title: IL-4_IL-6_IL-21_rep2

city: West Lafayette

first: Matt

last: Olson

address: 201 St University St

institute: Purdue University

data_processing:
The expression level of all genes in all RNA-seq libraries was quantified by cufflinks. Differntially expressed genes were determined using cuffdiff (adjusted q-value < 0.05; at least 2 fold change) between each pair of condition (i.e. Th0 vs Th0+IL6/21, Th0 vs Th0+IL4 and Th0 vs Th0+IL4+IL6/21).
Genome_build: GRCm38; mm10

source_name: Isolated and Treated Naive CD4+ Cells (Negative Magnetic Selection)

extract_protocol: RNA from in vitro Th cultures was harvested by placing 200,000-1,000,000 Th cells in Trizol reagent. RNA was isolated from these preparations via phenol-cholorofrm extraction. Illumina-sequenced reads from these cells were further quality filtered, aligned to the mouse genome (mm10), postprocessed, quantified and analyzed by Otogenetics.

treatment_protocol: Naive (CD4+ CD62L+) mouse CD4 T cells were isolated from the spleen and lymph nodes of 8-12 week old WT C57BL/6 mice using CD62L naive CD4+ T cell enrichment (Miltenyi Biotec, 130-093-227). After isolation, cell purity was monitored and was above 93% CD4+ CD62L+ and CD44- and were resuspended at 106 cells per ml in RPMI 1640 media supplemented with 10% fetal calf serum, penicilin (1000U/ml) and streptomycin (1mg/ml) (Gibco), 2mM L-glutamine (Lonza), 0.05mM 2-mercaptoethanol, and 20mM HEPES buffer.      After isolation, cells were incubated on anti-CD3-coated plates (2ug/ml) with soluble anti-CD28 (5ug/ml) in the presence of no additional cytokines, IL-4 (20ng/ml), IL-6 and IL-21 (20ng/ml and 100ng/ml) or a combinaiton of IL-4 and IL-6+IL-21. After 3 days, cells were expanded in 4 volumes of fresh media in uncoated plates with 1/2 the indicated cytokines. Cells were collected on day 5 of culture and placed in trizol for RNA isolation.

tag: sequencing method

value: PE 100bp RNAseq, HiSeq

value: Wildtype


title: IL-4_IL-6_IL-21_rep3

status: Public on Jul 18 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: treatment

tag: genotype


title: HCC-2 T/N ratio

status: Public on Jul 19 2020

type: RNA

city: Taoyuan

first: Yang-Hsiang

last: Lin

address: Wenhua 1st Rd., Guishan Dist.

department: Department of Biochemistry

country: Taiwan

institute: Chang Gung University

description: HCC-2 (paired)

hyb_protocol: Cy5 and Cy3 channel input cRNA amount for hybridization(micro gram)

scan_protocol: microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies, USA)

data_processing: Mean signal intensity of g(r) channel - mean background light intensity of g(r) channel. Normalized Expression Ratio is performed by the statistic method 'rank consistant lowess.

molecule: total RNA

organism: Homo sapiens

source_name: HCC

label_protocol: Cy5 and Cy3 channel input RNA amount for labeling(micro gram)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: tissue

value: HCC liver

source_name: adjacent normal tissue

value: adjacent normal liver


title: IL-4_IL-6_IL-21_rep1


title: IL-6_IL-21_rep3


title: IL-6_IL-21_rep2


title: LEPR+_PDGFRA-_CBM_YOUNG_3

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

data_processing:
RNAseq: Raw reads were trimmed using TrimmGalore! software and inspected using FastQC
RNAseq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using STAR software.
RNAseq: The featureCounts software was used to count reads on the basis of the RefSeq gene model
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Raw count matrix generated by featureCounts software

extract_protocol:
Stromal cells were isolated from mouse bone marrow by FACS and cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.

tag: strain

value: Bone marrow

tag: cell type

value: stromal cells

tag: phenotype

tag: age

value: YOUNG


title: IL-6_IL-21_rep1


title: LEPR+_PDGFRA-_CBM_YOUNG_1


title: IL-4_rep3


title: LEPR+_PDGFRA+_CBM_YOUNG_3


title: LEPR+_PDGFRA-_CBM_OLD_3

value: OLD


title: LEPR+_PDGFRA-_CBM_YOUNG_2


title: IL-4_rep2


title: LEPR+_PDGFRA-_CBM_OLD_1


title: ALCAM+_BLC_YOUNG_3


title: No cytokine_rep2


title: IL-4_rep1


title: LEPR+_PDGFRA-_CBM_OLD_2


title: LEPR+_PDGFRA+_CBM_YOUNG_1


title: ALCAM+_BLC_YOUNG_2


title: LEPR+_PDGFRA+_CBM_OLD_3


title: ALCAM+_BLC_YOUNG_1


title: ALCAM+_BLC_OLD_3


title: LEPR+_PDGFRA+_CBM_OLD_1


title: ALCAM+_BLC_OLD_2


title: DNA-PKcs_KO_3

city: New York

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

description: Since all our experimental mice carry the preassembled IgH on the 129  ackground, we replaced the IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6-based mm9 with the corresponding region in the AJ851868.3 (NCBI gene accession no. AJ851868.3) 129 IgH sequence (1415966–1592715) to generate the mm9sr (switch region replacement) genome.  1. Hu J, et al. (2016) Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc 11:853–871.

library_source: genomic

data_processing:
Library strategy: high-throughput genome translocation sequencing (HTGTS)
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3 using Bowtie2. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Mutation rate was calculated by custom Excel integrated VBA script. Mutations were determined by comparing the actual bait sequence of each IgH junction with the germ-line bait sequence based on the IgH sequence from 129/Sv strain (NCBI gene accession no. AJ851868.3). Only true mismatches (no insertion or deletion within 7 nt) were counted as a mutation.
Genome_build: mm9sr (to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3)
Supplementary_files_format_and_content: .xlsx files generated from tab-delimited text files after analysis for reads distribution and mutation rates.

molecule: genomic DNA

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice carrying preassembled IgH and IgK loci (129Sv background) were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)). Due to low splenic B cell number, DNA-PKcs KD/KDTp53-/- splenic cells were used for stimulation without purification.

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

value: anti-CD40 and Il4 activated B cells

value: DNA-Pkcs-/-


title: DNA-PKcs_KO_1


title: ALCAM+_BLC_OLD_1


title: No cytokine_rep1


title: DNA-PKcs_KO_2


title: Xrcc4_KO_1


title: DNA-PKcs_5A_5

value: DNA-Pkcs5A/5A p53+/-


title: No cytokine_rep3


title: DNA-PKcs_KO_4


title: DNA-PKcs_5A_3

value: DNA-Pkcs5A/5A p53-/-


title: DNA-PKcs_5A_4


title: DNA-PKcs_5A_1


title: P53_+-_1


title: P53_--_1


title: P53_+-_2


title: wildtype_2

value: wild type


title: P53_--_2


title: DVE-1_CHIP (L4440+atp-2) rep1

city: Beijing

first: Liwa

last: Shao

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description: DG-LA-CHIP

data_processing:
Adaptor in reads were filtered using in-house script then Trim Galore was used to do the quality control with following parameters: -q 20 --fastqc --illumina --stringency 6 -e 0 --length 50 --trim-n –paired.
Processed reads were mapped to the C. elegans genome (ce11) using bwa (v0.7.13-r1126) with default parameters.
Only proper paired uniquely mapping reads with mapping quality ≥20 and mismatches <8 were retained. PCR duplicates were removed by picard-2.17.6 (http://broadinstitute.github.io/picard) MarkDuplicates command.
MACS2 (v2.1.1) was used to obtain peak regions with following parameter: -g ce -f BAMPE --broad --SPMR.
ChIP-seq signals were calculated using deeptools (v2.4.2) by normalizing the read coverage to 10 million reads then subtracting input coverage from the ChIP samples to get final ChIP-seq signals.
Genome_build: C. elegans genome (ce11)
Supplementary_files_format_and_content: Bed files contain rep overalap called peaks.

organism: Caenorhabditis elegans

source_name: the whole organism

growth_protocol: Synchronized worms were raised on RNAi at 20°C. Synchronized from L1 to Day of adulthood stage

extract_protocol:
Worms were cross-linked by formaldehyde and homogenized by a glass homogenizer.Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared by DNA Sample Kit (NEB, E7370).

treatment_protocol: atp-2 RNAi bacterial culture solution was seeded after worms cultured on the empty vector RNAi clones.

tag: developmental stage

value: Day1 of adulthood

tag: chip antibody

value: GFP agarose (ChromoTek, gta-20)

tag: knockdown

value: L4440 and atp-2 RNAi


title: Xrcc4_KO_2


title: wildtype_1


title: brain of unmated reproductive ant departing on her mating flight (5GB)

city: Griffin

first: Brendan

middle: G.

last: Hunt

state: GA

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

data_processing:
Data were mapped to the Solenopsis invicta gnG genome assembly and refseq annotation
First, we filtered out reads in our data that aligned to Myrmecia croslandi (Australian bull ant) 18S rRNA, 5.8S rRNA, or 28S rRNA genes using BLAT (version 3.5). The remaining reads were trimmed with Trimmomatic version 0.32 (TRAILING:3, LEADING:3, SLIDINGWINDOW:4:15, MINLEN:36) (Bolger, Lohse, & Usadel, 2014). Reads were aligned to S. invicta assembly gnG (NCBI accession GCF_000188075.1, generated from an SB male) using STAR version 2.5.3a (Dobin et al., 2013; Wurm et al., 2011). We utilized previously published linkage mapping information to determine which scaffolds mapped to each linkage group as well as to the Sb supergene (Pracana, Priyam, et al., 2017; Wang et al., 2013).  In addition, we resequenced two libraries that had lower than expected numbers of sequenced reads (239AB and 1EB). Aligned reads were mapped to the NCBI annotation release 100 RefSeq gene models using the FeatureCounts function from the RSubread package (Liao, Smyth, & Shi, 2013).
Genome_build: GCF_000188075.1
Supplementary_files_format_and_content: For RNA-seq data: Tab delimited file: <gene_symbol> <aligned reads count> <LOC ID>

organism: Solenopsis invicta

growth_protocol: Alate (winged) gynes were field-caught by aspiration from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co., Georgia, USA on days of mating flights in April 2015.

extract_protocol: RNA was extracted from brains using the RNeasy Micro Kit and from ovaries using the RNeasy Mini Kit, both with DNase treatment (Qiagen, Valencia, CA).  Illumina sequencing libraries were prepared following the Smart-seq2 protocol.

tag: echotype

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

value: Single Brain

value: reproductively mature

value: Sb/Sb

tag: social form

value: Polygyne


title: ovaries of unmated reproductive ant departing on her mating flight (5AO)

value: Single Ovary

value: SB/Sb


title: DNA-PKcs_5A_2


title: brain of unmated reproductive ant departing on her mating flight (5AB)


title: ovaries of unmated reproductive ant departing on her mating flight (30GO)


title: 1025NEC

city: Tokyo

first: noriko

middle: muto

last: matsumoto

address: 1-1-5 Sendagi, Bunkyo-ku

department: Department of Plastic, Reconstructive and Regenerative Surgery

country: Japan

institute: Nippon Medical School

description: Gene expression of NECs

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent SureScan G4900DA Microarray Scanner at 3 micron resolution.

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.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NECs 6

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: RNA was prepared using Rneasy Mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For isolation of EC the resected specimen was placed in DMEM supplemented with 1x penicillin / streptomycin and 250μg/ml amphotericin B for transportation. Pieces of at least 2cm x 2cm seized tissue (depending on the tissue size) were cut and used for isolation of EC. Keloid tissues were cut in the center of the lesion. Normal skin tissues from patients without keloids were cut from the ‘dog ear’ skin in each surgical procedure. The tissues were washed three times with DMEM supplemented with 1x penicillin / streptomycin and 250μg/ml amphotericin B for transportation and were minced into approximately 3mm3 pieces with scissors. The pieces were digested in C tube with 1% BSA/DMEM (Wako), Enzyme P, Enzyme D, Enzyme A using Whole Skin Dissociation Kit (Miltenyi Biotech, Bergish Gladbach, Germany) for approximately 1 hour in a room temprature. Later, the tissues were squeezed through a mesh filter with a mesh size of 100μm and cells were harvested by centrifugation (300 xg, 10 Min, 4℃). Then, PEB buffer was added and well mixed. As for Magnetic EC sorting, first, Anti-CD45 MicroBeads and Anti-Fibroblast Microbeads were added and incubated for 10 minutes in room air. Second, Anti-CD31-PE was added and incubated in 4℃, in a shade. Then these cell suspensions were applied to magnetic sorting (MACS) using LS separation columns (Miltenyi Biotech, Bergish Gladbach, Germany) which were previously washed three times with PEB. Negative fraction was collected and centrifuged (300 xg, 10 Min, 4℃) then, supernatant was removed.   Finally, the Anti-PE-microbeads were added and mixed well after adding the PEB.   Then these cell suspensions were applied to LS separation columns which were previously washed three times with PEB. Positive fraction was collected and repeated this to purify the EC. The suspension was immediately placed in RNA later. A very small amount of suspension were used for flow cytometry using FACS can (BD Biosciences) The purity of these cells as measured by flow cytometry was more than 85% in all cases.

value: Lower abdomen skin tissue

tag: gender

value: female


title: 0912NEcs

description: Gene expression of NECs

source_name: NECs 4

value: Eyelid skin tissue

value: male


title: 1012KEC

description: Gene expression of KECs

source_name: KECs 5

value: Lower abdomen keloid skin tissue


title: 0905NEcs

description: Gene expression of NECs

source_name: NECs 2

value: Thigh skin tissue


title: ovaries of unmated reproductive ant departing on her mating flight (5GO)


title: ovaries of unmated reproductive ant departing on her mating flight (30EO)

value: SB/SB


title: wildtype_3

value: anti-CD40 and Il4 activated B cells

value: wild type


title: 0808NEcs

description: Gene expression of NECs

source_name: NECs 1


title: brain of unmated reproductive ant departing on her mating flight (30EB)


title: 0620K

description: Gene expression of KECs

source_name: KECs 3


title: 1017NEC

description: Gene expression of NECs

source_name: NECs 5


title: 0720KEcs

description: Gene expression of KECs

source_name: KECs 4

value: Upper arm keloid skin tissue


title: brain of unmated reproductive ant departing on her mating flight (30AB)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.


title: 0906NEcs

description: Gene expression of NECs

source_name: NECs 3

value: Back skin tissue


title: 2.5wk HRZE rep3

city: Worcester

first: Richard

middle: E

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
100-base paired-end reads were trimmed and aligned to the M. tuberculosis H37Rv genome to identify sites of himar1 insertion. Custom Perl programs available at https://github.com/sassettilab/Bellerose_et_al_mSystems_TnSeq_analyses were used for the read trimming and subsequently to summarize insertion counts at each genomic TA dinucleotide (see subdirectory 'TnSeq_insertion_counts_v6' under the aforementioned Github link).
Genome_build: NC_018143.1
Supplementary_files_format_and_content: Tab-delimited text files generated in the custom data processing pipeline: col 1, genome coordinate; col 2, unique insertion counts

organism: Mycobacterium tuberculosis H37Rv

source_name: homogenized mouse spleens

growth_protocol: 8-12 week old female BALB/cJ mice were infected with 10^6 CFU of M. tuberculosis H37Rv himar1 transposon library via the intravenous route.

extract_protocol:
Spleens were isolated and homogenized. Approximately one million CFU per mouse were plated on 7H10 agar with kanamycin (10µg/ml). Genomic DNA was extracted as  described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. 2015. Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279:79-95.
Libraries were prepared for Illumina sequencing using custom primers as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. 2015. Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279:79-95.

treatment_protocol: Antibiotics were administered in the drinking water (0.1g/L isoniazid, 0.6g/L ethambutol, 0.1g/L rifampicin, 15g/L pyrazinamide) as indicated. All four antibiotics were used in combination treatment (HRZE).

tag: infection

value: himar1 transposon library

tag: infected host

value: 8-12 week old female BALB/cJ mice

tag: time

value: 32 days post infection

tag: antibiotic treatment

value: combination


title: 0530K1.1

description: Gene expression of KECs

source_name: KECs 1

value: Shoulder keloid skin tissue


title: 2.5wk HRZE rep1


title: 2.5wk HRZE rep2


title: ovaries of unmated reproductive ant departing on her mating flight (240AO)

value: Single Ovary

value: reproductively mature

value: Monogyne


title: 1wk HRZE rep4

value: 21 days post infection


title: 1wk HRZE rep5


title: Duct cells at day 4 control donor 4

city: Jette

first: Jonathan

last: Baldan

address: Laerbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45°C and rotation opf 65rpm on Human GeneChip 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 System

data_processing: The data were analyzed with the transcriptome analysis console (TAC) using Affymetrix default analysis settings with FDR p-value < 0.05

label: biotin

source_name: FACS sorted CA19.9 positive fraction at day 4 control donor_4

label_protocol: 5.5 μg of single-stranded cDNA is required for fragmentation and labeling (GeneChip™ WT Pico Reagent Kit)

growth_protocol: Advanced RPMI, 5% FBS

extract_protocol: RNeasy micro kit (Qiagen; 74004).

treatment_protocol: Clusters were dissociated using Neurocult™ enzymatic dissociation kit for adult CNS tissue (Stemcell™ Technologies), incubated for 5 minutes at 37°C while resuspending constantly

value: Ductal exocrine pancreas

value: Duct cells


title: Duct cells at day 4 control donor 2

source_name: FACS sorted CA19.9 positive fraction at day 4 control donor_2


title: Acinar cells at day 4 control donor 3

source_name: FACS sorted CA19.9 negative fraction at day 4 control_donor 3

value: Non-ductal exocrine pancreas

value: Acinar cells


title: Acinar cells at day 4 control donor 1

source_name: FACS sorted CA19.9 negative fraction at day 4 control_donor 1


title: ovaries of unmated reproductive ant departing on her mating flight (30AO)

value: SB/Sb

value: Polygyne


title: Duct cells at day 4 control donor 3

source_name: FACS sorted CA19.9 positive fraction at day 4 control donor_3


title: Acinar cells at day 4 control donor 2

source_name: FACS sorted CA19.9 negative fraction at day 4 control_donor 2


title: Acinar cells at day 4 control donor 4

source_name: FACS sorted CA19.9 negative fraction at day 4 control_donor 4


title: Mixed exocrine at day 4 donor 3

source_name: Human pancreatic exocrine cells after 4 days of suspension culture_donor 3

treatment_protocol: No treatment

value: Mixed exocrine pancreas

value: exocrine cells


title: brain of unmated reproductive ant departing on her mating flight (30GB)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

value: Single Brain

value: Sb/Sb


title: brain of unmated reproductive ant departing on her mating flight (240AB)

value: SB/SB


title: Mixed exocrine at day 4 donor 2

source_name: Human pancreatic exocrine cells after 4 days of suspension culture_donor 2


title: 1wk HRZE rep2

value: himar1 transposon library

value: 8-12 week old female BALB/cJ mice

value: combination


title: ovaries of unmated reproductive ant departing on her mating flight (239AO)

value: Single Ovary

value: reproductively mature

value: Monogyne


title: 5wk PZA rep6

value: 49 days post infection

value: pyrazinamide


title: brain of unmated reproductive ant departing on her mating flight (239AB)


title: 1wk HRZE rep3

value: 21 days post infection


title: 5wk PZA rep4


title: 5wk PZA rep3


title: 5wk PZA rep5


title: 5wk PZA rep2


title: ovaries of unmated reproductive ant departing on her mating flight (235AO)


title: 1wk HRZE rep1


title: 5wk PZA rep1


title: HepG2_Ribo_WT_ADRplus_rep2

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
library strategy: Ribo-Seq
Raw reads were aligned to UCSC hg19 reference genome by STAR with parameters provided by RiboCode manual.
Transcripts annotation files were prepared as gff3 format.
Tthe length range of the RPF reads and  the P-site location was selected through interpretation of the metaplots drawing the distance between 5' end and start codon.
Translated ORFs were detected using RiboCode with parameters:  "-l no -g"
Genome_build: hg19
Supplementary_files_format_and_content: bed files recording the ORFs detected by RiboCode

growth_protocol: HepG2 cells were cultured in MEM medium (GIBCO) supplemented with 1.5 g/L NaHCO3, 110 mg/L sodium pyruvate and 10% foetal bovine serum plus antibiotics.Cells were maintained in a 5% CO2 atmosphere at 37 ℃.

extract_protocol:
The HepG2 cells were treated with 500 ng/mL ADR for 24 h, and then cycloheximide (CHX) was added to inhibit the translational elongation of ribosomes. The 26-30-nt RPFs were isolated to generate ribosome profiling sequencing libraries.
The ribosome profiling assay was performed as described in the Nature Method’s protocol and the Ribo-seq libraries were prepared according to Illumina’s instructions

treatment_protocol: HepG2-KO-p53 cells were treated with 500 ng/mL ADR for 24 h.

tag: cell line

value: wild type

tag: treatment

value: 500 ng/mL ADR for 24 h


title: brain of unmated reproductive ant departing on her mating flight (235AB)

tag: tissue

tag: genotype


title: 0615K

description: Gene expression of KECs

source_name: KECs 2

value: Chest keloid skin tissue

value: female


title: 2.5wk PZA rep5

value: 32 days post infection


title: HepG2_RNA_WT_ADRplus_rep2

description:
processed data file:
WT_ADRplus_vs_WT_ADRminus_DEseq2_expr.txt
KO_ADRplus_vs_WT_ADRplus_DEseq2_expr.txt

data_processing:
RNA-seq data reads were aligned to UCSC hg19 reference genome using hisat2 with default parameters
DESeq2 package was used to detect the differential expressed genes (p<0.05 and |FC|>2)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include the differential expression between 2 samples

growth_protocol: HepG2 and HepG2-KO-p53 cells were cultured in MEM medium (GIBCO) supplemented with 1.5 g/L NaHCO3, 110 mg/L sodium pyruvate and 10% foetal bovine serum plus antibiotics.Cells were maintained in a 5% CO2 atmosphere at 37 ℃.

extract_protocol:
For RNA-seq profiling, the total RNA was purified from HepG2 and HepG2-KO-p53 cells untreated or treated with 500 ng/mL ADR for 24 h, with two independent samples, respectively. The total RNA was isolated from cells using the RNA isolation reagent Trizol (Invitrogen).
Paired-end and strand-specific RNA-seq libraries were prepared according to Illumina’s instructions and sequenced on Xten (ANOROAD) with a sequence length of 150 bp.

treatment_protocol: HepG2 and HepG2-KO-p53 cells were untreated or treated with 500 ng/mL ADR for 24 h.


title: 2.5wk PZA rep4


title: 2.5wk PZA rep2


title: 2.5wk PZA rep1


title: HepG2_Ribo_WT_ADRplus_rep1


title: brain of unmated reproductive ant departing on her mating flight (233AB)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

value: Single Brain


title: 2.5wk PZA rep3


title: 1wk PZA rep4


title: 1wk PZA rep3


title: ovaries of unmated reproductive ant departing on her mating flight (232AO)

value: SB/SB


title: Mixed exocrine at day of isolation donor 2

source_name: Human pancreatic exocrine cells after isolation_donor 2

value: Mixed exocrine pancreas

tag: cell type

value: exocrine cells


title: Mixed exocrine at day 4 donor 1

source_name: Human pancreatic exocrine cells after 4 days of suspension culture_donor 1


title: Mixed exocrine at day of isolation donor 3

source_name: Human pancreatic exocrine cells after isolation_donor 3


title: brain of unmated reproductive ant departing on her mating flight (232AB)


title: 1wk PZA rep2

value: himar1 transposon library

value: 8-12 week old female BALB/cJ mice


title: 1wk PZA rep1


title: Mixed exocrine at day of isolation donor 1

source_name: Human pancreatic exocrine cells after isolation_donor 1


title: 5wk RIF rep3

value: rifampicin


title: HepG2_RNA_WT_ADRminus_rep2

description:
processed data file:
WT_ADRplus_vs_WT_ADRminus_DEseq2_expr.txt


title: ovaries of unmated reproductive ant departing on her mating flight (222AO)

value: Single Ovary

value: reproductively mature

value: Monogyne


title: HepG2_RNA_WT_ADRminus_rep1


title: 5wk RIF rep4

value: 49 days post infection


title: ovaries of unmated reproductive ant departing on her mating flight (233AO)


title: 5wk RIF rep2


title: brain of unmated reproductive ant departing on her mating flight (222AB)


title: HepG2_RNA_KO_ADRplus_rep2

description:
processed data file:
KO_ADRplus_vs_WT_ADRplus_DEseq2_expr.txt

value: p53 knockout


title: HepG2_RNA_WT_ADRplus_rep1

value: wild type

value: 500 ng/mL ADR for 24 h


title: ovaries of unmated reproductive ant departing on her mating flight (20IO)

value: Sb/Sb

value: Polygyne


title: HepG2_RNA_KO_ADRplus_rep1


title: 2.5wk RIF rep3

value: 32 days post infection


title: 2.5wk RIF rep4


title: 2.5wk RIF rep5


title: 5wk RIF rep1


title: Worker 4

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

data_processing:
Libraries were sequenced using the Illumina HiSeq 2500. Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings. Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
The RNA-seq reads that passed the quality filters were mapped to the fire ant reference genome (Si_gnG, official gene set v.2.2.3)  using the Tuxedo RNA-seq pipeline (Trapnell et al., 2013, Trapnell et al., 2009, Trapnell et al., 2010) in cyverse.org
Genome_build: GCA_000188075.1

source_name: brain

extract_protocol:
Brains were disssected in ice-cold PBS , flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq   Stranded Total RNA library Prep Kit was used with 1 ug of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols with the Illumina TruSeq  Stranded Total RNA library Prep Kit  with 1 ug of total RNA

value: brain

value: adult

value: polygyne

tag: Sex

value: female


title: 2.5wk RIF rep1

source_name: homogenized mouse spleens

value: himar1 transposon library


title: 2.5wk RIF rep2

value: 8-12 week old female BALB/cJ mice


title: ovaries of unmated reproductive ant departing on her mating flight (20DO)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

tag: age

value: SB/SB


title: brain of unmated reproductive ant departing on her mating flight (20IB)

value: Single Brain

value: reproductively mature


title: 1wk RIF rep5

value: 21 days post infection

value: rifampicin


title: brain of unmated reproductive ant departing on her mating flight (20DB)


title: 1wk RIF rep3


title: Worker 2

tag: developmental stage


title: 1wk RIF rep2


title: 1wk RIF rep4


title: ovaries of unmated reproductive ant departing on her mating flight (20AO)

value: Single Ovary

value: SB/Sb


title: Worker 1


title: 5wk EMB rep2

value: 49 days post infection

value: ethambutol


title: 5wk EMB rep1


title: 1wk RIF rep1


title: 40S Ribosome Footprints from DENR KO Hela Cell Line 2

city: Heidelberg

last: Bohlen

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ

description: DENR KO2 40S & DENR KO2 (Stop Codon)

data_processing:
Library strategy: Ribo-seq
Read trimming: Adapter sequences and randomized nucleotides were trimmed from raw reads using cutadapt.
tRNA and rRNA depletion: Ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2.
Read Alignment: Then, the remaining reads were separately aligned to the human transcriptome (Refseq Transcripts, GrCH38, Version of November 2018) using BBmap.
Read counting: Reads in coding sequences and Transcripts were counted using custom scripts supplied in the supplemental file to the manuscript.
Genome_build: Refseq Transcripts, GrCH38, Version of November 2018
Supplementary_files_format_and_content: Read counted in Protein Coding Sequences (80S Footprinting) or  on wholeTranscript of the indicated samples (Columns)

source_name: Hela Cells

growth_protocol: Hela control and DENRKO cells were seeded in 15 cm dishes at 3 million cells per dish in 20 ml growth medium. Two days later, cells were harvested for Ribo-seq and RNA-seq.

extract_protocol:
For RNA-seq, cells were lysed with TRIzol and total RNA was isolated following manufacturer’s protocol. For Ribo-seq, cells were briefly rinsed with ice-cold PBS containing 10 mM MgCl2, 400 μM cycloheximide (CHX). This solution was poured off, removed by gently tapping the dish onto paper towels, and cells were lysed with 150 µl of lysis buffer (0,25 M HEPES pH 7.5, 50 mM MgCl2, 1 M KCl, 5% NP40, 1000 μM CHX) per plate. Cells were scraped off and lysate was collected. After brief vortexing, lysate was clarified by centrifuging for 10 minutes at 20.000 g at 4C. Approximate RNA concentration was measured using a Nanodrop system and 100U of Ambion RNAse 1 was added per 120 µg of measured RNA. Lysates were incubated with RNAse for 5 minutes on ice.  Lysates were then pipetted onto 17.5-50% sucrose gradients and centrifuged at 35.000 rpm for 3.5 hours in Beckmann SW40 rotor. Gradients were fractionated using a Biocomp Gradient Profiler system and 80S fractions were collected for footprint isolation. RNA was isolated from these fractions using Acid-Phenol extraction and analysed on an Agilent Bioanalyzer system to asses RNA integrity.
RNA samples were depleted of ribosomal RNA using the Illumina Ribo-Zero Gold kit. Depleted total RNA was then fragmented using chemical cleavage in 50 mM NaHCO3 at pH 10, 95°C for 12 minutes. Then total RNA was processed in parallel with the depleted RNA from 80S ribosome fractions. For size selection, RNA was run on 15% Urea-Polyacrylamide gels and fragments from 25-35 nt were excised using reference ssRNA nucleotides of 25 and 35 basepairs run on a neighboring lane. RNA was extracted from the gel pieces and phosphorylated using T4 PNK. Deep sequencing libraries were prepared from these RNA fragments using the Bio-Scientific NEXTflex Small RNA-Seq Kit v3. DNA was amplified with 9 PCR cycles for the Ribo-seq samples and 11-13 cycles for the RNA-seq samples. Deep-sequencing libraries were sequenced on the Illumina Next-Seq 550 system.

treatment_protocol: not applicable

value: DENR KO

value: Hela

tag: library preparation kit

value: Takara/Clonentech

tag: rrna depletion

tag: index sequence

value: CGCTCATT


title: ovaries of unmated reproductive ant departing on her mating flight (209AO)

tag: echotype

tag: social form

value: Monogyne


title: brain of unmated reproductive ant departing on her mating flight (20AB)

value: Polygyne


title: 2.5wk EMB rep2

tag: infection

value: himar1 transposon library

value: 8-12 week old female BALB/cJ mice

value: 32 days post infection


title: 2.5wk EMB rep1

tag: infected host


title: 40S Ribosome Footprints from DENR KO Hela Cell Line 1

description: DENR KO1 40S & DENR KO1 (Stop Codon)

value: TCCGGAGA


title: 1wk EMB rep2

tag: time


title: 1wk EMB rep1

tag: antibiotic treatment


title: 40S Ribosome Footprints from WT Hela Cells

description: WT 40S & WT 40S (Stop codon)

value: WT

tag: cell line

value: ATTACTCG


title: 5wk INH rep1

value: isoniazid


title: Worker 3

value: brain

value: adult

value: polygyne

value: female


title: ovaries of unmated reproductive ant departing on her mating flight (207AO)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

value: Single Ovary

value: reproductively mature

value: SB/SB


title: 5wk INH rep2

value: 49 days post infection


title: 2.5wk INH rep2


title: brain of unmated reproductive ant departing on her mating flight (207AB)

value: Single Brain

value: Monogyne


title: 2.5wk INH rep1

value: himar1 transposon library

value: 8-12 week old female BALB/cJ mice


title: RNA-seq from DENR KO Hela Cell Line 2

description: DENR KO2 RNA-seq

data_processing:
Read trimming: Adapter sequences and randomized nucleotides were trimmed from raw reads using cutadapt.
tRNA and rRNA depletion: Ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2.
Read Alignment: Then, the remaining reads were separately aligned to the human transcriptome (Refseq Transcripts, GrCH38, Version of November 2018) using BBmap.
Read counting: Reads in coding sequences and Transcripts were counted using custom scripts supplied in the supplemental file to the manuscript.
Genome_build: Refseq Transcripts, GrCH38, Version of November 2018
Supplementary_files_format_and_content: Counted fragments in CDS (80S Fping) or whole transcript (RNA-seq) xlsx excel sheet
Supplementary_files_format_and_content: Read counted in Protein Coding Sequences (80S Footprinting) or  on wholeTranscript of the indicated samples (Columns)

value: DENR KO

value: Hela

value: Nextflex small RNA

value: Ribo Zero Gold Illumina

value: GAATGA


title: 1wk INH rep1

value: 21 days post infection

value: isoniazid


title: 49dpi untreated rep4


title: 1wk INH rep2


title: ovaries of unmated reproductive ant departing on her mating flight (1EO)

value: Polygyne


title: 49dpi untreated rep3


title: brain of unmated reproductive ant departing on her mating flight (1EB)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.


title: RNA-seq from WT Hela Cells

description: WT RNA-seq

value: WT

value: GCTGTA


title: 80S Ribosome Footprints from DENR KO Hela Cell Line 2

description: DENR KO2 80S

data_processing:
Library strategy: Ribo-seq
Read trimming: Adapter sequences and randomized nucleotides were trimmed from raw reads using cutadapt.
tRNA and rRNA depletion: Ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2.
Read Alignment: Then, the remaining reads were separately aligned to the human transcriptome (Refseq Transcripts, GrCH38, Version of November 2018) using BBmap.
Read counting: Reads in coding sequences and Transcripts were counted using custom scripts supplied in the supplemental file to the manuscript.
Genome_build: Refseq Transcripts, GrCH38, Version of November 2018
Supplementary_files_format_and_content: Counted fragments in CDS (80S Fping) or whole transcript (RNA-seq) xlsx excel sheet
Supplementary_files_format_and_content: Read counted in Protein Coding Sequences (80S Footprinting) or  on wholeTranscript of the indicated samples (Columns)

value: TACAAG


title: RNA-seq from DENR KO Hela Cell Line 1

description: DENR KO1 RNA-seq

value: ATTATA


title: 49dpi untreated rep2

value: 49 days post infection


title: 49dpi untreated rep1


title: ovaries of unmated reproductive ant departing on her mating flight (19GO)

value: Single Ovary

value: reproductively mature

value: Sb/Sb


title: 32dpi untreated rep6

value: himar1 transposon library

value: 8-12 week old female BALB/cJ mice

value: 32 days post infection


title: 80S Ribosome Footprints from DENR KO Hela Cell Line 1

description: DENR KO1 80S

value: DENR KO

value: Hela

value: Nextflex small RNA

value: Ribo Zero Gold Illumina

value: CTGATC


title: brain of unmated reproductive ant departing on her mating flight (19GB)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

value: Single Brain

value: Polygyne


title: brain of unmated reproductive ant departing on her mating flight (209AB)

value: SB/SB

value: Monogyne


title: 32dpi untreated rep5


title: 80S Ribosome Footprints from WT Hela Cells

description: WT 80S

value: WT

value: CGTGAT


title: 32dpi untreated rep4


title: ovaries of unmated reproductive ant departing on her mating flight (19DO)

value: Single Ovary

value: reproductively mature


title: 32dpi untreated rep3

value: himar1 transposon library


title: PF_Input_H3K64me3

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

country: India

institute: IITM

description: Input DNA

data_processing:
FastQC for quality analysis and Cutadapt for adaptor trimming.
ChIP seq reads were aligned to PlasmoDB-37 using Bowtie2-build.
Peak calling was performed using MACS2 tool.
ChIP-seq signals were background subtracted using MACS2 bdgcmp tool.
Integrative Genomics Viewer (IGV) was used for visualization. Graphpad Prim (version 8) was used for generating the bar graph representing the number of genes bound by H3K64me3. R script (http://r-project.org/) was used to visualize the H3K64me3 peaks chromosome-wide at three different stages of P. falciparum.
Genome_build: PlasmoDB-37
Supplementary_files_format_and_content: *_peaks.xls: Peak text files.

organism: Plasmodium falciparum 3D7

source_name: Plasmodium falciparum culture

growth_protocol: Asexual blood stages of P. falciparum 3D7 strain was cultured at 5% hematocrit using advanced RPMI 1640 supplemented with 2 mM L- glutamine, 0.6% Albumax II and 10% human O+ Serum.

extract_protocol:
The parasite was synchronized by 5% sorbitol treatment and parasites were released from infected RBCs by lysis with 0.15% saponin. Crosslinked chromatin was prepared by adding 1% formaldehyde to the culture for 5 min followed by the addition of glycine to 0.125 M final concentration for 5 minutes to stop the cross-linking. Chromatin was sheared by sonication in a Bioruptor UCD-200 (Diagenode) for 10 min at 30 s intervals, power setting high, to a size of 300–800 bp. ChIP was performed by adding 1.8 µg of H3K64me3 antibodies to ChIP buffer (100 mM NaCl, 20 mM Tris pH-7.5, 6 mM EDTA, 1% Triton X- 100). The three respective RBC stage samples of wild-type 3D7 were added to the mixture and incubated at 4 °C for overnight, followed by the addition of 15 μl protein A Dynabeads and further incubated for 4 h. After washing with buffers containing 180 mM NaCl, immuno-precipitated DNA was eluted and purified using PCR purification columns.
Libraries for ChIP sequencing were prepared using NEB Next Ultra II DNA Library preparation kit. In brief, ChIP DNA and the Input DNA are subjected to various enzymatic steps for repair the ends and tailing with dA-tail followed by ligation of adapter sequences. These adapter ligated fragments are then size selected using SPRI beads. Next, the size selected fragments are indexed during limited cycle PCR to generate final libraries for sequencing. The resulting libraries are quantified before getting sequenced on Illumina HiSeq 4000 system to generate 2X50 bp sequence reads.

treatment_protocol: Untreated

value: Wild type

tag: Stage

value: Trophozoite

tag: treatment

value: Untreated

tag: chip antibody


title: 32dpi untreated rep2

value: 8-12 week old female BALB/cJ mice

value: 32 days post infection


title: PF_Schizont_H3K64me3

description: ChIP DNA

tag: genotype

value: Schizont


title: brain of unmated reproductive ant departing on her mating flight (19DB)

tag: tissue


title: 21dpi untreated rep6

value: 21 days post infection


title: 21dpi untreated rep5


title: ovaries of unmated reproductive ant departing on her mating flight (19AO)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

tag: age

value: SB/Sb


title: 32dpi untreated rep1


title: 21dpi untreated rep4


title: 21dpi untreated rep2


title: brain of unmated reproductive ant departing on her mating flight (19AB)

value: Single Brain

value: Polygyne


title: ovaries of unmated reproductive ant departing on her mating flight (16GO)

value: Sb/Sb


title: 14dpi pretreatment  rep3

value: 14 days post infection


title: 21dpi untreated rep3


title: brain of unmated reproductive ant departing on her mating flight (16GB)


title: PF_Ring_H3K64me3

description: ChIP DNA

value: Ring


title: L108A_3

city: Pozuelo de Alarcón

first: joaquín

last: Giner Lamia

state: Madrid

address: Campus de Montegancedo

department: Biotecnologia

country: Spain

institute: CBGP-Universidad Politecnica de Madrid

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence,  then mapped to S. enterica serovar Typhimurium SL1344 (NC_016810.1) whole genome using bowtie v2.2.4 with default parameters for paired-end reads.
SAM files were filtered by average insert size (< 1000) and  transformed to BAM files using Samtools v1.2
Raw counts were calculated using htseq-count from Htseq framework v0.11.0 with default mode (union)
Genome_build: S. enterica serovar Typhimurium SL1344 (NC_016810.1)
Supplementary_files_format_and_content: raw counts of sequencing reads

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant L108A

growth_protocol: cells were grown to the exponential phase (~0.25) OD 600nm

extract_protocol:
Total RNA was obtained from 10 ml cultures of S. Typhimurium expressing RcsB WT or mutant variants in exponential phase (OD600 ~ 0.25) using the TRIzol. The samples for the strains expressing each RcsB variant were prepared from three independent biological replicates. Total RNA was further purified by treatment with TURBO DNA-free kit (#AM1907, Invitrogen). Quality of RNA was checked by Bioanalyzer with final yields in the range of 25-40 µg per sample (concentration of 500-800 ng/µl)
Purified RNA was then treated with Ribo-Zero™ rRNA Removal Reagent and magnetic core kit (Epicentre). rRNA-free RNA was resuspended in ethanol and subsequently used to prepare libraries using the ScriptSeq™ v2 RNA-Seq Library preparation kit (Epicentre and Illumina Company). The purifications were performed following manufacturer instructions and involving usage of MagSi-NGSPREP Plus (Magtivio). Size of the fragments composing the different libraries was monitored by capillary electrophoresis in a QIAxcel Advanced System (Qiagen) and quantification of the cDNA was made in a QuantiFluor dsDNA system (Promega)

treatment_protocol: Cells were collected after being growing in LB and reach exponential phase

tag: strain

value: {delta}rcsB L108A RcsB


title: H77A_3

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant H77A

value: {delta}rcsB  H77A RcsB


title: 14dpi pretreatment  rep2

value: himar1 transposon library


title: 14dpi pretreatment  rep1


title: ovaries of unmated reproductive ant departing on her mating flight (16DO)

value: Single Ovary

value: reproductively mature

value: SB/SB


title: 14dpi pretreatment  rep7

value: 8-12 week old female BALB/cJ mice


title: M88A_3

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant M88A

value: {delta}rcsB  M88A RcsB


title: 14dpi pretreatment  rep6


title: D56A_3

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant D56A

value: {delta}rcsB  D56A RcsB


title: in vitro input rep7

value: 0 days post infection


title: 14dpi pretreatment  rep4


title: brain of unmated reproductive ant departing on her mating flight (16DB)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.


title: PF_Trophozoite_H3K64me3

description: ChIP DNA

value: Wild type

value: Trophozoite

value: Untreated


title: H12A_3

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant H12A

value: {delta}rcsB  H12A RcsB


title: ovaries of unmated reproductive ant departing on her mating flight (16CO)

value: SB/Sb

value: Polygyne


title: in vitro input rep6


title: in vitro input rep5


title: 21dpi untreated rep1

value: 21 days post infection


title: Empty_plasmid_3

source_name: S. Typhimurium null ΔrcsB mutant

value: {delta}rcsB


title: brain of unmated reproductive ant departing on her mating flight (16CB)

value: Single Brain


title: WT_3

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB WT

value: {delta}rcsB RcsB WT


title: S207C_3

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant S207C

value: {delta}rcsB  S207A RcsB


title: in vitro input rep3

value: himar1 transposon library


title: in vitro input rep2

value: 8-12 week old female BALB/cJ mice


title: in vitro input rep1


title: brain of unmated reproductive ant departing on her mating flight (15GB)

value: reproductively mature

value: Sb/Sb


title: H77A_2

value: {delta}rcsB  H77A RcsB


title: L108A_2

value: {delta}rcsB L108A RcsB


title: 14dpi pretreatment  rep5

value: 14 days post infection


title: brain of unmated reproductive ant departing on her mating flight (15AB)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.


title: ovaries of unmated reproductive ant departing on her mating flight (15GO)

value: Single Ovary


title: Midbody

city: Boston

first: Michael

middle: Demian

last: Blower

address: 185 Cambridge St CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description: cells were synchronized by incubation in 2mM thymidine for 16 hours. Cells were relased from thymidine block for 5 hours then incubated with 0.1ug/ml nocodazole for 4-5 hours. Mitotic cells were collected by shake-off and incubated in fresh media for 65 minutes. Midbodies were purified as described in Skop et al. Science 2004.

data_processing:
basecalls were performed using Illumina Hi-Seq control software
reads were collapsed into unique reads using a custom Perl script (Schwarz and Blower. JCB. 2014)
reads were aligned to CHO Refseq sequences
reads were counted using a custom Perl script (Schwarz and Blower. JCB 2014)
Genome_build: CHO Refseq mRNAs 2013.
Supplementary_files_format_and_content: processed files were generated by merging counts from each library. Processed file contains read counts and RPKM values.

organism: Cricetulus griseus

source_name: CHO cells

extract_protocol:
Qiagen Rneasy. Exiqon dT LNA dT selection kit.
Illumina TruSeq RNA Sample Preparation v2 Kit

value: CHO

tag: cell cycle phase

value: Midbody

tag: rna source

value: microtubule-associated RNA


title: ovaries of unmated reproductive ant departing on her mating flight (15AO)

value: SB/Sb

value: Polygyne


title: in vitro input rep4

value: 0 days post infection


title: M88A_2

value: {delta}rcsB  M88A RcsB


title: Mitosis

description: cells were synchronized by incubation in 2mM thymidine for 16 hours. Cells were relased from thymidine block for 5 hours then incubated with 0.1ug/ml nocodazole for 4-5 hours. Mitotic cells were collected by shake-off and incubated in fresh media for 15 minutes. Microtubules were purified as described in Skop et al. Science 2004.

value: Mitosis


title: ovaries of unmated reproductive ant departing on her mating flight (107GO)


title: ovaries of unmated reproductive ant departing on her mating flight (15DO)

value: SB/SB


title: Interphase

description: cells were synchronized by incubation with 2 mM thymidine for 16h and microtubules were purified as described in Skop et al. Science. 2004.

value: Interphase


title: ovaries of unmated reproductive ant departing on her mating flight (107EO)

value: reproductively mature


title: brain of unmated reproductive ant departing on her mating flight (15DB)

value: Single Brain


title: brain of unmated reproductive ant departing on her mating flight (107EB)


title: WT_2

value: {delta}rcsB RcsB WT


title: brain of unmated reproductive ant departing on her mating flight (107GB)

value: Sb/Sb


title: Melanocytes Control

city: Brussels

first: Grégoire

last: de Streel

state: Woluwe-Saint-Lambert

address: 75 Avenue Hippocrate

department: de Duve Institute

institute: UCLOUVAIN

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 10.

label: Biotin

source_name: Melanocytes Control

label_protocol: Biotin

growth_protocol: Primary keratinocytes were derived from the detached epidermis layer from a healthy skin sample and were cultured in selective CnT-02 growth medium (Celltech). Dermal fibroblasts were obtained by mincing the dermal part of the skin sample and growing the cells in the same medium as the melanoma cell lines. Primary melanocytes and dermal endothelial cells (Promocell) were amplified in Medium 254 + HMGS2 (ThermoFischer Scientific) and Endothelial Cell Growth Medium (Promocell), respectively

extract_protocol: RNA was extracted using GITC and CsCl gradient method

treatment_protocol: The cultured cells were treated with either IFNγ (100 U/mL), IL-1b (10 ng/ml), TGF-b1 (5 ng/ml), TNFa (10 ng/ml) or no cytokine for 24 hours.

tag: origin

value: Cell line

tag: cell type

value: Melanocytes

value: control


title: Melanocytes + TNFa

source_name: Melanocytes + TNFa

value: TNFa


title: Empty_plasmid_2

value: {delta}rcsB


title: H12A_2

value: {delta}rcsB  H12A RcsB


title: D56A_2

value: {delta}rcsB  D56A RcsB


title: Subject 5 Post-vitC_SN22AF

city: mueang khon kaen

first: Laongthip

last: Ruknarong

state: Khon Kaen

address: 123 moo 16 mittraphap rd, nai mueang

department: Blood transfusion and clinical immunology

country: Thailand

institute: Faculty of Associated Medical Sciences

description: Total RNA includes miRNAs were extracted from archived plasma sample

hyb_protocol: miRNAs were hybridized to the color-coded probes at 65 °C at least 12 hours.

scan_protocol: Each sample was loaded into each well within one cartridge and was run at the same time.  The data were collected by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens at 196 fields of view. Images were processed internally, and each lane produces one RCC (Reporter Code Count).

data_processing: We analyzed daya by using nSolver Analysis Software v. 4.0. Background threshold of 100 counts was set to eliminate all targets with low expression. Six positive controls and cel-miR-254 were used for data normalization. The count of each miRNA expression was transformed to Log2 data.

source_name: Plasma from EDTA blood

label_protocol: Total RNA was ligated to a specific miR-Tag and purification before hybridization step

extract_protocol: Total RNA was extracted from 200 ul of plasma using the miRNeasy Serum/Plasma kit (Qiagen, Germany) according to the manufacturer’s instruction. Spike-in controls, cel-miR-39 and cel-miR-254, were added in this step.

treatment_protocol: Blood samples were collect from the participants before and after receiving 1,000 mg/day vitamin C for six weeks. The subjects who had increased plasma vitamin C levels, increased phagocytosis and oxidative burst, and reduced oxidative stress at the post-vitamin C supplementation timepoint compared to pre-supplementation were collected to investigate miRNA expression

tag: disease

value: poorly controlled type 2 diabetes mellitus

tag: gender

value: Female

tag: vitamin c supplement

value: 1,000 mg/day vitamin C for six weeks


title: Melanocytes + TGFb

source_name: Melanocytes + TGFb

value: TGFb


title: Melanocytes + IFNg

source_name: Melanocytes + IFNg

value: IFNg


title: Melanocytes + IL1b

source_name: Melanocytes + IL1b


title: Keratinocytes + IL1b

source_name: Keratinocytes + IL1b

value: Primary cell line

value: Keratinocytes


title: Keratinocytes + TNFa

source_name: Keratinocytes + TNFa


title: Keratinocytes Control

source_name: Keratinocytes Control


title: Keratinocytes + IFNg

source_name: Keratinocytes + IFNg


title: S207C_2

value: {delta}rcsB  S207A RcsB


title: L108A_1

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant L108A

value: {delta}rcsB L108A RcsB


title: Keratinocytes + TGFb

source_name: Keratinocytes + TGFb


title: ovaries of unmated reproductive ant departing on her mating flight (107AO)

tag: echotype

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

value: Single Ovary

value: reproductively mature

value: SB/Sb

tag: social form

value: Polygyne


title: brain of unmated reproductive ant departing on her mating flight (107AB)

value: Single Brain


title: Subject 4 Post-vitC_SN20AF


title: H77A_1

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant H77A

value: {delta}rcsB  H77A RcsB


title: Subject 5 Pre-vitC_SN22BF


title: ovaries of unmated reproductive ant departing on her mating flight (104GO)

value: Sb/Sb


title: Subject 4 Pre-vitC_SN20BF

value: poorly controlled type 2 diabetes mellitus


title: M88A_1

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant M88A

value: {delta}rcsB  M88A RcsB


title: Endothelial Cells + IL1b

source_name: Endothelial Cells + IL1b

value: Endothelial


title: Endothelial Cells + TGFb

source_name: Endothelial Cells + TGFb

value: TGFb


title: brain of unmated reproductive ant departing on her mating flight (104GB)


title: D56A_1

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant D56A

value: {delta}rcsB  D56A RcsB


title: Endothelial Cells + IFNg

source_name: Endothelial Cells + IFNg

value: Primary cell line

value: IFNg


title: Subject 3 Post-vitC_SN18AF

value: Male

value: 1,000 mg/day vitamin C for six weeks


title: H12A_1

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant H12A

value: {delta}rcsB  H12A RcsB


title: ovaries of unmated reproductive ant departing on her mating flight (104DO)

value: Alate (winged) gynes were aspirated from the tops of mounds and frozen on dry ice in the field in and around Athens-Clarke Co. on days of mating flights in April 2015.

value: Single Ovary

value: SB/SB


title: Endothelial Cells + TNFa

source_name: Endothelial Cells + TNFa

value: TNFa


title: ovaries of unmated reproductive ant departing on her mating flight (104AO)

value: reproductively mature

value: SB/Sb

value: Polygyne


title: brain of unmated reproductive ant departing on her mating flight (104DB)

value: Single Brain


title: Subject 3 Pre-vitC_SN18BF

source_name: Plasma from EDTA blood

value: poorly controlled type 2 diabetes mellitus


title: Empty_plasmid_1

source_name: S. Typhimurium null ΔrcsB mutant

value: {delta}rcsB


title: Subject 2 Pre-vitC_SN16BF

value: Female


title: Subject 2 Post-vitC_SN16AF


title: Subject 1 Post-vitC_SN15AF


title: brain of unmated reproductive ant departing on her mating flight (104AB)


title: Subject 1 Pre-vitC_SN15BF


title: Fibroblast + TGFb

source_name: Fibroblast + TGFb

value: Fibroblast

value: TGFb


title: S207C_1

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB variant S207C

value: {delta}rcsB  S207A RcsB


title: Fibroblast + IL1b

source_name: Fibroblast + IL1b

value: Primary cell line


title: Endothelial Cells Control

source_name: Endothelial Cells Control

value: Endothelial

value: control


title: jc5583_FOXA1_3487

status: Public on Jul 17 2020

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

description: jc5583_3487_foxa1-X-jc5583_3487_foxa1_input_peaks.narrowPeak.gz

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.2016 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

source_name: Primary breast tumour - ER+/pSTAT3+

growth_protocol: MCF7 cell were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin. T47D cells were grown in RPMI supplemented with 10% FBS, 2mM L-glutamine and 50 U/ml penicillin and 50 ug/ml streptomycin.

extract_protocol:
Cells were crosslinked with 2mM DSG for 20 min followed by crosslinking in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication for 15 minutes (Bioruptor plus, Diagenode). Chromatin was immunoprecipitated over night using specific antibodies. Beads were washed six times in RIPA buffer and eluted from beads using SDS buffer. After RNase and proteinase K treatment, DNA was purified by phenol/chloroform extraction.
Libraries were prepared using the Thruplex kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Cells were treated with human recombinant IL6 (206-IL-200, R&D systems) for 30 min.

value: Breast cancer


title: jc5573_ER_3487

description: jc5573_3487_er-X-jc5573_3487_er_input_peaks.narrowPeak.gz

value: ab3575 (abcam)/06-935 (Millipore)


title: jc5596_Input_3840


title: jc5555_pSTAT3_3487

description: jc5555_3487_pstat3-X-jc5555_3487_pstat3_input_peaks.narrowPeak.gz

value: 9145 (Cell signaling)


title: jc5572_ER_3840

description: jc5572_3840_er-X-jc5572_3840_er_input_peaks.narrowPeak.gz


title: jc5597_Input_3487


title: Fibroblast + TNFa

source_name: Fibroblast + TNFa

value: TNFa


title: Fibroblast + IFNg

source_name: Fibroblast + IFNg

value: IFNg


title: jc5554_pSTAT3_3840

description: jc5554_3840_pstat3-X-jc5554_3840_pstat3_input_peaks.narrowPeak.gz


title: WT_1

source_name: S. Typhimurium null ΔrcsB mutant expressing RcsB WT

value: {delta}rcsB RcsB WT


title: JC5090_Input_siFOXA1_IL6

tag: passages


title: JC5089_Input_siCtl_PBS


title: JC5092_Input_siFOXA1_PBS


title: JC5087_Input_siCtl_IL6


title: JC5085_Input_siCtl_PBS


title: JC5088_Input_siFOXA1_PBS


title: JC5086_Input_siFOXA1_IL6


title: JC5083_H3K27ac_siFOXA1_PBS

description: t47d_h3k27ac_sifoxa1_pbs-X-t47d_h3k27ac_sifoxa1_pbs_input_peaks.broadPeak.gz

value: ab4729 (Abcam)


title: JC5081_H3K27ac_siCtl_PBS

description: t47d_h3k27ac_sictl_pbs-X-t47d_h3k27ac_sictl_pbs_input_peaks.broadPeak.gz


title: JC5084_H3K27ac_siFOXA1_IL6

description: t47d_h3k27ac_sifoxa1_il6-X-t47d_h3k27ac_sifoxa1_il6_input_peaks.broadPeak.gz


title: JC5079_H3K27ac_siFOXA1_PBS


title: JC5080_H3K27ac_siFOXA1_IL6


title: JC5078_H3K27ac_siCtl_IL6

description: t47d_h3k27ac_sictl_il6-X-t47d_h3k27ac_sictl_il6_input_peaks.broadPeak.gz


title: Fibroblast Control

source_name: Fibroblast Control


title: JC5074_H3K27ac_siCtl_IL6


title: JC5091_Input_siCtl_IL6


title: JC5076_H3K27ac_siFOXA1_IL6


title: JC5075_H3K27ac_siFOXA1_PBS


title: JC5077_H3K27ac_siCtl_PBS


title: JC5066_pSTAT3_siCtl_IL6

description: t47d_pstat3_sictl_il6-X-t47d_pstat3_sictl_il6_input_peaks.narrowPeak.gz


title: JC5073_H3K27ac_siCtl_PBS


title: JC5069_H3K27ac_siCtl_PBS


title: JC5071_H3K27ac_siFOXA1_PBS


title: JC5067_pSTAT3_siFOXA1_PBS

description: t47d_pstat3_sifoxa1_pbs-X-t47d_pstat3_sifoxa1_pbs_input_peaks.narrowPeak.gz


title: JC5063_pSTAT3_siFOXA1_PBS


title: JC5068_pSTAT3_siFOXA1_IL6

description: t47d_pstat3_sifoxa1_il6-X-t47d_pstat3_sifoxa1_il6_input_peaks.narrowPeak.gz


title: JC5061_pSTAT3_siCtl_PBS

description: t47d_pstat3_sictl_pbs-X-t47d_pstat3_sictl_pbs_input_peaks.narrowPeak.gz


title: JC5072_H3K27ac_siFOXA1_IL6


title: JC5060_pSTAT3_siFOXA1_IL6


title: JC5064_pSTAT3_siFOXA1_IL6


title: JC5065_pSTAT3_siCtl_PBS


title: JC5062_pSTAT3_siCtl_IL6


title: JC5059_pSTAT3_siFOXA1_PBS


title: JC5058_pSTAT3_siCtl_IL6


title: JC5057_pSTAT3_siCtl_PBS


title: JC5082_H3K27ac_siCtl_IL6


title: JC5054_pSTAT3_siCtl_IL6


title: JC5056_pSTAT3_siFOXA1_IL6


title: JC5053_pSTAT3_siCtl_PBS


title: jc5864_Input IL6 MCF7


title: JC5070_H3K27ac_siCtl_IL6


title: jc5860_Input IL6 MCF7


title: jc5862_Input IL6 MCF7


title: jc5857_Input Veh MCF7


title: jc5859_Input Veh MCF7


title: jc5858_Input IL6 MCF7


title: jc5852_ER IL6 MCF7

description: mcf7_er_il6-X-mcf7_er_il6_input_peaks.narrowPeak.gz


title: jc5853_ER Veh MCF7

description: mcf7_er_pbs-X-mcf7_er_pbs_input_peaks.narrowPeak.gz


title: jc5854_ER IL6 MCF7


title: jc5855_ER Veh MCF7


title: jc5849_ER Veh MCF7


title: jc5851_ER Veh MCF7


title: jc5846_STAT3 IL6 MCF7

description: mcf7_stat3_il6-X-mcf7_stat3_il6_input_peaks.narrowPeak.gz

value: sc-482 (Santa Cruz)


title: jc5844_STAT3 IL6 MCF7


title: jc5842_STAT3 IL6 MCF7


title: jc5841_STAT3 Veh MCF7

description: mcf7_stat3_pbs-X-mcf7_stat3_pbs_input_peaks.narrowPeak.gz


title: jc5848_STAT3 IL6 MCF7


title: jc5840_pSTAT3 IL6 MCF7

description: mcf7_pstat3_il6-X-mcf7_pstat3_il6_input_peaks.narrowPeak.gz


title: jc5850_ER IL6 MCF7


title: jc5839_pSTAT3 Veh MCF7

description: mcf7_pstat3_pbs-X-mcf7_pstat3_pbs_input_peaks.narrowPeak.gz


title: jc5847_STAT3 Veh MCF7


title: jc5838_pSTAT3 IL6 MCF7


title: jc5837_pSTAT3 Veh MCF7


title: JC5055_pSTAT3_siFOXA1_PBS


title: jc5861_Input Veh MCF7


title: jc5835_pSTAT3 Veh MCF7


title: jc5836_pSTAT3 IL6 MCF7


title: jc5845_STAT3 Veh MCF7


title: jc5833_pSTAT3 Veh MCF7


title: jc5834_pSTAT3 IL6 MCF7


title: JC4724_Input IL6 MCF7


title: jc5863_Input Veh MCF7


title: jc5856_ER IL6 MCF7


title: JC4697_FOXA1 IL6 MCF7

description: mcf7_foxa1_il6-X-mcf7_foxa1_il6_input_peaks.narrowPeak.gz


title: jc5843_STAT3 Veh MCF7


title: JC4695_FOXA1 IL6 MCF7


title: JC4692_FOXA1 Veh MCF7

description: mcf7_foxa1_veh-X-mcf7_foxa1_veh_input_peaks.narrowPeak.gz


title: JC4693_FOXA1 IL6 MCF7


title: JC4691_FOXA1 IL6 MCF7


title: JC4690_FOXA1 Veh MCF7


title: JC4784_Input IL6 T47D


title: JC4783_Input Veh T47D


title: JC4782_Input Veh T47D


title: JC4757_pSTAT3 IL6 T47D

description:
Y705 phosphorylation
t47d_pstat3_il6-X-t47d_pstat3_il6_input_peaks.narrowPeak.gz


title: JC4755_pSTAT3 IL6 T47D


title: JC4754_pSTAT3 veh T47D

description:
Y705 phosphorylation
t47d_pstat3_veh-X-t47d_pstat3_veh_input_peaks.narrowPeak.gz


title: JC4756_pSTAT3 veh T47D


title: JC4753_pSTAT3 IL6 T47D


title: JC4752_pSTAT3 veh T47D


title: JC4751_pSTAT3 IL6 T47D


title: JC4725_Input IL6 MCF7


title: JC4750_pSTAT3 veh T47D


title: JC4749_FOXA1 IL6 T47D

description: t47d_foxa1_il6-X-t47d_foxa1_il6_input_peaks.narrowPeak.gz

value: ab5089 (Abcam)


title: JC4723_Input Veh MCF7


title: JC4748_FOXA1 veh T47D

description: t47d_foxa1_veh-X-t47d_foxa1_veh_input_peaks.narrowPeak.gz


title: JC4747_FOXA1 IL6 T47D


title: JC4722_Input Veh MCF7


title: JC4745_FOXA1 IL6 T47D


title: JC4746_FOXA1 veh T47D


title: JC4696_FOXA1 Veh MCF7


title: JC4744_FOXA1 veh T47D


title: JC4694_FOXA1 Veh MCF7


title: JC4743_FOXA1 IL6 T47D


title: JC4742_FOXA1 veh T47D


title: JC4741_STAT3 IL6 T47D

description: t47d_stat3_il6-X-t47d_stat3_il6_input_peaks.narrowPeak.gz


title: JC4785_Input IL6 T47D


title: JC4740_STAT3 veh T47D

description: t47d_stat3_veh-X-t47d_stat3_veh_input_peaks.narrowPeak.gz


title: JC4736_STAT3 veh T47D


title: JC4737_STAT3 IL6 T47D


title: JC4734_STAT3 veh T47D


title: JC4739_STAT3 IL6 T47D


title: JC4735_STAT3 IL6 T47D


title: JC4732_ER veh T47D

description: t47d_er_veh-X-t47d_er_veh_input_peaks.narrowPeak.gz


title: JC4730_ER veh T47D


title: JC4729_ER IL6 T47D

description: t47d_er_il6-X-t47d_er_il6_input_peaks.narrowPeak.gz


title: JC4727_ER IL6 T47D


title: JC5184_siFOXA1_PBS_4

description:
48h knock down, 1h treatment
t47d_siRNA_RPKM.tsv.gz

data_processing:
STAR, version 2.6.1a, was used to align reads against hg38 reference genome.
The read counting was performed using intrinsic function of STAR.
For normalized measurement of mRNA expression the read counts were converted into RPKM values.
Differential gene expression analysis was performed using DESeq2 workflow.
Genome_build: GRCh38
Supplementary_files_format_and_content: RPKM

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.
Libraries were prepared using the TruSeq mRNA Stranded Sample prep kit from Illumina.

treatment_protocol: Cells were treated with human recombinant IL6 (206-IL-200, R&D systems) for 1 hour. For the siRNA-mediated knock down experiments, T47D cells were transfected with ON-TARGETplus SMARTPools (Dharmacon) targeting STAT3, FOXA1, or ER. Non-targeting pool was used as a control. Media was changed 24 hours after transfection, and cells were treated with IL6 for 1 hour 48 hours after transfection.

value: Breast cancer cell line

tag: replicate


title: JC5185_siFOXA1_IL6_4


title: JC4728_ER veh T47D


title: JC5183_siER_IL6_4


title: JC5182_siER_PBS_4


title: JC5181_siSTAT3_IL6_4


title: JC5180_siSTAT3_PBS_4


title: JC5177_siFOXA1_IL6_3


title: JC5178_siCtl_PBS_4


title: JC4726_ER veh T47D


title: JC5176_siFOXA1_PBS_3


title: JC5179_siCtl_IL6_4


title: JC4738_STAT3 veh T47D


title: JC5172_siSTAT3_PBS_3


title: JC4733_ER IL6 T47D


title: JC5175_siER_IL6_3


title: JC5174_siER_PBS_3


title: JC5173_siSTAT3_IL6_3


title: JC4731_ER IL6 T47D


title: JC5169_siFOXA1_IL6_2


title: JC5167_siER_IL6_2


title: JC5170_siCtl_PBS_3


title: JC5171_siCtl_IL6_3


title: JC5165_siSTAT3_IL6_2


title: JC5168_siFOXA1_PBS_2


title: JC5164_siSTAT3_PBS_2


title: JC5166_siER_PBS_2


title: JC5163_siCtl_IL6_2


title: JC5161_siFOXA1_IL6_1


title: JC5162_siCtl_PBS_2


title: JC5159_siER_IL6_1


title: JC5158_siER_PBS_1


title: JC5157_siSTAT3_IL6_1


title: JC5156_siSTAT3_PBS_1


title: JC5155_siCtl_IL6_1


title: JC4387_KO2_EtOH_IL6_4

description:
EtOH: 3 hours -> IL6: 1hour
mcf7_clonal_RPKM.tsv.gz

source_name: P4B5_MCF7 STAT3 -/- clonal cell line


title: JC4385_KO1_EtOH_IL6_4

source_name: P3D9_MCF7 STAT3 -/- clonal cell line


title: JC5154_siCtl_PBS_1


title: JC4386_KO2_EtOH_PBS_4

description:
EtOH: 3 hours -> PBS: 1hour
mcf7_clonal_RPKM.tsv.gz


title: JC4384_KO1_EtOH_PBS_4


title: JC4383_WT_ICI_IL6_4

description:
ICI: 3 hours -> IL6: 1hour
mcf7_clonal_RPKM.tsv.gz

source_name: WT_MCF7 clonal cell line


title: JC4382_WT_ICI_PBS_4

description:
ICI: 3 hours -> PBS: 1hour
mcf7_clonal_RPKM.tsv.gz


title: JC4377_KO1_EtOH_IL6_3


title: JC4379_KO2_EtOH_IL6_3


title: JC4380_WT_EtOH_PBS_4


title: JC4376_KO1_EtOH_PBS_3


title: JC4381_WT_EtOH_IL6_4


title: JC4373_WT_EtOH_IL6_3


title: JC4374_WT_ICI_PBS_3


title: JC4370_KO2_EtOH_PBS_2


title: JC4378_KO2_EtOH_PBS_3


title: JC4371_KO2_EtOH_IL6_2


title: JC5160_siFOXA1_PBS_1


title: JC4372_WT_EtOH_PBS_3


title: JC4368_KO1_EtOH_PBS_2


title: JC4366_WT_ICI_PBS_2


title: JC4365_WT_EtOH_IL6_2


title: JC4367_WT_ICI_IL6_2


title: JC4364_WT_EtOH_PBS_2


title: JC4363_KO2_EtOH_IL6_1


title: JC4362_KO2_EtOH_PBS_1


title: JC4360_KO1_EtOH_PBS_1


title: JC4361_KO1_EtOH_IL6_1


title: JC4359_WT_ICI_IL6_1


title: JC4356_WT_EtOH_PBS_1


title: JC4358_WT_ICI_PBS_1


title: jc4228_IL6_6

description:
IL6 treatment (1 hour)
t47d_il6_RPKM.tsv.gz


title: JC4357_WT_EtOH_IL6_1


title: jc4227_veh_6

description:
Vehicle treatment
t47d_il6_RPKM.tsv.gz


title: JC4375_WT_ICI_IL6_3


title: jc4224_IL6_5


title: jc4215_veh_3

description:
Vehicle treatment
t47d_il6_RPKM.tsv.gz


title: jc4212_IL6_2


title: jc4220_IL6_4


title: jc4219_veh_4

description:
Vehicle treatment
t47d_il6_RPKM.tsv.gz


title: jc4211_veh_2

description:
Vehicle treatment
t47d_il6_RPKM.tsv.gz


title: jc4216_IL6_3


title: JC4369_KO1_EtOH_IL6_2


title: jc3264_IL6_4

description:
IL6 treatment (1 hour)
mcf7_il6_RPKM.tsv.gz


title: jc4208_IL6_1


title: jc4207_veh_1

description:
Vehicle treatment
t47d_il6_RPKM.tsv.gz


title: jc3258_IL6_2


title: jc3260_NT_3

description:
No treatment
mcf7_il6_RPKM.tsv.gz


title: jc3257_NT_2

description:
No treatment
mcf7_il6_RPKM.tsv.gz


title: jc3261_IL6_3


title: jc3255_IL6_1


title: jc4223_veh_5

description:
Vehicle treatment
t47d_il6_RPKM.tsv.gz


title: jc3254_NT_1

description:
No treatment
mcf7_il6_RPKM.tsv.gz


title: jc3263_NT_4

description:
No treatment
mcf7_il6_RPKM.tsv.gz


title: Synchronized RNA-seq_CrMTA1_time_4

city: BEIJING

first: Haili

last: Qian

address: 17 South Panjiayuan Lane, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with default parameters.
Transcript FPKM were calculated using Stringtie v1.3.4 with default parameters.
Genome_build: GRCH38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: colon

growth_protocol: HCT116 were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (HyClone) at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cell synchronization at the G1/S phase, 2 mM thymidine was used.

tag: time point

tag: cell line

value: colon

tag: morphology

value: epithelial

value: colorectal carcinoma

tag: genotype/variation


title: Synchronized RNA-seq_CrMTA1_time_7

tag: tissue


title: Synchronized RNA-seq_CrMTA1_time_5


title: Synchronized RNA-seq_CrMTA1_time_8


title: Synchronized RNA-seq_CrMTA1_time_3


title: Synchronized RNA-seq_CrMTA1_time_2


title: JD130_6_Q50_5

first: Myriam

last: Heiman

state: Massachusetts

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

data_processing:
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome build: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.
snRNA-seq: Basecalls converted to FASTQ with Cellranger v3.1.
snRNA-seq: FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome_build: snRNA-seq: GRCm38/mm10
Supplementary_files_format_and_content: snRNA-seq: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome_build: TRAP: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TRAP: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.

source_name: Striatum

extract_protocol:
TRAP: Striata or cortex were homogenized with a glass/Teflon power-driven Potter-Elvehjem homogenizer in an ice-cold lysis buffer (150 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5mM dithiothreitol, 100 μg/mL cycloheximide, 20 U/µL SUPERaseIn RNase Inhibitor, 40 U/µL RNasin Plus Rnase Inhibitor, and EDTA-free protease inhibitors).  Following homogenization, samples were centrifuged at 2,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  NP-40 (final concentration 1%) and 1,2-Diheptanoyl-sn-glycero-3-phosphocholine (DHPC, final concentration 15 mM) were subsequently added and samples were incubated on ice for 5 min.  Samples were centrifuged at 13,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  Streptavidin Dynabeads (ThermoFisher Scientific, Waltham MA) coated with biotin-linked mouse anti-GFP antibodies were then added to this supernatant and the samples were incubated overnight at 4°C with end-over-end rotation.  Beads were collected on a magnetic rack and washed three times with wash buffer (350 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/mL cycloheximide, 1% NP-40).  RNA was subsequently purified using the Absolutely RNA Isolation Nanoprep kit (Agilent Technologies, Santa Clara CA).
TRAP: Libraries were constructed using the Ovation RNA-Seq System v2 kit.

value: Striatum

tag: genotype

tag: tissue id


title: JD130_6_Q20_5


title: JD130_6_Q50_8


title: JD130_6_Q50_3


title: JD130_6_Q50_7


title: JD130_6_Q20_9


title: JD130_6_Q50_1


title: JD130_6_Q50_2


title: JD130_6_Q50_10


title: JD130_6_Q50_6


title: JD130_6_Q20_7


title: JD130_6_Q50_4


title: JD130_6_Q20_6


title: PC3_72hr_control_1

city: Kamigyo-ku, Kyoto

first: Keiko

last: Taniguchi

state: Kyoto

address: Kawaramachi-Hirokoji

department: Drug Discovery Medicine

institute: Kyoto Prefectural University of Medicine

hyb_protocol: 100 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) 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 Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

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 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: PC3 prostate cancer cells, 72hr, control siRNA

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The prostate cancer PC3 cell line was purchased from RIKEN BRC (Tsukuba, Japan). The cells were cultured in DMEM supplemented with 10% FBS (HyClone, South Logan, UT) and 1% penicillin and streptomycin (Wako Pure Chemical Industries, Osaka, Japan) and maintained at 37 ºC in 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from the cells lysed with Trizol (Thermo Fisher Scientific, Waltham, MA) and purified with the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: The synthesized siRNAs were purchased from RNAi Co. LTD, Tokyo, or Gene Design Inc, Osaka, Japan. The siRNAs were transfected into cells using Lipofectamine RNAi MAX (Invitrogen, Waltham, MA) according to the manufacturer’s protocol. The siRNA sequences were as follow; non-targeting, 5’-GUACCGCACGUCAUUCGUAUC-3’; GGCT, 5’- UGACUAUACAGGAAAGGUCTT-3’; AMPK, 5’-UGCCUACCAUCUCAUAAUA-3’. All siRNAs were transfected at a concentration of 10 nM. For simultaneous knockdown experiments, 20 nM of the non-targeting siRNA was transfected as a control. At 72 hours post-transfection, cells were collected and total RNA was extracted.

tag: transfection

value: 72hr control siRNA


title: PC3_72hr_control_3


title: PC3_72hr_GGCTKD_1

source_name: PC3 prostate cancer cells, 72hr, GGCT siRNA

value: 72hr GGCT siRNA


title: PC3_72hr_GGCTKD_2


title: PC3_72hr_GGCTKD_3


title: PC3_72hr_control_2


title: Synchronized RNA-seq_CrMTA1_time_6


title: JD130_6_Q20_8


title: Synchronized RNA-seq_CrMTA1_time_1


title: Synchronized RNA-seq_Control_time_8

value: control


title: JD130_6_Q20_2


title: JD130_6_Q20_4


title: Synchronized RNA-seq_Control_time_6


title: Synchronized RNA-seq_Control_time_5


title: Synchronized RNA-seq_Control_time_4


title: JD130_6_Q20_1


title: Synchronized RNA-seq_Control_time_2


title: Synchronized RNA-seq_Control_time_1


title: JD130_6_Q175_7


title: JD130_6_Q175_6


title: Synchronized RNA-seq_Control_time_3


title: JD130_6_Q175_8


title: JD130_6_Q20_10


title: JD130_6_Q175_4


title: JD130_6_Q175_3


title: JD130_6_Q175_2


title: Synchronized RNA-seq_Control_time_7


title: JD130_6_Q20_3


title: JD130_6_Q175_1


title: Spt6_E

city: Copenhagen

first: Kristoffer

last: Vitting-Seerup

address: Ole maaloesvej 5

department: Department of Biology

country: Denmark

institute: University of Copenhangen, Denmark

data_processing:
Reads were trimmed with Trimmomatic
Mapped to the genome with TopHat
Quantified with FeatureCount using Gencode v19 ( https://www.gencodegenes.org/human/release_19.html )
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression count matrix, tap seperated

extract_protocol: Random primed cDNA library, Unstranded single end

value: Patient Derived Xenograft Glioblastoma Cell Line

tag: treatment

value: Treated with siSUPT6H

value: SUPT6H KD


title: Spt6_D

tag: cell type


title: JD130_6_Q170_9


title: Spt6_C


title: JD130_6_Q175_9


title: JD130_6_Q170_8


title: CTRL_E

value: Treated with scrambled siRNA

value: Ctrl


title: CTRL_D


title: JD130_6_Q175_5


title: JD130_6_Q170_6


title: NIH3T3_GGCTOE_3

hyb_protocol: 100 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent Technologies) 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 Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

source_name: NIH3T3 fibroblast cell line

growth_protocol: The mouse fibroblast NIH3T3 cell line was purchased from American Type Culture Collection (Rockville, MD). The cells were cultured in DMEM supplemented with 10% FBS (HyClone, South Logan, UT) and 1% penicillin and streptomycin (Wako Pure Chemical Industries, Osaka, Japan) and maintained at 37 ºC in 5% CO2 atmosphere.

treatment_protocol: Stably GGCT-expressing NIH3T3 cells were established via retroviral infection with pCX4bsr vector. NIH3T3 cells were transfected with GGCT expression retroviral vector or control vector.

value: GGCT expression retroviral vector


title: NIH3T3_control_1


title: JD130_6_Q170_4


title: JD130_6_Q170_7


title: NIH3T3_control_2


title: NIH3T3_GGCTOE_2


title: NIH3T3_GGCTOE_1


title: ChIP-seq-Input

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
(RNA-seq) FastQC 0.11.4
(RNA-seq) STAR 2.5.1b
(RNA-seq) Cufflinks 2.2.1
(ChIP-seq) EDD
(ATAC-seq) Cutadapt0.5
(ATAC-seq) Bowtie2.2.6
(ATAC-seq) Sambamba0.6.5
(ATAC-seq) Samtools1.2.0
(ATAC-seq) Deeptools2.0.0
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: (RNA-seq) tab-delimited text file (gene_exp) include gene expression and differential expression for each sample. (ChIP-seq) Bed and Bedgraphs for ChIP-seq.

source_name: H7 derived cardiomyocytes

growth_protocol: iPSC lines and hESCs were maintained in chemically defined medium Essential 8 (E8 medium) (Life Technologies) on Matrigel-coated (BD Bioscience, San Jose, CA) plates at 37°C with 5% (vol/vol) CO2.

extract_protocol:
(RNA-seq) iPSC-CMs were detached from cell culture plates and RNA was extracted using a microRNeasy kit (QIAGEN). (ChIP-seq) Lysates were clarified from sonicated nuclei and LMNA-DNA complexes were isolated with antibody. (ATAC-seq) The samples were extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218)
(RNA-seq) RNA libraries were prepared for sequencing using standard Illumina protocols. (ChIP-seq) ChIP-seq libraries were prepared for sequencing using The Ion Proton™ System protocols. (ATAC-seq) ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (illumina).

treatment_protocol: iPSCs and hESCs were grown to 90% confluence and subsequently differentiated into beating cardiomyocytes, using a small-molecule-based monolayer method described previously. Ten days after cardiac differentiation, iPSC-CM and hESC-CM monolayers were purified using RPMI-1640 without glucose (Life Technologies) with B27 supplement (Life Technologies). Non-glucose culture medium was changed every 2 days. After 5 days, iPSC-CMs were reseeded onto Matrigel-coated plates in a culture medium containing glucose.

tag: cell-type

value: ES-derived cardiomyocyte

tag: day post-differentiation

value: day 40

value: wt/wt


title: NIH3T3_control_3


title: JD130_6_Q170_5


title: CTRL_C


title: ChIP-seq-IgG

tag: antibody

value: mouse normal IgG (Santa Cruz Biotechnology, sc-2025)


title: JD130_6_Q170_3


title: ChIP-seq-LMNA-sc7292

value: LMNA A/C (Santa Cruz Biotechnology, sc-7292X)


title: JD130_6_Q170_2


title: ChIP-seq-LMNA-sc6215

value: LMNA A/C (Santa Cruz Biotechnology, sc-6215)


title: JD130_6_Q170_10


title: JD130_6_Q170_1


title: JD130_6_Q170_11


title: JD130_6_Q111_9


title: Resistant - CMB9-Poly

city: Melbourne

first: Anna

last: Trigos

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Polysomal RNA
processed data file: Resistant_poly.txt

data_processing:
Sequencing reads were aligned with Tophat2 and reads counts were obtained with htseq (Anders et al., 2015) using the mouse genome (Ensembl release 78) as reference. We used our in-house bioinformatics pipeline, seqliner (http://bioinformatics.petermac.org/seqliner/).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Eμ-Myc B-lymphoma cells

growth_protocol: Eμ-Myc B-lymphoma cells (MSCV Gfp) were cultured in Anne Kelso DMEM, supplemented with 10% heat-inactivated (h.i.) fetal bovine serum (FBS), 100 μM L-asparagine (Merck), penicillin/streptomycin/glutamine (Thermo Fisher Scientific) and 0.5% beta-mercaptoethanol.

extract_protocol:
The cytoplasmic lysate was layered on top of a linear 10-40% sucrose gradient, ultracentrifuged (36,000 rpm, 2¼ hours, 4 °C) and fractionated using the Foxy Jr Fraction Collector with constant monitoring of absorbance at 260 nm by an ISCO UA-6 Absorbance Detector (Teledyne). Cytoplasmic (input) RNAs and polysomal RNAs from pooled fractions corresponding to four or more ribosomes were isolated using a TRIzol®- based method and purified using the Qiagen RNeasy® Minikit according to manufacturer’s instructions, and analysed by RNAseq.
cDNA libraries were generated using a ribodepletion method (TruSeq Ribo Profile Mammalian Kit, Illumina) from 1 µg of RNA sample. Fragment sizes were evaluated using the DNA 1000 kit and 2100 bioanalyzer (Agilent Technologies). Libraries were subjected to single-end sequencing (SE50bp) (Hiseq2500, Illumina) to generate ~30 million reads per sample using standard protocols.

treatment_protocol:
Acute study: Eµ-Myc B-cell lymphoma (MSCV Gfp; clone #4242) cells were transplanted into C57BL/6 mice as we performed previously (Bywater et al., 2012; Devlin et al., 2016). Lymphoma-bearing mice were treated on Day 10 post-transplant for 2 hours with CX-5461 (35 mg/kg), everolimus (EV; 5 mg/kg), or both (CX-5461+EV; 35 mg/kg CX-5461 and 5 mg/kg EV).
Resistance study: Early-passage Eμ-Myc B- lymphoma cells were isolated from the mice transplanted with Eµ-Myc B-cell lymphoma (MSCV Gfp; clone #107) cells who had succumbed to disease relapse following treatment with vehicles, everolimus, CX-5461 or CX-5461+EV at the end of a survival experiment in Figure 2B in Devlin et al. (Devlin et al., 2016). Specifically, lymph nodes isolated at endpoint of the in vivo experiment were manually disrupted by pressing with the plunger of a 3 ml syringe and the cell suspension was passed through 40 µm cell filters to obtain single cell suspensions. These cells were then cultured in Anne Kelso DMEM supplemented with 20% h.i. FBS (Gibco), 100 μM L-asparagine (Merck), penicillin/streptomycin/glutamine (Thermo Fisher Scientific) and 0.5% beta-mercaptoethanol until exponential growing phase was obtained (2-3 passages).

value: MSCV Gfp; clone #107

value: Resistant to CX5461+EV


title: Resistant - CMB31-Poly


title: Resistant - EV26-Poly

value: Resistant to EV


title: Resistant - CMB8-Poly


title: JD130_6_Q111_8

value: Striatum


title: Resistant - EV12-Poly


title: JD130_6_Q111_7


title: Resistant - EV4-Poly


title: Resistant - CX39-Poly

value: Resistant to CX5461


title: JD130_6_Q111_6


title: JD130_6_Q111_5


title: JD130_6_Q111_3


title: JD130_6_Q111_2


title: JD130_6_Q111_1


title: Resistant - Ctrl33-Poly

value: drug-naive


title: Resistant - CX14-Poly


title: Resistant - Ctrl38-Poly


title: Resistant - CX20-Poly


title: Resistant - CMB9-Input

description:
Cytosolic RNA
processed data file: Resistant_input.txt


title: JD130_6_Q111_10


title: DW167_6_Q50_7


title: JD130_6_Q111_4


title: DW167_6_Q50_8


title: Resistant - EV26-Input


title: DW167_6_Q50_6


title: DW167_6_Q50_5


title: DW167_6_Q50_9


title: Resistant - CMB8-Input


title: DW167_6_Q50_4


title: Resistant - Ctrl6-Poly


title: Resistant - EV4-Input


title: Resistant - EV12-Input


title: Resistant - CX39-Input


title: Resistant - CX20-Input


title: DW167_6_Q50_2


title: Resistant - CMB31-Input


title: DW167_6_Q50_1


title: Resistant - CX14-Input


title: Resistant - Ctrl38-Input


title: DW167_6_Q50_10


title: Resistant - Ctrl33-Input


title: DW167_6_Q20_8


title: Acute - CMB-6-POLY

description:
Polysomal RNA
processed data file: Acute_poly.txt

value: MSCV Gfp; clone #4242

value: Acute treatment to CX5461+EV


title: Resistant - Ctrl6-Input


title: DW167_6_Q20_7


title: Acute - CMB-5-POLY


title: DW167_6_Q20_6


title: DW167_6_Q20_5


title: Acute - CMB-4-POLY


title: DW167_6_Q20_3


title: DW167_6_Q20_4


title: Acute - CMB-2-POLY


title: DW167_6_Q20_2


title: Acute - CMB-3-POLY


title: DW167_6_Q50_3


title: Acute - EV-4-POLY

value: Acute treatment to EV


title: DW167_6_Q175_3


title: Acute - EV-5-POLY


title: DW167_6_Q20_1


title: DW167_6_Q175_4


title: DW167_6_Q175_2


title: Acute - EV-3-POLY


title: DW167_6_Q175_1


title: Acute - EV-2-POLY


title: Acute - EV-1-POLY


title: DW167_6_Q170_8


title: JD130_6_Q50_9


title: Acute - CX-6-POLY

value: Acute treatment to CX5461


title: Acute - CX-5-POLY


title: Acute - CX-3-POLY


title: Acute - CX-4-POLY


title: DW167_6_Q170_7


title: DW167_6_Q170_5


title: DW167_6_Q170_4


title: Acute - EV-6-POLY


title: Acute - CMB-1-POLY


title: Acute - CX-2-POLY


title: ADN0128

type: genomic

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
Data were pre-processed by ChAS and processed/analysed as described in Lesluyes et al. 2019 (PMID: 31243333)
Matrices include logRs (weighted for CytoScanHD), smooth signals (2N-centred for CytoScanHD) and allelic differences for all samples

source_name: Human sarcoma

label_protocol: Affymetrix standard procedure

growth_protocol: None (primary tumours)

extract_protocol: Affymetrix standard procedure

tag: histological subtype

value: Undifferentiated pleomorphic sarcoma

tag: group


title: Acute - CX-1-POLY


title: ADN0122


title: ADN0127

value: Leiomyosarcoma


title: ADN0119


title: DW167_6_Q170_2


title: ADN0118


title: Acute - CTRL-6-POLY

value: Acute treatment to Vehicle/Vehicle


title: ADN0111


title: DW167_6_Q170_1


title: DW167_6_Q170_3


title: DW167_6_Q170_9


title: ADN0105


title: ADN0108


title: Acute - CTRL-5-POLY


title: Acute - CTRL-4-POLY


title: DW167_6_Q170_10


title: DW167_6_Q170_6


title: ADN0101


title: DW167_6_Q111_9


title: Acute - CTRL-3-POLY


title: ADN0100


title: DW167_6_Q111_8


title: DW167_6_Q111_7


title: ADN0088


title: ADN0095


title: ADN0082


title: DW167_6_Q111_6


title: ADN0079


title: Acute - CMB-5-INPUT

description:
Cytosolic RNA
processed data file: Acute_input.txt


title: ADN0077


title: Acute - CTRL-1-POLY


title: DW167_6_Q111_5


title: Acute - CMB-4-INPUT


title: DW167_6_Q111_4


title: DW167_6_Q111_3


title: ADN0099


title: ADN0067


title: ADN0071


title: ADN0078


title: Acute - CMB-3-INPUT


title: ADN0066


title: ADN0080


title: DW167_6_Q111_2


title: ADN0098


title: ADN0076


title: Acute - CTRL-2-POLY


title: Acute - CMB-2-INPUT


title: DW167_6_Q111_1


title: ADN0063


title: ADN0062


title: Acute - CMB-6-INPUT


title: DW167_6_Q111_10


title: Acute - CMB-1-INPUT


title: ADN0060


title: ADN0058


title: Acute - EV-6-INPUT


title: ADN0072


title: ADN0056


title: ADN0057


title: DW167-6-Q175_8


title: Acute - EV-5-INPUT


title: ADN0055


title: ADN0046


title: ADN0054


title: Acute - EV-3-INPUT


title: DW167-6-Q175_7


title: Acute - EV-4-INPUT


title: Acute - EV-2-INPUT


title: ADN0065


title: ADN0052


title: Acute - EV-1-INPUT


title: ADN0041


title: ADN0045


title: DW167-6-Q175_5


title: ADN0039


title: Acute - CX-6-INPUT


title: ADN0037


title: ADN0032


title: Acute - CX-5-INPUT


title: ADN0031


title: ADN0030


title: CP73-6-Q50_8


title: CP73-6-Q50_9


title: CP73-6-Q50_7


title: DW167-6-Q175_6


title: ADN0027


title: ADN0049


title: ADN0025


title: Acute - CX-3-INPUT


title: ADN0024


title: ADN0021


title: CP73-6-Q50_5


title: ADN0040


title: DW167-6-Q175_10


title: DW167-6-Q175_9


title: Acute - CX-1-INPUT


title: ADN0018


title: ADN0019


title: Acute - CX-2-INPUT


title: CP73-6-Q50_6


title: ADN0017


title: Acute - CTRL-6-INPUT


title: ADN0038


title: CP73-6-Q50_3


title: CP73-6-Q50_4


title: ADN0016


title: Acute - CX-4-INPUT


title: ADN0006


title: ADN0004


title: Acute - CTRL-4-INPUT


title: CP73-6-Q50_1


title: Acute - CTRL-3-INPUT


title: CP73-6-Q50_2


title: ADN0020


title: CP73-6-Q50_10