title: Rv48

city: Burnaby

first: Heather

last: Coatsworth

state: BC

address: 8888 University Drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

description:
fed with DENV-2 infected bloodmeal
Cuffdiff_Transcript_Rv_36v48.txt
Cuffdiff_Transcript_Rv_24v48.txt
Cuffdiff_Transcript_RbvRv_48.txt
Cuffdiff_Transcript_RbvRv_Global.txt
Cuffdiff_Transcript_SvvRv_48.txt
Cuffdiff_Transcript_SvvRv_Global.txt
Cuffdiff_Gene_Rv_36v48.txt
Cuffdiff_Gene_Rv_24v48.txt
Cuffdiff_Gene_RbvRv_48.txt
Cuffdiff_Gene_RbvRv_Global.txt
Cuffdiff_Gene_SvvRv_48.txt
Cuffdiff_Gene_SvvRv_Global.txt
DESeq2_Gene_Rv_36v48.txt
DESeq2_Gene_Rv_24v48.txt
DESeq2_Gene_RbvRv_48.txt
DESeq2_Gene_RbvRv_Global.txt
DESeq2_Gene_SvvRv_48.txt
DESeq2_Gene_SvvRv_Global.txt
GFOLD_Gene_Rv_36v48.txt
GFOLD_Gene_Rv_24v48.txt
GFOLD_Gene_RbvRv_48.txt
GFOLD_Gene_RbvRv_Global.txt
GFOLD_Gene_SvvRv_48.txt
GFOLD_Gene_SvvRv_Global.txt

data_processing:
Basecalling completed by Fusion Genomics (Buranby, BC)
Sequence data was checked for quality using FastQC (v. 0.11.1). Sequences were then trimmed using Trimmomatic (v. 0.30) to reduce overrepresented sequences, as well as to remove sequences less than 90bp in length. Tophat2 was used to align and map reads and Samstat (v.1.09)  was used to check mapping quality.
[Differential Expression Analyses]: To investigate the effects of time, viral presence and mosquito strain, 24 separate differential expression (DE) tests were run using three programs – Cuffdiff (v. 2.2.1), DESeq2 (v. 1.16.0), and GFOLD (v. 1.1.1). Processed files include corresponding gene annotations including gene names, GO (Gene Ontology) terms, and KEGG (Kyoto Encyclopedia of Genes and Genomes) terms.
Genome_build: AaegL3
Supplementary_files_format_and_content: tab deliminated files containing differential expression output from all 24 comparasions for all 3 programs

organism: Aedes aegypti

source_name: Aedes aegypti midgut

extract_protocol:
Midguts were dissected in DEPC sterile water on a cold table, transferred to a microcentrifuge tub containing 200ul of RNAlater Stabilizaiton Solution. Total RNA was extracted using Trizol.
mRNA purification was performed using the Micro Poly A Purist Kit. 100ng of RNA was used to generate cDNAs using the Ultra RNA Library Prep Kit for Illumina. Purification was completed using AMPure XP Beads
Illumina miSeq RNASeq

value: Cali-Refractory (Cali-MIB)

value: midgut

value: 48 hours post blood meal


title: 44P_N: Patient 18 cancer with nodes_TUMOUR

status: Public on May 01 2020

type: RNA

city: Shatin

first: Katie

last: Meehan

state: Northern Territories

address: Rooms 84026 - 31, 6th Floor, Lui Che Woo Clinical Sciences Building

country: Hong Kong

institute: Chinese University of Hong Kong

hyb_protocol: Input RNA was hybridized to target sequence-specific capture probes and fluorescent-labelled reporter probes for 15-19 hours at 65°C. The mRNA-probe complexes were washed, and immobilized, and quantified by the nCounter Digital Analyzer as described by the manufacturer.

data_processing: Reporter probe counts for samples were subjected to sequential data-processing steps, starting with quality control (QC) metrics using the NSolver software v4.0 (NanoString Technologies). Samples that failed QC metrics were excluded. Remaining samples were normalised and differential expression analyzes was performed using three different software packages (NanoStringDiff, R v3.3.3, http://www.r-project.org; Degust v3.1, https://degust.erc.monash.edu/; NSolver Advanced Analysis module v2.0.115).

label: biotin and fluorescent probe

molecule: total RNA

organism: Homo sapiens

source_name: oral tongue

label_protocol: A minimum of 200ng of RNA was used to measure the expression of 730 immune-related genes and 40 housekeeping genes using the nCounter® platform (NanoString Technologies) and the PanCancer Immune Profiling Panel according to the manufacturer instructions.

extract_protocol: A FFPE section stained with hematoxylin and eosin (H&E) was examined by a head and neck pathologist to confirm the presence of invasive tumor. For RNA purification (High Pure RNA Isolation Kit, Roche Diagnostic), either 2-4 x 10μm scrolls were obtained or if the tumor percentage was <70%, macro-dissection was performed on multiple air-dried sections

tag: disease state

value: primary oral tongue squamous cell carcinoma

tag: tissue

value: oral tongue


title: 45LN_N: Patient 19 cancer with nodes_NODE

scan_protocol: The mRNA-probe complexes were washed, and immobilized, and quantified by the nCounter Digital Analyzer as described by the manufacturer.

source_name: involved lymph node

value: involved lymph node


title: SADRT24

type: SRA

city: Aberdeen

first: Ashish

last: Malik

address: St Machar drive

country: United Kingdom

institute: University of Aberdeen

library_source: transcriptomic

data_processing:
Resulting sequences from metatranscriptomic analysis were annotated with the Metagenomics Rapid Annotation using Subsystems Technology (MG-RAST) server version 4.0.3.
Functional classification was performed using the SEED Subsystems database and taxonomic annotations up to genus level were performed using the RefSeq database with a maximum e-value cut-off of 10-5, minimum identity cut-off of 60% and minimum length of sequence alignment of 15 nucleotides.
Abundance tables derived from MG-RAST (processed file attached) were imported into R for downstream analyses.
Supplementary_files_format_and_content: Processes data file contains gene adundances under Subsystems heirarchical classification. Sample IDs match the sample titles provided in this file.

organism: leaf litter metagenome

source_name: Leaf litter_Grass_Reduced_1d after wet-up_microbial community

growth_protocol: In situ

extract_protocol:
We carried out RNA extraction on a coarse-ground litter aliquot of 0.2 g for shrub and 0.5 g for grass using RNeasy PowerSoil Total RNA Kit following manufacturer instructions (Qiagen, Hilden, Germany). Due to a high amount of organic compounds co-extracted from shrub litter, a lower amount of starting material was used in the extraction protocol to increase the RNA yield. After resuspending the RNA pellet in solution SR7 in the final step, purity and concentration of total RNA was assessed using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA), Qubit fluorometer (LifeTechnologies, Carlsbad, CA, USA) and Nanodrop 2000 Spectrophotometer (Thermo Scientific, USA).
Ribosomal RNA was removed using a Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions with a modification that included combining magnetic beads from the yeast and bacteria kit as follows: 0.5x Yeast Removal Solution, 0.25x Gram Negative Bacteria Removal solution, and 0.25x Gram Positive Bacteria Removal Solution. Strand-specific and barcode indexed RNA-seq libraries were then generated using the Kapa RNA-seq Hyper kit (Kapa Biosystems, Cape Town, South Africa) following the instructions of the manufacturer. The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100. The libraries were quantified by fluorometry on a Qubit fluorometer and pooled in equimolar ratios. The pool was quantified by qPCR with a Kapa Library Quant kit (Kapa Biosystems). The pooled library was sequenced on 1 lane of an Illumina HiSeq 4000 (Illumina, San Diego, CA, USA) with single-end 100 bp reads. The sequencing was carried out at the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center.

treatment_protocol: A subsample of leaf litter was ground in a mixer (a quick whirl for 5 s) and used for RNA and metabolite extraction.

tag: vegetation type

value: Grass

tag: precipitation treatment

value: Reduced

tag: time point

value: 1d after wet-up


title: 44LN_N: Patient 18 cancer with nodes_NODE


title: SADRT22


title: 43P_N: Patient 17 cancer with nodes_TUMOUR


title: Heliotrine 0.1 mg/kg/bw_animal 1

city: Berlin

first: Stefanie

last: Hessel-Pras

address: Max-Dohrn-Str. 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

description:
mRNA, liver after 28 days oral treatment
gene expression data of livers of PA treated rats

hyb_protocol: hybridization to GeneChip cartridge, staining and washing on a GeneChip Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G

data_processing: microarray data was normalized using the package limma in R, then,  the dataset was filtered and only transcripts were kept for which annotations were available. The reduced dataset comprising 26480 probe sets was analyzed further using Qlucore Omics Explorer (version 3.3, Qlucore, Lund, Sweden). After a correction for batch-dependent differences of microarray chips, a comparison of all high-dose groups of single PA was performed using one-way analysis of variance

label: biotin

organism: Rattus norvegicus

source_name: PA treated rats

label_protocol: biotin-labeling with GeneChipWT plus reagent kit

extract_protocol: small pieces of the deep-frozen liver lobe 1 were homogenized under liquid nitrogen and transferred to RLT buffer (Qiagen, Hilden, Germany) containing 1 % β-mercaptoethanol  RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) in combination with QiaShredder (Qiagen, Hilden, Germany)

treatment_protocol: rats were orally exposed to 4 different doses pf 6 structurally different pyrrolizidine alkaloids daily, after 28 d liver samples were gained, snap frozen and stored at 80°C prior isoation of RNA

tag: strain

tag: gender

value: male

value: liver

tag: treatment

value: Heliotrine 0.1 mg/kg/bw


title: Echimidine 3.3 mg/kg/bw_animal 5

value: Echimidine 3.3 mg/kg/bw


title: SADRT21


title: Rv24

description:
fed with DENV-2 infected bloodmeal
Cuffdiff_Transcript_Rv_24v36.txt
Cuffdiff_Transcript_Rv_24v48.txt
Cuffdiff_Transcript_RbvRv_24.txt
Cuffdiff_Transcript_RbvRv_Global.txt
Cuffdiff_Transcript_SvvRv_24.txt
Cuffdiff_Transcript_SvvRv_Global.txt
Cuffdiff_Gene_Rv_24v36.txt
Cuffdiff_Gene_Rv_24v48.txt
Cuffdiff_Gene_RbvRv_24.txt
Cuffdiff_Gene_RbvRv_Global.txt
Cuffdiff_Gene_SvvRv_24.txt
Cuffdiff_Gene_SvvRv_Global.txt
DESeq2_Gene_Rv_24v36.txt
DESeq2_Gene_Rv_24v48.txt
DESeq2_Gene_RbvRv_24.txt
DESeq2_Gene_RbvRv_Global.txt
DESeq2_Gene_SvvRv_24.txt
DESeq2_Gene_SvvRv_Global.txt
GFOLD_Gene_Rv_24v36.txt
GFOLD_Gene_Rv_24v48.txt
GFOLD_Gene_RbvRv_24.txt
GFOLD_Gene_RbvRv_Global.txt
GFOLD_Gene_SvvRv_24.txt
GFOLD_Gene_SvvRv_Global.txt

tag: age

value: 24 hours post blood meal


title: Rv36

description:
fed with DENV-2 infected bloodmeal
Cuffdiff_Transcript_Rv_24v36.txt
Cuffdiff_Transcript_Rv_36v48.txt
Cuffdiff_Transcript_RbvRv_36.txt
Cuffdiff_Transcript_RbvRv_Global.txt
Cuffdiff_Transcript_SvvRv_36.txt
Cuffdiff_Transcript_SvvRv_Global.txt
Cuffdiff_Gene_Rv_24v36.txt
Cuffdiff_Gene_Rv_36v48.txt
Cuffdiff_Gene_RbvRv_36.txt
Cuffdiff_Gene_RbvRv_Global.txt
Cuffdiff_Gene_SvvRv_36.txt
Cuffdiff_Gene_SvvRv_Global.txt
DESeq2_Gene_Rv_24v36.txt
DESeq2_Gene_Rv_36v48.txt
DESeq2_Gene_RbvRv_36.txt
DESeq2_Gene_RbvRv_Global.txt
DESeq2_Gene_SvvRv_36.txt
DESeq2_Gene_SvvRv_Global.txt
GFOLD_Gene_Rv_24v36.txt
GFOLD_Gene_Rv_36v48.txt
GFOLD_Gene_RbvRv_36.txt
GFOLD_Gene_RbvRv_Global.txt
GFOLD_Gene_SvvRv_36.txt
GFOLD_Gene_SvvRv_Global.txt

value: 36 hours post blood meal


title: 43LN_N: Patient 17 cancer with nodes_NODE


title: SADRT20

source_name: Leaf litter_Grass_Ambient_1d after wet-up_microbial community

value: Ambient


title: Echimidine 3.3 mg/kg/bw_animal 3


title: SADRT23


title: 41P_N: Patient 16 cancer with nodes_TUMOUR


title: Echimidine 3.3 mg/kg/bw_animal 2


title: Echimidine 3.3 mg/kg/bw_animal 4


title: SADRT19


title: Rb36

description:
fed with non-infectious bloodmeal
Cuffdiff_Transcript_Rb_24v36.txt
Cuffdiff_Transcript_Rb_36v48.txt
Cuffdiff_Transcript_RbvRv_36.txt
Cuffdiff_Transcript_RbvRv_Global.txt
Cuffdiff_Gene_Rb_24v36.txt
Cuffdiff_Gene_Rb_36v48.txt
Cuffdiff_Gene_RbvRv_36.txt
Cuffdiff_Gene_RbvRv_Global.txt
DESeq2_Gene_Rb_24v36.txt
DESeq2_Gene_Rb_36v48.txt
DESeq2_Gene_RbvRv_36.txt
DESeq2_Gene_RbvRv_Global.txt
GFOLD_Gene_Rb_24v36.txt
GFOLD_Gene_Rb_36v48.txt
GFOLD_Gene_RbvRv_36.txt
GFOLD_Gene_RbvRv_Global.txt


title: Rb24

description:
fed with non-infectious bloodmeal
Cuffdiff_Transcript_Rb_24v36.txt
Cuffdiff_Transcript_Rb_24v48.txt
Cuffdiff_Transcript_RbvRv_24.txt
Cuffdiff_Transcript_RbvRv_Global.txt
Cuffdiff_Gene_Rb_24v36.txt
Cuffdiff_Gene_Rb_24v48.txt
Cuffdiff_Gene_RbvRv_24.txt
Cuffdiff_Gene_RbvRv_Global.txt
DESeq2_Gene_Rb_24v36.txt
DESeq2_Gene_Rb_24v48.txt
DESeq2_Gene_RbvRv_24.txt
DESeq2_Gene_RbvRv_Global.txt
GFOLD_Gene_Rb_24v36.txt
GFOLD_Gene_Rb_24v48.txt
GFOLD_Gene_RbvRv_24.txt
GFOLD_Gene_RbvRv_Global.txt


title: SADRT16

source_name: Leaf litter_Shrub_Reduced_Before wet-up_microbial community

value: Shrub

value: Before wet-up


title: Echimidine 3.3 mg/kg/bw_animal 1


title: 41LN_N: Patient 16 cancer with nodes_NODE


title: SADRT17


title: Sv48

description:
fed with DENV-2 infected bloodmeal
Cuffdiff_Transcript_Sv_36v48.txt
Cuffdiff_Transcript_Sv_24v48.txt
Cuffdiff_Transcript_SbvSv_48.txt
Cuffdiff_Transcript_SbvSv_Global.txt
Cuffdiff_Transcript_SvvRv_48.txt
Cuffdiff_Transcript_SvvRv_Global.txt
Cuffdiff_Gene_Sv_36v48.txt
Cuffdiff_Gene_Sv_24v48.txt
Cuffdiff_Gene_SbvSv_48.txt
Cuffdiff_Gene_SbvSv_Global.txt
Cuffdiff_Gene_SvvRv_48.txt
Cuffdiff_Gene_SvvRv_Global.txt
DESeq2_Gene_Sv_36v48.txt
DESeq2_Gene_Sv_24v48.txt
DESeq2_Gene_SbvSv_48.txt
DESeq2_Gene_SbvSv_Global.txt
DESeq2_Gene_SvvRv_48.txt
DESeq2_Gene_SvvRv_Global.txt
GFOLD_Gene_Sv_36v48.txt
GFOLD_Gene_Sv_24v48.txt
GFOLD_Gene_SbvSv_48.txt
GFOLD_Gene_SbvSv_Global.txt
GFOLD_Gene_SvvRv_48.txt
GFOLD_Gene_SvvRv_Global.txt

value: Cali-Susceptible

value: midgut


title: 40P_N: Patient 15 cancer with nodes_TUMOUR

value: primary oral tongue squamous cell carcinoma


title: Echimidine 1 mg/kg/bw_animal 4

value: Echimidine 1 mg/kg/bw


title: Sv36

description:
fed with DENV-2 infected bloodmeal
Cuffdiff_Transcript_Sv_24v36.txt
Cuffdiff_Transcript_Sv_36v48.txt
Cuffdiff_Transcript_SbvSv_36.txt
Cuffdiff_Transcript_SbvSv_Global.txt
Cuffdiff_Transcript_SvvRv_36.txt
Cuffdiff_Transcript_SvvRv_Global.txt
Cuffdiff_Gene_Sv_24v36.txt
Cuffdiff_Gene_Sv_36v48.txt
Cuffdiff_Gene_SbvSv_36.txt
Cuffdiff_Gene_SbvSv_Global.txt
Cuffdiff_Gene_SvvRv_36.txt
Cuffdiff_Gene_SvvRv_Global.txt
DESeq2_Gene_Sv_24v36.txt
DESeq2_Gene_Sv_36v48.txt
DESeq2_Gene_SbvSv_36.txt
DESeq2_Gene_SbvSv_Global.txt
DESeq2_Gene_SvvRv_36.txt
DESeq2_Gene_SvvRv_Global.txt
GFOLD_Gene_Sv_24v36.txt
GFOLD_Gene_Sv_36v48.txt
GFOLD_Gene_SbvSv_36.txt
GFOLD_Gene_SbvSv_Global.txt
GFOLD_Gene_SvvRv_36.txt
GFOLD_Gene_SvvRv_Global.txt


title: 40LN_N: Patient 15 cancer with nodes_NODE

value: involved lymph node


title: Echimidine 1 mg/kg/bw_animal 5


title: Rb48

description:
fed with non-infectious bloodmeal
Cuffdiff_Transcript_Rb_36v48.txt
Cuffdiff_Transcript_Rb_24v48.txt
Cuffdiff_Transcript_RbvRv_48.txt
Cuffdiff_Transcript_RbvRv_Global.txt
Cuffdiff_Gene_Rb_36v48.txt
Cuffdiff_Gene_Rb_24v48.txt
Cuffdiff_Gene_RbvRv_48.txt
Cuffdiff_Gene_RbvRv_Global.txt
DESeq2_Gene_Rb_36v48.txt
DESeq2_Gene_Rb_24v48.txt
DESeq2_Gene_RbvRv_48.txt
DESeq2_Gene_RbvRv_Global.txt
GFOLD_Gene_Rb_36v48.txt
GFOLD_Gene_Rb_24v48.txt
GFOLD_Gene_RbvRv_48.txt
GFOLD_Gene_RbvRv_Global.txt

value: Cali-Refractory (Cali-MIB)

value: 48 hours post blood meal


title: 39_NN: Patient 14  cancer without nodes_TUMOUR

value: oral tongue


title: SADRT15

value: Reduced


title: Echimidine 1 mg/kg/bw_animal 3

value: male

value: liver


title: Senecionine 0.1 mg/kg/bw_animal 3

value: Senecionine 0.1 mg/kg/bw


title: Echimidine 1 mg/kg/bw_animal 2


title: 38_NN: Patient 13 cancer without nodes_TUMOUR


title: SADRT13


title: Echimidine 1 mg/kg/bw_animal 1


title: Sb48

description:
fed with non-infectious bloodmeal
Cuffdiff_Transcript_Sb_36v48.txt
Cuffdiff_Transcript_Sb_24v48.txt
Cuffdiff_Transcript_SbvSv_48.txt
Cuffdiff_Transcript_SbvSv_Global.txt
Cuffdiff_Gene_Sb_36v48.txt
Cuffdiff_Gene_Sb_24v48.txt
Cuffdiff_Gene_SbvSv_48.txt
Cuffdiff_Gene_SbvSv_Global.txt
DESeq2_Gene_Sb_36v48.txt
DESeq2_Gene_Sb_24v48.txt
DESeq2_Gene_SbvSv_48.txt
DESeq2_Gene_SbvSv_Global.txt
GFOLD_Gene_Sb_36v48.txt
GFOLD_Gene_Sb_24v48.txt
GFOLD_Gene_SbvSv_48.txt
GFOLD_Gene_SbvSv_Global.txt


title: Sv24

description:
fed with DENV-2 infected bloodmeal
Cuffdiff_Transcript_Sv_24v36.txt
Cuffdiff_Transcript_Sv_24v48.txt
Cuffdiff_Transcript_SbvSv_24.txt
Cuffdiff_Transcript_SbvSv_Global.txt
Cuffdiff_Transcript_SvvRv_24.txt
Cuffdiff_Transcript_SvvRv_Global.txt
Cuffdiff_Gene_Sv_24v36.txt
Cuffdiff_Gene_Sv_24v48.txt
Cuffdiff_Gene_SbvSv_24.txt
Cuffdiff_Gene_SbvSv_Global.txt
Cuffdiff_Gene_SvvRv_24.txt
Cuffdiff_Gene_SvvRv_Global.txt
DESeq2_Gene_Sv_24v36.txt
DESeq2_Gene_Sv_24v48.txt
DESeq2_Gene_SbvSv_24.txt
DESeq2_Gene_SbvSv_Global.txt
DESeq2_Gene_SvvRv_24.txt
DESeq2_Gene_SvvRv_Global.txt
GFOLD_Gene_Sv_24v36.txt
GFOLD_Gene_Sv_24v48.txt
GFOLD_Gene_SbvSv_24.txt
GFOLD_Gene_SbvSv_Global.txt
GFOLD_Gene_SvvRv_24.txt
GFOLD_Gene_SvvRv_Global.txt

value: 24 hours post blood meal


title: SADRT12

source_name: Leaf litter_Shrub_Ambient_Before wet-up_microbial community


title: 36_NN: Patient 12  cancer without nodes_TUMOUR


title: SADRT11


title: 33_NN: Patient 11  cancer without nodes_TUMOUR


title: 32_NN: Patient 10  cancer without nodes_TUMOUR


title: SADRT14


title: 29_NN: Patient 9  cancer without nodes_TUMOUR


title: SADRT10


title: Echimidine 0.33 mg/kg/bw_animal 5

value: Echimidine 0.33 mg/kg/bw


title: Echimidine 0.33 mg/kg/bw_animal 4


title: 27_NN: Patient 8  cancer without nodes_TUMOUR


title: 26_NN: Patient 7  cancer without nodes_TUMOUR


title: SADRT9

value: Ambient


title: SADRT8

source_name: Leaf litter_Grass_Reduced_Before wet-up_microbial community

value: Grass


title: SADRT7

value: Before wet-up


title: Sb36

description:
fed with non-infectious bloodmeal
Cuffdiff_Transcript_Sb_24v36.txt
Cuffdiff_Transcript_Sb_36v48.txt
Cuffdiff_Transcript_SbvSv_36.txt
Cuffdiff_Transcript_SbvSv_Global.txt
Cuffdiff_Gene_Sb_24v36.txt
Cuffdiff_Gene_Sb_36v48.txt
Cuffdiff_Gene_SbvSv_36.txt
Cuffdiff_Gene_SbvSv_Global.txt
DESeq2_Gene_Sb_24v36.txt
DESeq2_Gene_Sb_36v48.txt
DESeq2_Gene_SbvSv_36.txt
DESeq2_Gene_SbvSv_Global.txt
GFOLD_Gene_Sb_24v36.txt
GFOLD_Gene_Sb_36v48.txt
GFOLD_Gene_SbvSv_36.txt
GFOLD_Gene_SbvSv_Global.txt

value: Cali-Susceptible

value: 36 hours post blood meal


title: Echimidine 0.33 mg/kg/bw_animal 2


title: Echimidine 0.33 mg/kg/bw_animal 3


title: Echimidine 0.33 mg/kg/bw_animal 1


title: Sb24

description:
fed with non-infectious bloodmeal
Cuffdiff_Transcript_Sb_24v36.txt
Cuffdiff_Transcript_Sb_24v48.txt
Cuffdiff_Transcript_SbvSv_24.txt
Cuffdiff_Transcript_SbvSv_Global.txt
Cuffdiff_Gene_Sb_24v36.txt
Cuffdiff_Gene_Sb_24v48.txt
Cuffdiff_Gene_SbvSv_24.txt
Cuffdiff_Gene_SbvSv_Global.txt
DESeq2_Gene_Sb_24v36.txt
DESeq2_Gene_Sb_24v48.txt
DESeq2_Gene_SbvSv_24.txt
DESeq2_Gene_SbvSv_Global.txt
GFOLD_Gene_Sb_24v36.txt
GFOLD_Gene_Sb_24v48.txt
GFOLD_Gene_SbvSv_24.txt
GFOLD_Gene_SbvSv_Global.txt

value: midgut


title: 25_NN: Patient 6  cancer without nodes_TUMOUR

value: primary oral tongue squamous cell carcinoma


title: 24_NN: Patient 5  cancer without nodes_TUMOUR


title: SADRT6


title: 23_NN: Patient 4  cancer without nodes_TUMOUR


title: SADRT5


title: Volunteer Control 05

city: Beijing

first: Li

last: Lingzhi

address: 45 Changchun Street

department: neurology

country: China

institute: Xuanwu hospital

description: We investigated the circRNAs expression profile of neutrophil transcriptome in patients with asymptomatic MMD.Microarray based circRNAs profiling was determined between neutrophil samples from patients with asymptomatic MMD and healthy subjects.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 15 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: peripheral blood

label_protocol: Total RNAs were digested with Rnase R to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: 5 ml of peripheral blood was drawn from each suject in K2EDTA-coated Vacutainer tubes. Neutrophils were isolated out of peripheral blood within three hours.Finally, neutrophil was disrupted and total RNA was extracted using TRIzol reagent, which was stored in Freezing Tube at -80℃ for further processing.

tag: cell

value: neutrophil

tag: status when enrolled

value: healthy

tag: ethnicity

value: Han

value: 50 years

tag: Sex

value: Female


title: SADRT4

source_name: Leaf litter_Grass_Ambient_Before wet-up_microbial community


title: Volunteer Control 03

value: 58 years

value: Male


title: 22_NN: Patient 3 cancer without nodes_TUMOUR

value: oral tongue


title: Volunteer Control 04


title: Echimidine 0.1 mg/kg/bw_animal 5

value: male

value: liver

value: Echimidine 0.1 mg/kg/bw


title: Volunteer Control 02

value: 49 years


title: Echimidine 0.1 mg/kg/bw_animal 4


title: Echimidine 0.1 mg/kg/bw_animal 3


title: Volunteer Control 01

value: 45 years


title: Echimidine 0.1 mg/kg/bw_animal 1


title: SADRT3

value: Grass

value: Ambient

value: Before wet-up


title: Vehicle 0.15 NaCl_animal 6

description:
mRNA, liver after 28 days oral treatment
gene expression data of livers of vehicle treated rats

source_name: vehicle treated rats

value: Vehicle 0.15 NaCl


title: Vehicle 0.15 NaCl_animal 5


title: Echimidine 0.1 mg/kg/bw_animal 2


title: SADRT2


title: 16_NN: Patient 1 cancer without nodes_TUMOUR

value: primary oral tongue squamous cell carcinoma


title: 17_NN: Patient 2 cancer without nodes_TUMOUR


title: 1_PM: Patient 38 NON cancer

value: non-cancer


title: EJ34

status: Public on Apr 30 2020

city: Montreal

first: Cindy

last: Audiger

state: Québec

address: 2900, boul. Édouard-Montpetit

institute: Univeristy of Montreal

data_processing:
illumine HiSeq system
Sequence reads were then aligned to the genome by using a standard illumine sequence analysis pipeline by the Laboratory of Statistical Genomics and Systems Biology at the University of Cincinnati
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: spleen

extract_protocol:
RNA was extracted according to the mir-VANA RNA extraction kit protocol
The NEBNext Ultra Directional RNA library Prep Kit was used for library preparation.
Bioanalyzer (Agilent, Santa Clara, CA) analyses using a DNA high sensitivity chip were performed to determine quality and yield f the purified library

value: 8-12 weeks old

value: spleen

tag: cell type

value: mcDC


title: SADRT1


title: EJ35


title: EJ31


title: EJ36


title: EJ33


title: EJ30


title: EJ29


title: Patient MMD 04

value: neutrophil

value: asymptomatic

value: Han

value: Female


title: Patient MMD 01

value: 54 years

value: Male


title: Patient MMD 02

value: 46 years


title: Patient MMD 05

value: 58 years


title: Patient MMD 03


title: HAP1 cells,  WT 175 T0

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

institute: University of Toronto

description: gRNA amplicon

library_source: genomic

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix

molecule: genomic DNA

source_name: HAP1 cell line

growth_protocol: Human HAP1 cells were maintained in low glucose (10 mM), low glutamine (1 mM) DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega).
Sequencing libraries were prepared in two PCR steps, the first to enrich guide-RNA regions from the genome, and the second to amplify guide-RNA and attach Illumina TruSeq adapters with i5 and i7 indices.

treatment_protocol: Cells were transduced with the genome-wide TKOv3 CRISPR guide RNA library using a lentiviral vector co-expressing SpCas9 at a low mulitplicity of infection (MOI~0.4) at >200-fold library representation. Succesfully transduced cells were selected using Puromycin (T0), split into three replicates (A,B,C) that were subsequently cultured independently at >200-fold libryary coverage and passaged every three days until day 18 (T18).

tag: cell line

tag: genotype

value: WT

tag: crispr library


title: HAP1 cells,  WT 181 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 181 T0

description: gRNA amplicon


title: HAP1 cells,  WT 181 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 175 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 175 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 145 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 145 T18 B

description: gRNA amplicon


title: Vehicle 0.15 NaCl_animal 4

value: male

value: liver


title: Vehicle 0.15 NaCl_animal 2

value: Vehicle 0.15 NaCl


title: HAP1 cells,  WT 145 T0

description: gRNA amplicon


title: EJ32


title: HAP1 cells,  WT 107 T0

description: gRNA amplicon


title: HAP1 cells,  WT 107 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 99 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 107 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 99 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 99 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 99 T0

description: gRNA amplicon


title: HAP1 cells,  WT 89 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 89 T0

description: gRNA amplicon


title: HAP1 cells,  WT 89 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 175 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 107 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 80 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 145 T18 C

description: gRNA amplicon


title: Vehicle 0.15 NaCl, animal 1


title: HAP1 cells,  WT 80 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 80 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 80 T0

description: gRNA amplicon


title: HAP1 cells,  WT 74 T17 A

description: gRNA amplicon


title: HAP1 cells,  WT 69 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 69 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 69 T0

description: gRNA amplicon


title: HAP1 cells,  WT 74 T0

description: gRNA amplicon


title: HAP1 cells,  WT 74 T17 B

description: gRNA amplicon


title: HAP1 cells,  WT 69 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 60 T19 B

description: gRNA amplicon


title: HAP1 cells,  WT 60 T19 A

description: gRNA amplicon


title: HAP1 cells,  WT 60 T19 C

description: gRNA amplicon


title: HAP1 cells,  WT 60 T0

description: gRNA amplicon


title: HAP1 cells,  WT 57 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 54 T17 C

description: gRNA amplicon


title: HAP1 cells,  WT 54 T17 B

description: gRNA amplicon


title: HAP1 cells,  WT 57 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 54 T17 A

description: gRNA amplicon


title: HAP1 cells,  WT 54 T0

description: gRNA amplicon


title: HAP1 cells,  WT 52 T19 C

description: gRNA amplicon


title: HAP1 cells,  WT 52 T19 B

description: gRNA amplicon


title: HAP1 cells,  WT 52 T19 A

description: gRNA amplicon


title: HAP1 cells,  WT 52 T0

description: gRNA amplicon


title: HAP1 cells,  WT 49 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 49 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 49 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 49 T0

description: gRNA amplicon


title: HAP1 cells,  WT 74 T17 C

description: gRNA amplicon


title: HAP1 cells,  WT 42 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 42 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 35 T17 B

description: gRNA amplicon


title: HAP1 cells,  WT 42 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 35 T17 A

description: gRNA amplicon


title: HAP1 cells,  WT 35 T17 C

description: gRNA amplicon


title: HAP1 cells,  WT 30 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 57 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 35 T0

description: gRNA amplicon


title: HAP1 cells,  WT 22 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 22 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 30 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 57 T0

description: gRNA amplicon


title: HAP1 cells,  WT 30 T0

description: gRNA amplicon


title: HAP1 cells,  WT 15 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 22 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 15 T0

description: gRNA amplicon


title: HAP1 cells,  WT 15 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 7 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 7 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 7 T0

description: gRNA amplicon


title: HAP1 cells,  WT 2 T18 C

description: gRNA amplicon


title: HAP1 cells,  WT 7 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 2 T18 A

description: gRNA amplicon


title: HAP1 cells,  WT 2 T0

description: gRNA amplicon


title: HAP1 cells,  WT 2 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 30 T18 B

description: gRNA amplicon


title: HAP1 cells,  WT 42 T0

description: gRNA amplicon


title: HAP1 cells,  C12orf49 T18 B

description: gRNA amplicon

value: C12orf49 knockout


title: HAP1 cells,  C12orf49 T18 C

description: gRNA amplicon


title: HAP1 cells,  C12orf49 T0

description: gRNA amplicon


title: HAP1 cells,  SREBF2 T18 C

description: gRNA amplicon

value: SREBF2 knockout


title: HAP1 cells,  C12orf49 T18 A

description: gRNA amplicon


title: HAP1 cells,  SREBF2 T18 B

description: gRNA amplicon


title: HAP1 cells,  SREBF2 T18 A

description: gRNA amplicon


title: HAP1 cells,  SREBF2 T0

description: gRNA amplicon


title: HAP1 cells,  LDLR T0

description: gRNA amplicon

value: LDLR knockout


title: HAP1 cells,  ACACA T0

description: gRNA amplicon

value: ACACA knockout


title: HAP1 cells,  SREBF1 T18 A

description: gRNA amplicon

value: SREBF1 knockout


title: HAP1 cells,  LDLR T18 A

description: gRNA amplicon


title: HAP1 cells,  SREBF1 T18 C

description: gRNA amplicon


title: HAP1 cells,  ACACA T18 A

description: gRNA amplicon


title: HAP1 cells,  FASN_3 T18 C

description: gRNA amplicon

value: FASN knockout


title: HAP1 cells,  WT 22 T0

description: gRNA amplicon


title: HAP1 cells,  WT 15 T18 C

description: gRNA amplicon


title: HAP1 cells,  ACACA T18 C

description: gRNA amplicon


title: HAP1 cells,  FASN_3 T18 A

description: gRNA amplicon


title: HAP1 cells,  SREBF1 T18 B

description: gRNA amplicon


title: HAP1 cells,  LDLR T18 C

description: gRNA amplicon


title: HAP1 cells,  ACACA T18 B

description: gRNA amplicon


title: HAP1 cells,  LDLR T18 B

description: gRNA amplicon


title: HAP1 cells,  FASN_3 T0

description: gRNA amplicon


title: HAP1 cells,  SREBF1 T0

description: gRNA amplicon


title: HAP1 cells,  FASN_3 T18 B

description: gRNA amplicon


title: HAP1 cells,  FASN_2 T18 A

description: gRNA amplicon


title: HAP1 cells,  FASN_2 T0

description: gRNA amplicon


title: HAP1 cells,  FASN_1 T18 C

description: gRNA amplicon


title: HAP1 cells,  FASN_2 T18 B

description: gRNA amplicon


title: HAP1 cells,  FASN_1 T0

description: gRNA amplicon


title: HAP1 cells,  FASN_2 T18 C

description: gRNA amplicon


title: HAP1 cells,  FASN_1 T18 B

description: gRNA amplicon


title: HEK293T, ZNF711 ChIP-exo in HEK293T -rep2

city: Los Angeles

first: Weiya

middle: Stephanie

last: Ni

state: California

address: 1450 Biggy Street

country: USA

institute: University of Southern California

data_processing:
Library strategy: ChIP-exo
Sequencing results were aligned to hg19 using bwa-mem (v0.7.9a)
Peaks were called using ChexMix
Genome_build: hg19
Supplementary_files_format_and_content: peak files with quantitative data

growth_protocol: HEK293T cells were grown according to ATCC protocol

extract_protocol:
Chromatins were prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked by 1%formedelhyde for 10 mins and lysised into nuclei. Nuclei were sonicated using BioRuptor to break into chromatin fragments.
Librarys were prepared by Peconic

value: kidney cell line HEK293T


title: HEK293T, ZNF711 ChIP-exo in HEK293T -rep1


title: ATAC_Nutlin

city: Boulder

first: Ignacio

middle: Javier

last: Tripodi

state: Colorado

address: 3415 Colorado Avenue

department: Computer Science

institute: University of Colorado, Boulder

description:
open chromatin DNA
ATAC-seq

data_processing:
ATACFlow pipeline (https://github.com/NCBI-Hackathons/ATACFlow/)
Genome_build: hg38
Supplementary_files_format_and_content: broadPeak files generated using MACS2

growth_protocol: Mccoys, 10%FBS, 1x Pen-strep

extract_protocol:
doi: 10.1002/0471142727.mb2129s109 except that steps 2 and 3were repeated 2x to further clean nuclei
doi: 10.1002/0471142727.mb2129s109
NextSeq V2 pair end 2x37

treatment_protocol: 10 cm plate at 70% conflunce treated with 10 ml media and 10 ul DMSO (control) or 10 μM Nutlin-3A (inhibitor of p53) in DMSO [Sigma SML0580]

tag: cells type

value: colon cancer

tag: perterbation

value: 10 uM Nutlin-3A (inhibitor of p53) in DMSO [Sigma SML0580]

tag: media

value: Mccoys, 10%FBS, 1x Pen-strep


title: ATAC_DMSO

description:
open chromatin DNA
ATAC-seq

value: DMSO


title: LN308-untreated-GCCAAT-R3 (Ribo-Seq)

city: Heidelberg

first: Grischa

last: Toedt

address: Meyerhofstr. 1

department: Computational Biology

institute: EMBL

description: ribosomal profiling RNA

data_processing:
Library strategy: Ribo-Seq
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh38 using STAR v2.5.4b with gencode.v26.annotation.  Parameters for Ribo-Seq: --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --alignSoftClipAtReferenceEnds No --chimSegmentMin 20 --chimSegmentReadGapMax 0 10 --best --strata  Parameters for RNA-Seq: --outFilterMultimapNmax 20 --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType Local --alignSoftClipAtReferenceEnds No --chimSegmentMin 20 --chimSegmentReadGapMax 0 --outMultimapperOrder Random --outSAMattributes Standard --outSAMmode Full --outSAMstrandField intronMotif --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMmultNmax -1
Gene level expression were quantified using HTSeq (Anders et al. 2015) and raw RNA-Sequencing count data normalized and fold changes computed using the DESeq2 library (Love et al. 2014). Translation efficiencies of ribosomal profiling data was computed using RiboDiff (Zhong et al. 2017).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited data files include ensembl gene ids and counts per sample.

source_name: LN308 cell line

growth_protocol: LN308 cells were cultured in DMEM supplemented with 10% FBS, 100 units/ml penicillin and 100µg/ml streptomycin at 37°C and at 5% CO2.

extract_protocol:
Ribo-Seq  TH- or TM-stimulated cells were treated with 0.1mg/ml cycloheximide for 5min.  After washing with ice-cold PBS (supplemented with cycloheximide), cells were harvested and lysed for 15min on ice in a buffer containing 5mM Tris pH7.4, 1.5mM KCl, 5mM MgCl2, 0.5% Triton-X, 0.5% sodium deoxycholate, 0.1mg/ml cycloheximide, RNasin and 1x cOmplete protease inhibitor cocktail (Roche).  The cell lysate was cleared by centrifugation and digested with 0.2U RNaseI (Ambion) per 1µg RNA for 15min.  To stop the reaction, 1U SUPERaseIn RNase Inhibitor (Invitrogen) was added per unit of RNaseI.  Ribosomal complexes were separated on 12ml 10-50% sucrose gradients (in a buffer containing 20mM Tris pH7.4, 75 mM NaCl, 5mM MgCl2, 0.1mg/ml cycloheximide, and 1mM DTT) by centrifugation at 4°C and 35,000rpm for 3h in a SW41 rotor.  Fractions were collected at 0.5ml/min with continuous monitoring of conductivity and UV absorption at 254nm.  Fractions containing 80S monosomes were diluted with an equal amount of RNase-free water followed by organic extraction with Phenol:Chloroform:Isoamylalkohol 25:24:1 (Roth) and ethanol precipitation.  RNAs were then separated by denaturing Urea-PAGE and visualized by SYBR Gold staining.  RNAs with a length of 27-33nt were excised from the gel and eluted overnight in a buffer containing 300mM NaOAc pH 5.5, 1mM EDTA, and 0.25% SDS followed by ethanol precipitation.
RNA-Seq  Total cellular RNA was extracted using TRIzol reagent according to the manufacturer’s instructions.
Ribo-Seq  After dephosphorylation for 1h at 37°C with 20U of T4 Polynucleotide Kinase (NEB), RNAs were ligated to a universal miRNA cloning linker (NEB) using truncated T4 RNA ligase 2.  After gelpurification reverse transcription was performed using SuperscriptIII reverse transcriptase and a primer complementary to the ligated adapter, followed by alkaline hydrolysis of the RNA strand.  The resulting cDNAs were gelpurified and contaminating sequences originating from rRNA were depleted by substractive hybridization to a mixture of biotinylated DNA oligonucleotides and Streptavidin magnetic beads (New England Biolabs).  The recovered RNAs were then circularized with CircLigase II ssDNA Ligase (Epicentre) according to the manufacturer’s instructions and subjected to PCR amplification to generate amplicons suitable for Illumina sequencing.  After gelpurification, DNA concentration was determined using a Qubit Fluorometer (Qubit 2.0, Thermo Fisher Scientific).  Bioanalyzer or TapeStation (Agilent) analyses were performed to assess the quality of the samples followed by deep sequencing on the Illumina platform.
RNA-Seq  RNA integrity was checked using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA), and concentration was measured with Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies).  Starting with ~300ng of total RNA as input, ribosomal RNA was removed by NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs).  Subsequently, stranded total RNA-seq libraries were prepared from rRNA free RNA sample using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the protocol.  RNA-seq barcoded libraries that passed the QC step, which was assessed on the Agilent Bioanalyzer system, were then pooled in equimolar amounts;  1.8 pM solution of this pool was loaded on the Illumina sequencer NextSeq 500 and sequenced bi-directionally.

treatment_protocol: To induce ER stress the medium was supplemented with 200nM Thapsigargin or 2.5µg/ml Tunicamycin (dissolved in DMSO); DMSO only served as a control.

value: Astrocytoma-derived p53-deficient glial cells

tag: time

value: 0 h

value: untreated


title: LN308-untreated-GCCAAT-R2 (Ribo-Seq)

description: ribosomal profiling RNA


title: HAP1 cells,  FASN_1 T18 A

description: gRNA amplicon

tag: time point


title: LN308-untreated-GCCAAT-R1 (Ribo-Seq)

description: ribosomal profiling RNA


title: LN308-2h-Thapsigargin-TACAAG (Ribo-Seq)

description: ribosomal profiling RNA

value: 2 h

value: thapsigargin


title: LN308-6h-Thapsigargin-GCTCAT (Ribo-Seq)

description: ribosomal profiling RNA

value: 6 h


title: LN308-6h-Tunicamycin-GAATGA-R3 (Ribo-Seq)

description: ribosomal profiling RNA

value: tunicamycin


title: LN308-6h-Tunicamycin-R1 (RNA-Seq)

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh38 using STAR v2.5.4b with gencode.v26.annotation.  Parameters for Ribo-Seq: --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --alignSoftClipAtReferenceEnds No --chimSegmentMin 20 --chimSegmentReadGapMax 0 10 --best --strata  Parameters for RNA-Seq: --outFilterMultimapNmax 20 --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType Local --alignSoftClipAtReferenceEnds No --chimSegmentMin 20 --chimSegmentReadGapMax 0 --outMultimapperOrder Random --outSAMattributes Standard --outSAMmode Full --outSAMstrandField intronMotif --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMmultNmax -1
Gene level expression were quantified using HTSeq (Anders et al. 2015) and raw RNA-Sequencing count data normalized and fold changes computed using the DESeq2 library (Love et al. 2014). Translation efficiencies of ribosomal profiling data was computed using RiboDiff (Zhong et al. 2017).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited data files include ensembl gene ids and counts per sample.


title: LN308-6h-Tunicamycin-GAATGA-R2 (Ribo-Seq)

description: ribosomal profiling RNA


title: LN308-2h-Thapsigargin-R1 (RNA-Seq)


title: LN308-2h-Tunicamycin-R3 (RNA-Seq)


title: LN308-2h-Tunicamycin-AGGAAT-R1 (Ribo-Seq)

description: ribosomal profiling RNA


title: LN308-6h-Tunicamycin-R2 (RNA-Seq)


title: LN308-2h-Tunicamycin-R2 (RNA-Seq)


title: LN308-2h-Tunicamycin-AGGAAT-R3 (Ribo-Seq)

description: ribosomal profiling RNA


title: LN308-6h-Tunicamycin-GAATGA-R1 (Ribo-Seq)

description: ribosomal profiling RNA


title: LN308-6h-Tunicamycin-R3 (RNA-Seq)


title: LN308-2h-Tunicamycin-AGGAAT-R2 (Ribo-Seq)

description: ribosomal profiling RNA


title: LN308-untreated-R3 (RNA-Seq)


title: LN308-untreated-R2 (RNA-Seq)


title: LN308-2h-Tunicamycin-R1 (RNA-Seq)


title: LN308-6h-Thapsigargin-R1 (RNA-Seq)


title: invivo_vehicle2_HDAC3_ChIP_seq

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

description: WT C57Bl6, MHD3KO, NS-DAD mice and their control littermates of 8-week-old were intraperitoneally injected with either phosphate-buffered saline (PBS, Sigma) or 10 mg/kg of purified LPS (Sigma E. Coli O111:B4) at 4PM. Without thioglycolate stimulation, peritoneal cells were harvested 6h after LPS or PBS injection at 10PM and passed through pre-separation filters (Miltenyi Biotec, 130-041-407) to obtain a single-cell suspension. Peritoneal macrophages were then isolated by MACS (Magnetic-Activated Cell Sorting) as previously described40, following the manufacturer instructions (Miltenyi Biotec, 130-110-434) and using MiniMACS columns (Miltenyi Biotec, 130-042-201)

data_processing:
All the reads were aligned to mouse genome, mm10, using Bowtie2 with option (--p 12 -N 1 -x ~/mm10/mm10).
All the redundant tags were eliminated except one per each genomic position before downstream analysis.
Peak calling was done using Homer and 1 rpm cutoff was further applied for peak tag counts within 200bp window.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and bed files of HDAC3, H3K27Ac, ATF2, ATF3, p65, NCoR1, NCoR2 ChIP_seqs

source_name: peritoneal macrophages

growth_protocol: Control and MHD3KO mice were euthanized, and bone marrow were extracted for hindlimb femurs. Bone marrow cells were cultured for 7 days in DMEM supplemented with 10% FBS and 30% L929 media for 7 days on petri dishes to allow macrophage differentiation.

extract_protocol:
ChIP was performed as described previously (Steger et al., 2008) , using HDAC3 (abcam7030),  H3K27Ac (Abcam 4729), ATF2 (Cell Signaling,D4L2X), ATF3 (Cell Signaling,D2Y5W) ,p65 (Cell Signaling,D14E12), NCoR1 (ell Signaling, E4S4N), NCoR2 (Millipore AntiSMRTe 06-981) antibodies
ChIP DNA was prepared for sequencing according to the amplification protocol provided by Illumina

treatment_protocol: After 7 days of differeniation, BMDM were replated, rested overnight before treated with BSA control, LPS(5ng/ml for 4 hours). For rescue macrophages, retrovirus expressing Y298F or WT HDAC3 were added to BMDM 4 days post harvest from femurs. For siRNA experiments, siRNA were addded 24 hours after replating of the macrophages on the 7th day post harvest.

tag: strain

value: 8 weeks

value: Control


title: invivo_vehicle3_HDAC3_ChIP_seq


title: invivo_LPS1_HDAC3_ChIP_seq

tag: agent

value: LPS


title: invivo_vehicle1_HDAC3_ChIP_seq


title: invivo_LPS2_HDAC3_ChIP_seq


title: HH_7.1_vs_H_G5

city: San Vicente del Raspeig

first: Julia

last: Esclapez

state: Alicante

address: Crta San Vicente del Raspeig s/n

department: Biochemistry

country: Spain

institute: University of Alicante

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Haloferax mediterranei

source_name: H. mediterranei HM26 (parental strain) cells were shifted to nitrogen starvation for 72h. Replicate 2.

label_protocol: Two-color microarray-based prokaryote analysis Fair Play III Labeling v1.3 (Agilent)

growth_protocol: H. mediterranei cultures were grown in a 25% (w/v) mixture of salts, 0,5% yeast extract  and the pH value of the media was adjusted to 7.3. Gln was added at a final concentration of 40 mM to maintain the mutant phenotype.   To induce nitrogen starvation, cells grown in a complex media + Gln 40 mM until mid-exponential growth phase were harvested by centrifugation, washed and transferred to a defined medium lacking all nitrogen source during  72h.

extract_protocol: Total RNA was isolated from these samples by using RNeasy Mini Kit (Qiagen) following product specifications

tag: sample id

value: wildtype

tag: growth condition

value: shifted to nitrogen starvation for 72h

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells were shifted to nitrogen starvation for 72h. Replicate 4.


title: CGG_B4_vs_CGH_2.1-2.2

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate 2.

value: complex medium with 40 mM Gln

source_name: H. mediterranei HM26 (parental strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate 4.


title: siC_2_LPS_HDAC3_ChIP_seq

source_name: bone marrow-derived macrophages

tag: age


title: CGH_3.1_vs_HH_6.1

source_name: H. mediterranei HM26 (parental strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate 2.

source_name: H. mediterranei HM26 (parental strain) cells were shifted to nitrogen starvation for 72h. Replicate 4.


title: CHIP_seq_HDAC3_input_LPS


title: siATF3_1_NA_HDAC3_ChIP_seq


title: sip65_1_NA_HDAC3_ChIP_seq


title: siC_2_NA_HDAC3_ChIP_seq


title: siATF3_1_LPS_HDAC3_ChIP_seq


title: siC_1_LPS_HDAC3_ChIP_seq


title: sip65_2_LPS_HDAC3_ChIP_seq


title: sip65_1_LPS_HDAC3_ChIP_seq


title: H_H5_vs_HH_8.1

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells were shifted to nitrogen starvation for 72h. Replicate 1.

source_name: H. mediterranei HM26 (parental strain) cells were shifted to nitrogen starvation for 72h. Replicate 3.


title: CGH_1.1-1.2_vs_CGG_A1-A2

source_name: H. mediterranei HM26 (parental strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate  1.

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate 3.


title: CGG_D3_vs_H_E5-E6

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate 1.

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells were shifted to nitrogen starvation for 72h. Replicate 3.


title: HH_5.1_vs_CGH_4.1

source_name: H. mediterranei HM26 (parental strain) cells were shifted to nitrogen starvation for 72h. Replicate 1.

source_name: H. mediterranei HM26 (parental strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate 3.


title: siATF3_2_LPS_HDAC3_ChIP_seq


title: H_F6_vs_CGG_C3

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells were shifted to nitrogen starvation for 72h. Replicate 2

source_name: H. mediterranei ΔglnA (deletion mutant strain) cells grown in complex medium with 40 mM Gln until mid-exponential growth phase. Replicate 4.


title: siATF3_2_NA_HDAC3_ChIP_seq


title: invivo_LPS3_HDAC3_ChIP_seq

source_name: peritoneal macrophages


title: siATF2_1_NA_HDAC3_ChIP_seq


title: siC_1_NA_HDAC3_ChIP_seq


title: siATF2_2_NA_HDAC3_ChIP_seq


title: siATF2_2_LPS_HDAC3_ChIP_seq


title: sip65_2_NA_HDAC3_ChIP_seq


title: 400nM_3_SAHA_HDAC3_ChIP_seq


title: 400nM_1_SAHA_HDAC3_ChIP_seq


title: 400nM_3_SAHA_LPS_HDAC3_ChIP_seq


title: 400nM_2_SAHA_HDAC3_ChIP_seq


title: 400nM_2_SAHA_LPS_HDAC3_ChIP_seq


title: 25nM_3_SAHA_HDAC3_ChIP_seq


title: 400nM_1_SAHA_LPS_HDAC3_ChIP_seq


title: 100nM_3_SAHA_LPS_HDAC3_ChIP_seq


title: 100nM_3_SAHA_HDAC3_ChIP_seq


title: 25nM_2_SAHA_HDAC3_ChIP_seq


title: 25nM_2_SAHA_LPS_HDAC3_ChIP_seq


title: 100nM_2_SAHA_HDAC3_ChIP_seq


title: 100nM_1_SAHA_HDAC3_ChIP_seq


title: 0nM_3_SAHA_HDAC3_ChIP_seq


title: 0nM_2_SAHA_HDAC3_ChIP_seq


title: 25nM_1_SAHA_HDAC3_ChIP_seq


title: 100nM_2_SAHA_LPS_HDAC3_ChIP_seq


title: siATF2_1_LPS_HDAC3_ChIP_seq


title: 0nM_1_SAHA_HDAC3_ChIP_seq


title: WT_P65_ChIP_LPS_2


title: 0nM_1_SAHA_LPS_HDAC3_ChIP_seq


title: WT_P65_ChIP_LPS_1


title: p65_wt3


title: 25nM_3_SAHA_LPS_HDAC3_ChIP_seq


title: 25nM_1_SAHA_LPS_HDAC3_ChIP_seq


title: 100nM_1_SAHA_LPS_HDAC3_ChIP_seq


title: 0nM_3_SAHA_LPS_HDAC3_ChIP_seq


title: p65_KO3


title: KO_P65_ChIP_LPS_1


title: KO_P65_ChIP_LPS_3


title: KO_P65_ChIP_LPS_2


title: p65_wt1


title: p65_KO2


title: NCoR2_LPS2


title: NCoR2_LPS1


title: 0nM_2_SAHA_LPS_HDAC3_ChIP_seq


title: NCoR2_LPS3


title: p65_KO1


title: NCOR1_LPS3


title: NCoR2_Ctrl_2


title: NCOR1_LPS2


title: NCoR2_Ctrl_1


title: NCoR2_Ctrl_3


title: NCOR1_LPS4


title: NCOR1_LPS1


title: WT_P65_ChIP_LPS_3


title: ATF3_wt_lps_3


title: ATF3_wt_lps_2


title: p65_wt2


title: NCoR1_1


title: NCoR1_3


title: ATF3_wt3


title: ATF3_wt_lps_1


title: ATF3_wt2


title: ATF3_wt1


title: ATF2_LPS_1


title: ATF2_LPS_3


title: NCoR1_2


title: ATF2_1


title: ATF2_2


title: H3K27_wt_lps_3


title: H3K27_wt_lps_2


title: H3K27_wt_lps_1


title: ATF2_LPS_2


title: H3K27_wt2


title: H3K27_KO_lps_1


title: H3K27_wt1


title: H3K27_KO3


title: H3K27_KO_lps_3


title: H3K27_KO1


title: H3K27_KO2


title: KO_LPS_2_GRO_seq

description: LPS_all_transcripts_all_bidirectional_eRNAs.bed

data_processing:
Library strategy: GRO-seq
adapter and poly-A sequence were trimmed off from the raw tags, then remaining tags were converted into FASTA format before alignment. Trimmed tags were aligned to the mouse genome, mm10, using Bowtie with the following options: inputs were in FASTA format (-f), three mismatches were allowed for each tags (-v 3), and only uniquely mapped tags were retained (-m 1).
All the alignments were adjusted to 50bp by extending toward 3'-end if their size is shorter than that to make libraries comparable.  For stack-height profiles, all the replicates for each condition were pooled. genomeCoverageBed in bedtools was used first to make bedGraph files for plus and minus strands separately, where minus strand values were converted into negative ones.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, bedgraph.tdf, and bed file of eRNA

extract_protocol:
Cells were washed twice with ice-cold PBS, then swelled in swelling buffer (10mM Tris pH 7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice. Cells were centrifuged at 400g for 10 min, then resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% Igepal) and incubated on ice for 5 min. Nuclei were washed twice with lysis buffer, then resuspended in freezing buffer (50mM Tris pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). Nuclei were counted, pelleted, and 5 x 106 nuclei were resuspended in 100ul freezing buffer. For each library, run-on was performed on 4 tubes of 5 x 106 nuclei.   For the run-on, cells were mixed with an equal volume of run-on buffer (10mM Tris pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-In, 1% Sarkosyl, 500uM ATP, GTP and Br-UTP, 2uM CTP) and incubated for 5 min at 30°C. Nuclear RNA was extracted with TRIzol (Invitrogen) and precipitated with NaCl and ethanol overnight. The pellet was resuspended in water and the RNA was DNase treated (Ambion) for 30 min. RNA was hydrolyzed using fragmentation reagents (Ambion) for 13 min at 70°C and purified through a Micro Bio-Spin p-30 column (Bio-Rad) according to manufacturer's instructions. RNA was treated with 1.5ul T4 polynucleotide kinase (New England Biolabs) for 1h at 37°C, then with an additional 1l for 1h more. RNA was denatured for 5 min at 65°C.   Anti-BrU agarose beads (Santa Cruz) were rotated for 1h in blocking buffer (0.5xSSPE, 1mM EDTA, 0.05% Tween-20, 0.1% PVP, and 1mg/ml BSA). Run-on RNA was rotated with beads for 1h, followed by washes twice in binding buffer (0.5xSSPE, 1mM EDTA, 0.05% Tween-20), twice in low salt buffer (0.2SSPE, 1mM EDTA, 0.05% Tween-20), once in high salt buffer (0.5x SSPE, 1mM EDTA, 0.05% Tween-20, 15mM NaCl), and twice in TET buffer (TE pH 7.4, 0.05% Tween-20). BrU-labeled RNA was eluted from the beads four times for 15 min with 10% elution buffer pre-heated to 42°C. RNA was ethanol-precipitated overnight.
Precipitated RNA was resuspended in water, denatured, and treated with poly(A)-polymerase (NEB) for 30 min at 37°C. cDNA synthesis was performed as described previously (Wang et al, Nature 2011) using oNTI223 primer ((5'-pGATCGTCGGACTGTAGAACTCT;CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3') where the p indicates 5' phosphorylation, indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. The reaction was treated with  3 ul exonuclease I (Fermentas) for 15 min at 37°C, followed by 2 ul 1M NaOH for 20 min at 98°C, and neutralized with 1ul 2M HCl. cDNA was run on 10% TBE-urea gel, then products were excised and eluted from shredded gel pieces for 4h in TE + 0.1% Tween and precipitated in ethanol overnight.   First-strand cDNA was circularized with CircLigase (Epicentre), denatured for 10 min at 80°C, and relinearized with APE I (NEB). Linearized DNA was amplified by PCR using Phusion Hot Start II Kit, according to manufacturer's instructions. The oligonucleotide primers oNTI200 (5'-CAAGCAGAAGACGGCATA-3') and oNTI201 (5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3') were used for amplification. The PCR product was run on a 10% TBE gel and eluted as before. Libraries were sequenced on an Illumina hi-Seq2000 with sequencing primer 5'CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3'.

treatment_protocol: After 7 days of differeniation, BMDM were replated, rested overnight before treated with PBS control, LPS(5ng/ml for 4 hours)


title: KO_LPS_3_GRO_seq


title: KO_3_GRO_seq

description: Ctrl_all_transcripts_all_bidirectional_eRNAs.bed

value: PBS


title: KO_LPS_1_GRO_seq


title: KO_2_GRO_seq


title: Control_LPS_3_GRO_seq

value: control


title: ATF2_3


title: KO_1_GRO_seq


title: Control_LPS_2_GRO_seq


title: Control_LPS_1_GRO_seq


title: H3K27_wt3


title: Control_3_GRO_seq


title: Control_2_GRO_seq


title: Control_1_GRO_seq


title: ChIP_seq_NCoR1_input_LPS


title: CHIP_seq_NCoR1_input_veh


title: CHIP_seq_HDAC3_input_veh


title: CHIP_seq_p65_input_LPS


title: CHIP_seq_p65_input_veh


title: CHIP_seq_H3K27Ac_input_veh


title: CHIP_seq_NCoR2_input_veh


title: CHIP_seq_ATF2_input_veh


title: CHIP_seq_ATF2_input_LPS


title: H3K27_KO_lps_2


title: CHIP_seq_H3K27Ac_input_LPS


title: CHIP_seq_ATF3_input_LPS


title: HDAC3_Y298F_LPS_3


title: HDAC3_Y298F_LPS_2


title: HDAC3_Y298F_LPS_1


title: HDA3_Y298F_3


title: HDA3_Y298F_2


title: CHIP_seq_NCoR2_input_LPS


title: HDAC3_WT_3


title: HDAC3_WT_LPS_2


title: HDA3_Y298F_1


title: HDAC3_WT_LPS_1


title: HDAC3_WT_LPS_3


title: HDAC3_WT_1


title: HDAC3_WT_2


title: CHIP_seq_ATF3_input_veh


title: HDAC3_KO_LPS_3

description: used for peak calling


title: HDAC3_KO_LPS_1

description: used for peak calling


title: HDAC3_KO_LPS_2

description: used for peak calling


title: HDAC3_KO_2

description: used for peak calling


title: HDAC3_KO_1

description: used for peak calling


title: HDAC3_KO_3

description: used for peak calling


title: H3K36me3 in DKO clone3- rep2

description: USC1422_H3K36me3_ChIPseq_DKO_clone3_rep2

data_processing:
Sequencing results were aligned to hg19 using bwa
Peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peak files with quantitative data

source_name: DKO clone3

extract_protocol:
Chromatins were prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked by 1%formedelhyde for 10 mins and lysised into nuclei. Nuclei were sonicated using BioRuptor to break into chromatin fragments.
Librarys were prepared using KAPA Hyper Prep Kit (Kapa #KK8505) according to provided protocol

tag: clone name

value: DKO clone3

tag: factor

tag: chip antibody

value: Cell Signaling Technology, 9763S, lot3


title: H3K36me3 in DKO clone2 - rep1

description: USC1419_H3K36me3_ChIPseq_DKO_clone2_rep1

source_name: DKO clone2

value: DKO clone2


title: H3K36me3 in DKO clone2 - rep2

description: USC1420_H3K36me3_ChIPseq_DKO_clone2_rep2


title: H3K36me3 in DKO clone3 - rep1

description: USC1421_H3K36me3_ChIPseq_DKO_clone3_rep1


title: H3K36me3 in DKO clone1 - rep2

description: USC1418_H3K36me3_ChIPseq_DKO_clone1_rep2

source_name: DKO clone1

value: DKO clone1


title: H3K36me3 in DKO clone1 - rep1

description: USC1417_H3K36me3_ChIPseq_DKO_clone1_rep1


title: H3K36me3 in HEK293T - rep2


title: H3K36me3 in HEK293T - rep1


title: HEK293T, ZFX ZF 9-13 FLAG ChIP in HEK293T

value: kidney cell line HEK293T

value: ZFX ZF 9-13 FLAG

value: Sigma, F1804, lot SLBX2256


title: HEK293T, ZFX ZF 1-8 FLAG ChIP in HEK293T

value: ZFX ZF 1-8 FLAG


title: 22Rv1, ZNF711 ChIP in 22Rv1 - rep2

value: prostate cell line 22Rv1

value: Thermo Fisher, PA5-31815


title: HEK293T, wt ZFX FLAG ChIP in HEK293T

value: wt ZFX FLAG


title: 22Rv1, ZFY ChIP in 22Rv1 - rep2

value: ZFY

value: Sigma, SAB2102775, lot QC8001


title: 22Rv1, ZFY ChIP in 22Rv1 - rep1


title: 22Rv1, ZFX ChIP in 22Rv1 - rep2

value: ZFX

value: CST, L28B6, lot 1


title: Replicate4_INO80_04_PE

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

institute: University Medical Center Göttingen

description: in vitro, plasmid DNA

data_processing:
fastq files were aligned to the SacCer3 (R64)genome using Bowtie (Lengmead et al. 2009). Multiple matches were omited. BAM files were imported into R Studio (RStudio Team, 2015) using GenomicAlignments (Lawrence et al. 2013). Then, reads were shifted by 73 bp to cover the nucleosome dyad and extended to 50 bp. Genome coverage was caluculated.
Coverage files containing single-end sequencing data were either aligned to in vivo +1 nucleosome positions, Reb1 sites (SLIM-ChIP hits (Gutin et al. 2019), Reb1 PWM hits (Badis et al. 2008) or Reb1 promotor hits), or BamHI, EcoRV or KpnI cut sites. Signal was normalized per gene in a 2000 bp window around the alignment point.
For promotor grouping according to Reb1 site orientation, Reb1 SLIM-ChIP hits which contain a PWM site (± 50 bp) and which are located within 400 bp upstream of in vivo +1 nucleosomes were used. Cluster 1 contains promotors where the Reb1 PWM motif is located on the sense strand and cluster 2, where the Reb1 PWM motif is located on the antisense strand. Cluster 3 contains Reb1 sites at bidirectional promotors.
Plus 1 nucleosome positions were called according to (Tirosh, 2012). In more detail, mono-nucleosomal fragments generated from BY4741 MNase digested chromatin were sequenced on an Illumina Genome analyzer, mapped to the sacCer3 genome with bowtie (Langmead et al., 2009) and shifted by 73 bp with respect to sequencing read directionality to obtain theoretical nucleosome dyads. The obtained dyad-density counts were smoothed with sliding Gaussian filter (width = 100, mean = 0, SD = 25) and resulting values were sorted by decreasing values. Iteratively, the position with the highest value was added to the list of “dyad centers” and all values for positions within +/-120 bp surrounding the position with the highest value were removed from further analysis. The top 90% of nucleosome dyad centers, by value, constituted the final list of nucleosome positions. Plus 1 nucleosome dyad positions were defined as the nearest nucleosome dyad position to TSS within a window 0 to +500 bp from the TSS, with respect to direction of transcription.
Paired-end sequencing data was used for a genome-wide principal component and DNA shape analysis. If not stated otherwise, functions were called with default parameters. Read pairs were aligned using bowtie2 (version 2.2.9) with options "-X 250 --no-discordant --no-mixed --no-unal". Only unique matches were kept, and orphaned mates removed. Nucleosomes were called on each sample using bioconductor/nucleR (2.16.0) on nucleosomal fragments defined by paired reads as follows: fragments were processed with trimming to 40 bp around the dyads and their coverage was calculated. Noise was removed using FFT filtering with parameter pcKeepComp=0.02 and peak detection was carried out with threshold 99%.  For each sample in an analysis set, sample-specific dyad positions obtained by nucleosome calling were enlarged to 20 bp and all positions were merged across the samples. Overlapping regions were joined. We excluded regions locating closer than 250 bp to tile borders and those residing in a region with high artifactual signals (chr III, 91000-93000 bp).   On this joint set of nucleosome dyads, we counted the number of overlapping fragments (reduced to their center position) for each sample. With x being the number of counts of sample-specific fragment centers overlapping one dyad region of the joint set and sum(x) being the sum of all counts across all dyad regions in the sample the data was normalized using the formula: normalized occupancy (dyad region) = log2(((x/sum(x))*1000)+0.001). The resulting matrix was subjected to principal component analysis. K-means clustering was applied to the resulting principal components to group nucleosomes based on similar occupancy patterns across sample conditions.  DNA shape features in windows of 320 bp around dyad positions were calculated with bioconductor/DNAshapeR (version 1.14.0).
Genome_build: SacCer3
Supplementary_files_format_and_content: bw (bigwig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

molecule: other

organism: Saccharomyces cerevisiae

source_name: in vitro reconstituted chromatin

growth_protocol: Salt Gradient Dialysis (SGD): For low and medium assembly degrees, 10 µg of plasmid library DNA (pGP546) was mixed with ~2 or 4 µg of histone octamers (endogenous or recombinant histones), respectively, in 100 µl assembly buffer (10 mM Tris-HCl, pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 0.2 µg BSA). Samples were transferred to Slide-A-lyzer mini dialysis devices, which were placed in a 3 L beaker containing 300 ml of high salt buffer (10 mM Tris-HCl pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 14.3 mM β-mercaptoethanol), and dialyzed against a total of 3 L low salt buffer (10 mM Tris-HCl pH 7.6, 50 mM NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 1.4 mM β-mercaptoethanol) added continuously via a peristaltic pump over a time course of 16 h under stirring conditions. β-mercaptoethanol was added freshly to all buffers. After complete transfer of low salt buffer, samples were additionally dialyzed against 1 L low salt buffer for 1 h at room temperature. DNA concentration of the SGD chromatin preparations was estimated with a DS-11+ spektrophotometer (Denovix) and if necessary stored at 4 °C for several weeks. To estimate the extend of the assembly degree, an aliquot of the sample was subjected to MNase digestion (as described below) for MNase-ladder read out.

extract_protocol:
MNase-seq  After apyrase addition, remodeling reactions were supplemented with CaCl2 to a final concentration of 1.5 mM and digested with 100 U MNase to generate mostly monoucleosomal DNA. Chd1-reaction were incubated with 20 U MNase to get the same extent of mononucleosomal DNA. 10 mM EDTA and 0.5% SDS (final concentrations) were added to stop the MNase digest. After proteinase K treatment for 30 min at 37°C, samples were ethanol precipitated and electrophoresed for 1.5 - 2 h at 100 V using a 1.5% agarose gel in 1x Tris-acetate-EDTA (TAE) buffer. Mononucleosome bands were excised and purified with PureLink Quick Gel Extraction Kit.
For library preparation, approximately 10 - 50 ng of mononucleosomal DNA was incubated with 1.25 U Taq polymerase (NEB), 3.75 U T4 DNA polymerase (NEB) and 12.5 U T4-PNK (NEB) in 1x ligation buffer (B0202S, NEB) for 15 minutes at 12 °C, 15 minutes at 37 °C and 20 minutes at 72 °C. To ligate NEBNext Adaptors (0.75 µM final concentration, from NEBNext Multiplex Oligos Kit) to the DNA, samples were incubated with T4 DNA ligase (NEB) at 25 °C  for 15 minutes, followed by incubation with 2 U USER enzyme (NEB) for 10 minutes at 37°C. Fragments were purified using 2 volumes AMPure XP beads (Beckman Coulter) and amplified for 8-10 cycles using NEBNext Multiplex Oligos, Phusion High-Fidelity DNA Polymerase (1 U, NEB), deoxynucleotide solution mix (dNTP, 2.5 mM, NEB) and Phusion HF Buffer (1x, NEB). The following protocol was applied for amplification: 98 °C for 30 s, 98°C for 10s, 65 °C for 30s, 72 °C for 30s with a final amplification step at 72 °C for 5 minutes. The Qubit dsDNA HS Assay Kit (Invitrogen) was used to assess the DNA content of 1 µL PCR reaction. DNA was purified from agarose gels via PureLink Quick Gel Extraction Kit, measured again with Qubit dsDNA HS Assay Kit and diluted to final concentration of 10 nM (calculation based on the assumption that the DNA fragment length is 272 bp, i. e., 147 bp nucleosomal DNA and 122 bp sequencing adaptor). Diluted samples were pooled according to sequencing reads (~6 Mio reads/ sample). The final pool was quantified by BioAnalyzer (Agilent) and analyzed on an Illumina HiSeq 1500 in the 50 bp single-end or paired-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

treatment_protocol: Genome-wide remodeling reaction: All remodeling reactions were performed at 30 °C in 100 µL with final buffer conditions of 26.6 mM HEPES-NaOH pH 7.5, 1 mM Tris-HCl pH 7.6, 85.5 mM NaCl, 8 mM KCl, 10 mM ammonium sulfate, 10 mM creatine phosphate (Sigma), 3mM MgCl2, 2.5 mM ATP, 0.1 mM EDTA, 0.6 mM EGTA, 1 mM DTT, 14% glycerol, 20 ng/µL creatine kinase (Roche Applied Science). Remodeling was started by adding 10 µl SGD chromatin and terminated by adding 0.8 U apyrase followed by incubation at 30 °C for 30 minutes.

tag: histone type

value: Drosophila melanogaster embryos

tag: remodeler

tag: remodeling barrier

tag: histone-dna ratio

tag: sequencing mode

value: paired-end


title: Replicate2_hs_INO80wt_04_PE

description: in vitro, plasmid DNA

value: recombinant Homo sapiens


title: 22Rv1, ZFX ChIP in 22Rv1 - rep1

tag: cell line


title: Replicate4_INO80_02_PE

description: in vitro, plasmid DNA


title: Replicate2_hs_SGDtl_04_PE

description: in vitro, plasmid DNA


title: Replicate2_hs_INO80tl_04_PE

description: in vitro, plasmid DNA

value: recombinant Homo sapiens without histone tails


title: Replicate2_hs_SGDwt_04_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-HSA1_04_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-ct_04_PE

description: in vitro, plasmid DNA

value: INO80-C. thermophilium


title: Replicate4_INO80-ct_02_PE

description: in vitro, plasmid DNA


title: Replicate1_hs_INO80tl_04_PE

description: in vitro, plasmid DNA


title: Replicate1_hs_SGDtl_04_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-HSA2-HMGII_04_PE

description: in vitro, plasmid DNA


title: HEK293T, ZNF711 ChIP in HEK293T - rep2

value: From Kristian Helin lab


title: Replicate4_INO80-HSA2-HMGII_02_PE

description: in vitro, plasmid DNA


title: HEK293T, ZNF711 ChIP in HEK293T - rep1

value: kidney cell line HEK293T


title: Replicate4_INO80-HSA1_02_PE

description: in vitro, plasmid DNA


title: 22Rv1, ZNF711 ChIP in 22Rv1 - rep1


title: Replicate4_INO80-HSA1-HMGII_04_PE

description: in vitro, plasmid DNA


title: HEK293T, ZFX and ZNF711 DKO - clone 3 - RNAseq, rep3

data_processing:
RNA-seq results were aligned to Gencode v19 and reads were counted using STAR.
Read count table is generated using STAR as well.
Genome_build: hg19
Supplementary_files_format_and_content: text files include read count for each gene.

source_name: HEK293T, ZFX and ZNF711 DKO - clone 3

extract_protocol:
Total RNA were extracted following the trizol protocol.
Libraries were prepared using Kapa Stranded mRNA kit with beads (Kapa #KK8421) according to provided protocol.

tag: genotype

value: ZFX and ZNF711 DKO

tag: grna

value: ZFX KO:g1, g2; ZNF711 KO:g1,g2

value: DKO #Lady


title: HEK293T, ZFX and ZNF711 DKO - clone 2 - RNAseq, rep1

source_name: HEK293T, ZFX and ZNF711 DKO - clone 2

value: DKO #Jake


title: HEK293T, ZFX and ZNF711 DKO - clone 2 - RNAseq, rep2


title: HEK293T, ZFX and ZNF711 DKO - clone1 - RNAseq, rep2

source_name: HEK293T, ZFX and ZNF711 DKO - clone1

value: DKO #Seven


title: Replicate4_INO80-HSA1-HMGII_02_PE

description: in vitro, plasmid DNA


title: Replicate4_SGD_04_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-HMGII_02_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-HMGII_04_PE

description: in vitro, plasmid DNA


title: Replicate4_SGD_02_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-DN_04_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-DNhp10_02_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-DN_02_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-DNhp10_04_PE

description: in vitro, plasmid DNA


title: HEK293T, ZNF711 single KO - clone 2 - RNAseq, rep3

source_name: HEK293T, ZNF711 single KO - clone 2

value: ZNF711 single KO

value: ZNF711 KO:g2,g3


title: HEK293T, ZFX and ZNF711 DKO - clone 3 - RNAseq, rep1


title: HEK293T, ZFX and ZNF711 DKO - clone 2 - RNAseq, rep3


title: HEK293T, ZFX and ZNF711 DKO - clone 3 - RNAseq, rep2


title: HEK293T, ZFX and ZNF711 DKO - clone1 - RNAseq, rep3


title: Replicate4_INO80-HSA2_04_PE

description: in vitro, plasmid DNA


title: Replicate4_INO80-HSA2_02_PE

description: in vitro, plasmid DNA


title: Replicate3_INO80_02_PE

description: in vitro, plasmid DNA


title: HEK293T, ZFX and ZNF711 DKO - clone1 - RNAseq, rep1


title: Ews1.crispr_lin28b_gfp

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

data_processing:
Alignment of the reads to the human transcriptome using RSEM
Genome_build: Human transcriptome according to Ensembl, version 79
Supplementary_files_format_and_content: Tab delimited files containg the TPM of each gene

molecule: polyA RNA

source_name: Spherogenic culture from Ewing sarcoma, sample 1, with sgRNA against GFP

growth_protocol: Primary EwS spheres were cultured in IMDM (Gibco, USA), supplemented with 20% KO serum (Gibco, USA), 10 ng/mL human recombinant EGF and bFGF (Invitrogen, USA), and 1% Pen/Strep (Gibco, USA) in ultra-low attachment flasks (Corning, USA)

extract_protocol:
Total RNA was isolated using miRCURY™ RNA Isolation Kit - Cell & Plant (Exiqon, Denmark) according to the manufacturer's recommendations
using the Illumina Tru-seq library preparation kit following the manufacturer instructions.

treatment_protocol: 1632 chemical inhibitor (Tocris, UK) was dissolved in DMSO according to the manufacturer’s recommendations. EwS spheres were dissociated and re-suspended in 6-well plates in complete medium containing either solvent (DMSO) or the 1632 inhibitor at day 0. The drug was added at a concentration of 50 µM or 250 µM, and an equal volume of DMSO without the drug was used as a control. Media were aspirated on day 4 and replaced with fresh DMSO and inhibitor. EWS-FLI-1 RNA stability EwS2 cells were treated with 10 µg/ml of Actinomycin D (ActD; Sigma-Aldrich A1410), or an equal volume of solvent (DMSO) as control. Cells were infected with sh CTRL or sh2 LIN28B lentiviral vectors, ActD or DMSO were added 36 hours later, and RNA was harvested at 0, 4, 8, 12 and 24 hours post ActD treatment.

tag: lin28b status

value: positive

tag: shRNA

tag: sgrna

value: GFP

tag: overexpression

tag: drug treatment


title: HEK293T, ZNF711 single KO - clone 1 - RNAseq, rep3

source_name: HEK293T, ZNF711 single KO - clone 1

value: ZNF711 KO:g1,g2

value: ZNF711 KO #4


title: Ews1.inhibitor_DMSO

source_name: Spherogenic culture from Ewing sarcoma, sample 1, treated with DMSO

value: DMSO


title: Replicate2_INO80_02_PE

description: in vitro, plasmid DNA

value: Drosophila melanogaster embryos

value: paired-end


title: Replicate1_SGD_04_PE

description: in vitro, plasmid DNA


title: TNBC-B1-2017-P4

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 11.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.

source_name: Triple negative breast cancer

label_protocol: DNAs from FFPE tissue were treated with DNAse 1 for 1 minute prior to Klenow-based labeling. In each case 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols. All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

growth_protocol: Formalin fixed paraffin embedded (FFPE) tissue samples were collected at room temperature.

extract_protocol: Excess paraffin was removed from each FFPE sample with a scalpel from either side of 40-60 μm scrolls). We used one to three 50 µm scrolls from each FFPE tissue block to obtain sufficient numbers of intact nuclei for subsequent sorting and molecular assays. Biopsies were dewaxed, digested then minced in the presence of NST buffer and DAPI according to published protocols (Holley et al, 2012). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Influx cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA). DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).

treatment_protocol: All samples were from treatment naïve surgical resections

tag: patient diagnosis

value: Lynch Syndrome

tag: tissue source

value: Flow sorted tumor from surgical resection

tag: tissue

value: Triple negative breast cancer

tag: tissue preparation

value: FFPE

tag: flow sort content

value: Human tumor

source_name: Reference Normal female genome

tag: sample type

value: Reference pooled 46XX


title: Ews2.sh_ewsfli1

source_name: Spherogenic culture from Ewing sarcoma, sample 2, with shRNA against EWSFLI1


title: PTCC-2008-P4

source_name: Papillary transitional cell carinoma of the thyroid


title: TNBC-B5-2017-P4


title: Duodenal Carcinoma-2008-P4

source_name: Duodenal carcinoma

value: Duodenal carcinoma


title: TNBC-B6-2017-P4


title: Replicate3_INO80-ct_02_PE

description: in vitro, plasmid DNA

tag: histone type

tag: remodeler

value: INO80-C. thermophilium

tag: remodeling barrier


title: HEK293T, ZNF711 single KO - clone 2 - RNAseq, rep1

tag: cell line

value: kidney cell line HEK293T

value: ZNF711 single KO

tag: clone name


title: Replicate3_SGD_02_PE

description: in vitro, plasmid DNA

tag: histone-dna ratio

tag: sequencing mode


title: HEK293T, ZNF711 single KO - clone 2 - RNAseq, rep2

tag: genotype

tag: grna

value: ZNF711 KO:g2,g3


title: Ews1.crispr_lin28b

source_name: Spherogenic culture from Ewing sarcoma, sample 1, with sgRNA against LIN28B

tag: lin28b status

value: positive

tag: shRNA

tag: sgrna

tag: overexpression


title: Replicate2_SGD_02_PE

description: in vitro, plasmid DNA


title: Ews1.sh_ewsfli1

source_name: Spherogenic culture from Ewing sarcoma, sample 1, with shRNA against EWSFLI1

tag: drug treatment


title: Ews2.sh_ewsfli1_gfp

source_name: Spherogenic culture from Ewing sarcoma, sample 2, with shRNA against GFP

value: GFP


title: Ews1.inhibitor

source_name: Spherogenic culture from Ewing sarcoma, sample 1, treated with LIN28B inhibitor


title: HEK293T, ZNF711 single KO - clone 1 - RNAseq, rep2

value: ZNF711 KO:g1,g2

value: ZNF711 KO #4


title: HEK293T, ZFX single KO - clone2 - RNAseq, rep3

source_name: HEK293T, ZFX single KO - clone2

value: ZFX single KO

value: ZFX KO:g1, g2

value: ZFX KO #58


title: Replicate1_SGD_02_PE

description: in vitro, plasmid DNA

source_name: in vitro reconstituted chromatin

value: Drosophila melanogaster embryos

value: paired-end


title: HEK293T, ZNF711 single KO - clone 1 - RNAseq, rep1


title: Ews1.sh_ewsfli1_gfp

source_name: Spherogenic culture from Ewing sarcoma, sample 1, with shRNA against GFP


title: HEK293T, ZFX single KO - clone2 - RNAseq, rep2


title: Ews3.over_lin28b_empty

source_name: Spherogenic culture from Ewing sarcoma, sample 3, with empty vector

value: negative

value: empty vector


title: Replicate1_INO80_02_PE

description: in vitro, plasmid DNA


title: HEK293T, ZFX single KO - clone2 - RNAseq, rep1


title: Replicate1_INO80_04_PE

description: in vitro, plasmid DNA


title: Ews3.over_lin28b

source_name: Spherogenic culture from Ewing sarcoma, sample 3, with LIN28B overexpression


title: Replicate7_dm_none_Ino80-WalkerB

description: in vitro, plasmid DNA

value: single-end


title: Ews2.sh_lin28b_gfp


title: HEK293T, ZFX single KO - clone1 - RNAseq, rep2

source_name: HEK293T, ZFX single KO - clone1

value: ZFX KO #48


title: Replicate7_dm_Reb1_INO80

description: in vitro, plasmid DNA

value: Reb1-20 nM


title: HEK293T, ZFX single KO - clone1 - RNAseq, rep3

value: kidney cell line HEK293T


title: HEK293T, ZFX single KO - clone1 - RNAseq, rep1


title: Ews1.sh_lin28b_gfp


title: Ews1.sh_lin28b

source_name: Spherogenic culture from Ewing sarcoma, sample 1, with shRNA against LIN28B


title: HEK293T, Control - RNAseq, rep3

source_name: HEK293T, Control

value: EGV


title: HEK293T, Control - RNAseq, rep2


title: Replicate_DSB2_dm_KpnI_INO80

description: in vitro, plasmid DNA

value: Double strand breaks (KpnI)


title: Replicate_DSB2_dm_KpnI_none

description: in vitro, plasmid DNA


title: Replicate_DSB2_dm_EcoRV_none

description: in vitro, plasmid DNA

value: Double strand breaks (EcoRV)


title: Replicate_DSB2_dm_EcoRV_INO80

description: in vitro, plasmid DNA


title: HEK293T, Control - RNAseq, rep1


title: Ews2

source_name: Spherogenic culture from Ewing sarcoma, sample 2

value: positive


title: Ews3

source_name: Spherogenic culture from Ewing sarcoma, sample 3


title: Ews1

source_name: Spherogenic culture from Ewing sarcoma, sample 1


title: Ews2.sh_lin28b

source_name: Spherogenic culture from Ewing sarcoma, sample 2, with shRNA against LIN28B


title: Replicate_DSB2_dm_BamHI_none

description: in vitro, plasmid DNA

value: Double strand breaks (BamHI)


title: Replicate7_hs_none_none

description: in vitro, plasmid DNA

value: recombinant Homo sapiens


title: Replicate_DSB2_dm_BamHI_INO80

description: in vitro, plasmid DNA


title: Replicate8_dm_none_none

description: in vitro, plasmid DNA


title: Replicate_DSB1_dm_none_none

description: in vitro, plasmid DNA


title: Replicate_DSB1_dm_BamHI_none

description: in vitro, plasmid DNA


title: Replicate8_dm_none_INO80

description: in vitro, plasmid DNA


title: Replicate8_hs_Reb1-6nM_INO80

description: in vitro, plasmid DNA

value: Reb1-6 nM


title: Replicate8_dm_Reb1_none

description: in vitro, plasmid DNA


title: Replicate8_hs_Reb1-2nM_INO80

description: in vitro, plasmid DNA

value: Reb1-2 nM


title: Replicate8_hs_none_none

description: in vitro, plasmid DNA


title: Replicate7_hs_none_Ino80-Rvb1-2

description: in vitro, plasmid DNA


title: Replicate8_dm_Reb1_INO80

description: in vitro, plasmid DNA


title: Replicate8_hs_Reb1_INO80

description: in vitro, plasmid DNA


title: Replicate8_hs_none_INO80

description: in vitro, plasmid DNA


title: Replicate7_dm_none_none

description: in vitro, plasmid DNA


title: Replicate7_dm_none_INO80

description: in vitro, plasmid DNA


title: Replicate6_hs_Reb1_INO80

description: in vitro, plasmid DNA


title: Ews4

source_name: Spherogenic culture from Ewing sarcoma, sample 4


title: Replicate7_hs_none_Ino80-WalkerB

description: in vitro, plasmid DNA


title: Replicate6_dm_none_INO80

description: in vitro, plasmid DNA


title: Replicate7_hs_none_INO80

description: in vitro, plasmid DNA


title: Replicate6_hs_none_INO80

description: in vitro, plasmid DNA


title: Replicate_DSB1_dm_BamHI_INO80

description: in vitro, plasmid DNA


title: Replicate5_hs_Reb1_INO80

description: in vitro, plasmid DNA


title: Replicate5_hs_none_INO80

description: in vitro, plasmid DNA


title: Replicate3_hs_Reb1_INO80

description: in vitro, plasmid DNA


title: Replicate4_hs_Reb1_INO80

description: in vitro, plasmid DNA


title: Replicate4_dm_none_INO80

description: in vitro, plasmid DNA


title: Replicate3_hs_none_none

description: in vitro, plasmid DNA


title: Replicate5_dm_none_INO80

description: in vitro, plasmid DNA


title: Day 14

first: Jiangping

last: Song

address: 167A Beilishi Road

department: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.2 with default parameters. The clonotype and annotation for BCR and TCR were determined by Cellranger vdj with default parameters.
Cells were accepted with greater than 200 and fewer than 5000 unique mapped genes. Analysis was performed on cells with less than 5% mitochondrial mapping.
Genome_build: mm10

source_name: Cardiac immune cells

growth_protocol: Balc/c mice were subcutaneously injected with 250 μg of the α-MyHC peptide (Ac-RSLKLMATLFSTYASADR-OH; AnaSpec, AS-62554) emulsified with complete Freund’s adjuvant (Sigma, F5881) (1:1, w/w) on days 0 and 7 to establish EAM. Mice were examined using echocardiography and sacrificed at various time points including normal control, acute phase, subacute phase  and chronic myopathy phase

extract_protocol:
Hearts were digested with 200 U/ml collagenase type II, then alive immune cells were isolated by FACS with antibody CD45
The scRΝΑ-seq libraries were prepared using the single cell 5’ solution v2 reagent kit (Chromium, 1000006) according to the protocol provided with the 10x Genomics Chromium Single Cell Immune Profiling Solution. Briefly, FACS-sorted Cd45+ immune cells (90-95% viability) were encapsulated into droplets. After the RT step, droplets were disrupted and barcoded cDNAs were purified with DynaBeads, followed by 14 cycles of PCR amplification (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, and 72°C for 1 min] x 14 cycles; 72°C for 1 min). The resulting amplified cDNAs were sufficient to construct 5’ gene expression libraries and T/B cell receptor enriched libraries. The cDNAs from single-cell transcriptomes (50 ng) were fragmented, subjected to two rounds of size selection with SPRI beads (avg. size 450 bp), and sequenced on the Illumina NextSeq platform (High Output V2 Kit, 150 cycles). The cDNAs encoding the TCR/BCR library (10 ng) were amplified with 10 cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, and 72°C for 1 min] x 10 cycles; 72°C for 1 min), followed by an additional 10 cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, and 72°C for 1 min] x 10 cycles; 72°C for 1 min) using DNA primers provided in the kit. After library construction, VDJ region-enriched libraries were subjected to size selection with SPRI beads (average size of 600 bp) and sequenced using an HiSeq X Ten instrument.

tag: cell type

value: Cd45+ immune cell

tag: tissue

value: heart

tag: week

value: 6-8 weeks

tag: strain

value: Balb/c

tag: phase

value: acute inflammatory phase


title: Replicate2_hs_none_none

description: in vitro, plasmid DNA

tag: histone type

tag: remodeler

tag: remodeling barrier

value: single-end


title: Replicate2_hs-tl_none_none

description: in vitro, plasmid DNA

value: recombinant Homo sapiens without histone tails

tag: histone-dna ratio


title: Replicate2_sc_none_INO80

description: in vitro, plasmid DNA

value: recombinant Saccharomyces cerevisiae

tag: sequencing mode


title: Replicate2_hs-tl_none_INO80

description: in vitro, plasmid DNA


title: Ews4

hyb_protocol: Hybridization was performed according to manufacturer’s guidelines, Affymetrix® GeneChip® miRNA 4.0 Arrays (Affymetrix, Santa Clara, CA).

scan_protocol: Not provided

data_processing: Background subtraction and RMA normalization using the “oligo” Bioconductor package

label_protocol: Flash Tag Biotin HSR RNA Labeling Kit (Thermo-Fischer) was used. Samples were end-labeled according to manufacturer’s guidelines.

growth_protocol: Primary EwS spheres were cultured in IMDM (Gibco, USA), supplemented with 20% KO serum (Gibco, USA), 10 ng/mL human recombinant EGF and bFGF (PROSPEC) and 1% Pen/Strep (Gibco, USA) in ultra-low attachment flasks (Corning, USA)

extract_protocol: Total RNA was isolated using miRCURY™ RNA Isolation Kit – Cell & Plant (Exiqon) according to the manufacturer's recommendations. 100 ng of total RNA were used as input.

value: Spherogenic culture

value: Ewing sarcoma

tag: lin28 status

value: negative


title: Ews2


title: Ews1


title: Ews3


title: Replicate1_hs_none_Ino80-Rvb1-2

description: in vitro, plasmid DNA


title: Replicate1_dm_none_none

description: in vitro, plasmid DNA

value: Drosophila melanogaster embryos


title: Replicate3_dm_none_INO80

description: in vitro, plasmid DNA


title: Replicate2_hs_none_Ino80-Rvb1-2

description: in vitro, plasmid DNA


title: Day 60

value: myopathy phase


title: Replicate2_hs_Reb1_INO80

description: in vitro, plasmid DNA

value: Reb1-20 nM


title: Replicate1_hs_Reb1-1_3_INO80

description: in vitro, plasmid DNA

value: recombinant Homo sapiens


title: Replicate1_hs_Reb1-1_10_INO80

description: in vitro, plasmid DNA


title: Replicate2_dm_none_INO80

description: in vitro, plasmid DNA


title: OE3

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

institute: Max Planck Institute for heart and lung research

data_processing:
Basecalls performed using CASAVA version 1.7
Raw reads were stripped of adaptor sequences and low quality bases (Q<=20) were removed using Cutadapt (https://cutadapt.readthedocs.io/en/stable/guide.html). The processed reads were aligned to fly genome (dm6) with STAR aligner (version 2.7.0f) and genes with differential alternative splicing between WT and KO cells was identified using RSEM (version 1.3.0). Significantly differentially spliced events are defined as FDR < 0.05 and fold change of exon usage > 2
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Drosophila melanogaster

source_name: ko

extract_protocol:
Total RNA was extracted with TRIzol according to the manufacturer’s instructions (Invitrogen). PolyA(+) mRNA was isolated from total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kc

tag: genotype/variation

value: ko


title: Replicate1_sc_none_INO80

description: in vitro, plasmid DNA


title: Replicate1_hs-tl_none_INO80

description: in vitro, plasmid DNA


title: Replicate1_sc_none_none

description: in vitro, plasmid DNA


title: Replicate1_dm_none_INO80

description: in vitro, plasmid DNA


title: WT3

source_name: wt

value: wild type


title: Replicate1_hs-tl_none_none

description: in vitro, plasmid DNA


title: Day 21

value: Cd45+ immune cell

value: heart

value: subacute inflammatory phase


title: Replicate1_hs_Reb1_INO80

description: in vitro, plasmid DNA


title: Day 0

value: 6-8 weeks

value: Balb/c

value: normal control


title: OE2


title: Replicate2_dm_none_none

description: in vitro, plasmid DNA

value: single-end


title: Replicate1_in vivo_MNase-seq

description: in vivo, genomic DNA

source_name: BY4741 nuclei, in vivo MNase-seq

value: in vivo


title: WT2


title: WT1


title: OE1


title: DKS14_WCE

city: PACIFICA

first: Hiten

last: Madhani

state: CA

institute: UCSF

description:
Affinity purified DNA
processed data file:

data_processing:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  genome with bowtie v 1.1.2
Analysis performed using custom scripts from bedgraph files normalized to wild type (untagged)
Genome_build: C. neoformans CNA3
Supplementary_files_format_and_content: .bedgraph: Signal of ChIP-seq of the sample normalized to the untagged (wild type, K1) sample and smoothed to a 50bp window

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: Samples were inoculated at less than an OD600 of 0.01 from starter cultures in YPAD or YNB at 30°C until reaching OD600 of 1.0, 5.0, or 10.0. An aliquot of the culture as it grew in optical density was taken and harvested by centrifugation at 2000xg for 5 minutes.

extract_protocol:
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNA was isolated by antibodies directed to our proteins of interest (10 mg anti-FLAG M2).  DNA was then isolated by incubation with SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
library preparation as described in Homer et al. 2016

value: mixed

tag: genotype

value: all

tag: optical density (od600)

tag: media

value: YNB

tag: antibody

value: anti-FLAG

tag: protocol

value: ChIP-seq


title: DKS14_nL1

value: Liv3-2xFLAG; nrg1_delta


title: DKS14_L2


title: DKS14_L1


title: DKS14_cL2

value: Liv3-2xFLAG; cqs2_delta


title: DKS14_cL1


title: DKS14_cN2

value: 3xFLAG-Nrg1; cqs21_delta


title: DKS14_qN2_log

value: 3xFLAG-Nrg1; qsp1_delta


title: RET SH-1, biological replicate 2

first: Ashik Ahmed

last: Abdul Pari

address: Im neuenheimer Feld 280

institute: German Cabcer Research Institute

hyb_protocol: 15 μg of cRNA was then converted to sensestrand DNA (ss-cDNA). After fragmentation and terminal labeling, 5,5 ug of biotinylated ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays.

scan_protocol: Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: All intensity data were quarantile normalized.

label: Biotin

source_name: RET (mouse melanoma cells)

label_protocol: Biotin-labeled ss-cDNA samples for hybridization on GeneChip™ Mouse Gene 2.0 ST Arrays (Affymetrix) were prepared according to Affymetrix's recommended sample labeling procedure as described in the Gene Chip WT Plus Reagent Kit guide. In brief, 100 ng total RNA was used for complementary DNA (cDNA) synthesis and in vitro transcription step to synthesize cRNA according to the Affymetrix® GeneChip® WT Plus Reagent Kit. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: Control and Angpt2 silenced melanoma cells  were cultured in DMEM high glucose supplemented with 10% FCS, 1% penicillin/streptomycin  and 1% non-essential amino acid

extract_protocol: Total RNA were isolated using  GenElute Mammalian Total RNA Purification Kit (Sigma) according to the manufacturer described protocol.

treatment_protocol: Equal number of control and Angpt2 silenced cells were seeded in a 6 well plate and cultured for 24h. Next, the cells were lysed and RNA was isolated.

value: Angpt2 shrna-1


title: RET SH-1, biological replicate 3


title: DKS14_qN1_OD1


title: DKS14_N1


title: DKS14_N2


title: DKS14_nC1

value: Cqs2-2xFLAG; nrg1_delta


title: DKS14_nC2


title: RET SH-1, biological replicate 1


title: RET GFP, biological replicate 1

value: non targeting shrna


title: DKS14_C2


title: RET GFP, biological replicate 3