title: B_wt_control_RNAseq

status: Public on Jun 08 2020

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

description:
B_control_RNAseq
processed data file:
A_B_control_merged_minus_strand.bedgraph
A_B_control_merged_plus_strand.bedgraph

data_processing:
Demultiplexing. Command: pyBarcodeFilter.py -f raw_file.fastq -b barcodes_file.txt
Adapter stripping and quality control. Command: flexbar -r file.fastq -a adapters.txt -ao 4 -m 11 -at RIGHT -u 2 -q TAIL -qf i1.8
Collapsing. Command: pyFastqDuplicateRemover.py -f file.fastq (Note that this step was used only for the CRAC analysis. RNAseq files were not collapsed)
Removal of low-complexity reads. Command: bbduk.sh in=file.fasta entropy=0.5 entropywindow=10 entropyk=6
Alignment. Command: novoalign -f file.fasta -r Random -o SAM -d genome.novoindex
samtools view -bS file.sam
samtools sort file.bam
Bedgraph files (+ strand). Command: bedtools genomecov -split -strand + -ibam sorted_file.bam -bg -scale variable > file_plus_strand.bedgraph
Bedgraph files (- strand). Command: bedtools genomecov -split -strand - -ibam sorted_file.bam -bg -scale variable > file_minus_strand.bedgraph
Read counting. Command: pyReadCounters.py -f file.bam --file_type=bam --sense --gtf=annotation_file.gtf
Genome_build: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping
Supplementary_files_format_and_content: The .txt files (generated using pyReadCounters.py) contain information on the number of reads mapping to each transcript. The bedgraph files show the distribution of reads across the genome. Individual replicates were merged into a single file to generate the bedgraph files.

organism: Saccharomyces cerevisiae

source_name: control

growth_protocol: For CRAC experiments (07-99), cells were cultured in SC -TRP medium containing 2% glucose to 0.4 OD. For the 'control', cells were then subjected to 100 mJ of 254nm UV-crosslinking (4-6 seconds), collected by filtration, resuspended in 50 mL of ice cold PBS, centrifuged to pellet, and frozen at -80°C. For all other conditions,  cells at 0.4 OD were first collected by filtration,  then transferred to the appropriate medium and cultured for either 30 seconds or 16 minutes prior to UV-crosslinking. All subsequent harvesting steps were identical to the control. For RNAseq experiments (A-F), we used the same approach as for CRAC but without the crosslinking step.

extract_protocol:
The CRAC protocol is based on Tuck and Tollervey, 2013.
Modifications are described in Bresson and Tollervey, 2020.

tag: cell/ploidy type

value: haploid cells

tag: genotype/variation

value: control


title: A5AbRi

status: Public on Jun 29 2020

type: SRA

city: London

first: Rocio Teresa

last: Martinez-Nunez

state: Greater London

address: 5th Floor Tower Wing, Guy’s Campus

department: Infectious Diseases

country: United Kingdom

institute: King's College London

description: RNA enriched in ribosome pellets

library_source: transcriptomic

data_processing:
Base Quality and Phred score were calculated employing the Illumina CASAVA v1.8 software with more than 92% of all reads for all samples having a Q30
Bowtie v2.2.3 was used to index the reference genome and trimmed paired-end reads were aligned using TopHat v2.0.12.
HTSeq v0.6.1 using the union mode was employed to count mapped reads and generate FPKM
Differential gene expression analysis was performed employing DESeq with Benjamini and Hochberg’s FDR correction

molecule: total RNA

organism: Rattus norvegicus

source_name: Ribosome-cushion Ab treated

extract_protocol: Library preparation and RNA sequencing was done by Novogene (Hong Kong). Libraries were made using polyadenylated mRNA isolation, employing NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Three samples had lower RNA amounts and a higher efficiency bead capture was employed for only those, maintaining the same library preparation kit otherwise. Base Quality and Phred score were calculated employing the Illumina CASAVA v1.8 software with more than 92% of all reads for all samples having a Q30. Bowtie v2.2.3 was used to index the reference genome and trimmed paired-end reads were aligned using TopHat v2.0.12.

tag: tissue

value: Primary rat cortical neurons

tag: treatment

value: Ribosome-cushion Ab treated


title: AcAPE1 seq_HCT116 cells_rep1

status: Public on Jun 02 2020

city: Omaha

first: Shrabasti

last: Roychoudhury

state: NE

address: S 42nd &, Emile St

country: USA

institute: University of Nebraska Medical Center

library_source: genomic

data_processing:
FASTQ files were generated after adaptor sequences, and low quality (Phred score < 20) ends were trimmed from the ChIP sequences using the Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). FASTQ files were aligned to the human genome (GRCh37/hg19) using the sequence aligner Bowtie2 (version 2.2.3)
The software package Picard routine Mark Duplicates (http://broadinstitute.github.io/picard/) was used to remove sequence duplications.
Biological replicates were then merged using SAMtools.
The merged files were used to call peaks using MACS2 peak caller software (version 2.1.1). A peak from a given antibody was considered significant if it had a fold change ≥2 over IgG, ≥15 reads, and a p-value<0.001.
All bigWig files generated using the deepTools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: HCT116 CELLS

growth_protocol: Cells were plated in a 150 mm cell culture dish with respective media and cultured for 24 hours.

extract_protocol:
Lysates were clarified from sonicated nuclei. ARP-tagged DNA was isolated with Streptavidin and DNA-protein complexes were isolated with antibody.
The library was made using New England Biolabs NEB Next Ultra II DNA Library Prep Kit. High-throughput sequencing was conducted at the UNMC Sequencing Core, using an Illumina HiSeq 2500 Genome Analyzer.

treatment_protocol: For mapping AP sites, 1 mM biotin-conjugated ARP (Life Technologies, #A10550) was fed to cells for 3 hours.

tag: cell line

tag: cell type

value: colon cancer cells

tag: passages

value: 3 to 5

tag: ip reagent

value: α-AcAPE1 (Chattopadhyay R, et al. (2008);Molecular and cellular biology 28(23):7066-7080)


title: E_wt_42C_16min_RNAseq

description:
E_42C_16min_RNAseq
processed data file:
E_F_42C_16min_merged_minus_strand.bedgraph
E_F_42C_16min_merged_plus_strand.bedgraph


title: F_wt_42C_16min_RNAseq

description:
F_42C_16min_RNAseq
processed data file:
E_F_42C_16min_merged_minus_strand.bedgraph
E_F_42C_16min_merged_plus_strand.bedgraph


title: C_wt_GE_16min_RNAseq

description:
C_GE_16min_RNAseq
processed data file:
C_D_GE_16min_merged_minus_strand.bedgraph
C_D_GE_16min_merged_plus_strand.bedgraph

value: GE


title: D_wt_GE_16min_RNAseq

description:
D_GE_16min_RNAseq
processed data file:
C_D_GE_16min_merged_minus_strand.bedgraph
C_D_GE_16min_merged_plus_strand.bedgraph


title: BG4 seq_APE1shRNA A549 cells_rep2

source_name: A549 CELLS

value: lung adenocarcinoma cells

value: α-BG4; Mouse monoclonal (Abosolute biology)


title: Actinomycin D_ AcOGG1_A549 cells

value: Actinomycin D

value: α-AcOGG1 (Bhakat KK, et.al. (2006),Molecular and cellular biology 26(5):1654-1665)


title: BG4 seq_A549 cells_rep3


title: AP seq_HCT116 cells

value: Biotinylated  ARP (Thermo fisher #A10550)


title: Actinomycin D_AcAPE1_A549 cells


title: BG4 seq_APE1shRNA A549 cells_rep1


title: BG4 seq_A549 cells_rep2


title: BG4 seq_A549 cells_rep1


title: AcAPE1 seq_A549 cells_rep3


title: A_wt_control_RNAseq

description:
A_control_RNAseq
processed data file:
A_B_control_merged_minus_strand.bedgraph
A_B_control_merged_plus_strand.bedgraph


title: AcOGG1 seq_A549 cells_rep1


title: AcAPE1 seq_A549 cells_rep2


title: AcAPE1 seq_A549 cells_rep1


title: AcAPE1 seq_HCT116 cells_rep2


title: APE1 seq_A549 cells_rep1

value: α-APE1; Mouse monoclonal (Novus biologicals #13B8E5C2)


title: APE1 seq_A549 cells_rep2


title: AP seq_A549 cells_rep1


title: AP seq_A549 cells_rep2


title: Actinomycin D_BG4_A549 cells


title: Actinomycin D_APE1_A549 cells

value: α-APE1; Rabbit polyclonal


title: 64

status: Public on Jul 20 2020

city: Portland

first: Suzy

middle: CP

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

data_processing:
Sequence reads were aligned to in silico bisulfite converted amplicon reference sequences (https://github.com/rose-driscoll/methylation-analysis/tree/master/reference_sequences/Bisulfite_Genome/CT_conversion) with bowtie2 using options -N 1 --dovetail -x
Samtools view -bS, samtools sort, and samtools mpileup -d 200000 were used to produce a vcf file for each sample
Custom python scripts available at https://github.com/rose-driscoll/methylation-analysis/blob/master/percent-methylation/methylation_pipeline_samtoolspythonandcat_20180605_RD.txt were employed to count the number of As, Cs, Ts, and Gs observed at each base, extract data for selected bases (CpG Cs, Ts and non-CpG Cs, and As and Gs, relative to the reference sequence), and calculate relevant statistics such as % methylation for CpG C bases and % error for A and G bases.
In a second pipeline, forward and reverse reads from each sample were combined using FLASH and aligned to in silico bisulfite converted amplicon reference sequences (https://github.com/rose-driscoll/methylation-analysis/tree/master/reference_sequences/Bisulfite_Genome/CT_conversion) with bowtie2 using options -N 1 -x in order to identify which amplicon they had come from
Reads from each of the four amplicons were extracted from the bowtie alignment, dereplicated with usearch -derep_fulllength -sizeout, and aligned with muscle along with a reference sequence.
Custom python scripts available at https://github.com/rose-driscoll/methylation-analysis/tree/master/epialleles were employed to identify CpG sites in the aligned reads.
Command line tools (cut and awk) were employed to paste together CpG bases and identify an 'epiallele' for each read, and count the number of times each unique epiallele appeared for each sample.
Supplementary_files_format_and_content: tab-delimited text files with % methylation per CpG site (all_CpGs_20180605_RD.txt), bisulfite conversion completeness per base (all_conversion_20180605_RD.txt), sequencing error per base (all_error_20180605_RD.txt), or epiallele abundance (all_haplotypes_w_AP6_20180612.tab) per sample.

organism: Pelvicachromis pulcher

source_name: pH_neutral_Day 30_trunk

extract_protocol:
Fish were euthanized with tricaine methanesulfonate and tissues were dissected out and placed in 95% EtOH. DNA was extracted by proteinase K digestion and phenol:chloroform purification. 500 ng genomic DNA was bisulfite treated using Zymo Research EZ Methylation-Gold kit.
Four regions were amplified (Bioline Immomix) from bisulfite-treated gDNA samples using primers with Illumina-compatible tails. Fragments were cleaned (Aline Biosciences PCRCLEAN DX) before a second round of PCR to attach sample-specific barcodes. Samples were pooled at equal concentrations and column purified to produce Illumina libraries.
DNA amplicon sequencing

value: neutral

tag: timepoint

value: Day 30

tag: sexual phenotype

value: trunk

tag: set

tag: molecule subtype

value: ampliconic DNA


title: O296

status: Public on Jun 01 2020

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description: gender: Too Young

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were alligned using Kallisto, and transcript level tpm values were summed up to gene level tpm values
Genome_build: GRCm38 version 95
Supplementary_files_format_and_content: tpm.tsv contains the transcript per million levels of each gene within each cell, in a tab deliminated matrix

organism: Mus musculus

source_name: Stratum Pyramidale

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

tag: morphological type

value: vBC

tag: axon morphology

value: BC

tag: dendrite morphology

value: Vertical

tag: gender

value: not determined

tag: location

value: Left

tag: age

tag: quality control

value: Passed


title: O299

description: gender: Too Young

value: Right


title: O303

description: gender: Too Young

value: Failed


title: O301

description: gender: Too Young


title: O297

description: gender: Too Young


title: O290

description: gender: Too Young


title: O286

description: gender: Too Young


title: O305

description: gender: Too Young


title: O285

description: gender: Too Young


title: O284

description: gender: Too Young


title: O255

description: gender: Too Young


title: O251

description: gender: Too Young


title: O300

description: gender: Too Young


title: O248

description: gender: Too Young

source_name: Stratum Oriens

value: hBC

value: Horizontal


title: O250

description: gender: Too Young


title: O242

description: gender: Too Young


title: O246

description: gender: Too Young


title: O221

description: gender: Too Young


title: O220

description: gender: Too Young


title: O218

description: gender: Too Young


title: O292

description: gender: Too Young


title: O205

description: gender: Too Young


title: O210

description: gender: Too Young


title: O211

description: gender: Too Young


title: O204

description: gender: Too Young


title: O282

description: gender: Too Young


title: O216

description: gender: Too Young


title: O160

value: Female


title: O240

description: gender: Too Young


title: O171


title: O164

value: AAC


title: O162


title: O159

value: hBIC

value: BIC


title: O165

value: vBIC


title: O147

value: Male


title: O304

description: gender: Too Young


title: O145


title: O141


title: O135


title: O138


title: O137


title: O132


title: O139


title: O131


title: O130


title: O125


title: O129


title: O128


title: O149


title: O113


title: O127


title: O114


title: O109


title: O117


title: O76


title: O111


title: O73


title: O89


title: O78


title: O66


title: O61


title: O60


title: O59


title: O56


title: O62


title: O65


title: O58


title: O287

description: gender: Too Young


title: O100


title: O48


title: O102


title: O49


title: O103


title: O47


title: O55


title: O44


title: O41


title: O36


title: O39


title: O222

description: gender: Too Young


title: O32


title: O35


title: O34


title: O26


title: O31


title: O24


title: O46


title: O243

description: gender: Too Young


title: O54


title: 16

value: neutral

value: Day 30

tag: tissue

value: trunk

value: ampliconic DNA


title: Muscle_PRE_GS20_Rep1

status: Public on May 29 2020

type: genomic

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

hyb_protocol: The amplification products were then fragmented, precipitated, resuspended, and then hybridised onto the BeadChips.

scan_protocol: The chips were washed and then stained prior to application on an HMEPIC array according to the manufacturer’s protocol. The HMEPIC arrays were then visualised and analysed using the Illumina HiScan instrument and GeneStudio software (Illumina).

data_processing: Any sample with > 10% of probes with detection p-value > 0.01 was removed (default parameter of the champ.load function). All probes with missing β-values, with a detection p-value > 0.01, probes with a bead count < 3 in at least 5% of samples, non-CG probes and probes aligning to multiple locations were removed, and for datasets containing males and females, probes located on the sex chromosomes were removed. SNP-related probes (“EUR” population probes in Zhou et al. 28) were also removed. β-values were obtained, and defined as  β-value =(intensity of the Methylated allele)/(intensity of the Unmethylated allele + intensity of the Methylated allele + 100)   Then, β-mixture quantile normalization (BMIQ) method was applied to adjust for the Type I and Type II probe designs for methylation profiles generated from the HM450 and HMEPIC arrays. To identify technical and biological sources of variation in each individual dataset, Singular Value Decomposition (SVD) was performed. In all pre-processed datasets, both the plate and the position on the plate were identified as significant technical effects. Thus, all β-values were converted to M-values and the ComBat function from the sva package used to adjust directly for these technical artefacts.

label: Cy5 and Cy3

source_name: Vastus lateralis, at baseline, from individual GS20, Rep1

label_protocol: For bisulphite conversion of gDNA for subsequent methylation arrays, 500 ng total gDNA was bisulfite converted using the EZ DNA methylation kit (ZYMO research) as per the manufacturer’s instructions. Bisulfite converted DNA (bDNA) was then used for the methylation array protocol. riefly, bDNA was used for amplification of the regions of interest for binding to the Infinium BeadChip arrays.

extract_protocol: Total gDNA was extracted from 15 mg muscle tissue using the Allprep DNA/RNA/miRNA universal kit (Qiagen). The manufacturer’s protocol was modified to include the use of a Bullet Blender Gold Homogeniser (NextAdvance) in combination with dry ice for complete tissue digestion to ensure no enzymatic digestion of the DNA. Following isolation, DNA quantity and quality was measured using the dsDNA Broad Range Qubit kit (ThermoFisher scientific) on a Qubit Flourometer V2.0.

tag: Sex

value: M


title: Muscle_PO_GS18_Rep2

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS18, Rep2


title: Muscle_PRE_GS19_Rep1

source_name: Vastus lateralis, at baseline, from individual GS19, Rep1


title: Muscle_PO_GS8_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS8, Rep1


title: Muscle_PO_GS7_Rep2

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS7, Rep2


title: Muscle_4WP_GS22_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS22, Rep1


title: Muscle_PRE_GS24_Rep1

source_name: Vastus lateralis, at baseline, from individual GS24, Rep1


title: Muscle_PO_GS24_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS24, Rep1


title: Muscle_4WP_GS5_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS5, Rep1


title: Muscle_PO_GS19_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS19, Rep1


title: Muscle_4WP_GS23_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS23, Rep1


title: Muscle_4WP_GS21_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS21, Rep1


title: Muscle_4WP_GS14_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS14, Rep1


title: Muscle_4WP_GS13_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS13, Rep1


title: Muscle_4WP_GS16_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS16, Rep1


title: Muscle_PRE_GS3_Rep1

source_name: Vastus lateralis, at baseline, from individual GS3, Rep1


title: Muscle_PO_GS6_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS6, Rep1


title: Muscle_PRE_GS9_Rep1

source_name: Vastus lateralis, at baseline, from individual GS9, Rep1


title: Muscle_PO_GS10_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS10, Rep1


title: Muscle_PO_GS17_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS17, Rep1


title: Muscle_PRE_GS23_Rep1

source_name: Vastus lateralis, at baseline, from individual GS23, Rep1


title: Muscle_PRE_GS12_Rep1

source_name: Vastus lateralis, at baseline, from individual GS12, Rep1


title: Muscle_PO_GS2_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS2, Rep1


title: Muscle_4WP_GS1_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS1, Rep1


title: Muscle_4WP_GS20_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS20, Rep1


title: Muscle_PO_GS25_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS25, Rep1


title: Muscle_4WP_GS4_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS4, Rep1


title: Muscle_PRE_GS11_Rep1

source_name: Vastus lateralis, at baseline, from individual GS11, Rep1


title: Muscle_PO_GS15_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS15, Rep1


title: Muscle_PO_GS16_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS16, Rep1


title: Muscle_PO_GS21_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS21, Rep1


title: Muscle_PRE_GS18_Rep1

source_name: Vastus lateralis, at baseline, from individual GS18, Rep1


title: Muscle_PO_GS7_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS7, Rep1


title: Muscle_4WP_GS3_Rep2

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS3, Rep2


title: Muscle_4WP_GS19_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS19, Rep1


title: Muscle_4WP_GS24_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS24, Rep1


title: Muscle_PO_GS11_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS11, Rep1


title: Muscle_PRE_GS1_Rep1

source_name: Vastus lateralis, at baseline, from individual GS1, Rep1


title: Muscle_PRE_GS21_Rep1

source_name: Vastus lateralis, at baseline, from individual GS21, Rep1


title: Muscle_PRE_GS16_Rep1

source_name: Vastus lateralis, at baseline, from individual GS16, Rep1


title: Muscle_4WP_GS15_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS15, Rep1


title: Muscle_PRE_GS25_Rep1

source_name: Vastus lateralis, at baseline, from individual GS25, Rep1


title: Muscle_PO_GS3_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS3, Rep1


title: Muscle_PO_GS20_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS20, Rep1


title: Muscle_4WP_GS7_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS7, Rep1


title: Muscle_PRE_GS10_Rep1

source_name: Vastus lateralis, at baseline, from individual GS10, Rep1


title: Muscle_4WP_GS2_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS2, Rep1


title: Muscle_PRE_GS4_Rep1

source_name: Vastus lateralis, at baseline, from individual GS4, Rep1


title: Muscle_PO_GS22_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS22, Rep1


title: Muscle_PRE_GS8_Rep1

source_name: Vastus lateralis, at baseline, from individual GS8, Rep1


title: Muscle_PO_GS23_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS23, Rep1


title: Muscle_PRE_GS17_Rep1

source_name: Vastus lateralis, at baseline, from individual GS17, Rep1


title: Muscle_4WP_GS9_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS9, Rep1


title: Muscle_4WP_GS12_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS12, Rep1


title: Muscle_PO_GS14_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS14, Rep1


title: Muscle_PO_GS5_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS5, Rep1


title: Muscle_PRE_GS13_Rep1

source_name: Vastus lateralis, at baseline, from individual GS13, Rep1


title: Muscle_PRE_GS22_Rep1

source_name: Vastus lateralis, at baseline, from individual GS22, Rep1


title: Muscle_4WP_GS17_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS17, Rep1


title: Muscle_PRE_GS15_Rep1

source_name: Vastus lateralis, at baseline, from individual GS15, Rep1


title: Muscle_4WP_GS6_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS6, Rep1


title: cd45+ cells sorted from CT26 tumor, 5P.Lib30

status: Public on May 22 2020

city: san diego

first: Ji

last: Wen

state: CALIFORNIA

address: 10777 science center dr

institute: Pfizer Inc.

data_processing:
Data were processed using the Cell Ranger v2.1.1 (10x Genomics) to generate count-level data for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx
Supplementary_files_format_and_content: All_CD45_Cell_Anno_Coordinates.txt: Cell type annotation, TSNE coordinates and UMAP coordinates for all CD45+ cells were included in this file. CD45- clusters have been removed. The information included in this file can be used to regenerate the published Figure 1. Please refer to the paper for analysis details.
Supplementary_files_format_and_content: Myeloid_Cell_Anno_Coordinates.txt: Cell type annotation, TSNE coordinates for only myeloid cells were included in this file. The information included in this file can be used to regenerate the published Figure 3. Please refer to the paper for analysis details.

source_name: cd45+ cells sorted from CT26 tumor

growth_protocol: 3x10^5 CT26 tumor cells were implanted s.c into each flank of female BALB/c mice and a single tumor resected 8 days post s.c. implantation. Following resection mice were treated with avelumab to monitor treatment response in the remaining bilateral tumor.

extract_protocol:
TILs were isolated by digesting tumor fragments using Mylteni mouse tumor disassociation kit with enzyme R at 1:10 per manufacturer's guidelines. 1 to 5 × 10^6 cells were stained using fluorescently labeled mouse CD45 antibody (clone 30F11) and Fixable Viability Dye eFluor 506 (Thermo Fisher Scientific; Waltham, MA) to sort for live CD45+ and CD45− cells using the FACSAria II cell sorter.
approximately 1.6x10^4 cells were onto Chromium Single Cell A chips and library construction performed using the Chromium Single Cell 5’ Library and Gel Bead Kit protocol (10x Genomics)
Libraries were sequenced using the NovoSeq 6000 platform (Illumina; San Diego, CA)

treatment_protocol: Sequenced tumors are from otherwise untreated mice

value: cd45+ cells sorted from CT26 tumor before avelumab treatment


title: cd45+ cells sorted from CT26 tumor, 5P.Lib23


title: cd45+ cells sorted from CT26 tumor, 5P.Lib27


title: cd45+ cells sorted from CT26 tumor, 5P.Lib26


title: cd45+ cells sorted from CT26 tumor, 5P.Lib29


title: cd45+ cells sorted from CT26 tumor, 5P.Lib25


title: cd45+ cells sorted from CT26 tumor, 5P.Lib28


title: cd45+ cells sorted from CT26 tumor, 5P.Lib21


title: cd45+ cells sorted from CT26 tumor, 5P.Lib24


title: cd45+ cells sorted from CT26 tumor, 5P.Lib22


title: cd45+ cells sorted from CT26 tumor, 5P.Lib19


title: Muscle_4WP_GS18_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS18, Rep1


title: cd45+ cells sorted from CT26 tumor, 5P.Lib18


title: cd45+ cells sorted from CT26 tumor, 5P.Lib20


title: Muscle_PO_GS12_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS12, Rep1


title: Muscle_PO_GS18_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS18, Rep1


title: Muscle_4WP_GS25_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS25, Rep1


title: cd45+ cells sorted from CT26 tumor, 5P.Lib16


title: cd45+ cells sorted from CT26 tumor, 5P.Lib9


title: cd45+ cells sorted from CT26 tumor, 5P.Lib13


title: cd45+ cells sorted from CT26 tumor, 5P.Lib11


title: cd45+ cells sorted from CT26 tumor, 5P.Lib10


title: cd45+ cells sorted from CT26 tumor, 5P.Lib15


title: cd45+ cells sorted from CT26 tumor, 5P.Lib12


title: cd45+ cells sorted from CT26 tumor, 5P.Lib8


title: cd45+ cells sorted from CT26 tumor, 5P.Lib6


title: cd45+ cells sorted from CT26 tumor, 5P.Lib7


title: cd45+ cells sorted from CT26 tumor, 5P.Lib4


title: cd45+ cells sorted from CT26 tumor, 5P.Lib3


title: cd45+ cells sorted from CT26 tumor, 5P.Lib2


title: cd45+ cells sorted from CT26 tumor, 5P.Lib17


title: cd45+ cells sorted from CT26 tumor, 5P.Lib14


title: cd45+ cells sorted from CT26 tumor, 5P.Lib1


title: cd45+ cells sorted from CT26 tumor, 5P.Lib5


title: anoxic_H2S_3

status: Public on Apr 30 2020

city: Vienna

first: Lena

last: König

address: Althanstrasse 14

country: Austria

institute: University of Vienna

description:
whole symbiotic marine nematodes
rRNA-depleted RNA containing both nematode and symbiont RNA

data_processing:
Based on quality assessment of raw sequencing reads using FastQC (Andrews, 2010) and prinseq-lite (Schmieder and Edwards, 2011), reads were trimmed and filtered using Trimmomatic (Bolger et al., 2014) and prinseq-lite as follows:  18 nucleotides were removed from the 5-prime end (HEADCROP), Illumina adapters were removed (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10), reads were trimmed when the average quality of a five-base sliding window dropped below a phred score of 20 (SLIDINGWINDOW:5:20), 3-prime poly-A tails were trimmed (-trim_tail_right 1), and only reads longer than 24 nucleotides were kept (MINLEN:25).
Trimmed reads were mapped to the symbiont (Ca. Thiosymbion oneisti) genome draft using BWA-backtrack (Li and Durbin, 2009) with default settings, only uniquely mapped reads were kept using SAMtools (Li et al., 2009), and the number of strand-specific reads per predicted gene were counted using HTSeq in the union mode of counting overlaps (Anders et al., 2014).
Genome_build: Ca. Thiosymbion oneisti GenBank accession JAAEFD000000000
Supplementary_files_format_and_content: txt files with 2 columns each; column 1 contains locus tag IDs (genes), column 2 contains read counts

organism: Laxus oneistus

source_name: Laxus oneistus associated with Ca. Thiosymbion oneisti

growth_protocol: Laxus oneistus individual worms were collected on multiple field trips (2016-2019) at approximately 1 m depth from sand bars off the Smithsonian Field Station, Carrie Bow Cay in Belize (16°48′11.01″N, 88°4′54.42″W). The nematodes were extracted from the sediment by gently stirring the sand and pouring the supernatant seawater through a 212 μm mesh sieve. The retained meiofauna was collected in a petri dish, and single worms of similar size (1-2 mm length, representing adult L. oneistus) were handpicked by forceps (Dumont 3, Fine Science Tools, Canada), under a dissecting microscope. Right after collection, the nematodes were incubated under four different conditions.

extract_protocol:
RNA was extracted using the NucleoSpin RNA XS Kit (Macherey-Nagel). Briefly, sets of 50 worms in RNA storage solution were thawed and the worms were transferred into 90 µl lysis buffer RA1 containing Tris (2-carboxyethyl) phosphine (TCEP) according to the manufacturer. The remaining RNA storage solution was centrifuged to collect any detached bacterial cells (10 min, 4°C, 16,100 x g), pellets were resuspended in 10 µl lysis buffer RA1 (plus TCEP) and then added to the worms in lysis buffer. To further disrupt cells, suspensions were vortexed for two minutes followed by three cycles of freeze (-80°C) and thaw (37°C), and homogenization using a pellet pestle (Sigma-Aldrich) for 60 s with a 15 s break after 30 s. Any remaining biological material on the pestle tips was collected by rinsing the tip with 100 µl lysis buffer RA1 (plus TCEP). Lysates were applied to NucleoSpin Filters and samples were processed as suggested by the manufacturer, including an on-filter DNA digest. RNA was eluted in 20 µl RNase-free water. To remove any residual DNA, a second DNase treatment was performed using the Turbo DNA-free Kit (Thermo Fisher Scientific), RNA was then dissolved in 17 µl RNase-free water, and the RNA quality was assessed using a Bioanalyzer (Agilent). To check whether all DNA was digested, real-time quantitative PCR using the GoTaq qPCR Master Mix (Promega) was performed targeting a 158 bp stretch of the sodB gene using primers specific for the symbiont (sodB-F: GTGAAGGGTAAGGACGGTTC, sodB-R: AATCCCAGTTGACGATCTCC, 10 µM per primer). Different concentrations of genomic Ca. T. oneisti DNA were used as positive controls. The program was as follows: 1x 95°C for 2 min, 40x 95°C for 15 s and 60°C for 1 min, 1x 95°C for 15 s, 55°C to 95°C over 20 min. Next, bacterial and eukaryotic rRNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Epidemiology) (Illumina) following the manufacturer’s instructions, but volumes were adjusted for low input RNA (Alberti et al., 2014). In short, 125 µl of Magnetic Beads Solution, 32.5 µl Magnetic Bead Resuspension Solution, 2 µl Ribo-Zero Reaction Buffer and 4 µl Ribo-Zero Removal Solution were used per sample. RNA was cleaned up via ethanol precipitation, dissolved in 9 µl RNase-free water, and rRNA removal was evaluated using the Bioanalyzer RNA Pico Kit (Agilent).
Strand-specific, indexed cDNA libraries were prepared using the SMARTer Stranded RNA-Seq Kit (Takara Bio USA). Library preparation was performed according to the instructions, with 8 µl of RNA per sample as input, 3 min fragmentation time, two rounds of AMPure XP Beads (Beckman Coulter) clean-up before amplification, and 18 PCR cycles for library amplification. The quality of the libraries was assessed via the Bioanalyzer DNA High Sensitivity Kit (Agilent). Libraries were sequenced on an Illumina HiSeq 200 instrument (single-read, 100 nt) at the next generation sequencing facility of the Vienna BioCenter Core Facilities (VBCF, https://www.viennabiocenter.org/facilities/). Demultiplexing was provided by the VBCF.

treatment_protocol: Batches of 50 freshly collected L. oneistus individuals per condition were incubated for 24 h in the dark in 13 ml-exetainers (Labco, Lampeter, Wales, UK) fully filled with 0.2 µm-filtered seawater. Moreover, different oxygen concentrations were applied: (1) high oxygen (exetainers were kept open and submerged in an aquarium constantly bubbled with air), (2) hypoxic (exetainers were kept open and were exposed to air), (3) anoxic (exetainers were kept inside polyethylene glove bags (AtmosBag; Sigma-Aldrich) that were flushed with N2 gas, together with incubation media and all vials, for at least 1 h before closing), and (4) anoxic with 11 µM sulfide (Na2S*9H2O) added ((exetainers were kept inside polyethylene glove bags (AtmosBag; Sigma-Aldrich) that were flushed with N2 gas, together with incubation media and all vials, for at least 1 h before closing). After the 24 h incubations, each set of 50 worms was quickly transferred into 2 ml RNA storage solution (13.3 mM EDTA disodium dihydrate pH 8.0, 16.6 mM sodium citrate dihydrate, 3.5 M ammonium sulfate, pH 5.2), kept at 4°C overnight, and finally stored in liquid nitrogen until RNA extraction.

tag: incubation condition

value: anoxic, with sulfide added

tag: replicate


title: anoxic_2

value: anoxic, without added sulfide


title: hypoxic_2

value: hypoxic


title: oxic_3

value: oxic


title: anoxic_H2S_1


title: anoxic_3


title: anoxic_H2S_2


title: oxic_2


title: hypoxic_3


title: anoxic_1


title: Sp.Bulk.TEM#2

status: Public on Apr 15 2020

city: San diego

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

department: Molecular Biology

institute: UCSD

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10
Supplementary_files_format_and_content: gct

source_name: D55 spleen P14 CD62Llo

extract_protocol:
Total RNA was extracted in TRIZoL reagent
PrepX RNA-seq library preperation kit (Integenex)

tag: strain

value: 6-16 Weeks

value: Spleen


title: Sp.TCM#1

source_name: D55 spleen P14 CD62LloCD127hi


title: Sp.TCM#2


title: oxic_1


title: Sp.LLTE#2

source_name: D55 spleen P14 CD62LloCD127lo


title: Sp.LLTE#1


title: EC9

status: Public on Apr 05 2020

city: San Francisco

first: Kun

last: Leng

state: Calfironia

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California San Francisco

data_processing:
Sequencing data generated from snRNA-seq libraries were demultiplexed using cellranger mkfastq.
To align reads, we first generated our own pre-mRNA GRCh38 reference genome using cellranger mkref in order to account for introns that may be eliminated using the default GRCh38 reference genome.
Alignment and gene expression quantification was then performed using cellranger count with default settings.
Genome_build: GRCh38 pre-mRNA
Supplementary_files_format_and_content: The processed data files are hdf5 formatted matrices of UMI counts, with rows as genes and columns as cell barcodes, obtained from running cellranger count.

source_name: Frozen post-mortem human brain tissue

extract_protocol:
Isolation of nuclei was performed similarly as described in Mo et al. [PMID: 26087164]. Briefly, frozen brain tissue was dounce homogenized in 5 ml of lysis buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15mM spermine, 0.5 mM spermidine, 1X protease inhibitor (Sigma, 4693159001), and RNAse Inhibitor (Promega, N2615)). Following initial dounce homogenization, IGEPAL-630 was added to a final concentration of 0.3% and the sample was homogenized with 5 more strokes. The solution was then filtered through a 40 um cell filter and mixed with Optiprep (Sigma, D1556-250ML) to create a 25% Optiprep solution. This solution was then layered onto a 30%/40% Optiprep gradient and centrifuged at 10,000g for 18 minutes using the SW41-Ti rotor. The nuclei were collected at the 30%/40% Optiprep interface.
Droplet-based single-nuclues RNA-sequencing (snRNA-seq) was performed using the Chromium Single Cell 3′ Reagent Kits v2 from 10X Genomics. Nuclei were resuspended to a concentration of 1000 nuclei/uL in 30% Optiprep solution before loading according to manufacturer’s protocol, with 10,000 nuclei recovered per sample as the target. cDNA fragment analysis was performed using the Agilent 4200 TapeStation System. Sequencing parameters and quality control were performed as described by The Tabula Muris Consortium [PMID 30283141].

tag: brain region

value: Entorhinal cortex

tag: batch

value: B

tag: donor id

tag: braak stage (ad neuropathological progression)

tag: age (years)


title: EC10

value: D


title: EC8


title: Sp.Bulk.TEM#1


title: EC6


title: EC4

value: C


title: EC1

value: Male


title: IEL.Trm#1

source_name: D55 siIEL P14

value: Small Intestine Epithelium


title: EC5


title: SFG8

value: Superior frontal gyrus


title: SFG9

value: A


title: EC7


title: SFG5


title: SFG6


title: SFG7


title: SFG4


title: SFG3


title: SFG2


title: hypoxic_1


title: SFG1


title: NG_Snap25_ip_SPF_3

status: Public on Mar 20 2020

city: New York

first: Paul

middle: Andrew

last: Muller

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: Actively translated mRNA

data_processing:
Library strategy: Ribo-Seq
Genome build: Ensembl Mus musculus release 91: GRCm38.p5 (GCA_000001635.7)

source_name: Immunoprecipitated ribosome-bound mRNA from the left and right nodose ganglion of germ free Snap25:RiboTag mice

extract_protocol: The nodose ganglion, dorsal root ganglion, and celiac superior mesenteric ganglion were dissected into PBS with cycloheximide (0.2 mg/mL) (PBS/CHX). The RiboTag immunoprecipitation protocol (http://depts.washington.edu/mcklab/RiboTagIPprotocol2014.pdf)  was then followed with the following modifications: All samples were homogenized by hand with a dounce homogenizer in 2.5 mL supplemented homogenization buffer (changes per 2.5 mL: 50 µl Protease Inhibitor, 75 µl heparin (100 mg/mL stock), 25 µl SUPERase In RNase Inhibitor). Samples were then centrifuged for 10 minutes at 10,000 G, after which 800 µl of supernatant was removed and 5µL of anti-HA antibody (Abcam, ab9110) was added. For input samples, 40uL of supernatant was removed and 60uL of PicoPure lysis buffer was added. These input samples were then put at -80°C. Immunoprecipitated samples were kept rotating at 4°C with antibody for 1 hour. 200 µl of Thermo Protein magnetic A/G beads were washed with homogenization buffer, added to the sample, and kept rotating for 30 minutes at 4°C. The beads were washed four times with high-salt buffer and samples were eluted with 100 µl of PicoPure lysis buffer.  RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.

value: Left and right nodose ganglion


title: Muscle_PRE_GS14_Rep1

source_name: Vastus lateralis, at baseline, from individual GS14, Rep1

value: M


title: SFG10


title: EC3


title: NG_Snap25_ip_SPF_1

description: Actively translated mRNA

source_name: Immunoprecipitated ribosome-bound mRNA from the left and right nodose ganglion of specific pathogen free Snap25:RiboTag mice


title: NG_Snap25_ip_GF_1_

description: Actively translated mRNA


title: IEL.Trm#2


title: 3M_H3K27ac_rep3

status: Public on Mar 10 2020

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Library strategy: CUT&RUN
Reads were quality trimmed 10 bp from the 5’ end and 5 bp from the 3’ end using Trim Galore! version 0.4.5. Quality check was performed using FastQC.
Reads were aligned against the Mus musculus genome (Ensembl version 84) and the Saccharomyces cerevisiae genome (Ensembl version 93) using bowtie2 (Langmead and Salzberg 2012) with additional parameters as detailed in the CUT&RUN protocol (Skene and Henikoff 2017). Deduplicated and high-quality mapped reads (MAPQ value of at least 30) were extracted using samtools.
Genome_build: GRCm38.p4 using Ensembl v84 annotation
Supplementary_files_format_and_content: BigWig files of unnormalized read counts at a bp-level

source_name: Rod photoreceptors

extract_protocol:
CUT&RUN was performed as previously described (Skene and Henikoff 2017) using 200-300,000 cells per experiment. Antibodies against H3K27ac (Rabbit, cat.no.  ab4729, Abcam, Cambridge, UK), and H3K27me3 (Rabbit, cat.no.  ab6002, Abcam, Cambridge, UK) were used at a concentration of 1:100 in 100 µl and pA-MNase conjugated to protein A (Steven Henikoff, Howard Hughes Medical Institute, Washington, USA) used at a concentration of 700 ng/ml. Released fragments were purified using QIAquick PCR Purification Kit (Qiagen, Hilden, Germany).
Libraries were generated using SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA, Inc, CA, USA) as per manufacturer instructions with 15 PCR cycles and 60°C extension, and sequenced pair-end using the HiSeq 2500 platform (Illumina, CA, USA) with read-length of 50 base pairs.

treatment_protocol: C57BL/6J mice expressing GFP under the control of the Nrl promoter (Nrlp-GFP and Nrlp-GFP;Nrl-KO mice (Akimoto et al. 2006)) were used to purify rod photoreceptors. Retinas from 3M, 12M, 18M and 24M were dissected in Hank’s Balanced Salt Solution (Life Technologies, NY, USA) and dissociated in Papain solution (Worthington Biochemical, NJ, USA) containing DNase I at 28°C for 8 min with constant agitation, pelleted at 200 g for 5 minutes and resuspended in a solution containing Albumin and DNase I (100 U/ml). Subsequently, cells were pelleted again and resuspended in 1 ml of HBSS. GFP positive cells were isolated by fluorescence-activated cell sorting (FACS) using FACS Aria II (Becton Dickinson, CA, USA). The purity of isolated GFP-positive cells was assessed by resorting and only cells that were over 98% pure were used in subsequent experiments. After sorting, cells were flash frozen with or without TRIzol (Invitrogen, CA, USA).

tag: individual

value: C57BL/6J (Nrlp-GFP)

tag: antibody


title: NG_Snap25_ip_SPF_2

description: Actively translated mRNA


title: 3M_H3K27me3_rep6


title: 3M_H3K27me3_rep5


title: NG_Snap25_ip_GF_2_

description: Actively translated mRNA


title: 3M_H3K27ac_rep2


title: 3M_H3K27ac_rep4


title: 3M_H3K27me3_rep4


title: 3M_H3K27me3_rep1


title: Muscle_PO_GS4_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS4, Rep1


title: EC2


title: Muscle_PRE_GS7_Rep1

source_name: Vastus lateralis, at baseline, from individual GS7, Rep1


title: WGBS_12M_rep1

data_processing:
Fastq files were generated from reads passing chastity filter.
Adapters, reads of low quality (Phred score < 20) and length < 20 were trimmed using Trim Galore! version 0.4.5
Quality control was performed using FastQC version 0.11.5. After inspection of M-bias plots, reads were further trimmed 20 base pairs from either end of both reads.
After removal of duplicate reads, CpG methylation was extracted using Bismark version 0.20.0 (Krueger and Andrews 2011) using the reference Mus musculus genome (Ensembl version 84) and values smoothened by applying a smoothing algorithm with the bsseq R package (Hansen et al. 2012).
CpGs with at least 2X coverage in at least 2 biological replicates of each time point were used for analysis. The R package bsseq was used to identify differential methylation between 3M and 24M sample using a cutoff of > 10% methylation difference, areaStat >20, and a quantile cutoff of the t-statistics of 0.001.
Genome_build: GRCm38.p4 using Ensembl v84 annotation
Supplementary_files_format_and_content: bigWig files containing the smoothed methylation values at CpGs with at least 2x coverage in at least 2 biological replicates at each time point

extract_protocol:
Genomic DNA was extracted using the Genomic DNA Mini Kit (Invitrogen, CA, USA) per manufacturer instructions and treated with bisulfite salt using the EZ DNA Methylation-Gold Kit (Zymo Research, CA, USA) on 100 ng of DNA following manufacturer instructions. Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, MI, USA) according to manufacturer’s instructions. A spike-in of unmethylated lambda DNA was used to determine bisulfite conversion. Paired-end sequencing was performed using the HiSeq 2500 platform (Illumina, CA, USA) with read-length of 125 base pairs.
Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, MI, USA) according to manufacturer’s instructions.

value: Rod photoreceptors


title: WGBS_3M_rep3


title: WGBS_18M_rep2


title: WGBS_3M_rep2


title: RNA-seq_24M_rep4

data_processing:
Fastq files were generated from reads passing chastity filter.
Transcript level quantitation was performed using Kallisto v0.42.5 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl v84 ftp site.
Gene level quantification was generated by summarization of the transcript level quantitation using tximport v0.99.9 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.13.9.
Differential expression (DE) analysis of the organoid data was performed for each time-wise culturing condition using limma (3.32.2) with voom and eBayes functions. Genes having a mean of 5 counts-per-million (CPM) expression in at least one group were used in the analysis and those showing Benjamini-Hochberg false discovery rate (FDR) of < 10% and minimum fold change of 1.2 were considered in significant DE category.
Genome_build: GRCm38.p4 using Ensembl v84 annotation
Supplementary_files_format_and_content: Tab delimited text files containing transcript level counts, gene level counts-per-million, normalized gene level counts-per-million, or differential expression results.

extract_protocol:
Total RNA from FACS-purified rod photoreceptors was extracted using TRIzol® (Invitrogen, Carlsbad, CA), treated with DNase and cleaned up using the MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems, Foster City, CA) following the manufacturer’s instructions. Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA, Mountain View, CA) with 4 ng of RNA and 13 PCR cycles library amplification.
Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA, Mountain View, CA) with 4 ng of RNA and 13 PCR cycles library amplification.


title: RNA-seq_24M_rep3


title: RNA-seq_24M_rep2


title: Muscle_4WP_GS8_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS8, Rep1


title: WGBS_18M_rep3


title: 3M_H3K27me3_rep2


title: WGBS_3M_rep1


title: Muscle_4WP_GS11_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS11, Rep1


title: Muscle_4WP_GS10_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS10, Rep1


title: RNA-seq_18M_rep3


title: Muscle_PRE_GS5_Rep1

source_name: Vastus lateralis, at baseline, from individual GS5, Rep1


title: RNA-seq_12M_rep3


title: 3M_H3K27ac_rep1


title: WGBS_24M_rep2


title: WGBS_24M_rep3


title: RNA-seq_12M_rep2


title: RNA-seq_12M_rep1


title: WGBS_24M_rep1


title: RNA-seq_18M_rep2


title: Muscle_PO_GS9_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS9, Rep1


title: WGBS_18M_rep1


title: RNA-seq_24M_rep1


title: Muscle_4WP_GS3_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT, from individual GS3, Rep1


title: RNA-seq_3M_rep3


title: Muscle_PRE_GS6_Rep1

source_name: Vastus lateralis, at baseline, from individual GS6, Rep1


title: WGBS_12M_rep2


title: RNA-seq_3M_rep4


title: 3M_H3K27me3_rep3


title: RNA-seq_3M_rep2


title: RNA-seq_3M_rep1


title: RNA-seq_18M_rep4


title: Red1 ChIP for top2-1 T=3 34C rep1

status: Public on Mar 06 2020

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
processed data file:
Red1-top2-4-411-498-535-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Bedgraph fileswere created from pooled replicates of ChIP-seq. Only 1 replicate available for TOP2-6HA sample.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

source_name: Red1 ChIP for top2-1 T=3 34C rep1

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606  which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012).
For ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads.

treatment_protocol: For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.

tag: genetic background

tag: treatment

value: 3 hour 34C

tag: strain id

tag: chip antibody


title: top2-1 T=3 input 34C for Red1 rep1

source_name: top2-1 T=3 input 34C for Red1 rep1


title: Muscle_PO_GS1_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS1, Rep1

tag: age


title: WT RNA-seq T=3

description:
processed data file:
2017.06.16_SK1Yue_EdgeR_tpm_AH119_3h.csv

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq and MNase-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). SNP-ChIP library reads were aligned to concatenated genome assemblies of SK1 and S288c genomes.  Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. The RNA-seq reads were mapped to the SK1 genome using Tophat2 with first strand library type, no novel junctions, and otherwise default options.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, 3' ends were extended to a final length of 146 and bandwidth was set to 350 using MACS2 2.1.1. MNase-seq pileups were SPMR-normalized, which was used for further analyses. For RNA-seq, mapped reads were counted using featureCounts and statistical analysis was performed using a count-based workflow with the edgeR Bioconductor package.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, the pileup was SPMR-normalized and used for further analyses. For RNA-seq, gene counts were normalized to counts per million and were then gene length-corrected for transcripts per million (tpm).
Bedgraph files and peak files for some samples were created from pooled replicates of ChIP-seq. MNase-seq data was pooled with published MNase-seq data from (Pan et al 2011). CSV file was created for RNA-seq.
Genome_build: SK1 and S288c (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph, BED6+3, CSV (RNA-seq)

source_name: WT RNA-seq T=3

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde.  The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). For quantitative ChIP-Seq (SNP-ChIP), S288c crosslinked meiotic cells were added to respective samples at 20% prior to ChIP processing (Vale Silva et al., 2018). For RNA-seq, 1.5 ml meiotic culture was taken at the 3-hr time point and RNA was extracted from mechanically lysed cells using the Qiagen RNeasy RNA isolation Kit and mRNA was extracted using Sera-Mag oligo-dT beads and fragmented.
For MNase-seq and ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads, 75 bp single-end reads, or 100 bp single-end reads.

value: 3 hour


title: Muscle_PO_GS13_Rep1

source_name: Vastus lateralis, after an acute bout of HIIT, from individual GS13, Rep1


title: Red1 ChIP for WT T=3 34C rep1

description:
processed data file:
Red1-WT-34C-410-495-528-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Red1 ChIP for WT T=3 34C rep1


title: WT T=3 input 34C for Red1 rep1

source_name: WT T=3 input 34C for Red1 rep1

value: none (input)


title: Red1 ChIP for top2-1 T=3 34C rep3

source_name: Red1 ChIP for top2-1 T=3 34C rep3


title: Red1 ChIP for top2-1 T=3 34C rep2

source_name: Red1 ChIP for top2-1 T=3 34C rep2


title: WT Mnase-seq T=3

description:
processed data file:
Nucleosome_reps-SK1-MACS2_treat_pileup.bdg

source_name: WT Mnase-seq T=3


title: top2-1 T=3 input 34C rep2

description:
processed data file:
Top2-top2-4-496-537-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: top2-1 T=3 input 34C rep2


title: Top2 ChIP for WT T=3 rep1

description:
processed data file:
Top2-wildtype-413-504-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz
Top2-wildtype-413-504-Reps-SK1Yue-PM_B3W3_MACS2_peaks.broadPeak

source_name: Top2 ChIP for WT T=3 rep1


title: WT T=3 input rep1

source_name: WT T=3 input rep1


title: Red1 ChIP for WT T=3 34C rep2

source_name: Red1 ChIP for WT T=3 34C rep2


title: WT T=3 input 34C rep1 for Top2 and Red1 ChIPs

description:
processed data file:
Top2-wildtype-34C-493-533-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: WT T=3 input 34C rep1


title: top2-1 T=3 input 34C rep1

source_name: top2-1 T=3 input 34C rep1


title: WT T=3 input 34C rep2

source_name: WT T=3 input 34C rep2


title: Muscle_PRE_GS2_Rep1

source_name: Vastus lateralis, at baseline, from individual GS2, Rep1


title: Top2 ChIP for WT T=3 rep2

source_name: Top2 ChIP for WT T=3 rep2


title: Myc ChIP for TOP1-13MYC T=3h rep1

description:
processed data file:
AH9847Myc-3h-735-841-Reps-SK1Yue-PM_B3W4_MACS2_FE.bdg.gz
AH9847Myc-3h-735-841-Reps-SK1Yue-PM_B3W4_MACS2_peaks.broadPeak

source_name: Myc ChIP for TOP1-13MYC T=3h rep1

value: anti-Myc


title: WT T=3 input rep2

source_name: WT T=3 input rep2


title: Myc ChIP for TOP1-13MYC T=3h rep2

source_name: Myc ChIP for TOP1-13MYC T=3h rep2


title: 34: Post-mortem dosolateral prefrontal cortex

status: Public on Feb 25 2020

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

data_processing:
10X Genomics Cellranger v2.1.0 mkfastq
10X Genomics Cellranger v2.1.0 count
Genome_build: Custom pre-mRNA reference produced with 10X Genomics Cellranger v2.0.0 mkref (provided, see  GRCh38-1.2.0_premrna.tar.gz)

extract_protocol: Chromium Single Cell 3’ Reagent Kits v2

tag: group

value: Major Depressive Disorder (MDD)

tag: ethnicity

value: Caucasian

tag: tissue

value: Brain


title: 32: Post-mortem dosolateral prefrontal cortex

tag: Sex


title: 30: Post-mortem dosolateral prefrontal cortex


title: 33: Post-mortem dosolateral prefrontal cortex


title: TOP1-13MYC T=3h input rep2

source_name: TOP1-13MYC T=3h input rep2


title: 29: Post-mortem dosolateral prefrontal cortex

value: Control


title: 31: Post-mortem dosolateral prefrontal cortex


title: TOP1-13MYC T=3h input rep1

source_name: TOP1-13MYC T=3h input rep1


title: 27: Post-mortem dosolateral prefrontal cortex


title: 26: Post-mortem dosolateral prefrontal cortex


title: 25: Post-mortem dosolateral prefrontal cortex

description:
25_MPS12342909_G05_7650_S1_L005
25_2_MPS12342750_D10_7390_S2_L003


title: 24: Post-mortem dosolateral prefrontal cortex

description:
24_MPS12342909_A07_7650_S2_L005
24_2_MPS12342750_D11_7390_S1_L008


title: 22: Post-mortem dosolateral prefrontal cortex


title: 18: Post-mortem dosolateral prefrontal cortex


title: 19: Post-mortem dosolateral prefrontal cortex


title: 23: Post-mortem dosolateral prefrontal cortex


title: 17: Post-mortem dosolateral prefrontal cortex


title: 15: Post-mortem dosolateral prefrontal cortex


title: 21: Post-mortem dosolateral prefrontal cortex


title: 11: Post-mortem dosolateral prefrontal cortex


title: 12: Post-mortem dosolateral prefrontal cortex


title: 16: Post-mortem dosolateral prefrontal cortex


title: 13: Post-mortem dosolateral prefrontal cortex


title: 20: Post-mortem dosolateral prefrontal cortex


title: 10: Post-mortem dosolateral prefrontal cortex


title: 28: Post-mortem dosolateral prefrontal cortex


title: 9: Post-mortem dosolateral prefrontal cortex


title: 6: Post-mortem dosolateral prefrontal cortex


title: 4: Post-mortem dosolateral prefrontal cortex


title: 3: Post-mortem dosolateral prefrontal cortex


title: 14: Post-mortem dosolateral prefrontal cortex


title: 8: Post-mortem dosolateral prefrontal cortex


title: 7: Post-mortem dosolateral prefrontal cortex


title: Weri-WT

status: Public on Feb 05 2020

city: shanghai

first: Hongyan

last: Ni

address: 639 zhizaoju Road

country: China

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using star
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: retinoblastoma cells

extract_protocol:
Total RNA from lncRNA CANT1-knockdown RB and WT RB cells was isolated and quantified. The concentration of each sample was measured by a NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by an Agilent2200 (Agilent, USA). The sequencing library of each RNA sample was prepared by using an Ion Proton Total RNA-Seq Kit v2 according to the protocol provided by manufacturer (Life Technologies, USA).
RNA libraries were prepared for sequencing using standard Ion PGM protocols

value: retina

value: 1 year

tag: genotype

value: wild type


title: Weri-CANT1

value: CANT1 overexpression


title: 1: Post-mortem dosolateral prefrontal cortex

value: Male


title: 2: Post-mortem dosolateral prefrontal cortex


title: PDAC-G ST1

status: Public on Jan 13 2020

first: Itai

last: Yanai

address: 435 E. 30th Street, 8th Floor

institute: Institute for Computational Medicine, NYU Langone Health

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop method were processed using a custom-built pipeline, available online (https://github.com/flo-compbio/singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the ST method were processed using a custom-built pipeline, available online (https://github.com/yanailab/celseq2). The pipeline was adapted to ST sequencing data using the following three steps: 1) Tagging and demultiplexing: the left-most 25 nucleotides (nt) of the R1 sequence contains the 18 nt for the spot-specific barcode and then 7 nt for UMI. The R2 sequence contains the transcript sequence, and its left-most 35 nt are used. The name of every read in the R2 file is tagged with the spot-specific barcode and UMI sequence that are extracted from the paired R1 read. The R2 file is demultiplexed to create the 1007 spot-specific FASTQ files. If the detected spot-specific barcode of a read is not present in the pre-defined barcodes list, the read is excluded from the downstream analysis. 2) Alignment of demultiplexed FASTQ files using Bowtie2. 3) Counting UMI using HTSeq. The reads that are aligned to a user-defined feature (by default: “gene_name”) are collapsed to count only once if they have same UMI. Here we used the version 2.3.1 of Bowtie2 with default parameters and the 0.9.1 version of HTSeq in the “union” mode. For demultiplexing spatial barcodes, PDAC-A ST1 was demultiplexed using the lot10001 barcode file, and PDAC-B ST1 was demultiplexed using the lot10003 barcode file (barcode files included in submission, and is also available at https://spatialtranscriptomics.com/resources/
Genome_build: hg38
Supplementary_files_format_and_content: for inDrop data: tab-delimited files with genes as rows and cells as columns. For ST data: tab-delimited files with genes as rows  and spots as columns (with first row is the coordinate of each spot along the array)

source_name: pancreatic adenocarcinoma tissue

extract_protocol:
For single-cell RNA-seq (inDrop platform), cell suspension was generated by incubating minced pancreatic cancer tissue with trypsin for 15' at 37C prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For spatial transcriptomics of pancreatic cancer tissue, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation.
For single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England Biolabs). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For spatial transcriptomics (ST) library construction, we followed the previously published ST protocol from Stahl et al. Science 2016, with minor changes. Briefly, after brightfield imaging of stained tissue, tissue was permeabilized with collagenase and 0.1% pepsin prior to an overnight RT step with SuperScript III on the ST slide. Tissue was digested away with proteinase K and 1% 2-mercaptoethanol prior to cleavage of probes from the slide surface with USER enzyme. Second strand synthesis was performed with DNA Pol I and RNase H (New england biolabs) followed by an in vitro transcription amplification step with the MEGAScript T7 kit (Thermofisher). Amplified RNA then underwent a second RT with random hexamers and SuperScript II (Invitrogen), eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).

value: pancreatic adenocarcinoma

tag: tissue preparation

value: tissue cryosections


title: Y79-WT

value: 2.5 years


title: PDAC-F ST1


title: PDAC-E ST1


title: PDAC-D ST1


title: PDAC-B ST3


title: PDAC-A ST3


title: 5: Post-mortem dosolateral prefrontal cortex


title: RR-ChIP seq WKKD

status: Public on Oct 22 2019

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

institute: Sir William Dunn School of Pathology,  University of Oxford

data_processing:
Library strategy: RR-ChIP-seq
For chrRNA-seq, adaptors were trimmed using Cutadapt. Paired-end reads for each sample were mapped to human genome reference assembly GRh37/hg19 (build 37.2, February 2009) with Tophat v. 2.0.13 with parameters -g 1 -r 3000 --no-coverage-search.
RR-ChIP-seq reads were demultiplexed and aligned to reference genome hg19/GRCh37 using Bowtie2 alignment software.Plus and minus strand were assigned to mapped reads using SAMtools. RR-ChIP-seq peaks were called using MACS2 algorithm with default options
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments; Raw alignment file

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10%FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and 1) RNA:DNA hybrids were isolated with S9.6 antibody for RDIP-seq 2) RNA:DNA hybrids were isolated with GFP antibody for RR-ChIP-seq
For the RDIP-seq and RR-ChIP-seq, the RNA component of the R-loop was used to prepare the library using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, (E7760S) according to manufacturer's guidelines. For the ChrRNA-seq and ChrCAP-seq, chromatin associated RNA was used for library prepration as for RDIP-seq.

treatment_protocol: Lipofectamine 2000 was used to deliver RNAseH1 over-expressing plasmid (pRNH1-GFP), RNaseH1 catalytically dead mutant (pRNH1-D210N-GFP) Rnase H1 non binding ctalytically dead mutant (pRNH1-WKKD-GFP) and pGFP.  For RDIP-seq experiments recombinant RNase H was added the sonicated HeLa cells before S9.6 immunoprecipitation. All HeLa cells used in Chromatin associated RNA-seq and ChrCAP-seq were GFP FACs sorted. For ChrCAP-seq, chromatin RNA were treated with Terminator exonuclease followed by calf intestine phosphatase before CAP-CLIP (5' pyrophosphatase) treatment.

tag: cell type

value: cervical cancer cells

tag: genotype/variation

value: WKKD


title: Replicate 1 RR-ChIP seq D210N

description: processed data file: GSE87607_RR-ChIP_D210N.peaks.txt


title: Wild type_H2O2 treated_rep3

status: Public on Sep 25 2019

city: Saint Paul

first: Sinisa

last: Vidovic

state: MN

address: 1971 Commonwealth Avenue

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the S. enterica (P125109) as a reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: S. enterica (P125109)
Supplementary_files_format_and_content: raw read counts

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Bacterial cells

growth_protocol: Each culture of the wild type and its yccT mutant was inoculated into 100 mL of freshly preapared LB broth followed incubation at 37 C with constant shaking 190 rpm.

extract_protocol: RNA was extracted using the RNAeasy Kit from Qiagen. All bacterial samples were re-suspended in RNAprotect bacterial agent (Qiagen, Valencia, CA, USA) and stored at -20°C until RNA extraction

treatment_protocol: The Salmonella cultures reaching their mid log growth phase (i.e., OD 600 nm 0.5) were treated with 3 uM of H2O2 followed by centrifugation and washing.

value: Wild type

value: H2O2 treatment


title: G164_Sph_r1

status: Public on Jan 01 2020

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description:
24h - low attachment flask. DMEM/F12 + 10% FBS
RPKM_cqn_monocultures.txt

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

source_name: G164 Spheroids

growth_protocol: DMEM/F12 (Gibco, UK)

extract_protocol:
RNA was prepared from cell cultures using the RNeasy Mini Kit and the RNase free DNase set (Qiagen)
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

treatment_protocol: SB431542 and GANT61 (Sigma-Aldrich, UK)

tag: cell types

tag: culture type

value: spheroids - monoculture

value: Untreated


title: G164_Sph_r3


title: G164_Sph_r2


title: Wild type_H2O2 treated_rep2


title: Replicate 2 RR-ChIP seq D210N


title: Y79-CANT1


title: Wild type_H2O2 treated_rep1


title: Wild type_untreated_rep3

value: No H2O2 treatment


title: Wild type_untreated_rep2


title: Wild type_untreated_rep1


title: E12.5 CM-specific RNASeq rep1

status: Public on Sep 13 2019

city: Boston

first: Brynn

middle: Nicole-Yoshiko

last: Akerberg

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: rRNA-depleted RNA

data_processing:
fastq files were aligned to mm9 genome using STAR aligner
gene count lists were obtained from STAR aligner
mm9
.txt files containing gene names for each sample and counts

source_name: heart

extract_protocol: RNA was purified using the Purelink RNA mini kit (Life Technologies). Ribosomal RNA was depleted using Ribo-Zero rRNA removal kits (MRZH11124, Epicentre). RNA-seq libraries were prepared using ScriptSeq v2 library kit (SSV21124, Epicentre).

treatment_protocol: For normal fetal and adult cardiomyocyte expression data, isolated, purified cardiomyocytes were used with 3 biological replicates per group. Adult CMs were dissociated and purified from 6 week old hearts by Langendorf collagenase perfusion followed by di

tag: strain

value: mixed mouse strain

tag: Stage

value: embryonic

tag: replicate

value: rep 1


title: E12.5 CM-specific RNASeq rep3

description: rRNA-depleted RNA

treatment_protocol: For normal fetal and adult cardiomyocyte expression data, isolated, purified cardiomyocytes were used with 3 biological replicates per group. Adult CMs were dissociated and purified from 6 week old hearts by Langendorf collagenase perfusion followed by differential sedimentation as described16. Fetal hearts were dissociated using the Neonatal mouse cardiomyocyte isolation kit (nc-6031, Cellutron Life Technologies) and purified using the mouse neonatal cardiomyocyte isolation kit (130-100-825, Miltenyi). CM preparations were over 90% pure by fluorescence microscopy.

value: rep 3


title: E12.5 CM-specific RNASeq rep2

description: rRNA-depleted RNA

value: rep 2


title: Fetal (E12.5) ventricle cardiomyocyte atac-seq rep1

data_processing:
Fastq files were aligned against mm9 using Bowtie2
aligned bam files were sorted, PCR duplicates and blacklisted regions removed and bam file indexed
peaks (accessible regions) were identified using peak caller MACS2
bigwig files were generated from peak files and aligned .bam files using deeptools (bin size 10bp) and normalized by RPKM
mm9

source_name: ventricle heart cardiomyoctes

extract_protocol:
E12.5 mouse hearts were dissected in ice cold optiMEM and cardiomyocytes were isolated using the Miltenyi Neonatal Mouse Cardiomyocyte Dissociation and Isolation Kits with the manufacturer’s suggested protocol (cat. 130-098-373; cat.130-100-825). The optimized-ATACSeq (omni-ATACSeq) libraries were generated from the isolated cardiomyocytes (2 biological replicates; 26K cells each) using the author’s recommended lysis steps and transposition protocol
omniATAC-Seq (updated ATAC-Seq protocol described by Corces et al., 2017 Nature Methods


title: Fetal (E12.5) ventricle cardiomyocyte atac-seq rep2

data_processing:
Fastq files were aligned against mm9 using Bowtie2
aligned bam files were sorted, PCR duplicates and blacklisted regions removed and bam file indexed
peaks (accessible regions) were identified using peak caller MACS2
bigwig files were generated from peak files and aligned .bam files using deeptools (bin size 10bp) and normalized by RPKM


title: PDAC-B ST2


title: 48432 (RB_14): Retinoblastoma

status: Public on Apr 30 2019

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

data_processing:
The raw fastq files generated in sequencing were first subjected to quality check to filter out substandard data and then adapter trimming was done using cutadapt v-1.8dev
The processed   data had no contamination from non-polyA tailed RNAs, mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences due to the usage of Bowtie2 v-2.2.4 (Langmead and Salzberg 2012).
The paired-end reads were aligned to reference human genome, GRCh37/hg19 [2] using HISAT v-0.1.7 (Kim, Langmead et al. 2015). The  gene expression in retina and RB tumours were calculated using FPKM values (Fragments Per Kilobase of transcript per Million mapped reads) using cufflinks v-2.2.1 (Trapnell, Roberts et al. 2012).
Genome_build: GRCh37 release 75 ftp://ftp.ensembl.org/pub/release75/gtf/homo_sapiens/Homo_sapiens.GRCh37
Supplementary_files_format_and_content: tab-delimited text files include count number reads per gene for each Sample

source_name: Retinoblastoma

growth_protocol: Retina is obtained from donor eye balls. Retinoblastoma tumour tissue is obtained by informed consent using Helsinki protocol in  the  Sankara Nethralaya institute Board (Ethical clearance no: 249B-2011-P). We stored the tissues at -80°C until further use.

extract_protocol:
RNA was extracted from tumors and normal retina using TRIzol reagent ((#15596026, Thermo Fisher Scientific) according to manufacturer’s protocol. The quality and concentration of RNA was determined on 2200 TapeStation using the RNA specific Tapes and reagents (#5067-5576, 5577, Agilent Technologies) and Qubit 3.0 Fluorimeter
After the RNA passed the defined quality control measures, the library was prepared using the TruSeq RNA Library Prep Kit V2 (#RS-122-2001/RS-122-2002, Illumina Inc.). Using divalent cations under high temperature, the Ribo-depleted RNA was fragmented. Initially, the first strand cDNA was developed from fragmented RNA by using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. A single ‘A’ base was added, and cDNA was then ligated to the adapters. This product was purified and amplified using PCR to make the final cDNA library. This library was quantified using Qubit DNA Assay and by using DNATapeStation D1000 Screen Tape (#5067-5582,5583, Agilent Technologies) amplified and sequenced on the HiSeq2500 with 100bp paired end chemistry. The TruSeq Universal Adapter is: 5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3’.T and the TruSeq Illumina Index Adapter is as follows: 5’GATCGGAAGAGCACACGTCTGAACTCCAGTCAC [INDEX] ATCTCGTATGCCGTCTTCTGCTTG3’. This was performed at Medgenome labs, Bangalore.

value: Retinoblastoma

value: 8 months


title: 48431 (Retina_5_years): Control Retina

source_name: Control Retina

value: Control Retina

value: 5 years


title: PDAC-A ST2

value: pancreatic adenocarcinoma

value: tissue cryosections


title: 48437 (768_13): Retinoblastoma

value: 6 years


title: 48434 (647_13): Retinoblastoma

value: 1 year


title: 48428 (348_12): Control Retina

value: 12 years


title: 48429 (67_13): Retinoblastoma


title: 48436 (172_22): Control Retina

value: 22 years


title: 334: ABA_1280min_rep2

status: Public on Apr 11 2019

city: Düsseldorf

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

data_processing:
Basecalling was done using Illumina Casava - version 1.9.
Any remaining adapter sequences as well as low-quality bases and Ns were trimmed using Trimmomatic - version 0.33.
Illumina reads were mapped against the reference transcriptome of Beta vulgaris (RefBeet-1.2.2; Dohm et al., 2014) using BLAT (Kent, 2002) in protein space. The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Reference transcripts were annotated based on their homology to representative Arabidopsis peptides (Araport11, www.araport.org) via BlastX (BLAST 2.6.0+ suite, parameters: -evalue 1e-5 -max_target_seqs 1).
Differential gene expression and log2-fold change of ABA-treated compared to mock-treated leaves were determined using DESeq2 (Love et al., 2010) with multiple hypothesis correction after Benjamini-Hochberg (1995).
Raw counts were normalized to reads per million (rpm) and reads per kilobase million (rpkm).
Reads per million (rpm) were used as an input for analysis of temporal patterns of transcript abundance using maSigPro (Nuedaet al., 2014) to identify genes with temporal patterns significantly different between the two treatments
Reads per kilobase million (rpkm) were used as an input for non-negative matrix factorisation and k-means clustering to assign genes to clusters based on time-dependent patterns of transcript abundance

organism: Talinum fruticosum

source_name: Leaf

growth_protocol: Two months old plants were used in this experiment. They were initially germinated in the green house and since the sixth week grown under 12 hr light, 25 °C/12 hr dark, 23°C regime in a controlled growth chamber. The adaptation lasted 11 days, until the treatments were performed.

extract_protocol:
Leaves were harvested at specified time points and shock frozen in liquid nitrogen. RNA was isolated from ground tissue using Monarch® Total RNA Miniprep Kit (New England Biolabs) and any co-extracted DNA was removed with DNase I (New England Biolabs). RNA integrity was examined using Fragment Analyzer™ with Standard Sensitivity RNA Analysis Kit (DNF-471, Advanced Analytical Technologies, Inc.).  Biolabs) and any co-extracted DNA was removed with DNase I (New England Biolabs). RNA integrity was controlled with
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (RS-122-2101, Illumina) and following PROTOKOL. Fragment size distribution was examined using Fragment Analyzer™ with High Sensitivity NGS Fragment Analysis Kit (1 bp – 6,000 bp) (DNF-474, Advanced Analytical Technologies, Inc.). Library concentration was determined with Qubit™ dsDNA HS Assay Kit (Invitrogen™) and pooled to final concentration for 2nM (12 samples per lane). Sequencing was performed in a single-end mode (150 bp read length) on HiSeq 3000 using HiSeq 3000/4000 SR Cluster Kit and HiSeq 3000/4000 SBS Kit (all Illumina).

treatment_protocol: Individual leaves were sprayed on adaxial surface either with mock solution (0.0995% methanol with 0.02% Tween 20) or 200µM ABA (also with 0.02% Tween-20).

value: leaf

tag: treatment

value: ABA

tag: time after treatment


title: 331: mock_1280min_rep1

value: mock


title: 48435 (1548_14): Retinoblastoma

value: 3 years


title: 330: ABA_640min_rep2


title: 48430 (1563_15): Retinoblastoma


title: 48433 (1630_15): Retinoblastoma


title: 326: ABA_320min_rep2


title: 329: mock_640min_rep2


title: 328: ABA_640min_rep1


title: 333: mock_1280min_rep2


title: RPFA0002_1_5B_BY_rgt2KanMX_to_BY

status: Public on Aug 12 2019

city: Minneapolis

first: Frank

middle: Wolfgang

last: Albert

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

data_processing:
Base calls were made on instrument using Illumina Real Time Analysis RTA 2.4.11
Basecalls were converted to Fastq using bcl2fastq v2.20.0.422
Reads were trimmed using trimmomatic version 0.38; using parameters ILLUMINACLIP:Trimmomatic-0.38/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Gene expression was quanitified using kalisto 0.44.0 using parameters kallisto quant -i Saccharomyces_cerevisiae.R64-1-1.cdna.all.kallistoIndex -t 28 --single -l 200 -s 30 --rf-stranded -b 100
Genome_build: sacCer3
Supplementary_files_format_and_content: We combined expression quantifications ("estimated counts" from the kalisto output ) from all samples into one tab-separated file. Sample are in columns and genes are in rows

molecule: polyA RNA

source_name: yeast culture

growth_protocol: Yeast cultures were grown in YNB in 1mL of medium in a 2mL deep well plate. To an average optical density (OD600) of 0.37

extract_protocol:
The plate was centrifuged for 3 min at 2,100g, the supernatant was removed, and each cell pellet was resuspended in 1 ml of H2O and transferred to a 1.5 ml centrifuge tube.  After centrifugation for 2 min at 16,000g, the supernatant was removed and the cell pellet was flash frozen by immersion of the tube in liquid nitrogen and stored at -80. Total RNA was isolated from cell pellets in 5 batches, with each batch containing a sample of each of the 5 strains, using the ZR Fungal/Bacterial RNA mini-prep kit, including the DNase I on-column digestion step (Zymo Research). Cell pellets chosen for RNA isolation had the most uniform OD600 reading across strains, with an average OD600=0.37 (range of 0.34 to 0.40). Each cell pellet was resuspended in lysis buffer and transferred to screw-capped tubes containing glass beads and the cells were broken open using a mini-beadbeater (Biospec Products) in 5 cycles of 2 min bead beating followed by 2 min at -80℃. The total RNA was eluted in 50 ul of DNAse/RNAse free water. Poly-A RNA was extracted from 550 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
PolyA RNA was used as input into the NEB Ultra II Directional RNA library kit for Illumina (NEB E7760) in two batches. NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set1) were used to amplify and barcode the libraries using the following cycling conditions: Initial Denaturation at 98℃ for 30s and 10 cycles of: 98℃ for 10 sec and 65℃ for 75 sec, followed by a 65℃ extension for 5 min. The amplified DNA was quantified using Qubit DNA HS. Sample concentrations ranged from 47-102 ng/ul. An equal concentration of each of the 25 barcoded libraries was pooled and the average fragment size of the library was determined using a Agilent High Sensitivity chip. High-output sequencing was performed on an Illumina NextSeq 550 at the University of Minnesota Genomics Core.


title: 322: ABA_160min_rep2


title: 324: ABA_320min_rep1


title: 320: ABA_160min_rep1


title: 319: mock_160min_rep1


title: 317: mock_80min_rep2


title: 318: ABA_80min_rep2


title: 316: ABA_80min_rep1


title: 315: mock_80min_rep1


title: 332: ABA_1280min_rep1


title: 327: mock_640min_rep1


title: 311: mock_40min_rep1


title: 313: mock_40min_rep2


title: 312: ABA_40min_rep1


title: RNA-seq_12M_rep4

source_name: Rod photoreceptors

value: Rod photoreceptors

value: C57BL/6J (Nrlp-GFP)


title: 325: mock_320min_rep2


title: 323: mock_320min_rep1


title: Pre_13

status: Public on Feb 11 2019

type: RNA

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

hyb_protocol: Probes and lysate were hybridized overnight at 65 ºC for 12-16 hours

scan_protocol: Hybridized samples were then run on the NanoString preparation station using their high sensitivity protocol per manufacturer’s instructions (NanoString Technologies, Seattle, WA).The samples were scanned at maximum scan resolution capabilities using the nCounter™ Digital Analyzer

data_processing: All sample and data normalization occurred within the nCounter™ digital analyzer software, nSolver™.  Specifically, the raw code count data was normalized using a positive control normalization factor based off the spiked-in positive control raw counts and also a content normalization factor derived from the raw counts of a set of relevant housekeeping genes. Transcripts with counts less than or equal to the highest embedded negative controls (background noise) in that sample are first set to its background. The gene count for each gene is then subtracted from this background so that each sample has the same footing where zero numbers represent undetectable noise.

label: biotin

label_protocol: Per sample, 50ng of total RNA isolated from FFPE was mixed with a 3′ biotinylated capture probe and a 5′reporter probe tagged with a fluorescent barcode, from a custom designed gene expression codeset

extract_protocol: RNA was isolated from slides of FFPE tissue using Qiagen RNeasy FFPE kit per manufacturer’s protocol (Qiagen, Valencia, CA)

tag: melanoma stage

value: IIIC

tag: recurrence

value: Male

tag: ldhcont

tag: ldhcat

value: normal

tag: primary

value: cutaneous

tag: patient id


title: Post_14

value: IIIB

tag: age

tag: Sex

value: elevated

value: unknown


title: Post_10


title: Pre_8


title: 321: mock_160min_rep2

tag: tissue


title: Pre_12

value: Female


title: Pre_10


title: Post_9


title: RNA-seq_18M_rep1


title: Post_7


title: Post_8


title: Pre_9

value: Normal


title: Post_6


title: Pre_6


title: Post_4


title: Post_5


title: 314: ABA_40min_rep2


title: Pre_4


title: Pre_5


title: Post_3


title: Pre_3


title: Pre_11


title: ndt80Δ T=3 input for pH2A ChIP rep2

status: Public on Jan 10 2019

description:
processed data file:
AH6179pH2AT3rep-344-348-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

data_processing:
Illumina output reads were processed as described in (Paul et al., 2017). The reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Bedgraph files were created from pooled replicates.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

source_name: ndt80Δ T=3 input for pH2A ChIP

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 2.0 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. Samples were processed as described in (Blitzblau et al., 2012).
Libraries for ChIP sequencing were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). Quality of the libraries was checked on 2100 Bioanalyzer or 2200 Tapestation. Libraries were quantified using qPCR prior to pooling. The ChIP libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads.

tag: meiotic time point

value: 3 hour

tag: genotype

tag: chip antibody


title: pH2A ChIP for ndt80Δ T=3  rep2

source_name: pH2A ChIP for ndt80Δ T=3

tag: strain


title: Post_2


title: Pre_1


title: Pre_2


title: pH2A ChIP for ndt80Δ T=3  rep1


title: Post_1


title: Pre_7


title: ndt80Δ T=3 input for pH2A ChIP rep1


title: Hop1 ChIP for pch2Δ ndt80Δ T=3 input rep2

description:
processed data file:
AH6639Hop1T3rep-226-216-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Hop1 ChIP for pch2Δ ndt80Δ T=3 input


title: pch2Δ ndt80Δ T=3 input rep1

source_name: pch2Δ ndt80Δ T=3 input


title: Hop1 ChIP for pch2Δ ndt80Δ T=3 input rep1


title: FFPE X221541965 [X81_X.77_plate1NHSII]

status: Public on Jan 08 2019

first: Rulla

middle: M

last: Tamimi

address: 181 Longwood Avenue

department: Medicine

institute: Brigham and Women's Hospital

hyb_protocol: Hybridization was performed according to standard protocols

scan_protocol: Scanning was performed according to standard protocols

data_processing: Gene expression data were normalized and summarized using Robust Multiarray Average (RMA)

source_name: breast tissue

label_protocol: Labeling was performed according to standard Affymetrix protocols

extract_protocol:
Formalin-fixed paraffin-embedded tissue blocks
Qiagen AllPrep RNA isolation kit was used to isolate total RNA

tag: tumor tumoradj

value: tumor

tag: cohort

tag: microarray batch

tag: age at dx

tag: dx year

tag: tumor size

tag: grade

tag: Stage

tag: surgery

value: mast

value: mixed

tag: recurrence months

tag: distant recurrence

tag: distant recurrence months

tag: er ihc

tag: pr ihc

tag: her2 ihc

tag: ki67 ihc

tag: molecularsubtype byihc

value: LumA

value: LumB

tag: proliferationscore modifiedmedianmethod

tag: rorptscore modifiedmedianmethod

tag: rorptgroup modifiedmedianmethod

value: med

tag: rorptscore subgroupspecificmethod

tag: rorptgroup subgroupspecificmethod

tag: sample id


title: FFPE X218287658 [X13_X.9_plate1NHSII]

tag: tumor tumoradj

tag: cohort

tag: microarray batch

tag: age at dx

tag: dx year

tag: tumor size

tag: grade

tag: treatment

tag: recurrence

value: low


title: FFPE X213978359 [X86_X.82_plate1NHSII]

value: tumor-adjacent normal

tag: Stage

tag: surgery

value: lump

tag: recurrence months

tag: distant recurrence

tag: distant recurrence months

tag: er ihc

tag: pr ihc

tag: her2 ihc

tag: ki67 ihc


title: FFPE X213310102 [X11_X.94_plate2NHSII_2]

tag: tumor tumoradj

tag: cohort

tag: molecularsubtype byihc

tag: proliferationscore modifiedmedianmethod

tag: rorptscore modifiedmedianmethod

tag: rorptgroup modifiedmedianmethod

tag: rorptscore subgroupspecificmethod

tag: rorptgroup subgroupspecificmethod

tag: sample id


title: FFPE X215716517 [X87_X.83_plate1NHSII]

tag: microarray batch

tag: age at dx

tag: dx year

tag: tumor size

tag: grade

tag: Stage

tag: surgery

tag: treatment

tag: recurrence


title: FFPE X217785175 [X5_X.88_plate2NHSII]

tag: tumor tumoradj

tag: cohort

tag: recurrence months

tag: distant recurrence

tag: distant recurrence months

tag: er ihc

tag: pr ihc

tag: her2 ihc

tag: ki67 ihc


title: FFPE X219656792 [X12_X.95_plate2NHSII]

tag: microarray batch

tag: age at dx

value: chemotx

tag: molecularsubtype byihc

tag: proliferationscore modifiedmedianmethod

tag: rorptscore modifiedmedianmethod

tag: rorptgroup modifiedmedianmethod

value: high

tag: rorptscore subgroupspecificmethod

tag: rorptgroup subgroupspecificmethod

tag: sample id


title: FFPE X215243359 [X89_X.85_plate1NHSII]

tag: tumor tumoradj

tag: cohort

tag: dx year

tag: tumor size

tag: grade

tag: Stage

tag: surgery

tag: treatment

tag: recurrence


title: FFPE X221541965 [X82_X.78_plate1NHSII]

tag: microarray batch

tag: age at dx

tag: recurrence months

tag: distant recurrence

tag: distant recurrence months

tag: er ihc

tag: pr ihc

tag: her2 ihc

tag: ki67 ihc


title: FFPE X215716517 [X88_X.84_plate1NHSII]

tag: tumor tumoradj

tag: cohort

tag: molecularsubtype byihc

tag: proliferationscore modifiedmedianmethod

tag: rorptscore modifiedmedianmethod

tag: rorptgroup modifiedmedianmethod

tag: rorptscore subgroupspecificmethod

tag: rorptgroup subgroupspecificmethod

tag: sample id


title: FFPE X215243359 [X90_X.86_plate1NHSII]

tag: microarray batch

tag: age at dx

tag: dx year

tag: tumor size

tag: grade

tag: Stage

tag: surgery

tag: treatment

tag: recurrence


title: FFPE X219853078 [X7_X.90_plate2NHSII]

tag: tumor tumoradj

tag: cohort

tag: recurrence months

tag: distant recurrence

tag: distant recurrence months

tag: er ihc

tag: pr ihc

tag: her2 ihc

tag: ki67 ihc


title: FFPE X219656792 [X13_X.96_plate2NHSII]

tag: microarray batch

tag: age at dx

tag: molecularsubtype byihc

tag: proliferationscore modifiedmedianmethod

tag: rorptscore modifiedmedianmethod

tag: rorptgroup modifiedmedianmethod

tag: rorptscore subgroupspecificmethod

tag: rorptgroup subgroupspecificmethod

tag: sample id


title: FFPE X213337254 [X14_X.97_plate2NHSII]

tag: tumor tumoradj

tag: cohort

tag: dx year

tag: tumor size

tag: grade

tag: Stage

tag: surgery

tag: treatment

tag: recurrence


title: FFPE X213337254 [X15_X.98_plate2NHSII]

tag: microarray batch

tag: age at dx

tag: recurrence months

tag: distant recurrence

tag: distant recurrence months

tag: er ihc

tag: pr ihc

tag: her2 ihc

tag: ki67 ihc


title: FFPE X221148853 [X8_X.91_plate2NHSII]

tag: tumor tumoradj

tag: cohort

tag: molecularsubtype byihc

tag: proliferationscore modifiedmedianmethod

tag: rorptscore modifiedmedianmethod

tag: rorptgroup modifiedmedianmethod

tag: rorptscore subgroupspecificmethod

tag: rorptgroup subgroupspecificmethod

tag: sample id