title: RNA_mouse_WT_IL2IL15IL12IL18IFNA_3

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36).
Transcript quantification was performed by salmon (v0.10.2) using arguments '-l IU --gcBias' and tximport (v1.8.0 or v1.10.1) using the UCSC mm10 known gene transcript assembly (v9).
Supplementary_files_format_and_content: Text files are raw estimated gene-level counts (1 count = 1 read pair) as quantified by salmon (v0.10.2) and imported by tximport (v1.8.0 or v1.10.1). Also provided are gene IDs (Entrez and Ensembl), gene names, gene descriptions, and chromosome (for human).

source_name: splenic NK cells

extract_protocol:
RNA was isolated from sorted and stimulated cell populations using TRIzol (Invitrogen) or the PicoPure RNA Isolation Kit (Thermo Fisher)
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.705-2ng total RNA with RNA integrity numbers ranging from 6.5 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech catalog # 63488), with 12 cycles of amplification. Subsequently, 10ng 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 or HiSeq 2500 in Rapid mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2, respectively (Illumina).  An average of 37 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 42% to 70%.

value: WT

value: ex-vivo NK cells

tag: replicate


title: 509 Spine-2

status: Public on Apr 29 2021

type: SRA

city: HOUSTON

first: Igor

middle: L.

last: Bado

state: Texas

address: One Baylor Plaza, Alkek Building N1130

department: Breast Center

country: USA

institute: Baylor College of Medicine

description:
509 Spine-2
mutation_count_matrix_509.txt

library_source: genomic

data_processing:
Library strategy: evolving barcode
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace. Only the R1 files were used in the following analysis and only the R1  files were submitted.
To identify the barcoding region, we globally aligned each distinct sequence to the A26 reference barcode using TraceQC package in R. The parameters used for alignment are: 2 for match score, -2 for mismatch score, -6 for gap opening penalty and -0.1 for gap extension penalty.
The adapter sequences were trimmed off and sequences with less than 200 alignment score or less than 10 counts were filtered out from the subsequent analysis. The barcode sequence  is 117 bp starting from 58 bp before predicted TSS.
The mutation events were categorized by the TraceQC package on each barcode into 4 attributes: 1) the mutation type (insertion, deletion or point mutation), 2) the starting position of mutation, 3) the length of mutation, and 4) the altered sequence.
The mutation events were normalized by the read count per million (RPM) approach and used to generate the feature count matrix for all the samples.
Supplementary_files_format_and_content: Processed data files are txt files including the count (RPM) of each mutation event.The mutation events are named in the form of A_B_C_D using below criteria: A, type of mutation, including insertion, deletion, or single nucleotide mutation (‘mutation’ in short); B, the starting position of mutation; C, the length of mutation; D, the altered sequence. For deletion, the value is -; for mutation, the value is the replaced nucleotide; for insertion, the value is the inserted sequence.

molecule: genomic DNA

organism: Homo sapiens

source_name: breast cancer cells implanted in mouse

growth_protocol: MDA-MB-231 FR and AT-3 FR cells were transduced with TLCV2-hgRNA A26 and selected by puromycin for 2 weeks. 1E5 barcoded cells were then implanted to the fourth pair of mammary fat pad of nude mice or C57BL/6 mice. 5 weeks later for MDA-MB-231 tumors or 18 days  later for AT-3 tumors, the mammary tumors were resected and mice were give with a single dose of 5mg/kg doxycycline weekly for 5 cycles or 4 cycles through I.P. injection. 2 weeks after Dox treatment, the tissues with metastases were collected, and total DNA were exacted. For IIA injection model, 1E5 barcoded MDA-MB-231 cells were then delivered to bone via IIA. 2 weeks later, a single dose of 5mg/kg doxycycline weekly for 5 cycles was applied to the mice carrying bone metastases through I.P. injection. 3 weeks after Dox treatment, lung, right and left hindlimbhind limbs were collected, and total DNA were exacted. For in vitro treatment samples, cells were treated with 100μg/ml doxycycline for 2 hours and then rinsed by pre-warmed PBS twice to completely remove doxycycline and then allow to grow in vitro for 4 days. Then 1 million cells were collected for barcode sequencing and 0.5 million cells were seeded back to the petri dish and received another round of doxycycline treatment 24 hours later.

extract_protocol:
The metastatic lesions were dissected with ex vivo BLI imaging, and the uninvolved tissues were removed. The surgery tools were sterilized with a bead-sterilizer following by 70% isopropanol between different lesions. The collected tissues was snap-frozen in the liquid nitrogen until DNA extraction. The tissues were then rinsed by the gDNA lysis buffer from Quick-DNA Miniprep Plus Kit (Zymo Research, D4068) and homogenized with Precellys Lysing Kit (Bertin Instruments, MK28-R). After the homogenization, samples were lysed at 55℃ for 3 h, followed by 0.33 mg/mL RNaseA treatment at 37℃ for 15 min. Nucleic acid was further extracted following the manufacturer’s instruction. The final DNA was assessed by NanoDrop 2000 (Thermo Scientific) and human/mouse DNA ratio was examined by q-PCR with primers targeting human and mouse GAPDH gene, respectively.
Barcodes were amplified by two rounds of PCR. The first round of PCR was performed with 100 ng genomic DNA using Platinum Taq DNA Polymerase (Invitrogen) with Barcode-For and Barcode-Rev primers in 15 cycles. The second round of PCR were performed in a real-time setting and stopped in mid-exponential phase using PowerUp SYBR Green Master Mix (Thermo Fisher) with Barcode-P5-For and Barcode-P7-Rev primers. PCR products were then column-purified with QIAquick PCR purification Kit (QIAGEN) and assessed with Qubit. The NEBNext Multiplex oligos for Illumina (Dual index primer set 1,NEB, E7600S) and the NEB library preparation kit for Illumina (NEB, #E7645S) were used for library preparation as previously described (Kalhor et al., 2017).

tag: injected cell line

tag: metastic sites

value: Spine

tag: host

value: Athymic Nude

tag: mouse id


title: A673_siSA2-Dh6_48h_R2

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

library_source: transcriptomic

data_processing:
Reads were trimmed with Atropos
Mapping and gene quantification were performed with STAR version 2.5.3 againt human genome (hg19, gencode V19). Option "--quantMode GeneCounts" was used to get abundance measurements.
DESEQ2 1.20.0 was used to perform differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files with raw counts for each genes.

molecule: polyA RNA

source_name: Ewing sarcoma cell line (A673)

growth_protocol: Cells were cultured in DMEM (A673) or RPMI (TC71 and EW1) supplemented with 10% fetal bovine serum. CHLA-10 and CHLA-258 were cultured in IMDM supplemented with 20% fetal bovine serum and 1X Insuline-Transferrin-selenium.

extract_protocol:
RNA was extracted using RNeasy plus mini kit and further processed for RNA-seq
The library construction was performed using TruSeq Stranded mRNA (Illumina, ref #20020594) according to manufacturer recommendations

treatment_protocol: Five different Ewing sarcoma cell lines were transfected with siCT or 2 different siRNAs targeting STAG2 (siSA2#6 or siSA2#8). RNA in A673 & TC71 (siSTAG2) was extracted 24, 48 and 72 hours post-transfection. RNA in EW1, CHLA-10 and CHLA-258 (siSTAG2 and siEWSR1-FLI1) was extracted 72 hours post-transfection.

tag: sirna

tag: timepoint


title: Ewing sarcoma sample EW103

type: RNA

first: Didier

last: Surdez

address: 26 rue d'ULM

hyb_protocol: As according to the manufacturer's instructions.

scan_protocol: GCOS 1.4

data_processing: All data were normalized using the gcrma package version 2.22.0 in R 2.12 environment with quantile normalization and hgu133plus2hsentrezg Brainarray annotation version 14  (http://brainarray.mbni.med.umich.edu/Brainarray/).

label: biotin

molecule: total RNA

source_name: Ewing sarcoma sample EW103

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA usin 3'IVT Express Kit.

growth_protocol: Tumor sample were fozen in liquid nitrogen or on dry ice

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

treatment_protocol: Tumor sample were stored at -80°C until extraction procedure

tag: gender

value: Male

tag: age

tag: tumor type

value: primary tumor


title: Ewing sarcoma sample EW110

source_name: Ewing sarcoma sample EW110

value: Female


title: TC71_siCT-Dh1_72h_R2

source_name: Ewing sarcoma cell line (TC71)


title: vec_minus_IP1

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Differential expression analysis was performed by DESeq2.
Peak calling was performed with exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: exomePeak output bed file

source_name: HEK cell

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

tag: technology

tag: condition

value: wild type

tag: sample type

value: IP


title: WT_RNA-Seq

city: London

first: Steve

last: West

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: mRNA-Seq

data_processing:
Sequenced reads were aligned and quantified against human genome version hg19 with Refseq transcript annotations using RSEM v1.2.31 and STAR v2.5.1b.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function (-scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.

source_name: HAP1 Wild-type Cells

growth_protocol: Human HAP1 WT and DSETX cells were cultured in IMDM (ThermoFisher) supplemented with 10% FBS and 1% Penicillin/Streptomycin (Sigma-Aldrich). Hap1 cells were grown at 37°C and in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cultured human and mouse cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including an on-column DNase treatment to eliminate any contaminating genomic DNA.
Illumina TruSeq Stranded mRNA Library Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.

treatment_protocol: Cells were harvested by trypsinization followed by two washes with ice-cold PBS.

tag: cell type

value: HAP1 cells derived from male CML cell line KBM7

tag: morphology

value: Fibroblast-like

tag: genotype

value: Wild-type


title: DSETX_RNA-Seq

description: mRNA-Seq

source_name: HAP1 SETX Knockout Cells

value: SETX Knockout


title: RNA_mouse_WT_IL2IL15IL12IL18IFNA_2

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

organism: Mus musculus

treatment_protocol: Mouse NK cells were stimulated for 3 hr with combinations of 20 ng/mL recombinant mouse IL-2,  20 ng/ml recombinant mouse IL-15, 20 ng/ml recombinant mouse IL-12, 10 ng/ml recombinant mouse IL-18, and/or 100 IU recombinant mouse IFN-α. Human NK cells were stimulated with 100 U/ml recombinant human IL-2, 50 ng/ml recombinant human IL-15, 20 ng/ml recombinant human IL-12, 50 ng/ml recombinant human IL-18 and/or 1000 U/ml recombinant human IFN-α.


title: Ewing sarcoma sample EW074

source_name: Ewing sarcoma sample EW074


title: vec_minus_Input2

value: input


title: RNA_mouse_WT_IL2IL15IL12IL18IFNA_1


title: A673_siSA2-Dh6_48h_R1


title: Ewing sarcoma sample EW122

source_name: Ewing sarcoma sample EW122


title: A673_siSA2-Dh6_24h_R2


title: vec_minus_Input1


title: A673_siSA2-Dh6_24h_R1


title: RNA_mouse_WT_IL2IL15IL12IL18_3


title: Alkbh5_mut_plus_IP2

value: over expression


title: RNA_mouse_WT_IL2IL15IL12IL18_2


title: Alkbh5_mut_plus_IP1


title: Control P7 Mixed Glial Cells

city: San Francisco

first: Leah

last: Dorman

state: CA

address: 499 Illinois St

department: Data Science

institute: CZBiohub

description:
Dorman_P7Glia_normalizedcounts.csv
DormanP7Glia_counts.csv
Dorman_P7_metadata_clustering.csv

data_processing:
Cell Ranger 2.2.0 (samples 1-2)/3.1.0 (samples 3-6) (STAR) alignment with Mus musculus transcriptome mm10-1.2.0 (samples 1-2)/ mm10-3.0.0 (samples 3-6)
Quality control to select cells with <10% mitochondrial RNA, 500-3,000 unique genes, and 1,200-15,000 unique mRNA counts
[normalized data only] SCT Transformation (samples 1-2) OR Log normalization (samples 3-6) (Seurat v3.2) with scale factor 10,000
[normalized data only] most variable genes scaled with "vst" algorithm and #genes/cell and %mitochondrial RNA regressed out (Seurat v3.2)
Genome_build: mm10
Supplementary_files_format_and_content: Counts: unnormalized count data for all cells included in the manuscript
Supplementary_files_format_and_content: Metadata: file containing age, individual, and cluster assignment for each cell

source_name: Barrel cortex

extract_protocol:
10x Genomics v2 3' Single Index (Chip Kit B) was used to make a single cell suspension in gel beads, and the v2 3' Library Kit was used to prepare cDNA
Sorted live cells after cold protease digestion (samples 1-2) or MACS bead isolated CD11b+ cells after tissue homogenization (samples 3-6)

tag: celltype

value: Mixed glial population

tag: dissociation method

value: Psychrophilic protease digestion on ice

tag: isolation method

value: Sorted live cells


title: Deprived P7 Mixed Glial Cells


title: RNA_mouse_WT_IL2IL15IL12IL18_1

value: WT

value: ex-vivo NK cells

tag: replicate


title: Ewing sarcoma sample EW107

source_name: Ewing sarcoma sample EW107


title: Ewing sarcoma sample EW085

source_name: Ewing sarcoma sample EW085


title: Ewing sarcoma sample EW099

source_name: Ewing sarcoma sample EW099


title: Ewing sarcoma sample EW083

source_name: Ewing sarcoma sample EW083


title: A673_siCT-Dh1_72h_R1


title: A673_siCT-Dh1_48h_R2


title: Ewing sarcoma sample EW060

source_name: Ewing sarcoma sample EW060


title: Alkbh5_mut_plus_Input1


title: Ewing sarcoma sample EW079

source_name: Ewing sarcoma sample EW079


title: Ewing sarcoma sample EW851

source_name: Ewing sarcoma sample EW851


title: Ewing sarcoma sample EW072

source_name: Ewing sarcoma sample EW072


title: A673_siCT-Dh1_48h_R1

source_name: Ewing sarcoma cell line (A673)


title: Alkbh5_mut_minus_IP2


title: A673_siCT-Dh1_72h_R2


title: Ewing sarcoma sample EW056

source_name: Ewing sarcoma sample EW056


title: Ewing sarcoma sample EW849

source_name: Ewing sarcoma sample EW849


title: RNA_mouse_WT_IFNAIL2IL15_1

source_name: splenic NK cells


title: Ewing sarcoma sample EW929

source_name: Ewing sarcoma sample EW929


title: A673_siCT-Dh1_24h_R2


title: Ewing sarcoma sample EW847

source_name: Ewing sarcoma sample EW847


title: Ewing sarcoma sample EW843

source_name: Ewing sarcoma sample EW843


title: RNA_mouse_WT_IL12IL18IFNA_3


title: Alkbh5_mut_plus_Input2

source_name: HEK cell


title: Alkbh5_mut_minus_Input2


title: A673_siCT-Dh1_24h_R1


title: Ewing sarcoma sample EW850

source_name: Ewing sarcoma sample EW850


title: Alkbh5_mut_minus_IP1


title: RNA_mouse_WT_IFNAIL2IL15_3


title: RNA_mouse_WT_IL12IL18IFNA_2


title: Alkbh5_mut_minus_Input1


title: RNA_mouse_WT_IFNAIL2IL15_2


title: RNA_mouse_WT_IL12IL18IFNA_1


title: RNA_mouse_WT_IL2IL15_3


title: RNA_mouse_WT_IL2IL15_2


title: Ewing sarcoma sample EW840

source_name: Ewing sarcoma sample EW840


title: RNA_mouse_WT_IL2IL15_1


title: RNA_mouse_WT_IL12IL18_3


title: CTRL-C2_RNA-Seq

description: mRNA-Seq

source_name: Lymphoblastoid Cell Line from Control Healthy Individual

growth_protocol: Lymphoblastoid cell lines (LCLs) from control and AOA2 patients were cultured in RPMI 1640 medium (ThermoFisher) containing 20% FBS (Sigma-Aldrich), 1% Penicillin/Streptomycin (P/S; Sigma-Aldrich), 2 mM L-glutamine (ThermoFisher) and 1% Non-Essential Amino Acids (ThermoFisher). All LCLs were grown at 37°C and in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including an on-column DNase treatment to eliminate any contaminating genomic DNA.
Illumina TruSeq Stranded mRNA Library Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.

tag: pair

value: Lymphoblastoid Cell Line transformed by Epstein-Barr Virus

value: Lymphoblast

value: Normal


title: 509 Lung L

description:
509 Lung Left
mutation_count_matrix_509.txt

source_name: breast cancer cells implanted in mouse

tag: injected cell line

tag: metastic sites

value: Lung

tag: host

value: Athymic Nude

tag: mouse id


title: Alkbh5_KO_plus_Input2

value: knock out


title: Alkbh5_KO_plus_IP1

value: IP


title: Alkbh5_KO_plus_IP2


title: Alkbh5_KO_plus_Input1


title: Alkbh5_KO_minus_IP2


title: RNA_mouse_WT_IL12IL18_2


title: A673_siSA2-Dh6_72h_HiChIP_CTCF_Rep2_Ad D362C80

data_processing:
All the processing steps were performed with HiC-Pro 2.10.1 pipeline.
Reads were mapped against human genome (GRCh37/hg19 version) with bowtie2.
Default HiC-Pro settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions and generate raw interaction matrices (5kb bins).
Genome_build: hg19
Supplementary_files_format_and_content: Raw interaction matrix (for each 5kb bin, count of valid pairs)

growth_protocol: A673 were cultured in DMEM supplemented with 10% fetal bovine serum. Four days before performing the ChIP experiments, cells were seeded in T150 flask at a concentration allowing to reach a cellular confluence of approximately 90% at the time of fixation of the cells with formaldehyde.

extract_protocol: Library for Illumina sequencing were prepared using 10 ng of chromatin and 0.5 µL of TN5 (15028211, Illumina). A first PCR in a final volume of 50µl with 5 cycles was performed (72 °C for 5 min, 98 °C for 1 min, then 5 cycles at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min). To determine how many additional PCR cycles were required for optimal library preparation, a QPCR with: 5µL of the first PCR product, 1 μL of Nextera Ad1_noMX and Nextera Ad2.X (each at 1.25 μM), 5 µl of phusion HF 2X (M0531S, New England Biolabs), 0,75 µL Evagreen® 20X (31000, Biotium) and 2,25 µL of water was runned (same program as first PCR but with 30 cycles). The optimal number of additional cycle was determined for each library by setting a threshold just before reaching the end of exponential amplification step. The 45µl left from the first PCR were further amplified using additional PCR cycles as determined above. Size selection was performed using Ampure XP beads (A63881, Beckman Coulter) to capture fragments greater than 300 bp. Libraries were quantified and analyzed using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and LabChIP (Perkin Elmer). A first validation of HiChIP experiments was performed using 150 bp paired-end sequencing on MiSeq-microV2-300-PE150 (Illumina). Deep 101 bp paired-end sequencing was then performed on NovaSeq 6000 systems (Illumina).

treatment_protocol: Cells were transfected for 72h with either siCT, siSA2#6 or siSA6#8 (Dharmacon). For each siRNA, CTCF HiChIP experiments were preformed. Several adaptations were made and are detailed below in an overview of the otherwise original protocol described by Mumbach and colleagues (PMID: 27643841).  Cells were fixed at room temperature for 10 min under gentle shaking platform (50mvt/min). 2 mL of glycine solution (2M) were added and cells were incubated for 5 additional min at room temperature under gentle shaking platform. The supernatant was removed and cells were washed 3 times with PBS at room temperature. Cells were scraped vigorously with ice cold PBS supplemented with protease inhibitor cocktail tablets (11836145001, Roche), and flushed five time through a syringe with a 21 gauge needle (301155, BD Microlance). In situ contact libraries were performed starting from 15 million nuclei digested overnight at 37°C with Mbo1 (R0147M, New England Biolabs). After proximity ligation (4 h at room temperature), the nuclear pellet was sonicated and the chromatin immunoprecipitation step was performed using the iDeal ChIP-seq kit for transcription factors (Diagenode) according to the supplier's recommendation with some modification. Nuclei were resuspended in IL1b and IL2 buffer following Diagenode protocol and all centrifugations were performed at 4°C for 5 min at 1,950 RCF for these steps. The chromatin was sonicated (5 million nuclei per tube) with Bioruptor pico (Diagenode) for 10 cycles (30-sec on, 30-sec off). The tubes were pooled and the chromatin was clarified by centrifugation at 4°C for 10 min at 16,000 RCF. Sonicated chromatin from 11 million nuclei were used for CTCF immunoprecipitation step using the equivalent of 3 ChIP reactions pooled in one tube for each HiChIP reaction (final volume was 1050 µl/tube). Immunoprecipitation was then carried out following Diagenode kit instructions by multiplying all reagents by a factor 3 until end of elution step (50µl). Biotin capture was performed following Mumbach et al. protocol (PMID: 27643841).

tag: sirna

tag: antibody

value: CTCF (provided in iDeal ChIP-seq kit Diagenode)

tag: timepoint


title: A673_siSA2-Dh8_72h_HiChIP_CTCF_Rep2_Ad D347C082


title: A673_siSA2-Dh8_72h_HiChIP_CTCF_Rep1_Ad D362C81


title: A673_siSA2-Dh6_72h_HiChIP_CTCF_Rep1_2_Ad D362C79


title: Ewing sarcoma sample EW739

source_name: Ewing sarcoma sample EW739

tag: gender

value: Female

tag: age

tag: tumor type

value: primary tumor


title: A673_siSA2-Dh8_72h_HiChIP_CTCF_Rep1_Ad D347C081


title: Ewing sarcoma sample EW837

source_name: Ewing sarcoma sample EW837


title: A673_siSA2-Dh8_72h_HiChIP_CTCF_Rep2_Ad D362C82


title: Ewing sarcoma sample EW833

source_name: Ewing sarcoma sample EW833

value: Male


title: Alkbh5_KO_minus_IP1

tag: technology

tag: condition

tag: sample type


title: A673_siSA2-Dh6_72h_HiChIP_CTCF_Rep1_1_Ad D362C78


title: Ewing sarcoma sample EW831

source_name: Ewing sarcoma sample EW831


title: RNA_mouse_WT_IL12IL18_1

tag: genotype

tag: cell type


title: Alkbh5_KO_minus_Input2

value: input


title: Ewing sarcoma sample EW740

source_name: Ewing sarcoma sample EW740


title: Ewing sarcoma sample EW741

source_name: Ewing sarcoma sample EW741


title: Ewing sarcoma sample EW736

source_name: Ewing sarcoma sample EW736


title: A673_siSA2-Dh6_72h_HiChIP_CTCF_Rep1_2_Ad D347C079

source_name: Ewing sarcoma cell line (A673)


title: Ewing sarcoma sample EW738

source_name: Ewing sarcoma sample EW738


title: Alkbh5_KO_minus_Input1


title: A673_siSA2-Dh6_72h_HiChIP_CTCF_Rep1_1_Ad D347C078


title: RNA_mouse_WT_IFNA_1

source_name: splenic NK cells

value: IFNA

tag: replicate


title: RNA_mouse_WT_IFNA_2


title: RNA_mouse_WT_IFNA_3


title: RNA_mouse_WT_UNSTIM_2

value: UNSTIM


title: A673_siCT-Dh1_72h_HiChIP_CTCF_Rep2_Ad D362C77


title: A673_siCT-Dh1_72h_HiChIP_CTCF_Rep1_2_Ad D362C76


title: RNA_mouse_WT_UNSTIM_3


title: A673_siSA2-Dh6_72h_HiChIP_CTCF_Rep2_Ad D347C080


title: RNA_mouse_WT_UNSTIM_1


title: Ewing sarcoma sample EW735

source_name: Ewing sarcoma sample EW735


title: MCF10A replicate3-24h CDK4/6i

city: Stanford

first: Tobias

last: Meyer

address: 318 Campus Dr

institute: Stanford University

data_processing:
Quality control: FastQC v0.11.3
Read alignment: Tophat v2.1.1 against GENCODE v25 gene model and GRCh38.p7 genome assembly (index built using Bowtie 2 v2.2.9)
Count tabulation: featureCounts (Subread v1.5.1) against GENCODE v25 gene model
Genome_build: hg38 (GRCh38.p7)
Supplementary_files_format_and_content: *.feature_counts.txt: tab-delimited text files include gene counts for each gene in a sample
Supplementary_files_format_and_content: GEO_raw_counts.txt: matrix table (tab-delimited text file) with raw gene counts for every gene and every sample

source_name: Breast epithelial cell line, non-transformed (MCF10A)

growth_protocol: MCF10A cells (obtained from ATCC, CRL-10317) were cultured in phenol red-free DMEM/F12 (Invitrogen) supplemented with 5% horse serum (ATCC), 20 ng/mL EGF (PeproTech), 10 µg/mL insulin (Sigma-Aldrich), 0.5 µg/mL hydrocortisone (Sigma-Aldrich), 100 ng/mL cholera toxin (Sigma-Aldrich), 50 U/mL penicillin and 50 µg/mL streptomycin (Thermo Fisher).

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN) according to manufacturer instructions. RNA quality control was performed using an Agilent Bioanalyzer 2100.
Sequencing library preparation was performed at the Stanford Functional Genomics Facility using the KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads (Roche) according to manufacturer instructions. Single-index 6-mer adapters were added, and the libraries were sequenced with 75 bp single-end reads on an Illumina NextSeq platform (Stanford Functional Genomics Facility).

treatment_protocol: To serum starve cells, cells were cultured for 2~3 days in phenol red-free DMEM/F12 (Invitrogen) supplemented with 0.5 µg/mL hydrocortisone (Sigma-Aldrich), 100 ng/mL cholera toxin (Sigma-Aldrich), 0.3% bovine serum albumin (Sigma-Aldrich), 50 U/mL penicillin and 50 µg/mL streptomycin (Thermo Fisher). To serum release cells, cells were treated with full growth media with 0.1% DMSO or 1µM palbociclib (Selleck Chemicals S1116) for the indicated period of time before extraction.

tag: time since release (hours)

tag: drug treatment

value: Palbociclib


title: A673_siCT-Dh1_72h_HiChIP_CTCF_Rep2_Ad D347C077


title: MCF10A replicate3-9h CDK4/6i


title: Ewing sarcoma sample EW733

source_name: Ewing sarcoma sample EW733


title: A673_siCT-Dh1_72h_HiChIP_CTCF_Rep1_1_Ad D362C75


title: MCF10A replicate3-15h CDK4/6i


title: MCF10A replicate3-12h CDK4/6i


title: MCF10A replicate3-24h DMSO

value: DMSO


title: Ewing sarcoma sample EW723

source_name: Ewing sarcoma sample EW723


title: Ewing sarcoma sample EW729

source_name: Ewing sarcoma sample EW729


title: A673_siCT-Dh1_72h_HiChIP_CTCF_Rep1_2_Ad D347C076


title: MCF10A replicate3-15h DMSO


title: ATAC_mouse_WT_IL2IL15IL12IL18IFNA_3

description: pkLstAssign_oneFeatGene_Project_09547_IDR_peaks.bed

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
ATAC-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on Tn5-shifted, concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated from BAM files using the bamCoverage function from deepTools (v3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled pileups of reads aligned to the genome. BED files are genomic ranges that represent the reference peak atlas used for analysis, with names representing unique peak IDs for each atlas.

extract_protocol:
Fresh cells were prepared as previously described (Buenrostro et al., 2013). Briefly, sorted, stimulated cells were washed in cold PBS and lysed. The transposition reaction was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004).
DNA was amplified for 5 cycles. After evaluation by real-time PCR, 8-11 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 36 million paired reads were generated per sample.

treatment_protocol: NK cells were stimulated for 3 hr with combinations of 20 ng/mL recombinant mouse IL-2,  20 ng/ml recombinant mouse IL-15, 20 ng/ml recombinant mouse IL-12, 10 ng/ml recombinant mouse IL-18, and/or 100 IU recombinant mouse IFN-α.

value: WT

value: ex-vivo NK cells


title: A673_siCT-Dh1_72h_HiChIP_CTCF_Rep1_1_Ad D347C075


title: ATAC_mouse_WT_IL2IL15IL12IL18IFNA_1


title: ATAC_mouse_WT_IL2IL15IL12IL18IFNA_2


title: Ewing sarcoma sample EW720

source_name: Ewing sarcoma sample EW720


title: Ewing sarcoma sample EW722

source_name: Ewing sarcoma sample EW722


title: MCF10A replicate3-12h DMSO


title: A673_siSA2-Dh8_72h_H3K27ac_spike_R1

data_processing:
Reads were mapped with bowtie2 against human genome (hg19)
Peaks were called with MACS2 2.1.1 with the option narrow for FLI1, CTCF and cohesin members ChIP-seq and broad for histone marks. For each cell line, ChIP-seq were normalized according to the input DNA sample.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

extract_protocol: The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations

treatment_protocol: Cells were transfected for 72h with either siCT, siSA2#6 or siSA6#8 (Dharmacon). For each siRNA, we performed ChIP-seq for CTCF, cohesin members (RAD21, SMC1A, STAG1 and STAG2), EWS-FLI1 and H3K27ac. Input of A673 WT was used as normalization controls. ChIP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors (ref C01010170, Diagenode) and by adding Spike-in Chromatin (ref 53083, Active motif) and Spike-in Antibody (ref 61686, Active motif)  to normalize the experiments. Ewing cell lines were fixed for 10 minutes with 1% of methanol-free formaldehyde (ref 28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor Pico, Diagenode) for 10 minutes (30-sec on, 30-sec off) to generate Chromatin fragments with an average size around 150-300pb.


title: A673_siSA2-Dh8_72h_FLI1_spike_R1


title: ATAC_mouse_WT_IL2IL15IL12IL18_3


title: MCF10A replicate3-9h DMSO


title: MCF10A replicate3-6h DMSO


title: MCF10A replicate3-3h DMSO


title: ATAC_mouse_WT_IL2IL15IL12IL18_1


title: MCF10A replicate3-0h


title: ATAC_mouse_WT_IFNAIL2IL15_3


title: Ewing sarcoma sample EW728

source_name: Ewing sarcoma sample EW728


title: Ewing sarcoma sample EW718

source_name: Ewing sarcoma sample EW718


title: A673_siSA2-Dh8_72h_CTCF_spike_R1

value: CTCF


title: A673_siSA2-Dh8_72h_RAD21_spike_R1


title: MCF10A replicate2-15h CDK4/6i


title: ATAC_mouse_WT_IFNAIL2IL15_2


title: A673_siSA2-Dh8_72h_STAG1_spike_R1


title: Ewing sarcoma sample EW715

source_name: Ewing sarcoma sample EW715


title: Ewing sarcoma sample EW302

source_name: Ewing sarcoma sample EW302


title: Ewing sarcoma sample EW707

source_name: Ewing sarcoma sample EW707


title: ATAC_mouse_WT_IL12IL18IFNA_3


title: Ewing sarcoma sample EW246

source_name: Ewing sarcoma sample EW246


title: MCF10A replicate2-12h CDK4/6i


title: A673_siSA2-Dh8_72h_SMC1_spike_R1


title: ATAC_mouse_WT_IL12IL18IFNA_2


title: ATAC_mouse_WT_IL12IL18IFNA_1


title: Ewing sarcoma sample EW160

source_name: Ewing sarcoma sample EW160


title: MCF10A replicate2-15h DMSO


title: A673_siSA2-Dh8_72h_STAG2_spike_R1

source_name: Ewing sarcoma cell line (A673)


title: MCF10A replicate2-12h DMSO


title: A673_siSA2-Dh6_72h_FLI1_spike_R1


title: Ewing sarcoma sample EW189

source_name: Ewing sarcoma sample EW189


title: ATAC_mouse_WT_IL2IL15_3

source_name: splenic NK cells


title: A673_siSA2-Dh6_72h_CTCF_spike_R1


title: MCF10A replicate2-9h DMSO


title: Ewing sarcoma sample EW233

source_name: Ewing sarcoma sample EW233


title: ATAC_mouse_WT_IL2IL15_2


title: Ewing sarcoma sample EW192

source_name: Ewing sarcoma sample EW192


title: A673_siSA2-Dh6_72h_RAD21_spike_R1


title: Ewing sarcoma sample EW154

source_name: Ewing sarcoma sample EW154


title: A673_siSA2-Dh6_72h_STAG2_spike_R1


title: MCF10A replicate2-9h CDK4/6i

source_name: Breast epithelial cell line, non-transformed (MCF10A)


title: ATAC_mouse_WT_IL2IL15_1


title: MCF10A replicate2-3h DMSO


title: MCF10A replicate2-6h DMSO


title: Ewing sarcoma sample EW150

source_name: Ewing sarcoma sample EW150


title: A673_siSA2-Dh6_72h_H3K27ac_spike_R1


title: MCF10A replicate2-0h


title: Ewing sarcoma sample EW091

source_name: Ewing sarcoma sample EW091


title: A673_siSA2-Dh6_72h_SMC1_spike_R1


title: MCF10A replicate1-24h CDK4/6i


title: Ewing sarcoma sample EW077

source_name: Ewing sarcoma sample EW077


title: ATAC_mouse_WT_IL12IL18_1


title: ATAC_mouse_WT_IL12IL18_2


title: Ewing sarcoma sample EW983

source_name: Ewing sarcoma sample EW983


title: Ewing sarcoma sample EW068

source_name: Ewing sarcoma sample EW068


title: A673_siCT-Dh1_72h_STAG2_spike_R1


title: MCF10A replicate1-15h CDK4/6i


title: ATAC_mouse_WT_IFNA_2


title: ATAC_mouse_WT_IL2IL15IL12IL18_2


title: A673_siCT-Dh1_72h_STAG1_spike_R1


title: Ewing sarcoma sample EW115

source_name: Ewing sarcoma sample EW115


title: A673_siCT-Dh1_72h_SMC1_spike_R1


title: ATAC_mouse_WT_UNSTIM_3


title: ATAC_mouse_WT_IFNA_1


title: A673_siSA2-Dh6_72h_STAG1_spike_R1


title: ATAC_mouse_WT_IL12IL18_3


title: MCF10A replicate1-12h CDK4/6i


title: Ewing sarcoma sample EW980

source_name: Ewing sarcoma sample EW980


title: MCF10A replicate1-9h CDK4/6i


title: A673_siCT-Dh1_72h_RAD21_spike_R1


title: Ewing sarcoma sample EW977

source_name: Ewing sarcoma sample EW977


title: ATAC_mouse_WT_UNSTIM_2


title: MCF10A replicate1-15h DMSO


title: A673_siCT-Dh1_72h_H3K27ac_spike_R1


title: Ewing sarcoma sample EW975

source_name: Ewing sarcoma sample EW975


title: ATAC_mouse_WT_UNSTIM_1


title: Ewing sarcoma sample EW976

source_name: Ewing sarcoma sample EW976


title: Ewing sarcoma sample EW982

source_name: Ewing sarcoma sample EW982


title: Ewing sarcoma sample EW743

source_name: Ewing sarcoma sample EW743


title: MCF10A replicate1-9h DMSO


title: MCF10A replicate1-24h DMSO


title: Ewing sarcoma sample EW742

source_name: Ewing sarcoma sample EW742


title: MCF10A replicate1-6h DMSO


title: A673_SA1m#1_FLI1_SPIKE

data_processing:
Reads were mapped with bowtie2 against human genome (hg19)
Peaks were called with MACS2 2.1.1 with the option narrow for FLI1, CTCF and cohesin members ChIP-seq and broad for histone marks. For each cell line, ChiP-seq were normalized according to their respective input DNA sample.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: Ewing sarcoma cell line (A673)

growth_protocol: A673 and TC71 were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum. Two days before performing the ChIP experiments, cells were seeded in T150 flask at a concentration allowing to reach a cellular confluence of approximately 90% at the time of fixation of the cells with formaldehyde.

extract_protocol:
ChIP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode). For some ChIP experiments (labeled as "SPIKE" in their name) Spike-in Chromatin (ref 53083, Active motif) and Spike-in Antibody (ref 61686, Active motif) was added to normalize the experiments. Ewing cell lines were fixed for 10 minutes with 1% of methanol-free formaldehyde (28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor, Diagenode) for 20 cycles (30-sec on, 30-sec off) set at position “high” to generate DNA fragments with an average size around 150-300pb.
The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations

value: SA1 KO


title: A673_WT_FLI1_SPIKE


title: MCF10A replicate1-3h DMSO


title: DTC, Input

city: Boston

first: Stephen

last: Buratowski

state: MA

address: 240 Longwood Avenue

department: BCMP

institute: Harvard Medical School

data_processing:
Analysis of ChIP-seq data was performed using the pipeline described in Soares et al. (Soares LM, He PC, Chun Y, Suh H, Kim T, Buratowski S. Determinants of Histone H3K4 Methylation Patterns. Mol Cell. 2017 Nov 16;68(4):773-785.e6.
Sequence reads were demultiplexed using SABRE (https://github.com/najoshi/sabre.git) allowing for one mismatch in the barcode. For S. pombe spike-in normalization, demultiplexed reads were first aligned to the S. pombe genome (version ASM294v2.31). The unaligned reads were subsequently aligned to the S. cerevisiae genome (version R64-1-1). Only sequence reads that could be exclusively assigned to each genome were considered for total number of reads. Normalization factors were calculated by first calculating the proportion of reads of S. pombe versus total reads in input reads, and dividing the value by the square root (to account for the sequence tags per million reads (SPMR) normalization) of the proportion of reads of S. pombe vs. total reads in each immunoprecipitation reads. All alignment was performed using BOWTIE 2 excluding the first base and multi-aligned reads.
All alignment was performed using BOWTIE 2 excluding the first base and multi-aligned reads
Genome_build: S. pombe genome (version ASM294v2.31), S. cerevisiae genome (version R64-1-1)
Supplementary_files_format_and_content: Bam files with mapped reads and values normalized to the internal spike-in controls.

organism: Saccharomyces cerevisiae

source_name: Input

growth_protocol: Yeast cells (250ml) were grown in synthetic media -URA to OD600~ 0.5. Cells were cross linked with formaldehyde followed by lysis

extract_protocol:
Cells were lysed with glass beads followed by chromatin purification and sonication. Protein-chromatin complexes were isolated using antibodies (ChIP).
Libraries were prepared according to the protocol:  https://doi.org/10.1002/0471142727.mb0711s101.

tag: chip antibody

tag: strain

value: DTC_CTR9/ YSB 3681

tag: treatment

value: Trestle and C'truncation of CTR9


title: DC, Input

value: DC_CTR9/ YSB 3680

value: C' truncation of CTR9


title: Ewing sarcoma sample EW737b

source_name: Ewing sarcoma sample EW737b


title: A673_SA2m#1_FLI1_SPIKE

value: SA2 KO


title: DT, Input

value: DT_CTR9/ YSB3679

value: Trestle truncation of CTR9


title: WT, Input

value: WT CTR9 / YSB3678

value: Wild type


title: MCF10A replicate1-0h

source_name: Breast epithelial cell line, non-transformed (MCF10A)


title: Ewing sarcoma sample EW732

source_name: Ewing sarcoma sample EW732

value: Male

value: primary tumor


title: 9934R

description:
9934 Right Hindlimb
mutation_count_matrix_9928&9934.txt

source_name: breast cancer cells implanted in mouse

tag: injected cell line

tag: metastic sites

value: Right Hindlimb

tag: host

value: Athymic Nude

tag: mouse id


title: A673_SA1m#1_H3K27ac_SPIKE

tag: antibody


title: PairFedVehicle_rep5

city: Indianapolis

first: Kyle

last: Haas

state: IN

address: 893 Delaware St

institute: Eli Lilly and Company

data_processing:
cutadapt (v1.9.1) for quality trimming
GSNAP (v2013-11-27, parameters -B 5 -A sam -N 1 -t 8 -s splicesites --quality-protocol=sanger --gunzip --sam-multiple-primaries --maxsearch=1000 --npaths=100) for alignment
count quantification using a custom Perl script
"Rollup" pipeline: exons excluded if more than 80% of samples have less than 10 counts; robust linear model used to obtain gene level signals; mean signal of log2 transformed gene level were median normalized.
Quantile normalization
Genome_build: m38.p3
Supplementary_files_format_and_content: normalized counts

source_name: brown adipose tissue

extract_protocol:
TRIzol reagent and RNeasy lipid mini kit
polyA selection

tag: tissue

value: brown adipose tissue

value: PairFedVehicle


title: PairFedVehicle_rep6


title: A673_siCT-Dh1_72h_FLI1_spike_R1

tag: sirna

tag: timepoint


title: PairFedVehicle_rep4


title: DTC_RPB3

source_name: ChIPseq for Rpb3

value: a-Rpb3(Neoclone, W0012)


title: PairFedVehicle_rep3


title: A673_SA2m#1_H3K27ac_SPIKE


title: MCF10A replicate1-12h DMSO

value: DMSO


title: DC_RPB3


title: 9934Lung

description:
9934 Lung
mutation_count_matrix_9928&9934.txt

value: Lung


title: A673_siCT-Dh1_72h_CTCF_spike_R1

value: CTCF


title: DT_RPB3


title: 9934L

description:
9934 Left Hindlimb
mutation_count_matrix_9928&9934.txt

value: Left Hindlimb


title: PairFedVehicle_rep2


title: D044C39: A673_WT_H3K27ac_rep4

data_processing:
Library strategy: HiChIP
All the processing steps were performed with HiC-Pro 2.10.1 pipeline.
Reads were mapped against human genome (GRCh37/hg19 version) with bowtie2.
Default HiC-Pro settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions and generate raw interaction matrices (5kb bins).
Genome_build: hg19
Supplementary_files_format_and_content: Raw interaction matrix (for each 5kb bin, count of valid pairs)

growth_protocol: A673 and TC71 isogenic models were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum.

extract_protocol:
Several adaptations were made and are detailed below in an overview of the otherwise original protocol described by Mumbach and colleagues (PMID: 27643841). Cells were plated 2 days before starting the experiment to reach a 90-95% confluence at the time of fixation (1% of methanol-free formaldehyde (28908, Thermo-Scientific) in freshly prepared respective cell culture media, 20ml/T150 flask). Cells were fixed at room temperature for 10 min under gentle shaking platform (50mvt/min). 2 mL of glycine solution (2M) were added and cells were incubated for 5 additional min at room temperature under gentle shaking platform. The supernatant was removed and cells were washed 3 times with PBS at room temperature. Cells were scraped vigorously with ice cold PBS supplemented with protease inhibitor cocktail tablets (11836145001, Roche), and flushed five time through a syringe with a 21 gauge needle (301155, BD Microlance). In situ contact libraries were performed starting from 15 million nuclei digested overnight at 37°C with Mbo1 (R0147M, New England Biolabs). After proximity ligation (4 h at room temperature), the nuclear pellet was sonicated and the chromatin immunoprecipitation step was performed using the iDeal ChIP-seq kit for transcription factors (Diagenode) according to the supplier's recommendation with some modification. Nuclei were resuspended in IL1b and IL2 buffer following Diagenode protocol and all centrifugations were performed at 4°C for 5 min at 1,950 RCF for these steps. The chromatin was sonicated (5 million nuclei per tube) with Bioruptor pico (Diagenode) for 10 cycles (30-sec on, 30-sec off) set at position “high”. The tubes were pooled and the chromatin was clarified by centrifugation at 4°C for 10 min at 16,000 RCF. Sonicated chromatin from 11 and 3 million nuclei were used respectively for CTCF and H3K27ac immunoprecipitation step using the equivalent of 3 ChIP reactions pooled in one tube for each HiChIP reaction (final volume was 1050 µl/tube). Immunoprecipitation was then carried out following Diagenode kit instructions by multiplying all reagents by a factor 3 until end of elution step (50µl). Biotin capture was performed following Mumbach et al. protocol (PMID: 27643841).
Library for Illumina sequencing were prepared using 10 ng of chromatin and 0.5 µL of TN5 (15028211, Illumina). A first PCR in a final volume of 50µl with 5 cycles was performed (72 °C for 5 min, 98 °C for 1 min, then 5 cycles at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min). To determine how many additional PCR cycles were required for optimal library preparation, a QPCR with: 5µL of the first PCR product, 1 μL of Nextera Ad1_noMX and Nextera Ad2.X (each at 1.25 μM), 5 µl of phusion HF 2X (M0531S, New England Biolabs), 0,75 µL Evagreen® 20X (31000, Biotium) and 2,25 µL of water was runned (same program as first PCR but with 30 cycles). The optimal number of additional cycle was determined for each library by setting a threshold just before reaching the end of exponential amplification step. The 45µl left from the first PCR were further amplified using additional PCR cycles as determined above. Size selection was performed using Ampure XP beads (A63881, Beckman Coulter) to capture fragments greater than 300 bp. Libraries were quantified and analyzed using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and LabChIP (Perkin Elmer). A first validation of HiChIP experiments was performed using 150 bp paired-end sequencing on MiSeq-microV2-300-PE150 (Illumina). Deep 75 bp paired-end sequencing was then performed on HiSeq 2500 or NovaSeq 6000 systems (Illumina).

value: Ewing sarcoma cell line (A673)

value: WT

value: H3K27ac (ab4729, Abcam)


title: 9928R

description:
9928 Right Hindlimb
mutation_count_matrix_9928&9934.txt


title: WT_RPB3


title: PairFedVehicle_rep1


title: DTC_H3

source_name: ChIPseq for H3

value: a-H3 (abcam, ab1791)

value: DTC_CTR9/ YSB 3681

value: Trestle and C'truncation of CTR9


title: TZP_rep6

value: TZP


title: DC_H3

value: DC_CTR9/ YSB 3680

value: C' truncation of CTR9


title: D044C38: A673_WT_CTCF_rep5

value: CTCF (provided in iDeal ChIP-seq kit Diagenode)


title: TZP_rep5

value: brown adipose tissue


title: DT_H3

value: DT_CTR9/ YSB3679

value: Trestle truncation of CTR9


title: 9928L

description:
9928 Left Hindlimb
mutation_count_matrix_9928&9934.txt

value: Athymic Nude


title: TZP_rep4


title: TZP_rep3


title: MDA231+Dox4

description:
MDA-MB-231 cells with 4 rounds of Dox treatment
mutation_count_matrix_MDA.txt

source_name: breast cancer cells

value: not injected


title: MDA231+Dox3

description:
MDA-MB-231 cells with 3 rounds of Dox treatment
mutation_count_matrix_MDA.txt


title: D075C53: A673_SA2r_H3K27ac_rep4

value: Rescue of SA2 in SA2 KO cell


title: DTC_H3K4me2

source_name: ChIPseq for H3K4me2


title: D075C43: A673_SA2r_H3K27ac_rep2


title: D075C44: A673_SA2r_H3K27ac_rep3


title: TZP_rep2


title: WT_H3

value: WT CTR9 / YSB3678

value: Wild type


title: A673_WT_H3K27ac_SPIKE

value: WT


title: MDA231+Dox2

description:
MDA-MB-231 cells with 2 rounds of Dox treatment
mutation_count_matrix_MDA.txt


title: DC_H3K4me2


title: DT_H3K4me2


title: TZP_rep1


title: MDA231+Dox1

description:
MDA-MB-231 cells with 1 round of Dox treatment
mutation_count_matrix_MDA.txt


title: 9928Lung

description:
9928 Lung
mutation_count_matrix_9928&9934.txt

value: Lung


title: D044C35: A673_SA2r_H3K27ac_rep1

value: Ewing sarcoma cell line (A673)

value: H3K27ac (ab4729, Abcam)


title: D075C54: A673_SA2r_H3K27ac_rep5


title: SETX-KO_Input DNA

description: Input DNA sequencing

data_processing:
Sequenced reads were aligned to the human hg19 genome assembly using Burrows Wheeler Aligner (BWA, RRID:SCR_010910) with default settings.
Only reads that aligned with no more than 2 mismatches and mapped uniquely to the genome were used for subsequent analyses.  PCR duplicate reads were removed.
The sequence reads represented the 5’-ends of the IP-fragments, hence the reads were extended in silico using proprietary software from Active Motif at their 3’-ends to a length of 150 bp to match the fragment length of the library. To identify the density of fragments, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. The resulting metric (“fragment density”) was used for the peak metrics in further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files representing normalised coverage, created using the standard Active Motif MeDIP-seq pipeline.

source_name: HAP1 SETX Knockout Cells

growth_protocol: Human HAP1 WT and DSETX cells were cultured in IMDM (ThermoFisher) supplemented with 10% FBS (Sigma-Aldrich) and 1% Penicillin/Streptomycin (Sigma-Aldrich). Cells were grown at 37°C and in a humidified atmosphere containing 5% CO2.

extract_protocol:
Genomic DNA was extracted and sonicated to ~150-300 bp using a Misonix Sonicator 300 equipped with a microtop. Illumina adaptors were added to the sonicated DNA and immunoprecipitated using a mouse monoclonal antibody against 5-methylcytosine (5meC; Clone 33D3, Active Motif) following the protocol described in the Active Motif MeDIP kit (Active Motif, Catalog No. 55009).
Libraries were prepared according to Illumina's instructions. Deep sequencing libraries were generated from the DNA immunoprecipitates and input DNA by the standard consecutive enzymatic steps of end-polishing, dA-addition and adaptor ligation. After a final PCR amplification step using barcoded primers, the resulting DNA libraries were quantified and sequenced.

value: HAP1 cells derived from male CML cell line KBM7

tag: morphology

value: Fibroblast-like

value: SETX Knockout


title: LAGIPRA_rep6

value: LAGIPRA


title: D075C42: A673_SA2r_CTCF_rep3

tag: genotype

value: CTCF (provided in iDeal ChIP-seq kit Diagenode)


title: D075C41: A673_SA2r_CTCF_rep2


title: WT_Input DNA

description: Input DNA sequencing

source_name: HAP1 Parental Cells

tag: cell type

value: Wild-type


title: D044C34: A673_SA2r_CTCF_rep1


title: DTC_H3K4me3

source_name: ChIPseq for H3K4me3

value: DTC_CTR9/ YSB 3681

value: Trestle and C'truncation of CTR9


title: MDA231+Veh

description:
Parental MDA-MB-231 cells
mutation_count_matrix_MDA.txt


title: LAGIPRA_rep4

value: brown adipose tissue


title: LAGIPRA_rep3


title: LAGIPRA_rep2


title: D075C55: A673_SA1m#1_CTCF_rep2

value: SA1 KO


title: WT_H3K4me2


title: D044C21: A673_SA2m#1_CTCF_rep5

value: SA2 KO


title: D044C36: A673_SA1m#1_CTCF_rep1


title: DSETX_Input DNA_Replicate 2

data_processing:
Sequenced reads were aligned against human genome version hg19 using BWA-MEM v0.7.15.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function.  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over is presented.

extract_protocol:
Cells were lysed in ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% NP-40 and protease inhibitors) and incubated 5 min on ice. Nuclei were pelleted by centrifugation at 3,900 g for 5 min at 4°C. Nuclei were then resuspended in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS and protease inhibitors) and sheared to fragments between 200-500 bp using a bioruptor sonication system (Diagenode). Sonicated chromatin was clarified by centrifugation at 20,000 g for 15 min at 4°C. The clarified chromatin was incubated with the RNAPII (4H8) antibody-conjugated Protein A Dynabeads (Invitrogen, ThermoFisher) overnight at 4°C.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were harvested by trypsinization and fixed in suspension with 1% formaldehyde for 10 min at room temperature. The crosslinking reaction was quenched with 125 mM glycine for 5 min, followed by two washes with ice-cold PBS.

tag: replicate


title: SETX-KO_MeDIP-Seq

description: MeDIP-Seq

value: anti-5meC clone 33D3


title: DC_H3K4me3

value: DC_CTR9/ YSB 3680

value: C' truncation of CTR9


title: DT_H3K4me3

value: DT_CTR9/ YSB3679

value: Trestle truncation of CTR9


title: WT_H3K4me3

value: WT CTR9 / YSB3678

value: Wild type


title: LAGIPRA_rep1


title: TC71_SA2m#2_input

data_processing:
Reads were mapped with bowtie2 against human genome (hg19)
Peaks were called with MACS2 2.1.1 with the option narrow for FLI1, CTCF and cohesin members ChIP-seq and broad for histone marks. For each cell line, ChIP-seq were normalized according to their respective input DNA sample.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: Ewing sarcoma cell line (TC71)

extract_protocol:
ChiP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode). For this, Ewing cell lines were fixed for 10 minutes with 1% of methanol-free formaldehyde (28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor, Diagenode) for 20 cycles (30-sec on, 30-sec off) set at position “high” to generate DNA fragments with an average size around 150-300pb.
The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations

tag: cell line

value: Ewing sarcoma cell line

value: input


title: DTC_H3K36me2

source_name: ChIPseq for H3K36me2

value: a-H3K36me2 (abcam ab9049)


title: WT_MeDIP-Seq

description: MeDIP-Seq

value: HAP1 cells derived from male CML cell line KBM7

value: Fibroblast-like


title: WT_Input DNA_Replicate 2

value: Wild-type


title: DTC_H3K36me3

source_name: ChIPseq for H3K36me3

value: a-H3K36me3 (abcam ab9050)

value: DTC_CTR9/ YSB 3681

value: Trestle and C'truncation of CTR9


title: Vehicle_rep4

value: brown adipose tissue

value: Vehicle


title: WT_ChIP-Seq_Replicate 2

value: anti-RNAPII CTD clone 4H8


title: A673_SA2r rep3

source_name: Ewing sarcoma cell line (A673)

growth_protocol: A673 and TC71 were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum. Two days before RNA extraction, cells were seeded in 6 well plate dishes at a concentration allowing to reach a cellular confluence of approximately 90% at the time of RNA extraction.

extract_protocol:
RNA was extracted using RNeasy plus mini kit (Qiagen, ref 74134)
The library construction was performed using TruSeq Stranded mRNA (Illumina, ref #20020594) according to manufacturer recommendations.

value: Rescue of SA2 in SA2 KO cell

value: Ewing sarcoma cell line (A673)


title: DSETX_ChIP-Seq_Replicate 2

value: SETX Knockout


title: DT_H3K36me2

value: DT_CTR9/ YSB3679

value: Trestle truncation of CTR9


title: DSETX_Input DNA_Replicate 1


title: LAGIPRA_rep5

value: LAGIPRA


title: A673_SA2r rep1


title: WT_Input DNA_Replicate 1


title: DC_H3K36me2

value: DC_CTR9/ YSB 3680

value: C' truncation of CTR9


title: Vehicle_rep5


title: DT_H3K36me3


title: TC71_SA2m#1_input

value: Ewing sarcoma cell line

value: SA2 KO

value: input


title: WT_H3K36me3

value: a-H3K36me3 (abcam ab9050)

value: WT CTR9 / YSB3678

value: Wild type


title: A673_SA1m#1 rep3

value: SA1 KO


title: A673_WT rep2

value: WT


title: Vehicle_rep6

value: brown adipose tissue

value: Vehicle


title: Vehicle_rep2


title: Vehicle_rep3


title: A673_WT rep3

value: Ewing sarcoma cell line (A673)


title: GN_rep3

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

country: Germany

institute: Max Planck Insititue for Biology

description:
Tn5-tagmented native chromatin
GSE155344_GN.ATACseq.bw

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using cutadapt version 1.9.
Reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 version 2.1.0.
Reads were filtered for duplicate reads using Picard tools MarkDuplicates version 1.141.
Biological replicates were subsequently merged for downstream analysis after confirming high correlation among replicates.
For data visualization, log2 ratio bigwig coverage files relative to input were generated using the deepTools version 2.2.4 utility bamCoverage with a bin size of 10 bp.
Peaks were called using the MACS2 version 2.1.0 callpeak function using -B -q 1e-5 -f BAMPE
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: *.bw: ATAC-seq coverage normalised to 1x Arabidopsis genome coverage. Data is generated from merged replicates.
Supplementary_files_format_and_content: *.bed: Peak BED files of different ATAC-seq peaks groups

organism: Arabidopsis thaliana

source_name: Germ cell nuclei

extract_protocol:
For GN, SN and VN ATAC-seq, ~50,000 FACS-purified nuclei were immediately resuspended in 25 μl transposase reaction mix (12.5 μl 2x TD buffer, 2.0 μl Nextera Tn5 [Illumina Cat #FC-121-1030] and nuclease-free water). For microspore ATAC-seq, FACS-purified spores were centrifuged at 800 g for 5 minutes at 4°C and the spore pellet resuspended in 500 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1 % IGEPAL CA-630). The microspores were pelleted once more at 500 g for 10 minutes at 4°C and ~50,000 added to a 25 μl transposase reaction mix (12.5 μl 2x TD buffer, 2.0 μl Nextera Tn5 [Illumina Cat #FC-121-1030] and nuclease-free water). The Tn5 reaction mixes were incubated at 37°C for 1 hour and tagmented DNA fragments recovered with a MinElute PCR Purification Kit (Qiagen).
Sequencing-ready libraries were generated as described previously (Buenrostro et al., 2015). The libraries were sequenced on an Illumina Hiseq 2500 using 50 bp paired-end reads. All ATAC-seq profiles were generated with at least two independent biological replicates.

tag: ecotype


title: WT_H3K36me2

tag: chip antibody

value: a-H3K36me2 (abcam ab9049)


title: A673_SA2r rep2

data_processing:
Reads were trimmed with Atropos
Mapping and gene quantification were performed with STAR version 2.5.3 againt human genome (hg19, gencode V19). Option "--quantMode GeneCounts" was used to get abundance measurements.
DESEQ2 1.20.0 was used to perform differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files with raw counts for each genes.

value: Rescue of SA2 in SA2 KO cell


title: Vehicle_rep1

tag: strain


title: DSETX_ChIP-Seq_Replicate 1

value: HAP1 cells derived from male CML cell line KBM7

value: Fibroblast-like

value: SETX Knockout

value: anti-RNAPII CTD clone 4H8


title: WT_ChIP-Seq_Replicate 1

value: Wild-type


title: Deprived P7 Microglia

description:
Dorman_P5_P7MG_normalizedcounts.csv
Dorman_P5_P7MG_counts.csv
Dorman_P5_P7MG_metadata_clustering.csv

source_name: Barrel cortex

extract_protocol:
10x Genomics v3.1 3' Single Index (Chip Kit B) was used to make a single cell suspension in gel beads, and the v3 3' Library Kit was used to prepare cDNA
Sorted live cells after cold protease digestion (samples 1-2) or MACS bead isolated CD11b+ cells after tissue homogenization (samples 3-6)

tag: celltype

value: Macrophages (CD11b+)

tag: dissociation method

value: Mechanical homogenization

tag: isolation method

value: MACS column with CD11b beads


title: DC_H3K36me3

value: a-H3K36me3 (abcam ab9050)

value: DC_CTR9/ YSB 3680

tag: treatment

value: C' truncation of CTR9


title: mouse leukemia WT NUP98-HOXA9 (GFP) GFP IP

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: Dept of Biochemistry and Biophysics

institute: UNC Lineberger Comprehensive Cancer Center

data_processing:
All reads were mapped to the human genome (hg19), drosophila (dm3) or mouse genome (mm10) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools. We filter out reads with a mapping quality score of < 20 for downstream analysis.
Profiles of ChIP-seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: GRCh37/hg19 or GRCm38/mm10

source_name: Oncogene-transformed murine hematopoietic stem/progenitor cells (HSPCs)

growth_protocol: HEK 293 cells were grown in DMEM base medium plus 10% FBS and 1% antibiotics. The fusion-transformed mouse HSPCs (leukemia-causing cells) were grown in Opti-MEM base medium plus 10% FBS, 2% of supernatant containing home-made murine stem cell factor (from mSCF-producing CHO cells), 1% of supernatant containing murine FLT3 ligand (from FLT3L-producing cells), 1% antibiotics and 50uM of beta-mercaptoethanol.

extract_protocol:
Fixed cells were sonicated in a Bioruptor sonication device for 45 cycles at a high-energy setting to enrich the sonicated DNA to be ~300bp as described in our method. The sonicated samples were incubated with the indicated antibodies pre-bound to the protein-G/A beads for overnight. Across 293 cell samples with GFP-tagged chimera, the cleared cell lysates from sonicated nuclei were added with the same fraction of the sonicated and cleared chromatin of Drosophila S2 cells (see our Method), and then protein-DNA complexes were isolated with antibodies against GFP and those against Drosophila-specific histone H2Av (Active Motif cat# 39715). Beads were then washed with various washing buffers (please see our method). Bead-bound DNA was eluted and subject to reverse crosslinking and sequential treatments of RNase and protease K. Finally, ChIP DNA was purified with a PCR cleanup kit (Qiagen) and used for library construction.
Multiplexed ChIP-seq sequencing libraries were prepared using the NEBNext Ultra II kit (NEB, #E7645L) following the manufacture’s instruction. ChIP-seq libraries were pooled together and sequenced on a Nextseq 550 system using a Nextseq 550 High Output Kit v2.5 or sent to UNC High-Throughput Sequencing Facility (HTSF) for sequencing by using an Illuminia Hiseq 2500/4000 system.

treatment_protocol: For ChIP-seq experiments, HEK293 cells with stable expression of IDR-WT or IDR-mutated NUP98-HOXA9 and FUS-HOXA9 (GFP-tagged or 3XHA-3XFLAG-tagged) were grown in DMEM medium and fixed with 1% of formaldehyde in PBS for 10 min at room temperature. For 1,6-Hexanediol treatment, growth medium was removed and cells then incubated with 10% of 1,6-hexanediol in PBS for 1 min. Then, formaldehyde was added directly to make up the final concentration formaldehyde to be 1%, followed by incubation at room temperature for 10 min.

tag: antibody used

value: Rabbit anti-GFP antibody(ab290)

tag: treatment condition

value: GFP tagged WT NUP98-HOXA9


title: A673_SA1m#1 rep1

value: SA1 KO


title: GN_rep2


title: A673_SA1m#1 rep2

value: Ewing sarcoma cell line (A673)


title: Control P7 Microglia


title: mouse leukemia WT NUP98-HOXA9 (GFP) input

value: n/a (input)


title: Deprived P5 Microglia


title: Control P5 Microglia


title: GN_rep1


title: Sample_107026: 31°C exposure for 12 days rep4

status: Public on Apr 28 2021

city: Ann Arbor

first: Hiroyuki

middle: A

last: Mori

state: MI

address: 1000 Wall Street

institute: University of Michigan

data_processing:
Illumina Hi-Seq platform
Read files were downloaded and concentrated into a single fastq file for each sample. Quality of raw read data was checked using FastQC (version v0.11.30) to identify features of the data that may indicate quality problems (i.e. low-quality scores, over-represented sequences, inappropriate GC content).
The Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, reads were aligned to the UCSC reference genome using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1). FastQC was used for the second round of quality control post-alignment to ensure that only high-quality data was input to expression quantitation and differential expression analysis.
Differential expression analysis was done using HTSeq/DESeq2, using UCSC build mm10 as the reference genome sequence.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: normalized abundance measurements of genes (rlog normalized counts) from DESeq2. Each sample is represented by a column in the table.
Supplementary_files_format_and_content: raw gene counts for every gene and every sample
Supplementary_files_format_and_content: differential expression data for 0 vs 1 day of cold exposure
Supplementary_files_format_and_content: differential expression data for 0 vs 12 days of cold exposure

source_name: 31°C exposure for 12 days_MSCs

growth_protocol: Cells were maintained in 5% CO2 and DMEM/F12 1:1 media (Gibco; Invitrogen) supplemented with 15% FBS (Atlas Biologicals), primocin (InVivoGen), and 10 ng/ml recombinant bFGF (PeproTech). For induction of adipogenesis, recombinant bFGF was removed and replaced with 10% FBS containing 0.5 mM methylisobutylxanthine, 1 μM dexamethasone, 5 μg/ml insulin, and 5 μM troglitazone. On day 2, cells were fed 5 μg/ml insulin plus 5 μM troglitazone. On day 4 and every 2 days thereafter, cells were fed with 10% FBS.

extract_protocol:
Total RNA was prepared from cells by using RNA Stat60 according to the manufacturer’s protocol (Tel-Test Inc.)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Move to the incubator maintained at 31°C

tag: cell type source

value: Mesenchymal stem cells (MSCs)

value: differentiated adipocytes from MSC


title: Sample_107025: 31°C exposure for 12 days rep3


title: Sample_107920: 31°C exposure for 12 days rep5


title: Sample_107024: 31°C exposure for 12 days rep2


title: MG1655 ade, rep 2

city: San Diego

first: Anand

last: Sastry

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text file include raw read counts for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 MG1655

growth_protocol: The E. coli cells were grown overnight in LB medium. RNA sequencing data were generated after growth under aerobic exponential growth conditions in M9 medium supplemented with adenosine. The wild type MG1655 strain was grown as a control for the isogenic punR mutant strain. Pre-cultures for the RNA sequencing experiments were started for growing the cells in LB medium. Cells were then washed twice with M9 medium and inoculated at an OD600 of 0.05.

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pelleted cells were stored at -80oC, and after cell resuspension and partial lysis, they were ruptured with a bead beater; the total RNA was extracted using a Qiagen RNA purification kit.

value: WT


title: MG1655 ade, rep 1


title: del_ydhB ade, rep 2

value: ydhB mutant


title: del_ydhB ade, rep 1


title: Sample_107023: 31°C exposure for 12 days rep1


title: vehicle group, 34_02

city: Wuhan

first: Zhi-Qiang

last: Li

state: Hubie

address: No.169 Donghu road

department: neurosurgery

country: China

institute: Zhongnan Hospital of Wuhan university

data_processing:
The obtained sequencing reads were quality-filtered using the following steps: (i) the end bases with mass less than 20, possible adapter sequences, and sequences shorter than 100 bp were removed (TrimGalore v0.4.5); (ii) the paired sequences from double-terminal sequencing were spliced after which the merged low-quality sequences (base with mass less than 20 is more than 90%) were removed (FLASH2 v2.2.00); (iii) the primer sequences and sequences containing N bases/homopolymer >6 bp were removed (mothur v.1.39.3); (iv) the sequences with a total base error rate of >2 and length <100 bp were removed (usearch v10).
Operational taxonomic units (OTUs) were clustered using a similarity cut-off value of 97%, and chimeric sequences were removed after singleton removal (usearch v10).
A standard curve equation based on the spike-in sequence of each sample was created, and the absolute copy number of each OTU in each sample was calculated.
Sequences were aligned to the RDP 16S rRNA database (trainset 16/release 11.5) with a credibility of >80% using mothur v.1.39.3.
Genome_build: RDP 16S rRNA database
Supplementary_files_format_and_content: quantification_otu_table.txt (table contains OTU numbers in each sample with taxonomic annotation for absolute and relative quantification separately (spike-in sequence was not included)).

organism: mouse gut metagenome

source_name: mouse feces

extract_protocol:
Bacterial genomic DNA was extracted by the FastDNATM Spin Kit for Soil. The V3-V4 region of the bacterial 16S ribosomal DNA was amplified using the following primer pair: 341F and 805R.A synthetic spike-in plasmid was used as internal reference to quantitatively detect the total number of bacterial 16S rRNA genes.Sample (10 ng/μL) and spike-in internal reference DNAs were used as templates for PCR. 250x2 bp were sequenced using the Illumina MiSeq/HiSeq Benchtop Sequencer.
A total of 48 samples were collected, and bacterial genomic DNA was extracted by the FastDNATM Spin Kit for Soil (MP Biomedicals, USA) according to the manufacturer’s protocols. Extracted DNA was quantified using the Invitrogen Qubit3.0 Spectrophotometer (Thermo Fisher Scientific, USA). Quality and integrity of the DNA were evaluated using NanoDrop 2000 (Thermo Fisher Scientific, USA) followed by 1.5% agarose gel electrophoresis. Isolated DNA was stored at -20°C until processing. The V3-V4 region of the bacterial 16S ribosomal DNA was amplified using the following primer pair: 341F and 805R. A synthetic spike-in plasmid was used as internal reference to quantitatively detect the total number of bacterial 16S rRNA genes. PCR amplified products were purified using equal volume of Agencourt AMPure XP PCR Purification Beads (Beckman Coulter, USA). The mixed-sample library was identified using the Agilent 2100Bioanalyzer (Agilent Technologies, USA) to detect the size of the inserted fragments in the sequencing library (confirming no specific amplification between 120 and 200 bp) and the concentration of these sequencing inserts were quantified.

treatment_protocol: After a 7-day adaptive feeding, mice were randomly allocated to two groups (i.e., vehicle- and TMZ- treated groups, n=6/group) and underwent intracranial GL261 cells implantation. TMZ gavage started at 7 days after implantation (T1) with the dosage of 50 mg/kg/d for five consecutive days (days 8-12 after implantation). TMZ solution was freshly prepared for gavage. The vehicle-treated mice received the gavage of 0.5% sodium carboxymethyl cellulose. The stool samples from the mice were collected at four time points: days 1 (the day of glioma cells implantation, T0), 7 (the day before TMZ gavage, T1), 14 (7 days after first TMZ gavage, T2), and 28 (21 days after first TMA gavage, T3).

tag: host

value: Specific-pathogen-free mouse

tag: host age

value: 8-10 weeks

tag: host strain

tag: host sex

value: male

tag: group

value: Vehicle group

value: SCC gavage started at 7 days after implantation (T1) for five consecutive days (days 8-12 after implantation)

tag: time point

value: T1 (the day before TMZ gavage)

tag: tissue

value: mouse feces


title: vehicle group, 34_04

value: T3 (21 days after first TMA gavage)


title: vehicle group, 34_03

value: T2 (7 days after first TMZ gavage)


title: vehicle group, 19_02


title: vehicle group, 34_01

value: T0 (the day of glioma cells implantation)


title: vehicle group, 19_03


title: vehicle group, 19_04


title: vehicle group, 19_01


title: Sample_107919: 31°C exposure for 1 day rep5

source_name: 31°C exposure for 1 day_MSCs

tag: cell type


title: C26 AAV9-FoxO1-shRNA

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from pooled muscle tissue of three animals in the C26 AAV9-FoxO1-shRNA group.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: tibialis anterior muscle tissue

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: CD2F1 male mice purchased from Charles River laboratory were injected subcutaneously in each flank with 5x10^5 colon 26 adenocarcinoma tumor cells diluted in 100 μL of sterile PBS (C26 group), or injected with sterile PBS alone (Sham group).

extract_protocol: Skeletal muscles were homogenized in Trizol, and RNA extracted according to manufacturer's instructions using a chloroform-based method.

treatment_protocol: AAV vectors diluted in 20 μL of Lactated Ringer solution to a final concentration of 1x10^11 vector genome were injected through the skin into the mid-belly of the tibialis anterior muscle two weeks before C26 tumor cell inoculation.

tag: gender

value: tibialis anterior muscle

value: C26 AAV9-FoxO1-shRNA


title: Sham AAV9-scrambled-shRNA

description: Gene expression data from pooled muscle tissue of three animals in the Sham AAV9-scrambled-shRNA group.

tag: strain

value: Sham AAV9-scrambled-shRNA


title: Sample_107021: 31°C exposure for 1 day rep3

value: Mesenchymal stem cells (MSCs)


title: Sample_107020: 31°C exposure for 1 day rep2

value: differentiated adipocytes from MSC


title: vehicle group, 17_02


title: C26 AAV9-FoxP1-shRNA

description: Gene expression data from pooled muscle tissue of three animals in the C26 AAV9-FoxP1-shRNA group.

value: C26 AAV9-FoxP1-shRNA


title: Sample_107918: 31°C exposure for 1 day rep4


title: vehicle group, 17_03


title: vehicle group, 15_04


title: vehicle group, 17_01


title: vehicle group, 15_03


title: C26 AAV9-scrambled-shRNA

description: Gene expression data from pooled muscle tissue of three animals in the C26 AAV9-scrambled-shRNA group.

value: C26 AAV9-scrambled-shRNA


title: Sample_107917: 31°C exposure for 0 days (culture at 37°C) rep5

source_name: 31°C exposure for 0 days (culture at 37°C)_MSCs


title: Sample_107018: 31°C exposure for 1 day rep1


title: Sample_107016: 31°C exposure for 0 days (culture at 37°C) rep4


title: Sample_107015: 31°C exposure for 0 days (culture at 37°C) rep3


title: vehicle group, 14_04

value: Specific-pathogen-free mouse


title: vehicle group, 15_02

value: 8-10 weeks


title: vehicle group, 15_01

value: male


title: Sample_107014: 31°C exposure for 0 days (culture at 37°C) rep2


title: vehicle group, 17_04

value: Vehicle group


title: Sample_107012: 31°C exposure for 0 days (culture at 37°C) rep1


title: vehicle group, 14_01

value: SCC gavage started at 7 days after implantation (T1) for five consecutive days (days 8-12 after implantation)


title: vehicle group, 14_02

value: T1 (the day before TMZ gavage)


title: vehicle group, 12_04

value: mouse feces


title: vehicle group, 14_03


title: vehicle group, 12_01


title: TMZ group, 9_01

value: TMZ group

value: TMZ gavage started at 7 days after implantation (T1) for five consecutive days (days 8-12 after implantation)


title: TMZ group, 9_02


title: TMZ group, 8_03

value: T2 (7 days after first TMZ gavage)


title: TMZ group, 8_04

value: T3 (21 days after first TMA gavage)


title: TMZ group, 9_03


title: TMZ group, 8_01

value: T0 (the day of glioma cells implantation)


title: vehicle group, 12_03


title: TMZ group, 9_04


title: MG-63: Sarcoma Cell Sample 16

city: Sendai

first: Hideharu

last: Yamada

state: Miyagi

address: 4-1 Seiryocyo, Aobaku,

department: Department of Clinical Oncology

country: Japan

institute: Institute of Development, Aging and Cancer, Tohoku University

description: gene expression in sarcoma cell line where pazopanib was resistant

hyb_protocol: 0.6 ug of each Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x fragmentation buffer and 10x Blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the each fragmentation mix and hybridized to a SurePrint G3 Human Gene Expression 8x60K Microarray (G4112A) and hybridized to an Agilent rotary hybridization oven for 17 hours at 65°C. After hybridization, the microarray was washed with GE Wash Buffer 1 (Agilent) for 1 minute at room temperature and GE Wash Buffer 2 (Agilent) at 37°C for 1 minute.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20180928) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cell line, Resistant

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

growth_protocol: The medium included 10 % fetal bovine serum. The cells were grown at 37 °C under 5 % CO2.

extract_protocol: Total RNA from the 16 sarcoma cell lines was extracted using RNeasy Mini kit (QIAGEN, Germantown, MD, USA) and quantitated by NanoDrop ND-1000 v3.8.1 Spectrophotometer (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: A total of 16 bone or soft tissue sarcoma cell lines were used in this study. SW872, SK-LMS-1, RD, ISO-HAS-B, HS-sch2, S462, HS-SY-II, Yamato-SS, and MG63 were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose. HT1080, A204, FMS-1, YST-1, and SaOs2 were maintained in RPMI-1640 medium. SFT8611 and SFT 9817 were maintained in DMEM / F12 medium.

tag: sarcoma subtypes

value: Osteosarcoma

tag: cell line


title: S462: Sarcoma Cell Sample 10

value: Malignant peripheral nerve sheath tumor


title: SFT8611: Sarcoma Cell Sample 12


title: HS-sch2: Sarcoma Cell Sample 14


title: SW872: Sarcoma Cell Sample 5

value: Liposarcoma


title: vehicle group, 12_02


title: TMZ group, 7_02


title: TMZ group, 7_04


title: TMZ group, 7_03


title: TMZ group, 8_02


title: RD: Sarcoma Cell Sample 8

value: Rhabdomyosarcoma

value: RD


title: SK-LMS-1: Sarcoma Cell Sample 7

value: Leiomyosarcoma


title: Saos2: Sarcoma Cell Sample 15


title: HT1080: Sarcoma Cell Sample 6

value: Fibrosarcoma


title: Yamato-SS: Sarcoma Cell Sample 4

description: gene expression in sarcoma cell line where pazopanib was sensitive

source_name: Cell line, Sensitive

value: Synovial sarcoma

value: Yamato-SS


title: HS-SY-II: Sarcoma Cell Sample 3

value: HS-SY-II


title: TMZ group, 7_01

value: Specific-pathogen-free mouse

value: 8-10 weeks

value: male


title: TMZ group, 2_04

value: TMZ group

value: TMZ gavage started at 7 days after implantation (T1) for five consecutive days (days 8-12 after implantation)

value: mouse feces


title: FMS-1: Sarcoma Cell Sample 11


title: ISO-HAS-B: Sarcoma Cell Sample 9

value: Angiosarcoma

value: ISO-HAS-B


title: TMZ group, 2_03

value: T2 (7 days after first TMZ gavage)


title: TMZ group, 2_02

value: T1 (the day before TMZ gavage)


title: TMZ group, 11_04

value: T3 (21 days after first TMA gavage)


title: TMZ group, 2_01

value: T0 (the day of glioma cells implantation)


title: TMZ group, 11_03


title: YST-1: Sarcoma Cell Sample 2

value: Malignant schwannoma


title: TMZ group, 11_02


title: SFT9817: Sarcoma Cell Sample 13

value: Malignant peripheral nerve sheath tumor


title: NR-14: Sarcoma Tissue Sample 23

description: gene expression in sarcoma patient FFPE tissue where pazopanib was clinically ineffective

hyb_protocol: Following protocol, 20 μl of each Cy3-labeled cDNA (specific activity >10.0 pmol Cy3/ug cDNA) was added in a volume of 30 μl hybridization master mix containing 2x Hi-RPM Hybridization Buffer and 10x Gene Expression Blocking Agent and hybridized to a SurePrint G3 Human Gene Expression 8x60K Microarray (G4112A) and hybridized to an Agilent rotary hybridization oven (Agilent) for 17 hours at 65°C. After hybridization, the microarray was washed with GE Wash Buffer 1 (Agilent) for 1 minute at room temperature and GE Wash Buffer 2 (Agilent) at 37°C for 1 minute.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20180928) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 23 cases were included in the final analysis after quality check process.

source_name: FFPE, Non-Responder

label_protocol: From each RNA, cDNA was synthesized using the Transplex Whole Transcriptome Amplification kit (Sigma Aldrich St. Louis, MO, USA). Cyanine-3 (Cy3) labeled cDNA was prepared from 1.8 ug cDNA using SureTag DNA Labelling Kit (Agilent) according to the manufacturer's instructions, followed by purification. The purification kit is included in the same kit. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 v3.8.1 Spectrophotometer (ThermoFisher Scientific Inc. Waltham, MA, USA).

extract_protocol: Total RNA from FFPE tissues was extracted using the RNeasy FFPE kit (QIAGEN, Germantown, MD, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: A total of 39 bone and soft tissue sarcoma tissue (patient tissue) were available and used in this study. All of these patient tissues were surgically resected prior to treatment with pazopanib. From these formalin-fixed, paraffin-embedded (FFPE) tissue blocks, for each eligible case, 10 μm-thick FFPE tissue sections were thinly sliced in all specimens and used for RNA extraction.

value: Undifferentiated pleomorphic sarcoma


title: A204: Sarcoma Cell Sample 1

value: Rhabdomyosarcoma


title: NR-11: Sarcoma Tissue Sample 22

value: Leiomyosarcoma


title: NR-08: Sarcoma Tissue Sample 20

value: Ewing sarcoma family tumor


title: NR-09: Sarcoma Tissue Sample 21

value: Myxoid liposarcoma


title: TMZ group, 01_03

value: Specific-pathogen-free mouse

value: 8-10 weeks

value: male


title: WAF014_v_null

city: Durham

first: Rachel

last: Johnston

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

data_processing:
Reads were trimmed with cutadapt version 2.3 (Martin, 2011) (parameters: -q 20 -e 0.2 --times 5 --overlap 2 -a AGATCGGAAGAGC -a "T(1000 Genomes Project Consortium)" --minimum-length=20).
Trimmed reads were mapped to the Damaraland mole-rat v1.0 genome (DMR_v1.0) (Fang et al., 2014) using two pass mapping with STAR (Dobin et al., 2013). Only uniquely mapped reads were retained.
HTseq (Anders et al., 2014) was used to quantify read counts mapping to genes (using the v1.0.92 gtf file from Ensembl; we extended the genomic coordinates of the SERPINE1 gene by 2000 basepairs in both directions due to very high expression directly adjacent to the annotated coordinates).
Genome_build: DMR_v1.0
Supplementary_files_format_and_content: molerat_rawcounts.txt is a tab delimited text file showing the output from HTseq, which provides the number of reads mapping to each gene for each RNA-Seq sample/library.

organism: Fukomys damarensis

source_name: bone marrow derived cells from pooled lumber vertebrae (LV1-LV5)

growth_protocol: Bone marrow was collected from bones using microcentrifuge. Cells were incubated in red blood cell lysis buffer for 3 minutes at room temperature, strained through a 70 µm cell strainer, and plated at 1.6 x 10^5 cells per cm^2 in bMSC media (MEM-alpha [ThermoFisher, Waltham, MA, USA] + 15% fetal bovine serum [Hyclone, Logan, UT, USA] + 1% penicillin/streptomycin + 2 ng/ml recombinant human fibroblast growth factor-basic [Biocam, Centurion, Gauteng, South Africa] + 10 nM ROCK inhibitor Y-27632 [RI; Cayman Chemical, Ann Arbor, MI, USA]). 24 hours post-plating, cells were carefully washed 3x with 1xPBS. Once bMSC clusters were visible (2-9 days post plating), plates were fed bMSC media without RI or fed bMSC media without RI + 10 nM estradiol (E2). Twenty-four hours later, cells were collected into buffer RLT.

extract_protocol:
Qiagen RNeasy Micro Kit
NEBNEXT LOW INPUT RNA LIBRARY PREP KIT

treatment_protocol: Cells were treated for 24 hours with 10 nM estradiol (E2) or vehicle control.

tag: breeding status

value: breeder

tag: social status

tag: cell culture treatment

tag: animal age (days)


title: TMZ group, 01_04

value: TMZ group

tag: treatment

value: TMZ gavage started at 7 days after implantation (T1) for five consecutive days (days 8-12 after implantation)

value: mouse feces


title: TMZ group, 01_02

tag: host

value: T1 (the day before TMZ gavage)


title: TMZ group, 11_01

tag: host age


title: WAF014_v_E2

value: 10 nM estradiol (E2)


title: TMZ group, 01_01

tag: host strain

value: T0 (the day of glioma cells implantation)


title: NR-06: Sarcoma Tissue Sample 19

value: Solitary fibrous tumour


title: WAF011_v_null

value: nonbreeder

value: helper


title: WAF014_lb_null

source_name: bone marrow derived cells from pooled long bones


title: NR-01: Sarcoma Tissue Sample 14


title: NR-05: Sarcoma Tissue Sample 18

value: Myxofibrosarcoma


title: WAF014_lb_E2


title: NR-03: Sarcoma Tissue Sample 16


title: R-14: Sarcoma Tissue Sample 12

description: gene expression in sarcoma patient FFPE tissue where pazopanib was clinically effective

source_name: FFPE, Responder


title: WAF011_v_E2


title: WAF011_lb_null


title: WAF011_lb_E2


title: NR-04: Sarcoma Tissue Sample 17

value: Clear cell sarcoma


title: LAF007_vert_null


title: R-12: Sarcoma Tissue Sample 10


title: LAF008_vert_null


title: R-13: Sarcoma Tissue Sample 11


title: NR-02: Sarcoma Tissue Sample 15

value: Fibroblastic osteosarcoma


title: R-10: Sarcoma Tissue Sample 8

value: Epitherioid sarcoma


title: R-11: Sarcoma Tissue Sample 9

value: Leiomyosarcoma


title: R-08: Sarcoma Tissue Sample 7

value: Osteosarcoma


title: R-15: Sarcoma Tissue Sample 13

value: Angiosarcoma of soft tissue


title: R-07: Sarcoma Tissue Sample 6


title: R-06: Sarcoma Tissue Sample 5

value: Alveolar soft part sarcoma


title: LAF007_lb_null

value: breeder


title: LAF007_lb_E2


title: R-05: Sarcoma Tissue Sample 4

value: Undifferentiated sarcoma


title: DVF008_v_null


title: R-02: Sarcoma Tissue Sample 2


title: LAF008_lb_null


title: DVF008_lb_null


title: R-01: Sarcoma Tissue Sample 1

value: Undifferentiated pleomorphic sarcoma


title: R-03: Sarcoma Tissue Sample 3


title: DVF008_v_E2


title: DVF008_lb_E2


title: DVF007_v_null


title: DVF007_v_E2


title: DVF007_lb_null


title: WEF002_lb_null


title: WEF002_v_null


title: WEF002_lb_E2


title: G11S87

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

data_processing: Illumina Casava1.7 software used for basecalling.  Read quality was observed using FastQC v. 0.11.2  quality trimming was performed using FastX-Toolkit version 0.0.14 with a trimscore of 30 and a trim length of 50  Topha2t version 2.1.0 was used to align trimmed reads to the human genome with default parameters other than that 1 mismatch was allowed  The htseq-count script was used in HTSeq v 0.6.1 to count the number of reads mapping to each gene. HTSeq used Biopython v.2.7.3.  BPSC in R, version 0.99.1 was used to determine normalize genes based on library size and to identify differentially expressed genes. A Benjamini-Hochmerg FDR of 0.05 was used as the cutoff.  IPA version  Genome_build: ENSEMBL version GrCh38.p7  Supplementary_files_format_and_content: counts generated from HTSeq are provided, along with 5 rows at the end of the matrix which include information about where reads aligned in the genome, how many alignments there were for each, etc.

source_name: low passage patient-derived PDAC cells

growth_protocol: All cells were maintained at 37 degrees Celsius in 5% Carbon dioxide and grown in DMEM. Patient-derived cells were only passaged up to 10 times.

extract_protocol: The C1 fluidigm instrument was used to capture single cells, extract RNA, reverse transcribe cDNA using the SMARTer system. The Nextera kit was used to prepare the library.

treatment_protocol: To transfect cells 1x10^5 cells were plated per well of a 6-well plate and allowed to attach overnight. The next day Lipofectamine RNAiMax reagent was used to transfect according to the manufacturer's protocol. After 16 hrs transfection normal growth media was added and cells recovered for 24 hr. Then the cells were place in a hypoxia chamber at 1% O2 for 24 hr prior to isolation for RNA sequencing.

tag: condition

value: Hypoxia

tag: transfection

value: Hypoxia APEX1 knock down


title: G10S79


title: H11S88


title: H7S56


title: G12S95


title: H9S72


title: WEF001_v_null

value: solitaire


title: G9S71


title: AR2659_03

city: Bunkyo-ku Tokyo

first: Aya

last: Fukuizumi

address: 1-1-5 Sendagi

department: Department of Pulmonary Medicine and Oncology,

institute: Nippon Medical School

description: gene expression on lung adenocarcinoma cell line

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA from cells was extracted using the NucleoSpin RNA Kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) following the manufacturer's recommendations.

treatment_protocol: All cell lines were cultured in RPMI1640 (Wako, Osaka, Japan) containing 10% fetal bovine serum (FBS; BioWest, Nuaille, France) and 1% penicillin and streptomycin (Wako Pure Chemical Industries, Osaka, Japan) at 37°C in a 5% CO2 incubator.

value: lung adenocarcinoma

tag: drug sensitivity

value: Osimertinib resistant


title: AR2659_01

tag: tissue

value: EGFR-TKIs sensitive


title: G7S55


title: AR2659_04


title: AR2659_02

value: Afatinib resistant


title: WEF001_v_E2

value: nonbreeder

value: 10 nM estradiol (E2)


title: AR2659_05


title: F12S94


title: H8S64


title: WEF001_lb_null


title: AR2659_06


title: F10S78


title: F11S86


title: F9S70


title: NOF007_v_null

value: helper


title: NOF009_lb_E2


title: NOF007_v_E2


title: F8S62


title: NOF007_lb_null


title: E12S93


title: E11S85


title: E9S69


title: NOF007_lb_E2


title: NOF009_lb_null


title: D12S92


title: E7S53


title: MAF003_v_null


title: MAF003_lb_null


title: D11S84


title: MAF006_lb_E2


title: MAF006_lb_null


title: MAF006_v_E2


title: G4F020_lb_null


title: C12S91


title: G4F020_v_null


title: D10S76


title: C11S83


title: D7S52


title: G4F020_lb_E2


title: G4F019_v_E2


title: G4F019_v_null


title: C10S75


title: G4F019_lb_null


title: F7S54


title: G1F025_v_null


title: C9S67


title: G1F025_lb_null


title: B12S90


title: B11S82


title: C8S59


title: G1F022_lb_E2


title: B10S74


title: B9S66


title: GB2-3-48hrs

city: Emeryville

first: John

last: Gladden

address: 5885 Hollis Street

institute: Agile BioFoundry

data_processing:
Illumina MiSeq GenerateFASTQ protocol
Sequenced reads were trimmed and filtered using BBDuk
Trimmed and filtered reads were mapped to Rhodosporidium toruloides IFO0880 reference genome using hisat2
Mapped reads were assigned to genes using featureCounts
Genome_build: https://mycocosm.jgi.doe.gov/Rhoto_IFO0880_4/
Supplementary_files_format_and_content: a tab-delimited text file that includes counts for all samples

organism: Rhodotorula toruloides

source_name: R. toruloides cells

growth_protocol: Cells were grown in synthetic defined medium + 2% glucose with starting OD of 0.1 and sampled at 18 and 48 hours of growth

extract_protocol:
Total RNA was isolated by disrupting harvested cells using an MP Biomedicals FastPrep bead beater (MP Biomedicals, Irvine, CA, USA) followed by purification using the QIAGEN RNeasy Mini kit with on-column DNase treatment following the manufacturer’s protocol.
10 ug of RNA was then used to prepare a sequencing library with the TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA, USA).

tag: genotype

value: IFO0880/P_GAPDH-BIS, P_ANT-BIS

tag: time

value: 48 hours


title: GB2-2-48hrs

tag: strain


title: B8S58


title: D8S60


title: GB2-1-48hrs


title: Bis3-3-48hrs


title: Bis3-1-48hrs


title: A11S81


title: B7S50


title: A7S49


title: Bis18-3-48hrs


title: Bis14-3-48hrs


title: Bis14-2-48hrs


title: H6S48

value: Hypoxia Scrambled Control


title: Bis14-1-48hrs


title: Bis18-2-48hrs


title: H5S40


title: Bis18-1-48hrs


title: G1F022_lb_null


title: H4S32


title: H3S24


title: H2S16


title: WT-5-48hrs


title: WT-6-48hrs


title: G6S47


title: A12S89


title: H1S8


title: Bis3-2-48hrs


title: A10S73


title: G4S31


title: WT-2-48hrs


title: G5S39


title: WT-3-48hrs


title: WT-4-48hrs


title: WT-1-48hrs


title: A8S57


title: Bis3-3-18hrs

value: 18 hours


title: GB2-1-18hrs


title: F6S46


title: GB2-2-18hrs


title: GB2-3-18hrs


title: F5S38


title: G1S7


title: F4S30


title: F3S22


title: Bis14-3-18hrs


title: G3S23


title: Bis3-1-18hrs


title: F2S14


title: Bis14-1-18hrs


title: Bis14-2-18hrs


title: Bis18-2-18hrs


title: Bis18-3-18hrs


title: G2S15


title: E5S37


title: E6S45


title: E4S29


title: E3S21


title: E1S5


title: WT-4-18hrs


title: E2S13


title: WT-6-18hrs


title: Bis18-1-18hrs


title: Bis3-2-18hrs


title: WT-3-18hrs


title: WT-1-18hrs


title: D5S36


title: D3S20


title: D2S12


title: D4S28


title: D1S4


title: D6S44


title: F1S6