06_FFPE_008

value: No

value: pair 008

value: FFPE tumor


title: J06_FFPE_013

value: pair 013

value: breast cancer


title: RNA_Ome_2

value: 15 min exposure to RNA_Ome


title: J06_FFPE_007

value: pair 007


title: LNA_2

value: 15 min exposure to LNA


title: RNA_F_2

value: 15 min exposure to RNA_F


title: J06_FFPE_006

value: pair 006


title: 7C_M_1283


title: 7C_M_1280


title: 7C_M_1281


title: RNA_MOE_2

value: 15 min exposure to RNA_MOE


title: 7C_M_128


title: J06_FFPE_002

value: pair 002


title: 7C_M_1279


title: J06_FFPE_003

value: FFPE

value: pair 003


title: 7C_M_1278


title: Control_2

value: 15 min exposure to water


title: KFFN3_1

value: 15 min exposure to KFFN3


title: 7C_M_1277


title: J06_FFPE_001

value: Yes

value: pair 001


title: J06_FF_027

source_name: FF tumor

value: FF

value: No

value: pair 027

value: FF tumor


title: J06_FF_026

value: pair 026

value: breast cancer


title: J06_FF_029

value: pair 029


title: J06_FF_028

value: pair 028


title: J06_FF_030

value: pair 030


title: 7C_M_1276


title: JVPep112_1

value: 15 min exposure to KFF


title: J06_FF_023

value: pair 023


title: PNA_21_1

value: 15 min exposure to PNA


title: J06_FF_025

value: pair 025


title: J06_FF_031

value: pair 031


title: J06_FF_024

value: pair 024


title: J06_FF_022

value: pair 022


title: J06_FF_021

value: pair 021


title: J06_FF_019

value: FF

value: pair 019


title: 7C_M_1274


title: J06_FF_020

value: No

value: pair 020


title: 7C_M_1275


title: DNA_PTO_1

value: 15 min exposure to DNA_PTO


title: PMO_1

value: 15 min exposure to PMO


title: J06_FF_018

value: pair 018

value: FF tumor

value: breast cancer


title: 7C_M_1273


title: 7C_M_1272


title: 7C_M_1271


title: LNA_1

value: 15 min exposure to LNA


title: RNA_F_1

value: 15 min exposure to RNA_F


title: 7C_M_1270


title: RNA_Ome_1

value: 15 min exposure to RNA_Ome


title: J06_FF_016

value: pair 016


title: J06_FF_014

value: pair 014


title: J06_FF_015

value: pair 015


title: RNA_MOE_1

value: 15 min exposure to RNA_MOE


title: J06_FF_017

value: pair 017


title: J06_FF_013

value: FF

value: pair 013


title: Control_1

value: 15 min exposure to water


title: 7C_M_127


title: J06_FF_012

value: No

value: pair 012


title: 7C_M_1268


title: J06_FF_009

value: pair 009


title: J06_FF_008

value: pair 008


title: J06_FFPE_015

value: FFPE

value: FFPE tumor


title: 7C_M_1267


title: J06_FF_007

value: pair 007

value: FF tumor

value: breast cancer


title: J06_FF_005

value: pair 005


title: J06_FF_003

value: Yes

value: pair 003


title: J06_FF_001

value: pair 001


title: J06_FF_002

value: pair 002


title: J06_FF_004

value: FF

value: pair 004


title: J06_FF_006

value: pair 006


title: J06_FF_010

value: No

value: pair 010


title: J06_FF_011

value: pair 011


title: J05_FFPE_015

value: pair 015


title: 7C_M_1269


title: 7C_M_1266


title: 7C_M_1265


title: 7C_M_1263


title: J05_FFPE_014

value: pair 014


title: 7C_M_1262


title: 7C_M_1260


title: J05_FFPE_012

value: pair 012

value: FFPE tumor


title: J05_FFPE_013

value: pair 013


title: 7C_M_1264


title: J05_FFPE_011

value: breast cancer


title: J05_FFPE_008

value: pair 008


title: J05_FFPE_003


title: J05_FFPE_004


title: J05_FFPE_009

value: pair 009


title: J05_FFPE_001


title: J05_FF_014

value: FF tumor


title: J05_FF_015


title: 7C_M_1261


title: J05_FFPE_006


title: J05_FFPE_007

value: pair 007


title: J05_FFPE_002

value: pair 002


title: 7C_M_126


title: 7C_M_1259


title: 7C_M_1258


title: 7C_M_1257


title: 7C_M_1256


title: J05_FF_013


title: J05_FF_008


title: J05_FF_009


title: J05_FF_011


title: J05_FF_010


title: 7C_M_1255


title: J05_FF_007


title: J05_FF_003

value: pair 003


title: J05_FF_004

value: pair 004


title: Juvenile wildtype replicate5

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon (v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.5.3) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: processed_data_DESeq_count.txt: Tab-delimited text file includes normalized read count matrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and heterozygous mouse pups in one cage.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Hippocampus

tag: Sex

value: male

tag: genotype

value: wildtype


title: J05_FF_002


title: 7C_M_1254


title: Juvenile wildtype replicate3


title: J05_FF_006

value: pair 006


title: Juvenile wildtype replicate2


title: J05_FF_012


title: Juvenile wildtype replicate1


title: 7C_M_1252


title: J05_FFPE_010

value: pair 010


title: Juvenile heterozygous replicate4

value: heterozygous Adnp


title: Juvenile heterozygous replicate2


title: Juvenile heterozygous replicate3


title: Juvenile heterozygous replicate5


title: 7C_M_1251


title: Juvenile wildtype replicate4


title: 7C_M_1250


title: 7C_M_125


title: Adult wildtype replicate3

value: 4 months


title: J05_FF_001

value: pair 001


title: 7C_M_1253


title: Juvenile heterozygous replicate1


title: NP9 sample, nucleus pulposus

type: genomic

city: Warsaw

first: Szymon

middle: Piotr

last: Baluszek

state: mazowieckie

address: Wilhelma Konrada Roentgena 5

department: Department of Molecular and Translational Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

hyb_protocol: DNA from 32 skull base chordomas and 4 NP samples were bisulfite converted with EZ-96 DNA  Methylation kit (Zymo Research, Orange, CA, USA)

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

data_processing: minfi was utilized to generate beta values and funnorm-normalized m-values (supplementary file). Probes containing SNPs and high p-value were dropped.

label: Cy5 and Cy3

source_name: nucleus pulposus

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA and total RNA from tissue samples were isolated using AllPrep DNA/RNA/miRNA Universal  Kit (Qiagen). The procedure included tissue homogenizing with rotor stator homogenizer Omni Tissue  Master (Omni International). The concentration of samples was measured both spectrophotometrically  using NanoDrop 2000 (Thermo Scientific) and with fluorescence-based method using QuantiFluor Dye kit  (Promega) and Quantus (Promega) instrument. Isolated total RNA was stored at -80 o C, whereas genomic  DNA was stored at -20 o C.

value: nucleus pulposus

tag: methylation cluster


title: Adult wildtype replicate1


title: NP1 sample, nucleus pulposus

value: female


title: 7C_M_1248


title: 7_19 sample, chordoma

source_name: chordoma

value: chordoma

tag: craniocervical junction

value: no

tag: days survival

tag: alive at censor point


title: NP4 sample, nucleus pulposus


title: Adult heterozygous replicate3


title: Adult heterozygous replicate4


title: 74_19 sample, chordoma

value: yes


title: 9_20 sample, chordoma


title: 92_15 sample, chordoma


title: Adult wildtype replicate5


title: NP8 sample, nucleus pulposus


title: Adult heterozygous replicate2


title: Adult heterozygous replicate5


title: Adult heterozygous replicate1


title: 7C_M_1246


title: 7C_M_1247


title: Treg, Il10 stably expressing, rep3 [ATAC_G3_stable]

first: Stanislav

last: Dikiy

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

description:
counts_ATAC_AllSamples.txt
merged_atlas.bed

data_processing:
Adapter trimming: Trimmomatic (version 0.39): TrimmomaticPE Sample_R1.fastq.gz Sample_R2.fastq.gz -baseout Sample.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment: STAR (version 2.7.3a): STAR --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir mm39_100 --readFilesIn Sample_1P.fastq.gz Sample_2P.fastq.gz --outFileNamePrefix Sample --outSAMtype BAM Unsorted --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.35 --outFilterMatchNmin 30 --alignIntronMax 1 --alignEndsType Local
Sort: samtools (version 1.12): samtools sort -@ 4 -n -o Sample.bam SampleAligned.out.bam
Mate coordinates: samtools (version 1.12): samtools fixmate -@ 4 -rm Sample.bam Sample.fixmate.bam
Sort: samtools (version 1.12): samtools sort -@ 4 -o Sample.resort.bam Sample.fixmate.bam
Remove duplicates: samtools (version 1.12): samtools markdup -@ 4 -l 1500 -r -d 100 -s Sample.resort.bam Sample.duprm.bam
Index: samtools (version 1.12): samtools index -@ 4 -b Sample.duprm.bam
Sort: samtools (version 1.12): samtools sort -@ 4 -n -o Sample.byname.bam Sample.duprm.bam
Call peaks: Genrich (version 0.5): Genrich -t Sample_r1.byname.bam,Sample_r2.byname.bam,Sample_r3.byname.bam -o ./Gen_out/Peak/Celltype.narrowPeak -j -d 25 -g 5 -v -q 0.01 -a X; Celltype stands in for each cell population, Sample (r1-3) represent the three replicates, and X is 0.002% of the mean number of uniquely aligned reads for each cell population
Merge peak atlases: R (version 4.0.4): custom script
Count reads: GenomicAlignments (R, version 1.26.0): summarizeOverlaps (default parameters)
Assembly: mm39 (custom with Foxp3, Il10, and Gt(ROSA)26Sor loci altered)
Supplementary files format and content: counts_ATAC_AllSamples.txt: text files with all raw counts generated by GenomicAlignments summarizeOverlaps
Supplementary files format and content: merged_atlas.bed: BED files with final merged atlas across all samples

source_name: Colon

extract_protocol:
Combined protocol for extraction and library preparation, see below
After sorting, cells were pelleted in a fixed rotor benchtop centrifuge at 500g for 5 minutes at 4°C. Cells were then washed in 1ml cold 1x PBS and pelleted again. Supernatant was aspirated and cells were resuspended in 50µl ice-cold cell lysis buffer (10mM Tris-Cl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% NP-40) to disrupt plasma membranes. Nuclei were pelleted at 1000g for 10 minutes. Supernatant was aspirated and nuclei were resuspended in 50µl transposition reaction mixture (25µl TD buffer; 2.5µl TDE1; 22.5µl ddH2O; llumina, 20034197). Samples were incubated in a ThermoMixer at 1100rpm for 45 minutes at 42°C. DNA was then purified using a MinElute PCR Purification Kit (QIAGEN, 28004), per manufacturer instructions. DNA was eluted in 10µl buffer EB. Libraries were then barcoded and amplified with NEBNext High-Fidelity Master Mix and primers from (Buenrostro et al., 2013) (50µl reaction with 10µl DNA and 2.5µl of 25µM primers – 1 cycle of 5min at 72°C, 30sec at 98°C; 5 cycles of 10sec at 98°C, 20sec at 63°C, 1min at 72°C). A qPCR on the product determined that an additional 7 cycles (10sec at 98°C, 20sec at 63°C, 1min at 72°C) were required. Library was purified and size selected with AMPure beads (Beckman Coulter, A63881): 45µl of PCR product was incubated with 18µl beads and supernatant was collected (beads bound larger >2000bp fragments). Supernatant (63µl) was then incubated with an additional 63µl of beads for 5 minutes, supernatant was removed, beads were washed 2x with 75% ethanol, and DNA was eluted into 50µl H2O by incubating for 2 minutes.
After quantification and quality control by Agilent BioAnalyzer, pooled libraries were run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina). The loading concentration was 3nM and a 5% spike-in of PhiX was added to the run to increase diversity and for quality control purposes. The run yielded average 36M reads per sample.

treatment_protocol: Mice treated with tamoxifen 21 days prior to cell isolation to activate an Il10 linked CreER, inducing permanent YFP labeling of Il10 expressing cells

value: Colon

tag: cell line

tag: cell type

value: regulatory T cell

tag: il10 expression

value: Positive

tag: il10 history

value: Yes


title: Treg, Il10 expressing, rep3 [ATAC_G3_pos]

value: No


title: Treg, Il10 negative, rep3 [ATAC_G3_neg]

value: Negative


title: 7C_M_1249


title: 6_16 sample, chordoma

value: male


title: Treg, Il10 stably expressing, rep2 [ATAC_G2_stable]


title: Treg, Il10 expressing, rep2 [ATAC_G2_pos]


title: 7C_M_1244


title: 81_15 sample, chordoma


title: Adult wildtype replicate4

value: Hippocampus

value: wildtype


title: 53_18 sample, chordoma


title: Treg, Il10 negative, rep2 [ATAC_G2_neg]


title: Treg, Il10 stably expressing, rep1 [ATAC_G1_stable]


title: 62_15 sample, chordoma


title: 7C_M_1243


title: Treg, Il10 expressing, rep1 [ATAC_G1_pos]


title: 7C_M_1242


title: Treg, Il10 negative, rep1 [ATAC_G1_neg]


title: Adult wildtype replicate2


title: Treg, Il10 stably expressing, rep3 [RNA_G3_stable]

description:
SMARTer Amp library
RNA_G3_stable

data_processing:
Adapter trimming: Trimmomatic (version 0.39): TrimmomaticPE Sample_R1.fastq.gz Sample_R2.fastq.gz -baseout Sample.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment: STAR (version 2.7.3a): STAR --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir mm39_100_RNA --readFilesIn Sample_1P.fastq.gz Sample_2P.fastq.gz --outFileNamePrefix Sample --outSAMtype BAM Unsorted --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.35 --outFilterMatchNmin 30 --alignEndsType EndToEnd
Sort: samtools (version 1.12): samtools sort -@ 4 -n -o Sample.bam SampleAligned.out.bam
Mate coordinates: samtools (version 1.12): samtools fixmate -@ 4 -rm Sample.bam Sample.fixmate.bam
Sort: samtools (version 1.12): samtools sort -@ 4 -o Sample.resort.bam Sample.fixmate.bam
Remove duplicates: samtools (version 1.12): samtools markdup -@ 4 -l 1500 -r -d 100 -s Sample.resort.bam Sample.duprm.bam
Index: samtools (version 1.12): samtools index -@ 4 -b Sample.duprm.bam
Count reads: GenomicAlignments (R, version 1.26.0): summarizeOverlaps (default parameters)
Assembly: mm39 (custom with Foxp3, Il10, and Gt(ROSA)26Sor loci altered)
Supplementary files format and content: text files with all raw counts generated by GenomicAlignments summarizeOverlaps

molecule: polyA RNA

extract_protocol:
Cells sorted directly into Trizol LS; phase separation was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in 13 µL nuclease-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 122-400pg total RNA with RNA integrity numbers ranging from undetectable to 9 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 4ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50 run using the HiSeq 3000/4000 SBS Kit (Illumina).


title: 7C_M_1241


title: Treg, Il10 expressing, rep3 [RNA_G3_pos]

description:
SMARTer Amp library
RNA_G3_pos


title: 55_19 sample, chordoma


title: 7C_M_1240


title: 68_18 sample, chordoma


title: Treg, Il10 stably expressing, rep2 [RNA_G2_stable]

description:
SMARTer Amp library
RNA_G2_stable


title: Treg, Il10 expressing, rep2 [RNA_G2_pos]

description:
SMARTer Amp library
RNA_G2_pos


title: 5_16 sample, chordoma


title: Treg, Il10 negative, rep2 [RNA_G2_neg]

description:
SMARTer Amp library
RNA_G2_neg


title: 7C_M_1239


title: 7C_M_1245


title: Treg, Il10 negative, rep1 [RNA_G1_neg]

description:
SMARTer Amp library
RNA_G1_neg


title: 54_15 sample, chordoma


title: 7C_M_124


title: [miRNA] Cartilage progenitor cells, Passage 3 + FFSS, rep3

city: Xi'an

first: Xu

last: Lingfeng

state: Shaanxi

address: 169 Changle West Road

country: China

institute: Air Force Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 (Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
Summarizing all alignments and annotations obtained before. In the alignment 3 / 5 and annotation before, some small RNA tags may be mapped to more than one category. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: known miRNA > rRNA > tRNA > snRNA > snoRNA > repeat > gene > NAT-siRNA > gene > novel miRNA > ta-siRNA. The total rRNA proportion was used a marker as sample quality indicator. Usually it should be less than 60% in plant samples and 40% in animal samples as high quality。
Assembly: Rattus_norvegicus.Rnor_6.0.97
Supplementary files format and content: Readcount_TPM.txt

organism: Rattus norvegicus

source_name: condylar cartilage

extract_protocol:
RNA was harvested using TRizol Reagent(Ambion).
Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing on Illumina sequencing with SE50. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: condylar cartilage

value: primary culturecell

value: Cartilage progenitor cells

value: WT

value: flow fluid shear stress


title: 45_17 sample, chordoma

value: chordoma

value: female


title: Treg, Il10 stably expressing, rep1 [RNA_G1_stable]

description:
SMARTer Amp library
RNA_G1_stable


title: 7C_M_1238


title: 4_19 sample, chordoma

value: no

value: yes


title: 39_18 sample, chordoma


title: 7C_M_1237


title: 50_19 sample, chordoma


title: [miRNA] Cartilage progenitor cells, Passage 3 + FFSS, rep1


title: [miRNA] Cartilage progenitor cells, Passage 3 + FFSS, rep2


title: [miRNA] Cartilage progenitor cells, Passage 9, rep3

value: In vitro culture to passage 9


title: 7C_M_1236


title: [miRNA] Cartilage progenitor cells, Passage 9, rep2


title: [miRNA] Cartilage progenitor cells, Passage 9, rep1


title: 40_18 sample, chordoma


title: [miRNA] Cartilage progenitor cells, Passage3, rep3

value: In vitro culture to passage 3


title: 7C_M_1234


title: [RNA] Cartilage progenitor cells, Passage 3 + FFSS, rep3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads 1 containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Rattus_norvegicus.Rnor_6.0.97
Supplementary files format and content: processed_data.xlsx

extract_protocol:
RNA was harvested using TRizol Reagent(Ambion).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: [RNA] Cartilage progenitor cells, Passage 3 + FFSS, rep2


title: 7C_M_1233


title: [miRNA] Cartilage progenitor cells, Passage3, rep1


title: [miRNA] Cartilage progenitor cells, Passage3, rep2


title: [RNA] Cartilage progenitor cells, Passage 3 + FFSS, rep1


title: [RNA] Cartilage progenitor cells, Passage 9, rep3


title: [RNA] Cartilage progenitor cells, Passage 9, rep2


title: 7C_M_1232


title: 50_15 sample, chordoma


title: 7C_M_1231


title: [RNA] Cartilage progenitor cells, Passage 9, rep1


title: Treg, Il10 expressing, rep1 [RNA_G1_pos]

description:
SMARTer Amp library
RNA_G1_pos

value: Colon

value: regulatory T cell

value: Positive


title: [RNA] Cartilage progenitor cells, Passage3, rep3


title: [RNA] Cartilage progenitor cells, Passage3, rep2


title: 7C_M_123


title: 7C_M_1229


title: Liver, DL.reuteri_8

city: Shanghai

first: Shang

last: Li

address: 845 Lingshan Road

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed to remove the poor-quality reads, the adapters, and the polluted reads using Seqtk.
The trimmed reads were mapped to the reference genome using Hisat2 (2.0.4).
The fragments per kilobase of exon model per million mapped reads (FPKM) values were calculated.
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: FPKM values for each gene and each sample.

source_name: Liver

extract_protocol:
Liver samples were collected, snap frozen using liquid nitrogen, and RNA was harvested using Trizol reagent.The libraries were prepared with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (#NR604-02, Vazyme Biotech).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A total of 24 female rats of 6-week-old were equally and randomly divided into 3 groups: control, darkness, and darkness+L.reuteri. Control rats were under a circadian rhythm of 12:12 h light-dark cycle (lights on at 7:30 a.m. and off at 7:30 p.m.), orally given with saline once a day. Darkness rats and darkness+L.reuteri rats were respectively given with saline or L.reuteri (1010 CFU/ml, 100 mg/d) by daily oral gavage during 8-week constant darkness housing.

value: Sprague-Dawley

value: L.reuteri, 8-week darkness housing

value: Liver


title: Treg, Il10 negative, rep3 [RNA_G3_neg]

description:
SMARTer Amp library
RNA_G3_neg

value: Negative

value: No


title: 7C_M_1235


title: Liver, DL.reuteri_7


title: [RNA] Cartilage progenitor cells, Passage3, rep1

value: condylar cartilage

value: primary culturecell

value: Cartilage progenitor cells


title: Liver, DL.reuteri_5


title: 7C_M_1228


title: 35_17 sample, chordoma

value: chordoma

value: male


title: 38_17 sample, chordoma

value: female

value: no


title: Liver, DL.reuteri_3


title: 7C_M_1226


title: 37_19 sample, chordoma

value: yes


title: 7C_M_1227


title: Liver, DL.reuteri_4


title: Liver, DL.reuteri_1


title: Liver, DL.reuteri_2


title: 7C_M_1225


title: Liver, Dark_8

value: saline, 8-week darkness housing


title: Liver, Dark_7


title: Liver, Dark_6


title: 31_14 sample, chordoma


title: 7C_M_1222


title: 28_20 sample, chordoma


title: Liver, Dark_4


title: 7C_M_1221


title: Liver, Dark_3


title: Liver, Dark_2


title: Liver, Dark_5


title: 7C_M_1220


title: Liver, Dark_1


title: Liver, Control_8

value: saline


title: Liver, Control_7


title: 31_20 sample, chordoma


title: 7C_M_122


title: 32_14 sample, chordoma


title: Liver, Control_6


title: 7C_M_1219


title: Liver, Control_4


title: Liver, Control_2


title: 7C_M_1218


title: 26_15 sample, chordoma


title: Liver, DL.reuteri_6


title: Liver, Control_5


title: Liver, Control_1


title: 7C_M_1217


title: Liver, Control_3


title: 7C_M_1216


title: COVID_ADpos, subject 238, region BA9

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

data_processing:
Reads were processed with the NGS-Data-Charmer pipeline. In brief, adaptors and low-quality bases were removed with Trim Galore.
Trimmed reads were aligned to the human genome with HISAT2 and alignments were de-duplicated with samtools rmdup.
Gene expression was calculated using featureCounts with parameters "-p -O --fraction -t gene" to the GENCODE annotation (v38).
Assembly: hg38
Supplementary files format and content: counts_matrix.txt is a tab-delimited text file containing the gene expression matrix.

extract_protocol:
Samples collected and homogenized in RNAzol RT (Molecular Research Center, Inc.) were then processed using the Zymo Clean and concentrator Kit (Zymo Research) to collect total RNA following the manufacturers protocols.
cDNA library construction and sequencing were conducted by Genewiz (Azenta Life Sciences). RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations, where enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Brain

tag: alzheimers status

value: ADpos

tag: covid status

value: COVID

value: Female


title: COVID_ADpos, subject 244, region BA9

tag: tissue

value: Male


title: COVID_ADpos, subject 141, region HP

tag: brain region

value: HP


title: COVID_ADpos, subject 238, region HP

tag: age


title: COVID_ADpos, subject 244, region HP


title: 7C_M_1215

tag: strain


title: COVID_ADpos, subject 141, region BA9


title: COVID_ADpos, subject 134, region HP


title: 26_16 sample, chordoma


title: 7C_M_1214


title: COVID_ADpos, subject 134, region BA9


title: COVID_ADneg, subject 143, region BA9

value: ADneg


title: 7C_M_1212


title: COVID_ADneg, subject 135, region HP


title: COVID_ADneg, subject 135, region BA9


title: COVID_ADneg, subject 131, region BA9


title: 7C_M_1213


title: 4C.NlaIII-DpnII_NT_DMSO_P4HA3_rep3

city: Amsterdam

first: Isabel

last: Mayayo-Peralta

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
library strategy: 4C-seq
Fastq files have been demultiplexed by Cutadapt (http://journal.embnet.org/index.php/embnetjournal/article/view/200)
Fastq mapping was performed on Hg38/GRCm38 genome assembly and signal normalized by pipe4C (v1.1) R-package in “cis” mode and with default parameters.
Assembly: Hg38/GRCm38 (UCSC source)
Supplementary files format and content: Normalized 4C-seq signal for each replicate is available in a wig.gz file.

source_name: lung cancer

extract_protocol:
Experiments of 4C-seq were performed as previously described (Krijger et al., Methods 170, 17–32 (2020)). Briefly, for each restriction enzyme (RE) combination (RE1 NlaIII, RE2 DpnII; New England Biolabs), replicate and treatment about 10×106 cells were collected, pelleted and cross-linked by 2% methanol-free formaldehyde for 10 minutes. Nuclei were isolated and permeabilized to allow digestion of the chromatin by the primary RE (NlaIII, New England Biolabs). Chromatin fragments were then diluted and ligated before crosslinking reversion. Purified DNA was digested by the secondary RE (DpnII, New England Biolabs) and circularized again by ligation. Re-purified circular fragments were amplified by PCR with View-Point specific primers (see Supplementary Table in corresponding paper) using the Expand Long Template PCR System (Roche).
Resulting amplicons were purified with a 0.8x ratio of AMPure XP beads (Beckman Coulter) and amplified using standard indexed Illumina primers as previously described (Krijger et al., Methods 170, 17–32 (2020)) using the Expand Long Template PCR System (Roche).
Second-round PCR products were purified with PCR purification columns (Qiagen) and quan-tified by 2100 Bioanalyzer (Agilent, DNA 7500 kit). 4C library was prepared by equimolar mix of the samples. The pooled library was cleaned-up by AMPure XP beads (0.8× ratio) to remove PCR dimers before sequencing through Illumina MiSeq with a 75bp Single-End reads setup.

value: lung cancer

value: NT

tag: time

tag: treatment

value: DMSO


title: 7C_M_1211


title: 20_17 sample, chordoma

value: chordoma

tag: Sex


title: 4C.NlaIII-DpnII_NT_DMSO_P4HA3_rep2

tag: genotype


title: 7C_M_1210


title: 19_19 sample, chordoma

tag: craniocervical junction

tag: methylation cluster


title: COVID_ADneg, subject 131, region HP


title: 11_18 sample, chordoma

value: male

tag: days survival

tag: alive at censor point


title: 18_16 sample, chordoma


title: 4C.NlaIII-DpnII_NT_DMSO_FKBP5-iso357266_rep3

tag: cell line

tag: cell type


title: 4C.NlaIII-DpnII_NT_DMSO_P4HA3_rep1


title: CONTROL_ADpos, subject 181, region HP

value: CONTROL


title: 7C_M_1209


title: 4C.NlaIII-DpnII_NT_DMSO_FKBP5-iso357266_rep2


title: CONTROL_ADpos, subject 181, region BA9


title: CONTROL_ADpos, subject 93, region HP


title: 7C_M_1208


title: 7C_M_121


title: 24_18 sample, chordoma

value: female


title: 7C_M_1223


title: CONTROL_ADpos, subject 15, region HP


title: CONTROL_ADpos, subject 15, region BA9


title: COVID_ADneg, subject 130, region HP


title: 7C_M_1207


title: CONTROL_ADpos, subject 7, region HP


title: COVID_ADneg, subject 130, region BA9


title: 4C.NlaIII-DpnII_NT_DMSO_CDKN1B-TSS_rep3


title: 7C_M_1206


title: CONTROL_ADneg, subject 98, region HP


title: CONTROL_ADneg, subject 96, region BA9


title: CONTROL_ADneg, subject 98, region BA9


title: 7C_M_1205


title: CONTROL_ADpos, subject 93, region BA9


title: COVID_ADneg, subject 143, region HP


title: CONTROL_ADneg, subject 96, region HP


title: CONTROL_ADneg, subject 44, region HP


title: 4C.NlaIII-DpnII_NT_Dex_P4HA3_rep3

value: 100nM Dexamethasone


title: 4C.NlaIII-DpnII_NT_DMSO_CDKN1B-TSS_rep2


title: CONTROL_ADneg, subject 44, region BA9


title: CONTROL_ADneg, subject 11, region HP


title: 7C_M_1203


title: CONTROL_ADneg, subject 11, region BA9


title: 4C.NlaIII-DpnII_NT_DMSO_FKBP5-iso357266_rep1


title: 7C_M_1204


title: 7C_M_1202


title: 4C.NlaIII-DpnII_NT_Dex_P4HA3_rep2


title: 4C.NlaIII-DpnII_NT_Dex_P4HA3_rep1


title: LNCaP_clone2, ATAC

city: Budapest

first: Andras

last: Furedi

state: HU

address: Magyar tudosok krt 2

department: Molecular Life Sciences

country: Hungary

institute: HUN-REN RCNS

data_processing:
Illumina Casava1.7 software used for basecalling.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Reads were aligned to hg19 using BWA.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: LNCaP

growth_protocol: LNCaP metastatic prostate cancer cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
The omni-ATAC protocol was performed.
ATAC-seq libraries were prepared using Nextera library preparation kit (Illumina). Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in length using Agencourt AMPure XP beads (Beckman Coulter). Library fragment size distributions were analyzed using 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: Transposase accessible chromatin (ATAC) signal intensities were interrogated at the IRX4 genomic region in single copy IRX4 enhancer (47bp long allele) knock in isogenic cell lines (clone 1 (C1) and clone 2(C2)) compared to the wild type (carrying 4 21 bp short allele) parental LNCaP cell line.

value: LNCaP

value: human metastatic prostate cancer


title: CONTROL_ADpos, subject 7, region BA9

value: Brain


title: 7C_M_1201


title: 7C_M_1200


title: LNCaP_parental, ATAC


title: LNCaP_clone1, ATAC


title: 4C.NlaIII-DpnII_NT_Dex_FKBP5-iso357266_rep3


title: 7C_M_120


title: 4C.NlaIII-DpnII_NT_Dex_FKBP5-iso357266_rep2


title: LNCaP_parental, H3K27ac

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Reads were aligned to hg19 using BWA.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the ThruPLEX DNA-seq Kit (Takara). 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in length using Agencourt AMPure XP beads (Beckman Coulter). Library fragment size distributions were analyzed using 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent).
Diagenode Cat# C15410196 H3K27ac antibody was used.

treatment_protocol: H3K27ac signal intensities were interrogated at the IRX4 genomic region in single copy IRX4 enhancer (47bp long allele) knock in isogenic cell lines (clone 1 (C1) and clone 2(C2)) compared to the wild type (carrying 4 21 bp short allele) parental LNCaP cell line.

tag: chip antibody

value: H3K27ac Diagenode (Cat# C15410196)


title: 4C.NlaIII-DpnII_NT_Dex_FKBP5-iso357266_rep1


title: 7C_M_12


title: LNCaP cells, IRX4 overexpression rep1

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
Invariant genes (genes that have no counts or only single count across all samples) were removed.
DESeq2 package were used for differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files, including GeneID, symbol and abundance measurements.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and 200 ng of total RNA was used for the construction of each sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

treatment_protocol: Lenti viral IRX4 over expression (oe) and knock-down (kd) was performed compared to vector control (vc) samples in LNCaP cell lines.

value: metastatic prostate cancer

value: WT

value: IRX4 overexpression rep1

value: Day 10


title: 4C.NlaIII-DpnII_NT_DMSO_CDKN1B-TSS_rep1


title: LNCaP cells, IRX4 overexpression rep2

value: IRX4 overexpression rep2


title: LNCaP cells, IRX4 knock down rep2

value: IRX4 knock down rep2


title: 7C_M_1199


title: 4C.NlaIII-DpnII_NT_Dex_CDKN1B-TSS_rep3

value: lung cancer

value: NT


title: LNCaP cells, IRX4 knock down rep1

value: IRX4 knock down rep1


title: LNCaP cells, vector control rep2

value: vector control rep2


title: 4C.NlaIII-DpnII_NT_Dex_CDKN1B-TSS_rep2


title: 4C.NlaIII-DpnII_NT_Dex_CDKN1B-TSS_rep1


title: 7C_M_1197


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_P4HA3_rep3


title: gq_sample_99

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

data_processing:
All sequencing data was extracted from FASTQ files and processed using CASAVA 1.8+
Illumina adapter sequences were trimmed using the Fastx_toolkit
Bowtie was used to align reads to the human genome
Rfam database was used to map reads to known snoRNAs
Sequencing data was normmalized with the Bioconductor-DESeq2 package
Assembly: GRch37

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated from whole blood using PAXgene Blood RNA kit (Qiagen) according to manufacturer's instructions
Libraries prepared using Illumina TruSeq Small RNA protocol following manufactuer's instructions.

value: Peripheral blood

value: Placebo

tag: sample type

value: Week 8 Responder


title: 7C_M_1196


title: gq_sample_94

value: Duloxetine

value: Week 0 Non-Responder


title: 7C_M_1195


title: gq_sample_95


title: gq_sample_98

value: Week 0 Responder


title: gq_sample_93


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_P4HA3_rep1

value: 100nM Dexamethasone


title: gq_sample_92


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_P4HA3_rep2


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_FKBP5-iso357266_rep3


title: 7C_M_1194


title: gq_sample_91


title: gq_sample_97


title: gq_sample_89


title: 7C_M_1198


title: 7C_M_1192


title: gq_sample_87


title: 7C_M_1193


title: 7C_M_1191


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_FKBP5-iso357266_rep2


title: gq_sample_9


title: gq_sample_88

value: Week 8 Non-Responder


title: gq_sample_85


title: LNCaP cells, vector control rep1

value: LNCaP

value: metastatic prostate cancer

value: WT

value: vector control rep1


title: gq_sample_90


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_CDKN1B-TSS_rep3


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_CDKN1B-TSS_rep2


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_FKBP5-iso357266_rep1


title: 4C.NlaIII-DpnII_PAXIP-KO_DMSO_CDKN1B-TSS_rep1


title: gq_sample_82


title: gq_sample_84


title: gq_sample_81


title: 7C_M_119


title: gq_sample_83


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_P4HA3_rep3


title: 7C_M_1188


title: gq_sample_96


title: gq_sample_80


title: 7C_M_1190


title: 7C_M_1189


title: gq_sample_8


title: gq_sample_86


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_P4HA3_rep2


title: gq_sample_78


title: 7C_M_1187


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_P4HA3_rep1


title: gq_sample_77


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_FKBP5-iso357266_rep3


title: gq_sample_76


title: gq_sample_75


title: gq_sample_73


title: gq_sample_72


title: 7C_M_1186


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_FKBP5-iso357266_rep2


title: gq_sample_74


title: gq_sample_7


title: 7C_M_1185


title: gq_sample_70


title: 7C_M_1183


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_CDKN1B-TSS_rep3


title: 7C_M_1184


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_CDKN1B-TSS_rep2


title: 7C_M_1182


title: gq_sample_69


title: gq_sample_66


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_FKBP5-iso357266_rep1


title: gq_sample_68


title: 7C_M_1181


title: gq_sample_67


title: gq_sample_79


title: 4C.NlaIII-DpnII_PAXIP-KO_Dex_CDKN1B-TSS_rep1


title: 7C_M_1180


title: gq_sample_65


title: gq_sample_63


title: 7C_M_118


title: gq_sample_71


title: gq_sample_62


title: gq_sample_61


title: gq_sample_60


title: 7C_M_1178


title: gq_sample_59


title: gq_sample_6


title: gq_sample_58


title: gq_sample_57


title: 7C_M_1176


title: gq_sample_56


title: gq_sample_54


title: gq_sample_55


title: gq_sample_53


title: Treg, Il10 positive, HTO-derived cDNA [E2_Il10pos_hto]

description: Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and ncBI RefSeq annotations.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each sample
Library strategy: scRNA-seq / CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Colon, lung, mesenteric lymph node, mediastinal lymph node

extract_protocol:
Cells were sorted into 0.04% BSA/PBS, pelleted, and then resuspended at 1000-1500 cells/ul
Library was prepared using Chromium Single Cell 3ʹ v3 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v3 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we followed the protocol provided by BioLegend (HTO, TotalSeq-A)

value: regulatory T cell

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC-I :LILP:TotalSeq-A0301 ; mesLN:TotalSeq-A0302 ; Lung:TotalSeq-A0303 ; medLN:TotalSeq-A0304

tag: il10 expression

value: Positive


title: 7C_M_1177

tag: brain region

tag: age


title: gq_sample_52

tag: tissue


title: gq_sample_64

tag: treatment


title: 7C_M_1174

tag: strain


title: 7C_M_1173


title: gq_sample_516


title: Treg, Il10 negative, HTO-derived cDNA [E2_Il10neg_hto]

value: Colon, lung, mesenteric lymph node, mediastinal lymph node

value: Negative


title: 7C_M_1175


title: gq_sample_515

value: Peripheral blood

value: Placebo


title: gq_sample_514

value: Duloxetine

value: Week 8 Responder


title: Treg, Il10 positive, mRNA-derived cDNA [E2_Il10pos]

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: gq_sample_512


title: gq_sample_511


title: gq_sample_51

value: Week 0 Non-Responder


title: gq_sample_510


title: Treg, Il10 negative, mRNA-derived cDNA [E2_Il10neg]


title: gq_sample_509


title: gq_sample_507


title: gq_sample_508

value: Week 8 Non-Responder


title: 7C_M_1169


title: 7C_M_1171


title: 7C_M_117


title: 7C_M_1172


title: 7C_M_1168


title: 7C_M_1170


title: gq_sample_506


title: 7C_M_1167


title: gq_sample_504


title: gq_sample_503


title: MDCK Mix culture_3

city: Noda-shi

first: Shunsuke

last: Kon

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

institute: Tokyo University of Science

description: Gene expression after 24h of tetracycline treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned using an Agilent SureScan (G4900DA).

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

organism: Canis lupus familiaris

source_name: MDCK-pTR GFP-RasV12 cells co-cultured with cells at a ratio of 1:10

label_protocol: For cRNA amplification and labeling, Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) were used following the manufacter’s instructions.

growth_protocol: MDCK and MDCK-pTR GFP-RasV12 cells were cultured in Dulbecco's Modified Eagle Medium, High Glucose supplemented with 10% Fetal Bovine Serum and penicillin/Streptomycin at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells using ISOGEN II (NIPPON GENE Co., Ltd).

treatment_protocol: MDCK-pTR GFP-RasV12 cells or a 10:1 mix culture of MDCK and MDCK-pTR GFP-RasV12 cells were cultured at a density of 1.2×107 cells on collagen-coated 10 cm dishes (CORNING). After incubation with tetracycline for 24 h at 37 ºC in a humidified incubator with 5% CO2, GFP-positive RasV12 cells was separated with an analytical flow cytometer.

tag: culture condition

value: mixed culture


title: gq_sample_502


title: gq_sample_513


title: gq_sample_501


title: gq_sample_5

value: Week 0 Responder


title: gq_sample_505


title: MDCK Mix culture_1


title: 7C_M_1165

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: MDCK Mix culture_2

source_name: MDCK-pTR GFP-RasV12 cells co-cultured with cells at a ratio of 1:100


title: gq_sample_499


title: 7C_M_1163


title: 7C_M_1164


title: MDCK Single culture_3

source_name: MDCK-pTR GFP-RasV12 cells culture alone

value: single culture


title: MDCK Single culture_2


title: MDCK Single culture_1


title: gq_sample_495


title: gq_sample_494


title: 7C_M_1161


title: 231 shHSF1 Rep2

city: Bloomington

first: Richard

middle: L

last: Carpenter

state: IN

department: Biochemistry and Molecular Biology

institute: Indiana University

data_processing:
The sequence data were mapped to the human reference genome hg38 with STAR
FeatureCounts was used to quantify gene expression
The data were further normalized using RPKM (Reads Per Kilobase Million)
Assembly: hg38
Supplementary files format and content: Excel table including gene information (Symbol, chromosome, start position, end position, strand, and gene length) and RPKM values

source_name: breast

growth_protocol: growth: 21% O2, 5% CO2 in DMEM + 10% FBS + 1% P/S

extract_protocol:
RNA Extraction: Qiagen Rneasy kit with Qiashredder
KAPA mRNA Hyperprep Kit

value: breast

tag: disease state

value: Adenocarcinoma

value: epithelial

tag: genotype

value: HSF1 shRNA


title: gq_sample_498


title: 231 shHSF1 Rep3


title: 231 shHSF1 Rep1


title: 7C_M_1162


title: 7C_M_1166


title: 7C_M_1160


title: gq_sample_500


title: gq_sample_496


title: gq_sample_491


title: gq_sample_497


title: 231 shCTL Rep3

value: CTL


title: gq_sample_492


title: gq_sample_493


title: gq_sample_50


title: 7C_M_116


title: gq_sample_49


title: gq_sample_489


title: 7C_M_1159


title: 231 shCTL Rep1


title: gq_sample_487


title: 7C_M_1158


title: RNA-seq of LuCaP 92 Rep 1

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

data_processing:
RNA sequence reads were trimmed and aligned to the mouse and human genomes in parallel to remove reads mapping to both genomes using Disambiguate.
Human-only reads were realigned to GRCh37 using STAR.
FeatureCounts was used to compute the raw reads for each transcript feature.
Assembly: GRCh37
Supplementary files format and content: tab-separated values file contains raw counts for each sample

source_name: prostate cancer

growth_protocol: LuCaP PDX tissues were processed into single cells, depleted for mouse cells using the mouse cell depletion kit (Miltenyi), and plated as organoids using optimized culture conditions for each model. Existing organoid-based cultures were maintained using optimized conditions. Organoids were grown in 5% matrigel on low-attachmentplates, supplemented with neuregulin 1 for adenocarcinoma models only.

extract_protocol:
RNA was recovered from organoids using the Qiagen RNeasy Mini Plus Kit following the manufacturer's recommended protocol.
RNA was assembled into paired-end Illumina-compatible libraries following PolyA enrichment of mRNA using the Illumina TruSeq kit.

value: prostate cancer

value: LuCaP 92

tag: Sex

value: male


title: gq_sample_484

value: Peripheral blood

value: Placebo


title: RNA-seq of LuCaP 77 Rep 1

value: LuCaP 77


title: gq_sample_483

value: Week 8 Responder


title: 7C_M_1156

source_name: C57BL/6J Male P56 Mouse Brain


title: RNA-seq of LuCaP 77 Rep 2


title: 7C_M_1155


title: gq_sample_485

value: Duloxetine


title: gq_sample_480


title: gq_sample_481

value: Week 8 Non-Responder


title: gq_sample_48

value: Week 0 Non-Responder


title: gq_sample_486


title: gq_sample_482


title: 7C_M_1154


title: gq_sample_490


title: gq_sample_479


title: RNA-seq of LuCaP 73 Rep 4

value: LuCaP 73


title: gq_sample_478


title: 7C_M_1153


title: 231 shCTL Rep2


title: gq_sample_477


title: gq_sample_488


title: RNA-seq of NCI-PC35-1 Rep 5


title: gq_sample_476


title: RNA-seq of NCI-PC35-1 Rep 4


title: gq_sample_475


title: 7C_M_1157


title: 7C_M_1152


title: gq_sample_474

value: Week 0 Responder


title: 7C_M_1151


title: RNA-seq of NCI-PC35-1 Rep 3


title: RNA-seq of LuCaP 73 Rep 3


title: gq_sample_472


title: 7C_M_1150


title: RNA-seq of NCI-PC35-1 Rep 2


title: gq_sample_471


title: gq_sample_473


title: 7C_M_115


title: gq_sample_47


title: gq_sample_469


title: RNA-seq of LuCaP 141CR Rep 1

value: LuCaP 141CR


title: gq_sample_467


title: 7C_M_1149


title: RNA-seq of LuCaP 35CR Rep 1

value: LuCaP 35CR


title: gq_sample_470


title: RNA-seq of LuCaP 73 Rep 2


title: gq_sample_466


title: RNA-seq of NCI-PC155 Rep 1


title: gq_sample_463


title: gq_sample_465


title: RNA-seq of NCI-PC44 Rep 1


title: gq_sample_462


title: gq_sample_464


title: 7C_M_1146


title: 7C_M_1145


title: gq_sample_461


title: RNA-seq of NCI-PC35-2 Rep 1


title: gq_sample_468


title: gq_sample_460


title: gq_sample_459


title: gq_sample_46


title: 7C_M_1148


title: 7C_M_1143


title: gq_sample_457


title: gq_sample_458


title: gq_sample_456


title: RNA-seq of LuCaP 49 Rep 1

value: LuCaP 49


title: 7C_M_1142


title: gq_sample_454


title: 7C_M_1144


title: RNA-seq of NCI-PC60 Rep 1


title: gq_sample_455


title: 7C_M_1147


title: RNA-seq of NCI-PC35-1 Rep 1


title: 7C_M_1141


title: gq_sample_453


title: RNA-seq of LuCaP 147CR Rep 2

value: LuCaP 147CR


title: gq_sample_452


title: gq_sample_451


title: 7C_M_1140


title: RNA-seq of LuCaP 147CR Rep 1


title: gq_sample_450


title: 7C_M_114


title: gq_sample_449


title: RNA-seq of LuCaP 189.4 Rep 2

value: LuCaP 189.4


title: RNA-seq of LuCaP 189.4 Rep 1

value: prostate cancer


title: 7C_M_1139


title: RNA-seq of LuCaP 73 Rep 1


title: gq_sample_447


title: gq_sample_448


title: 7C_M_1138


title: gq_sample_446


title: gq_sample_444


title: gq_sample_443


title: 7C_M_1137


title: 7C_M_1136


title: RNA-seq of LuCaP 170.2CR Rep 1

value: LuCaP 170.2CR


title: gq_sample_445


title: RNA-seq of LuCaP 167CR Rep 2

value: LuCaP 167CR

value: male


title: gq_sample_441

value: Peripheral blood


title: 7C_M_1135


title: gq_sample_440


title: gq_sample_44


title: gq_sample_439


title: RNA-seq of LuCaP 167CR Rep 1


title: gq_sample_438


title: gq_sample_45


title: 7C_M_1133


title: RNA-seq of LuCaP 136CR Rep 2

value: LuCaP 136CR


title: 7C_M_1132


title: gq_sample_436

value: Placebo


title: RNA-seq of LuCaP 170.2CR Rep 2


title: gq_sample_435


title: RNA-seq of LuCaP 136CR Rep 1


title: gq_sample_442

value: Duloxetine

value: Week 8 Responder


title: gq_sample_434

value: Week 8 Non-Responder


title: 7C_M_1131


title: RNA-seq of LuCaP 189.3 Rep 2

value: LuCaP 189.3


title: gq_sample_433


title: RNA-seq of LuCaP 189.3 Rep 1


title: gq_sample_432


title: 7C_M_1130


title: 7C_M_113


title: RNA-seq of LuCaP 70CR Rep 2

value: LuCaP 70CR


title: gq_sample_431


title: gq_sample_43

value: Week 0 Non-Responder


title: gq_sample_430


title: 7C_M_1134


title: gq_sample_429


title: 7C_M_1129


title: gq_sample_428


title: RNA-seq of LuCaP 70CR Rep 1


title: gq_sample_437


title: gq_sample_426


title: gq_sample_427


title: gq_sample_425


title: 7C_M_1128


title: 7C_M_1127


title: gq_sample_424


title: RNA-seq of LuCaP 70 Rep 2

value: LuCaP 70


title: RNA-seq of LuCaP 176 Rep 2

value: LuCaP 176


title: 7C_M_1126


title: RNA-seq of LuCaP 176 Rep 1


title: gq_sample_423


title: gq_sample_422


title: gq_sample_421


title: gq_sample_420


title: gq_sample_42

value: Week 0 Responder


title: 7C_M_1124


title: 7C_M_1125


title: gq_sample_419


title: gq_sample_418


title: gq_sample_416


title: gq_sample_414


title: RNA-seq of LuCaP 173.2 Rep 2

value: LuCaP 173.2


title: 7C_M_1123


title: RNA-seq of LuCaP 174.1 Rep 2

value: prostate cancer

value: LuCaP 174.1


title: 7C_M_1122


title: gq_sample_415


title: RNA-seq of LuCaP 173.2 Rep 1


title: gq_sample_417


title: gq_sample_412


title: 7C_M_1120


title: 7C_M_1121


title: RNA-seq of LuCaP 173.1 Rep 2

value: LuCaP 173.1


title: gq_sample_411


title: RNA-seq of LuCaP 173.1 Rep 1

value: male


title: gq_sample_410

value: Peripheral blood


title: 7C_M_112


title: RNA-seq of LuCaP 174.1 Rep 1


title: RNA-seq of LuCaP 170.3 Rep 2

value: LuCaP 170.3


title: RNA-seq of LuCaP 170.3 Rep 1


title: gq_sample_409


title: gq_sample_407


title: 7C_M_1118


title: RNA-seq of LuCaP 70 Rep 1


title: gq_sample_406


title: gq_sample_405


title: RNA-seq of LuCaP 170.2 Rep 2

value: LuCaP 170.2


title: gq_sample_404

value: Duloxetine


title: gq_sample_403


title: gq_sample_413

value: Week 8 Responder


title: 7C_M_1117


title: 7C_M_1116


title: RNA-seq of LuCaP 170.2 Rep 1


title: gq_sample_402

value: Placebo

value: Week 8 Non-Responder


title: 7C_M_1115


title: gq_sample_400


title: RNA-seq of LuCaP 167 Rep 2

value: LuCaP 167


title: gq_sample_401


title: gq_sample_40

value: Week 0 Non-Responder


title: RNA-seq of LuCaP 167 Rep 1


title: 7C_M_1114


title: gq_sample_4


title: gq_sample_41


title: gq_sample_399


title: gq_sample_408


title: 7C_M_1119


title: gq_sample_398


title: RNA-seq of LuCaP 147 Rep 2

value: LuCaP 147


title: gq_sample_397


title: 7C_M_1112


title: gq_sample_396


title: RNA-seq of LuCaP 147 Rep 1


title: gq_sample_395


title: gq_sample_394


title: RNA-seq of LuCaP 145.2 Rep 2

value: LuCaP 145.2


title: RNA-seq of LuCaP 145.2 Rep 1


title: 7C_M_1110


title: gq_sample_392

value: Week 0 Responder


title: gq_sample_393


title: gq_sample_391


title: gq_sample_390


title: 7C_M_111


title: 7C_M_1109


title: gq_sample_389


title: gq_sample_39


title: gq_sample_388


title: 7C_M_1113


title: 7C_M_1108


title: RNA-seq of LuCaP 145.1 Rep 2

value: LuCaP 145.1


title: gq_sample_386


title: RNA-seq of LuCaP 145.1 Rep 1

value: prostate cancer


title: RNA-seq of LuCaP 141 Rep 2

value: LuCaP 141


title: gq_sample_385


title: 7C_M_1107


title: RNA-seq of LuCaP 23.1 Rep 2

value: LuCaP 23.1


title: gq_sample_384


title: 7C_M_1111


title: gq_sample_387


title: gq_sample_383


title: 7C_M_1105


title: 7C_M_1106


title: RNA-seq of LuCaP 136 Rep 2

value: LuCaP 136

value: male


title: gq_sample_382

value: Peripheral blood


title: RNA-seq of LuCaP 136 Rep 1


title: gq_sample_380


title: gq_sample_38


title: gq_sample_379


title: gq_sample_378


title: RNA-seq of LuCaP 105 Rep 2

value: LuCaP 105


title: 7C_M_1103


title: 7C_M_1102


title: RNA-seq of LuCaP 105 Rep 1


title: gq_sample_376

value: Duloxetine


title: gq_sample_377


title: gq_sample_375

value: Week 8 Responder


title: RNA-seq of LuCaP 96 Rep 2

value: LuCaP 96


title: RNA-seq of LuCaP 141 Rep 1


title: gq_sample_374

value: Placebo

value: Week 8 Non-Responder


title: 7C_M_1101


title: gq_sample_372

value: Week 0 Non-Responder


title: 7C_M_1100


title: gq_sample_373


title: gq_sample_381


title: RNA-seq of LuCaP 96 Rep 1


title: gq_sample_371


title: 7C_M_110


title: RNA-seq of LuCaP 93 Rep 2

value: LuCaP 93


title: gq_sample_37


title: RNA-seq of LuCaP 93 Rep 1


title: 7C_M_1104


title: gq_sample_370


title: 7C_M_11


title: gq_sample_369


title: gq_sample_368


title: RNA-seq of LuCaP 23.1 Rep 1


title: 7C_M_1099


title: gq_sample_367


title: gq_sample_366


title: 7C_M_1098


title: gq_sample_364


title: gq_sample_363


title: AGS

city: wuhan

first: Meimei

last: Yang

address: Bayi Road

department: China Center for Type Culture Collection

institute: Wuhan University

description: AGS

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: MGC-803 cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: MGC-803 cell line

value: AGS


title: gq_sample_362


title: 7C_M_1096


title: gq_sample_361


title: gq_sample_360


title: 229 T25_3

city: Hangzhou

first: Yike

last: Chen

state: Zhejiang

address: Jiefang Road 88, Hangzhou

department: Department of Neurosurgery

institute: Second Affiliated Hospital, School of Medicine, Zhejiang University

data_processing:
Raw data was qualified with FastQC, and QC results were integrated with multiQC.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to hg19 using HISAT2
Sort and convert data to bam format, and remove duplicates using Sametools
Supplementary files format and content: hg19
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: GBM

growth_protocol: LN229 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Library Prep Kit following manufacturer's protocols.

value: GBM

value: TRIM25 knockdown


title: gq_sample_36

value: Week 0 Responder


title: 229 T25_2


title: 7C_M_1095


title: gq_sample_359


title: gq_sample_358


title: 7C_M_1093


title: gq_sample_355


title: 7C_M_1094


title: 229 NC_3

value: WT


title: gq_sample_353


title: gq_sample_356


title: 229 T25_1


title: 7C_M_1092


title: 7C_M_1097


title: 229 NC_2


title: HeLa

description: HeLa

value: HeLa


title: gq_sample_352


title: 7C_M_1091


title: gq_sample_365


title: 229 NC_1


title: gq_sample_350


title: gq_sample_351


title: gq_sample_35


title: 7C_M_109


title: gq_sample_349


title: gq_sample_348


title: gq_sample_357


title: 7C_M_1089


title: gq_sample_347


title: gq_sample_354


title: gq_sample_346


title: Homo sapiens, symptomatic individual, 16

city: Guangzhou

first: Jinbao

last: Gu

address: No.1023, South Shatai Road

institute: Southern Medical University

data_processing:
Cutadapt (v1.16) and SOAPnuke were used to trim the adaptor reads, repeat reads and low-quality reads, followed by rRNA removal using bowtie2 (v2.2.9) with default settings.
Trimmed reads were mapped to human genome annotation hg19 using Hisat (v2-2.0.5).
The expression levels of transcripts were calculated using StringTie-eB (v1.3.3b) and normalized to Fragments Per Kilobase Per Million reads (FPKM), and the low-abundance transcripts with FPKM value < 0.5 were discarded.
LncRNA identification was based on the criteria that more than two exons, bases greater than 200 bp, and locations do not overlap with mRNAs. The known lncRNAs were annotated using the Cuffcompare (v2.1.1). Further, CPC (cpc-0.9-r2) and Pfam-scan (v1.3) were used to predict the unknown transcripts; the transcripts identified by one tool as having coding potential were classified as the transcripts of uncertain coding potential (TUCPs), while those identified by both tools as having no coding potential were predicted as novel lncRNAs.
The Ballgown package in R was used to filter the differentially expressed transcripts with a fold change of > 1.5 (|log2 fold change| > 0.5849625) and a p-value of < 0.05.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM of all transcripts identified in every samples.

source_name: peripheral blood mononuclear cell

extract_protocol:
PBMCs were isolated by density gradient centrifugation, followed by total RNA isolation and purification according to the manufacturer's procedure.
After ribosomal RNA removal, strand-specific RNA sequencing libraries were generated using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina.

value: symptomatic

value: peripheral blood mononuclear cell


title: Homo sapiens, symptomatic individual, 14


title: gq_sample_345

value: Peripheral blood


title: 7C_M_1088

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute


title: Homo sapiens, symptomatic individual, 13


title: 7C_M_1087


title: gq_sample_344


title: gq_sample_343


title: Homo sapiens, symptomatic individual, 12


title: 7C_M_1090


title: gq_sample_341


title: 7C_M_1086


title: gq_sample_34


title: Homo sapiens, symptomatic individual, 11


title: 7C_M_1085


title: gq_sample_340

value: Duloxetine


title: 7C_M_1083


title: Homo sapiens, symptomatic individual, 15


title: gq_sample_337

value: Week 8 Responder


title: Homo sapiens, symptomatic individual, 9


title: gq_sample_338


title: 7C_M_1082


title: gq_sample_335


title: Homo sapiens, symptomatic individual, 8


title: 7C_M_1081


title: gq_sample_336


title: gq_sample_334


title: gq_sample_332


title: gq_sample_333


title: gq_sample_331


title: gq_sample_342


title: Homo sapiens, symptomatic individual, 6


title: gq_sample_33


title: 7C_M_1079


title: Homo sapiens, symptomatic individual, 10


title: Homo sapiens, symptomatic individual, 7


title: gq_sample_330


title: Homo sapiens, symptomatic individual, 4


title: gq_sample_339


title: gq_sample_329


title: gq_sample_327


title: gq_sample_328


title: 7C_M_1078


title: Homo sapiens, symptomatic individual, 5


title: Homo sapiens, symptomatic individual, 3


title: gq_sample_325


title: 7C_M_1077


title: gq_sample_326


title: gq_sample_324


title: Homo sapiens, symptomatic individual, 2


title: gq_sample_323


title: 7C_M_1076


title: Homo sapiens, symptomatic individual, 1


title: gq_sample_322


title: 7C_M_1080


title: 7C_M_108


title: 7C_M_1075


title: 7C_M_1074


title: gq_sample_320


title: Homo sapiens, asymptomatic individual, 11

value: asymptomatic


title: Homo sapiens, asymptomatic individual, 10


title: gq_sample_32

value: Placebo


title: gq_sample_318


title: 7C_M_1073


title: gq_sample_317


title: 7C_M_1072


title: gq_sample_316


title: Homo sapiens, asymptomatic individual, 9


title: gq_sample_315


title: 7C_M_1071


title: gq_sample_314

value: Week 8 Non-Responder


title: Homo sapiens, asymptomatic individual, 7


title: gq_sample_313

value: Week 0 Non-Responder


title: gq_sample_312


title: 7C_M_1070


title: Homo sapiens, asymptomatic individual, 6


title: gq_sample_311


title: 7C_M_107


title: gq_sample_321


title: gq_sample_310


title: Homo sapiens, asymptomatic individual, 5


title: gq_sample_31


title: 7C_M_1069


title: gq_sample_309


title: gq_sample_319


title: gq_sample_308


title: 7C_M_1068


title: 7C_M_1067


title: Homo sapiens, asymptomatic individual, 3


title: gq_sample_307


title: gq_sample_304


title: gq_sample_306


title: Homo sapiens, asymptomatic individual, 4


title: Homo sapiens, asymptomatic individual, 8


title: gq_sample_305


title: Homo sapiens, asymptomatic individual, 2


title: Homo sapiens, healthy control, 13

value: healthy control


title: 7C_M_1065


title: gq_sample_301


title: 7C_M_1066


title: gq_sample_303


title: gq_sample_302


title: gq_sample_300


title: 7C_M_1064


title: gq_sample_30


title: Homo sapiens, healthy control, 11


title: 7C_M_1063


title: Homo sapiens, healthy control, 10


title: 7C_M_1062


title: gq_sample_298


title: gq_sample_3


title: gq_sample_297


title: Homo sapiens, healthy control, 9


title: gq_sample_296


title: gq_sample_294


title: gq_sample_295


title: Homo sapiens, healthy control, 8


title: 7C_M_1060


title: Homo sapiens, healthy control, 7


title: gq_sample_292


title: gq_sample_291


title: 7C_M_106


title: Homo sapiens, healthy control, 6


title: Homo sapiens, healthy control, 12


title: 7C_M_1059


title: gq_sample_289


title: Homo sapiens, healthy control, 5


title: gq_sample_29


title: 7C_M_1058


title: gq_sample_288


title: Homo sapiens, healthy control, 4


title: gq_sample_287


title: gq_sample_286


title: 7C_M_1057


title: 7C_M_1061


title: 7C_M_1056


title: gq_sample_285


title: gq_sample_284


title: gq_sample_293


title: Homo sapiens, healthy control, 2


title: gq_sample_283


title: Homo sapiens, healthy control, 3


title: 7C_M_1054


title: Homo sapiens, healthy control, 1


title: gq_sample_290


title: gq_sample_281


title: gq_sample_280


title: 7C_M_1053


title: gq_sample_28


title: 7C_M_1051


title: gq_sample_278


title: gq_sample_277


title: 7C_M_1052


title: gq_sample_275


title: gq_sample_274


title: gq_sample_276


title: gq_sample_273


title: NCI-H295R cells, MET-2

city: Seoul

first: Soo Hyun

address: Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

data_processing:
Raw sequence reads were trimmed for adaptor sequence using Cutadapt (version 2.8).
Trimmed sequence reads were mapped to GRCh38 using STAR Aligner (version 2.7.10b).
Read count extraction and normalization were performed using RSEM (version 1.3.3).
Assembly: GRCh38
Supplementary files format and content: A tab-delimited text file includes TPM (transcripts per million) counts for all samples

extract_protocol:
Total RNA was extracted using the microRNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality was evaluated by RNA integrity number (>9.5) by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples were then subjected to ribosomal RNA depletion using Ribo-Zero™reagent (Illumina, San Diego, CA, USA).
cDNA libraries were prepared using the TruSeq™ Stranded Total RNA Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Adrenocarcinoma

value: Metyrapone (30 μM)

tag: time


title: NCI-H295R cells, MET-4

tag: cell line


title: NCI-H295R cells, CJ28-4

tag: cell type


title: NCI-H295R cells, MET-1


title: 7C_M_1049

city: La Jolla

address: 10010 North Torrey Pines Road


title: NCI-H295R cells, MET-3


title: gq_sample_282


title: 7C_M_105


title: gq_sample_272


title: gq_sample_271


title: 7C_M_1048


title: gq_sample_27


title: gq_sample_269


title: gq_sample_270


title: NCI-H295R cells, CJ28-3


title: gq_sample_268


title: NCI-H295R cells, CJ28-2


title: 7C_M_1047


title: 7C_M_1050


title: gq_sample_267


title: gq_sample_266


title: NCI-H295R cells, VEH-4

value: Vehicle (0.1% DMSO)


title: gq_sample_265


title: 7C_M_1045


title: NCI-H295R cells, VEH-3


title: gq_sample_261


title: gq_sample_26


title: gq_sample_260


title: gq_sample_263


title: gq_sample_299


title: NCI-H295R cells, VEH-2


title: gq_sample_262


title: 7C_M_1042


title: 7C_M_1044


title: 7C_M_1041


title: 7C_M_1040


title: NCI-H295R cells, VEH-1


title: 7C_M_104


title: gq_sample_257


title: gq_sample_258


title: gq_sample_256


title: gq_sample_255


title: 7C_M_1046


title: gq_sample_264


title: gq_sample_253


title: ATAC-Seq LNCaPabl_MPC309_2

first: Michael

last: Garabedian

address: 500 First Ave

institute: NYU School of Medicine

data_processing:
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt. Quality scores were assessed using FastQC. Reads were aligned to the Homo sapiens genome build hg19 using bowtie2. Per-sample quality assessment plots were generated with HOMER and Mosaics. Peaks were called using MACS26 (with input/IgG controls background subtracted if provided). Peak overlaps and differential binding were calculated using the DiffBind R library. Differential binding was calculated at gene promoter sites. Read distribution percentages, identity heatmaps, and FRiP plots were generated as part of the QC step using ChIPQC R library and HOMER. HOMER was also used to generate known and de novo motifs and perform functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies.
Assembly: hg19
Supplementary files format and content: bigWig includes indexed binary files which contain alignment data to the genome for each sample

source_name: LNCaP-ABL

growth_protocol: LNCaP-ABL cells were cultured under androgen deprivation

extract_protocol:
Cells (1x105) were washed in cold PBS and lysed in cold lysis buffer (10 mM Tris-HCl, pH = 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The transposition reaction (Illumina) was performed at 42C for 45 min. After purification of the DNA with the MinElute PCR purification kit (QIAGEN)
After purification of the DNA with the MinElute PCR purification kit (QIAGEN), the material was amplified for 5 cycles using NEB Next Ultra DNA Library Prep (New England BioLabs), and size was verified on Tapestation. Normalized libraries were sequenced on a HiSeq2500 1T in a 50bp/50bp Paired-end run at the Genome Technology Center at NYU, using the TruSeq SBS Kit v3 (Illumina).

treatment_protocol: LNCaP-ABL cells were treated with vehicle (DMSO), 1μM backbone, 1μM MPC309, 10nM DHT, or 10μM enzalutamide overnight

value: LNCaP-ABL

value: prostate


title: ATAC-Seq LNCaPabl_Backbone_2

value: Backbone


title: gq_sample_254

value: Week 0 Responder


title: ATAC-Seq LNCaPabl_MPC309_1


title: 7C_M_1039


title: ATAC-Seq LNCaPabl_Backbone_1


title: 7C_M_1038


title: gq_sample_251


title: ATAC-Seq LNCaPabl_DHT_2

value: DHT


title: ATAC-Seq LNCaPabl_DHT_1


title: gq_sample_259


title: gq_sample_250


title: gq_sample_25


title: gq_sample_247


title: 7C_M_1036


title: gq_sample_252


title: 7C_M_1035


title: ATAC-Seq LNCaPabl_Enzalutamide_2

value: Enzalutamide


title: 7C_M_1037


title: ATAC-Seq LNCaPabl_Enzalutamide_1


title: gq_sample_248

value: Peripheral blood


title: gq_sample_246

value: Duloxetine


title: gq_sample_245


title: gq_sample_244


title: NCI-H295R cells, CJ28-1

last: Kim


title: 7C_M_1034


title: ATAC-Seq LNCaPabl_Vehicle_2

value: Vehicle


title: gq_sample_242


title: ATAC-Seq LNCaPabl_Vehicle_1


title: 7C_M_1033


title: 7C_M_1032


title: gq_sample_249

value: Week 8 Responder


title: gq_sample_240

value: Placebo


title: ChIP-Seq LNCaPabl_MPC309_AR

extract_protocol:
Cells were double crosslinked with formaldehyde and the bifunctional protein crosslinker disuccinimidyl glutarate (DSG) to preserve protein-DNA and protein-protein interactions. A mixture of two antibodies for AR ChIP was used (AR 441 mouse monoclonal, Santa Cruz Biotechnology; Cat#sc-7305 and AR D6F11 rabbit monoclonal, Cell Signaling Technology; Cat #5153) to maximize AR enrichment and minimize epitope masking. Inputs were used for normalization, and additional IgG controls were included to ensure any low occupancy peaks were specific to AR and not the background.
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit, quantified on Qubit, pooled at equimolar concentrations.


title: gq_sample_24


title: 7C_M_1031


title: gq_sample_239


title: ChIP-Seq LNCaPabl_MPC309_IgG


title: 7C_M_1030


title: gq_sample_238


title: ChIP-Seq LNCaPabl_MPC309_Input


title: gq_sample_237


title: ChIP-Seq LNCaPabl_Enzalutamide_AR


title: 7C_M_103


title: ChIP-Seq LNCaPabl_Enzalutamide_IgG


title: gq_sample_235


title: gq_sample_234


title: 7C_M_1029


title: gq_sample_232


title: gq_sample_233


title: gq_sample_243


title: 7C_M_1028


title: gq_sample_241

value: Week 8 Non-Responder


title: gq_sample_231


title: ChIP-Seq LNCaPabl_Enzalutamide_Input


title: gq_sample_23

value: Week 0 Non-Responder


title: 7C_M_1027


title: ChIP-Seq LNCaPabl_DHT_AR


title: gq_sample_229


title: 7C_M_1026


title: ChIP-Seq LNCaPabl_DHT_IgG


title: gq_sample_228


title: 7C_M_1025


title: gq_sample_227


title: gq_sample_226


title: ChIP-Seq LNCaPabl_DHT_Input


title: gq_sample_236


title: gq_sample_225


title: 7C_M_1024


title: gq_sample_224


title: gq_sample_222


title: ChIP-Seq LNCaPabl_Backbone_Input


title: gq_sample_230


title: gq_sample_22


title: 7C_M_1023


title: ChIP-Seq LNCaPabl_Backbone_IgG


title: gq_sample_221


title: 7C_M_1022


title: gq_sample_223


title: gq_sample_220


title: 7C_M_1021


title: gq_sample_218


title: gq_sample_219


title: ChIP-Seq LNCaPabl_Vehicle_AR


title: ChIP-Seq LNCaPabl_Vehicle_IgG


title: gq_sample_216


title: gq_sample_215


title: 7C_M_102


title: gq_sample_214


title: 7C_M_1019


title: RNA-Seq LNCaPabl_Backbone_2

data_processing:
Data were analyzed by ROSALIND®, with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt. Quality scores were assessed using FastQC68. Reads were aligned to the Homo sapiens genome build hg19 using STAR3. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using the DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC. DEseq2 was also used to calculate fold changes and p values and perform optional covariate correction. The clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library. Functional enrichment analysis of pathways, gene ontology, domain structure, and other ontologies was performed using HOMER. Several databases were referenced for enrichment analysis, including Interpro, NCBI, MSigDB REACTOME, and WikiPathways. Enrichment was calculated relative to a set of background genes relevant to the experiment. Additional gene enrichment is available from the following partner institutions: Advaita. Differentially expressed genes were analyzed using the Enrichr platform from the Ma’ayan Laboratory.
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text file includes nomalized counts for each sample

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen).
Libraries were prepared for sequencing using the NEBNext Ultra II RNA Library Prep Kit for Illumina with polyA selection


title: gq_sample_212


title: ChIP-Seq LNCaPabl_Backbone_AR


title: gq_sample_211


title: RNA-Seq LNCaPabl_Backbone_1


title: gq_sample_279


title: RNA-Seq LNCaPabl_Vehicle_2


title: gq_sample_217


title: gq_sample_21


title: gq_sample_208


title: 7C_M_1020


title: 7C_M_1016


title: gq_sample_210


title: gq_sample_207


title: RNA-Seq LNCaPabl_Enzalutamide_2


title: 7C_M_1017


title: RNA-Seq LNCaPabl_Vehicle_1


title: 7C_M_1015


title: gq_sample_209


title: ChIP-Seq LNCaPabl_Vehicle_Input


title: gq_sample_213


title: gq_sample_205


title: RNA-Seq LNCaPabl_Enzalutamide_1


title: 7C_M_1014


title: gq_sample_204


title: gq_sample_203


title: gq_sample_202


title: 7C_M_1013


title: 7C_M_1018


title: 7C_M_1012


title: RNA-Seq LNCaPabl_DHT_2


title: gq_sample_200


title: gq_sample_206


title: gq_sample_20


title: gq_sample_199


title: RNA-Seq LNCaPabl_MPC309_2


title: 7C_M_1010


title: gq_sample_196


title: gq_sample_198


title: gq_sample_2


title: RNA-Seq LNCaPabl_DHT_1


title: gq_sample_195


title: 7C_M_1011


title: gq_sample_201


title: gq_sample_193


title: gq_sample_194


title: 7C_M_101


title: gq_sample_192


title: gq_sample_190


title: 7C_M_1008


title: RNA-Seq LNCaPabl_MPC309_1


title: gq_sample_19


title: 7C_M_1007


title: 7C_M_1006


title: gq_sample_189


title: LNCaPabl_Ethisterone_2

data_processing:
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt. Quality scores were assessed using FastQC. Reads were aligned to the Homo sapiens genome build hg19 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several databases were referenced for enrichment analysis, including Interpro, NCBI, KEGG, MSigDB, REACTOME, WikiPathways. Enrichment was calculated relative to a set of background genes relevant for the experiment.
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text file includes nomalized counts for each sample

treatment_protocol: LNCaP-ABL cells were treated with vehicle (DMSO), 1μM MPC309 or 10μM ethisterone overnight

value: Ethisterone


title: LNCaPabl_MPC309_1


title: LNCaPabl_Ethisterone_1


title: LNCaPabl_MPC309_2


title: LNCaPabl_Vehicle_2


title: gq_sample_197


title: gq_sample_188


title: 7C_M_1009


title: 7C_M_1005


title: gq_sample_187


title: LNCaPabl_Vehicle_1


title: gq_sample_186


title: gq_sample_191


title: 7C_M_1004


title: gq_sample_184


title: gq_sample_185


title: 7C_M_1003


title: gq_sample_183


title: donor3_biorepl1_techrepl2

city: Seattle

first: Asia

last: Mendelevich

state: WA

address: 2211 Elliott Ave

institute: Altius

description:
donor no. 3 peripheral blood monocytes
Donor no. 3 peripheral blood monocytes, biological replicate 1, library preparation replicate 2
STARA_E3.Human_only.counts.tsv

data_processing:
Sequence reads were aligned on two alellic pseudogenomes using STAR v2.7.9a (with parameters –outSAMattributes vA vG).
Uniquely aligned reads were assigned towards one of the alleles according to their SNP calls and alignment quality (see https://github.com/gimelbrantlab/fastq2allelictabs).
Allelic gene counts were calculated using featurecounts v2.0.2.
Supplementary files format and content: Tab-delimited text files include allelic gene count values for each sample.

source_name: peripheral blood monocytes

extract_protocol:
Qiagen Mini
SMART-Seq v4 PLUS kit (Takara)

value: peripheral blood monocytes

value: WT

value: donor no. 3


title: donor1_biorepl1_techrepl2

description:
donor no. 1 peripheral blood monocytes
Donor no. 1 peripheral blood monocytes, biological replicate 1, library preparation replicate 2
STARA_E3.Human_only.counts.tsv

value: donor no. 1


title: gq_sample_181


title: gq_sample_182


title: 7C_M_1002


title: donor2_biorepl1_techrepl2

description:
donor no. 2 peripheral blood monocytes
Donor no. 2 peripheral blood monocytes, biological replicate 3, library preparation replicate 2
STARA_E3.Human_only.counts.tsv

value: donor no. 2


title: gq_sample_18


title: gq_sample_180


title: 7C_M_1001


title: gq_sample_179


title: 7C_M_1000


title: gq_sample_176


title: 7C_M_100


title: donor3_biorepl1_techrepl1

description:
donor no. 3 peripheral blood monocytes
Donor no. 3 peripheral blood monocytes, biological replicate 1, library preparation replicate 1
STARA_E3.Human_only.counts.tsv


title: gq_sample_175


title: gq_sample_177


title: donor1_biorepl2_techrepl1

description:
donor no. 1 peripheral blood monocytes
Donor no. 1 peripheral blood monocytes, biological replicate 2, library preparation replicate 1
STARA_E3.Human_only.counts.tsv


title: 7C_M_10


title: gq_sample_174


title: gq_sample_173


title: 7C_M_1


title: gq_sample_172


title: donor1_biorepl2_techrepl2


title: gq_sample_171


title: gq_sample_170


title: 7C_M_0


title: 4T1 shHSF1 Rep3

data_processing:
The sequence data were mapped to the mouse reference genome mm10 with STAR
FeatureCounts was used to quantify gene expression
The data were further normalized using RPKM (Reads Per Kilobase Million)
Assembly: mm10
Supplementary files format and content: Excel table including gene information (Symbol, chromosome, start position, end position, strand, and gene length) and RPKM values

value: breast

value: Adenocarcinoma

value: epithelial

value: HSF1 shRNA


title: gq_sample_169

value: Peripheral blood


title: H3_repl2

description:
GM12878.DF1 cell line, biological replicate 3, library preparation replicate 2
LOVSON_E1.Human_only.counts.tsv

source_name: clonal pro-B cell line GM12878.DF

extract_protocol:
Agilent Mini
NEBNext® Single Cell/Low Input RNA

value: clonal pro-B cell line GM12878.DF

value: pro-B cells


title: H3_repl3

description:
GM12878.DF1 cell line, biological replicate 3, library preparation replicate 3
LOVSON_E1.Human_only.counts.tsv


title: 4T1 shHSF1 Rep2


title: gq_sample_17

value: Week 0 Responder


title: gq_sample_168

value: Placebo


title: H3_repl1

description:
GM12878.DF1 cell line, biological replicate 3, library preparation replicate 1
LOVSON_E1.Human_only.counts.tsv


title: gq_sample_167

value: Duloxetine

value: Week 8 Responder


title: gq_sample_166


title: 4T1 shHSF1 Rep1


title: donor1_biorepl1_techrepl1

description:
donor no. 1 peripheral blood monocytes
Donor no. 1 peripheral blood monocytes, biological replicate 1, library preparation replicate 1
STARA_E3.Human_only.counts.tsv


title: gq_sample_178


title: gq_sample_162

value: Week 8 Non-Responder


title: H2_repl3

description:
GM12878.DF1 cell line, biological replicate 2, library preparation replicate 3
LOVSON_E1.Human_only.counts.tsv


title: gq_sample_165


title: 4T1 shCTL Rep2

value: CTL


title: gq_sample_161


title: H2_repl2

description:
GM12878.DF1 cell line, biological replicate 2, library preparation replicate 2
LOVSON_E1.Human_only.counts.tsv

value: WT


title: donor2_biorepl1_techrepl1

description:
donor no. 2 peripheral blood monocytes
Donor no. 2 peripheral blood monocytes, biological replicate 1, library preparation replicate 1
STARA_E3.Human_only.counts.tsv

value: peripheral blood monocytes


title: 4T1 shCTL Rep3


title: gq_sample_163


title: H2_repl1

description:
GM12878.DF1 cell line, biological replicate 2, library preparation replicate 1
LOVSON_E1.Human_only.counts.tsv


title: gq_sample_160

value: Week 0 Non-Responder


title: gq_sample_16


title: 4T1 shCTL Rep1


title: gq_sample_159


title: H1_repl3

description:
GM12878.DF1 cell line, biological replicate 1, library preparation replicate 3
LOVSON_E1.Human_only.counts.tsv


title: gq_sample_158


title: H1_repl2

description:
GM12878.DF1 cell line, biological replicate 1, library preparation replicate 2
LOVSON_E1.Human_only.counts.tsv


title: gq_sample_156


title: H1_repl1

description:
GM12878.DF1 cell line, biological replicate 1, library preparation replicate 1
LOVSON_E1.Human_only.counts.tsv


title: gq_sample_155


title: gq_sample_157


title: 4T1 shHSF1 Tumor scRNAseq

library_source: transcriptomic single cell

data_processing:
CellRanger 6.1  was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger wereused for further analysis.
Assembly: mm10
Supplementary files format and content: HDF5 file of filtered gene-barcode matrices

source_name: breast tumor

growth_protocol: growth: injected into Balb/c mice and growth for 3 weeks

extract_protocol:
Tumor dissociated with Miltenyi tumor dissociation kit using gentleMACS. Single cell suspension processed with 10X genomics
Library was performed according to the manufacturer’s instructions (single cell 3’ protocol, 10x Genomics).

value: breast tumor

value: epithelial cells

value: BALB/c

value: 4T1 shHSF1 cells


title: 4T1 shCTL Tumor scRNAseq

value: 4T1 shCTL cells


title: gq_sample_154

value: Peripheral blood


title: gq_sample_153


title: gq_sample_164


title: gq_sample_152