title: para-carcinoma tissue 04

city: Shanghai

first: Gong

middle: Ke

last: Tao

address: Jimo Road 150#

institute: easthospital

data_processing:
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
LncRNA & mRNA: The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Genome_build: hg19

source_name: hepatocellular carcinoma

growth_protocol: Five pairs of primary HCC and adjacent non-tumor tissues were obtained from patients undergoing surgery.

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions.

treatment_protocol: Total RNA were extracted from tissue using Trizol reagent (Life Technologies Corporation, Carlsbad, CA, USA).

value: para-carcinoma tissue in liver


title: para-carcinoma tissue 05

status: Public on Dec 09 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: CD8_Memory_IFNa_HD_GU0003

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

description: CD8 Memory T-Cell

data_processing:
Illumina’s bcl2fastq2.17 software was used to de-multiplex the reads into individual fastq files for each sample.
Reads were mapped to human genome GRCh38, Ensemble version 91, using CLC Genomics Workbench v20 (QIAGEN) and “total exon reads” counted for each gene.
Genome_build: GRCh38, Ensemble version 91
Supplementary_files_format_and_content: table of raw counts of "total exon reads"

molecule: polyA RNA

source_name: PBMC

growth_protocol: PBMCs were thawed with X-Vivo media (Lonza, MD) containing Benzonase nuclease (50 U/ml; Millipore Sigma, MO) and cultured in the absence or presence of rhIL-27 (100 ng/ml).

extract_protocol:
Total RNA extraction from approx. 50,000 sorted cells of each sample was performed using Qiagen RNeasy Plus Universal mini kit (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, CA) and RNA integrity was analyzed using Agilent TapeStation 4200 (Agilent Technologies, CA).
cDNA was converted by using SMARTer kit (Clontech, CA), and sequencing libraries were prepared using Illumina Nextera XT Library Preparation Kit (NEB, MA).

treatment_protocol: After overnight culture, PBMCs from HIV infected participants were stimulated with HIVGag peptide pool (2 ug/ml, NIH AIDS Reagent Program), and PBMCs from healthy donors were stimulated with the CMV, EBV and Influenza (CEF) peptide pools (5ug/ml, NIH AIDS Reagent Program). DMSO was used as control in the unstimulated culture condition. After 2 hours of stimulation, Brefeldin A (10 ug/ml, Calbiochem, CA) was added and cultured for additional 4 hours. Cells were harvested and stained with Live/Dead staining (Invitrogen, CA). Cells were incubated with human IgG (10 ug/ml, Sigma, MO) to block Fc receptors followed by a cocktail of mAbs as described in manuscript Table S2, Panel 2.  T cell sorting and mRNA-Seq analysis: T cell subsets were sorted based on surface expression of CD45RA and CD27. Naïve (CD45RA+CD27+) and Memory (CD45RA-CD27+) CD4 and CD8 T cell subsets from PLWH (n= 5) and healthy controls (n= 3) were sorted in BD FACS Aria based on surface staining with antibody cocktail of mAbs (Table S2, Panel 3). Sorted cells were spun down and rested 3 hours for subsequent in vitro simulation for 90 minutes at 37°C and 5% CO2 with rhIFN-α (100 U/ml, PBL Biomedical Laboratories, N), rhIL-6 (100 ng/ml, PeproTech, NJ), rhIL-27 (100 ng/ml; PeproTech, NJ) or media as unstimulated control. After stimulation, the cells were washed with cold PBS, resuspended in TRIzol (Invitrogen, CA) and stored at -80°C.

tag: t-cell type

tag: ex-vivo stimulation

value: IFNa

tag: donor hiv status

value: HD

tag: donorid


title: para-carcinoma tissue 03


title: para-carcinoma tissue 02


title: CD8_Naive_Unstim_HD_GU0003

description: CD8 Naive T-Cell

value: Unstim


title: para-carcinoma tissue 01


title: 20120a037_01

city: Tuebingen

first: Christoph

last: Trautwein

address: Roentgenweg 13

department: Werner Siemens Imaging Center

country: Germany

institute: University of Tuebingen

data_processing:
Read quality of RNA-seq data in FASTQ files was assessed using ngs-bits (v.2020_06), to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR v2.7.3a (Dobin et al., 2013) to the GRCh37 and alignment quality was analyzed using ngs-bits and visually inspected in the Integrative Genome Viewer (v2.7.2).
Normalized read counts for all genes were obtained using Subread (v2.0.0).
The distribution of logarithmized cpm-normalized expression values shows similar characteristics over all samples. Based on the filtered data set, samples were investigated with respect to their pairwise similarity. Spearman’s rank correlation coefficient was calculated for each pair of samples.
A hierarchical clustering was performed on the resulting similarity values. Differential gene expression analysis was conducted based on the filtered gene expression data set. A statistical model incorporating the group property of samples was tested by fitting a negative binomial distribution using a generalized linear model (GLM) approach.
Genome_build: GRCh37
Supplementary_files_format_and_content: The full processed and annotated gene expression values are given in the file "Processed_Data_Spreadsheet_Glioma_Study.xlsx". Simple boxplots between genes and groups of interest were used for the publication.

source_name: glioma tissue

extract_protocol:
Tissue collection: Archival tumor samples were available after tissue acquisition according to a standardized routine bio banking procedures. In brief, after removal of tumor tissue from the resection cavity in the operating room, samples were immediately frozen in liquid nitrogen, the tumor content was assessed on a cryo-slide by a neuropathologist, and only tissue samples with sufficient tumor content (> 70-80%) were stored as bio samples in the biobank at -80°C.
Tissue homogenization: Tissue samples were cryogenically pulverized (Covaris CryoPREP CP02) and aliquots of 5 mg used for RNA analysis.
RNA was purified from lyophilized tissue using the QIAsymphony RNA kit (Qiagen). More precisely, tissue was thawed at room temperature and 800 µl of Buffer RTL Plus was added to the tissue. Homogenization was performed twice for 2 minutes at 25 Hz using the TissueLyser II (Qiagen). Resulting homogenates were centrifuged for 3 minutes at maximum speed in a microcentrifuge and 400 µl of the resulting lysate was loaded on the QIAsymphony SP (Qiagen) using the RNA CT 400 protocol. At the end of the protocol, the RNA was eluted in 35 µl of RNase-free water.
For library preparation, mRNA fraction was enriched using polyA capture from 200ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) using the liquid handler Biomek i7 (Beckman). Next, mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. Library molarity was determined by measuring the library size (approximately 400 bp) using the Fragment Analyzer with the High NGS Fragment 1-6000bp assay (Agilent) and the library concentration (approximately 5 ng/µl) using the Infinite 200Pro (Tecan) and the Quant-iT HS Assay Kit (Thermo Fisher Scientific).
The libraries were denatured, diluted to 270 pM and sequenced as paired-end 100bp reads on an Illumina NovaSeq6000 (Illumina, San Diego, CA, USA) with a sequencing depth of approximately 25 million clusters per sample.

tag: diagnosis

value: Diffuse glioma

value: Glioma

tag: histology

value: Astro

tag: genotype

tag: treatment

value: Untreated

tag: paired patient


title: 20120a038_01

value: Treated (Radiotherapy)


title: HCC tissue 05

value: hepatocellular carcinoma tissue


title: 20120a015_01

value: Oligo

tag: paired patien


title: 20087P01F05_01

value: Glio


title: CD8_Naive_IL6_HD_GU0003

description: CD8 Naive T-Cell


title: CD8_Naive_IL27_HD_GU0003

description: CD8 Naive T-Cell


title: 20087P01E05_01


title: HCC tissue 03


title: 20087P01G05_01


title: CD8_Naive_IFNa_HD_GU0003

description: CD8 Naive T-Cell


title: 20087P01H05_01


title: HCC tissue 04


title: 20120a003_01


title: HCC tissue 02


title: CD8_Memory_IL6_HD_GU0003

description: CD8 Memory T-Cell


title: HCC tissue 01


title: CD4_Naive_IL6_HD_GU0003

description: CD4 Naive T-Cell


title: CD4_Naive_Unstim_HD_GU0003

description: CD4 Naive T-Cell


title: 20087P01C05_01


title: CD4_Naive_IL27_HD_GU0003

description: CD4 Naive T-Cell


title: CD4_Memory_Unstim_HD_GU0003

description: CD4 Memory T-Cell


title: CD4_Naive_IFNa_HD_GU0003

description: CD4 Naive T-Cell


title: Liver _Fibrosis.C9

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

source_name: Liver Fibrosis

growth_protocol: six human liver fibrotic tissues were obtained from patients undergoing surgery.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Liver Fibrosis tissue


title: Liver _Fibrosis.C10


title: Liver _Fibrosis.C3


title: Liver _Fibrosis.C11


title: 20087P01H04_01


title: 20087P01A05_01


title: 20087P01D05I2_01


title: Sample 23_Whole_Ovaries

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0) with the RefSeq annotated transcripts as a guide.
Raw counts were generated using featureCounts (version 1.6.0.4)
Differential gene expression was assayed by edgeR (version 3.16.5), using a false discovery rate of (FDR) of 0.05, and genes with 4-fold or higher were considered significant.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: raw counts

organism: Drosophila melanogaster

source_name: Drosophila ovaries

growth_protocol: Ovaries dissected in 1x PBS.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, 15596026) or phenol-chloroform treatment, treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907), and then run on a 1% agarose gel to check integrity of the RNA. To generate mRNA-enriched libraries total RNA was treated with poly(A)tail selection beads and then following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes.
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

treatment_protocol: For samples with suffixes "_T" (Total) or "_P" (Polysome) samples were loaded onto polysome gradients prior to RNA isolation.

tag: age

value: dissected 1-5 days post-eclosion

tag: genotype/variation

value: ovaries


title: Liver _Fibrosis.C12


title: Liver _Fibrosis.C13


title: CD4_Memory_IL27_HD_GU0003

description: CD4 Memory T-Cell


title: Sample 22_S19bRNAi_P2

value: S19b RNAi>UAS-Dcr2;nosGAL4

tag: molecule subtype

value: Polysome


title: Sample 20_S19bRNAi_P1


title: H9 PUS7KO RPF replicate 2

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
Library strategy: Ribo-Seq
The raw sequence data were clipped using the 3' adaptor sequence (AGATCGGAAGAGCACACGTCT) by fastx_clipper of FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The sequence reads were aligned to an rRNA reference using Bowtie v1.1.2. The unaligned reads were collected while the rRNA alignments were discarded to reduce rRNA contamination. TopHat v2.1.0 was used to align the non-rRNA sequencing reads to hg38. The .bam files from TopHat and a custom protein coding gene annotation constructed with one transcript for each gene from GENCODE v35 were used to determine P-site offsets for the ribosome profiling data, count the number of read alignments, and calculate read densities (RPKM) per gene for exons, 5’ UTRs, coding regions, and 3’ UTRs by Plastid. Ribowaltz was used for quality control the data including the percentage of P-sites falling into the annotated transcript regions and the trinucleotide periodicity of ribosome footprints along coding sequences.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: H9 cells

growth_protocol: Cells were grown in mTeSR media on matrigel coated plates

extract_protocol:
Cells were lysed in Mammalian Lysis Buffer supplemented with CHX and cleared by centrifugation
Ribo-seq libraries were obtained following Art-Seq Ribosome Profiling Kit (Mammalian) Epicentre (cat# RPHMR12126)

treatment_protocol: Cells were treated for 1min with translation elongation inhibitor cyclohexamide (CHX)

tag: cell line


title: CD4_Memory_IL6_HD_GU0003

description: CD4 Memory T-Cell


title: 20087P01G04_01


title: 20087P01F04I2_01


title: H9 PUS7KO RPF replicate 1


title: 20087P01B05_01


title: Donor 5 Peripheral LungRep 1

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
donor5_periph_rep1
Healthy Donor
mRNA

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.h5: HDF5; Cell ranger HDF5 Feature Barcode Matrix Format, this file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.

source_name: Peripheral lung tissue

extract_protocol:
Peripheral samples: 2cm deep from the pleura, airway or vessel visible structures >2mm removed. Proximal airway: 5 generations of airway from main stem bronchus.
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two or one biological replicates were generated per sample. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. Sequencing libraries were loaded at 2.1pM on an Illumina Hiseq 2500 with 2 × 100 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

value: Healthy

value: Peripheral lung

tag: Sex

value: female


title: H9 WT RPF replicate 2

value: WT


title: Donor 4 Peripheral LungRep 1

description:
donor4_periph_rep1
Healthy Donor
mRNA

value: male


title: Sample 17_hsbam_T2

value: bam RNAi; hsbam>nosGAL4

value: Total/input


title: Sample 18_hsbam_P2


title: H9 WT RPF replicate 1


title: CD4_Memory_IFNa_HD_GU0003

description: CD4 Memory T-Cell

value: IFNa

value: HD


title: CD8_Naive_Unstim_HD_GU1118

description: CD8 Naive T-Cell

value: Unstim


title: 20087P01E04_01

value: Diffuse glioma

value: Glioma

value: Astro

value: Untreated


title: 20087P01D04_01

value: Glio


title: 20087P01B04_01


title: Donor 6 Proximal LungRep 2

description:
donor6_prox_rep2
Healthy Donor
mRNA

source_name: Proximal Airway Epithelium

value: Proximal airway epithelium


title: Sample 21_S19bRNAi_T2

value: dissected 1-5 days post-eclosion

value: S19b RNAi>UAS-Dcr2;nosGAL4

value: ovaries


title: 20120a047_01


title: Donor 3 Proximal LungRep 2

description:
donor3_prox_rep2
Healthy Donor
mRNA

value: Healthy

value: female


title: H9 PUS7KO Total replicate 2

data_processing:
The raw sequence data were clipped using the 3' adaptor sequence (AGATCGGAAGAGCACACGTCT) by fastx_clipper of FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The sequence reads were aligned to an rRNA reference using Bowtie v1.1.2. The unaligned reads were collected while the rRNA alignments were discarded to reduce rRNA contamination. TopHat v2.1.0 was used to align the non-rRNA sequencing reads to hg38. The .bam files from TopHat and a custom protein coding gene annotation constructed with one transcript for each gene from GENCODE v35 were used to determine P-site offsets for the ribosome profiling data, count the number of read alignments, and calculate read densities (RPKM) per gene for exons, 5’ UTRs, coding regions, and 3’ UTRs by Plastid. Ribowaltz was used for quality control the data including the percentage of P-sites falling into the annotated transcript regions and the trinucleotide periodicity of ribosome footprints along coding sequences.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files


title: Sample 19_S19bRNAi_T1


title: Donor 3 Proximal LungRep 1

description:
donor3_prox_rep1
Healthy Donor
mRNA


title: 20087P01H03_01


title: Donor 6 Proximal LungRep 1

description:
donor6_prox_rep1
Healthy Donor
mRNA

value: male


title: Sample 16_hsbam_P1

value: bam RNAi; hsbam>nosGAL4

value: Polysome


title: 20087P01C04_01


title: Sample 15_hsbam_T1

value: Total/input


title: Donor 3 Peripheral LungRep 2

description:
donor3_periph_rep2
Healthy Donor
mRNA

value: Peripheral lung


title: 20087P01A04_01


title: Sample 14_bamRNAi_S19b2

value: bam RNAi;S19b mutant>nosGAL4; S19b mutant


title: 20087P01G03_01

value: Diffuse glioma


title: H9 WT Total replicate 2

value: WT


title: H9 PUS7KO Total replicate 1


title: 20087P01F03_01

value: Glioma


title: H9 WT Total replicate 1


title: 20087P01D03_01

value: Untreated


title: Donor 2 Peripheral LungRep 2

description:
donor2_periph_rep2
Healthy Donor
mRNA


title: Sample 12_bamRNAi2

value: bam RNAi>nosGAL4


title: Donor 2 Peripheral LungRep 1

description:
donor2_periph_rep1
Healthy Donor
mRNA


title: Sample 11_bamRNAi1


title: Donor 1 Peripheral LungRep 2

description:
donor1_periph_rep2
Healthy Donor
mRNA


title: 20087P01B03_01

value: Glio


title: 20087P01C03_01

value: Astro


title: Donor 1 Peripheral LungRep 1

description:
donor1_periph_rep1
Healthy Donor
mRNA


title: Sample 9_NC2bRNAi1

value: dissected 1-5 days post-eclosion

value: NC2b RNAi>UAS-Dcr2;nosGAL4


title: Sample 10_NC2bRNAi2

value: ovaries


title: Sample 7_MSL3RNAi2

value: msl3 RNAi>UAS-Dcr2;nosGAL4


title: COPD 3 Peripheral LungRep 2

description:
copd3_periph_rep2
Disease - COPD
mRNA

value: COPD

value: male


title: 20087P01A03_01


title: 20087P01G02_01


title: 20087P01H02_01


title: COPD 3 Peripheral LungRep 1

description:
copd3_periph_rep1
Disease - COPD
mRNA


title: Sample 8_MSL3RNAi1


title: Donor 3 Peripheral LungRep 1

description:
donor3_periph_rep1
Healthy Donor
mRNA

value: Healthy

value: female


title: Sample 6_Set2RNAi2

value: Set2 RNAi>UAS-Dcr2;nosGAL4


title: Sample 13_bamRNAi_S19b1

value: bam RNAi;S19b mutant>nosGAL4; S19b mutant


title: 20087P01E03I2_01

value: Diffuse glioma


title: COPD 2 Peripheral LungRep 2

description:
copd2_periph_rep2
Disease - COPD
mRNA

value: Peripheral lung


title: Sample 5_Set2RNAi1


title: 20087P01F02I2_01

value: Glioma


title: COPD 4 Peripheral LungRep 1

description:
copd4_periph_rep1
Disease - COPD
mRNA


title: 20087P01E02I2_01

value: Untreated


title: COPD 2 Peripheral LungRep 1

description:
copd2_periph_rep1
Disease - COPD
mRNA


title: Sample 4_hsbam4

value: bam RNAi; hsbam>nosGAL4


title: Sample 3_hsbam3


title: Ifnar1-/-_HD-Tam x 48 hrs_3

type: RNA

city: St. Louis

first: Jose

middle: Bernardo

last: Saenz

state: Missouri

address: 660 S. Euclid Avenue

department: Medicine

institute: Washington University in St. Louis School of Medicine

description:
Ifnar1-/-_ HD-Tam x 48 hours_3
Mouse 3

hyb_protocol: Following fragmentation, cDNA was hybridized using slides with defined attached probes (GeneChip 2.0).

scan_protocol: Gene chips were scanned using the Affymetrix Genechip 3000.

data_processing: Data were processed using the Transcriptome Analysis Console (TAC; Thermo Fisher).

label: biotin

organism: Mus musculus

source_name: Gastric corpus

label_protocol: RNA was submitted to the Genome Technology Access Center at Washington University in St. Louis. cDNA was prepared according to the standard Affymetrix protocol using at least 1 µg RNA per sample using the WT Plus assay.

extract_protocol: The day after the final HD-Tam injection, mouse stomachs were harvested, and the gastric corpora were removed and snap-frozen in liquid nitrogen and stored at -80°C until further use. RNA was isolated from tissue sections using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Wild-type C57BL/6 cagemate/littermate mice or age-matched Ifnar1-/- mice were intra-peritoneally injected with two daily injections of HD-Tam (5 mg tamoxifen/20 g body weight). Mice were sacrificed one day after the last injection.

tag: strain

value: HD-Tam


title: Ifnar1-/-_HD-Tam x 48 hrs_1

description:
Ifnar1-/-_ HD-Tam x 48 hours_1
Mouse 1


title: Sample 1_hsbam1

tag: tissue


title: 20087P01D02_01

value: Glio


title: COPD 1 Peripheral LungRep 1

description:
copd1_periph_rep1
Disease - COPD
mRNA


title: 20087P01C02_01


title: Ifnar1-/-_HD-Tam x 48 hrs_2

description:
Ifnar1-/-_ HD-Tam x 48 hours_2
Mouse 2


title: Sample 2_hsbam2

value: dissected 1-5 days post-eclosion


title: WT_HD-Tam x 48 hrs_2

description:
WT_HD-Tam x 48 hours_2
Mouse 2

value: WT


title: 20087P01B02_01


title: WT_HD-Tam x 48 hrs_1

description:
WT_HD-Tam x 48 hours_1
Mouse 1


title: WT_HD-Tam x 48 hrs_3

description:
WT_HD-Tam x 48 hours_3
Mouse 3


title: COPD 1 Peripheral LungRep 2

description:
copd1_periph_rep2
Disease - COPD
mRNA


title: UN_476

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the hg38 human reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et.al. 2016), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Gene expression heatmaps were produced with GENE-E (Broad Institute).
Genome_build: hg38

source_name: Human Lymphatic Endothelial Cells (HLEC)

growth_protocol: HILEC were grown and mantained in Endothelial Cell Growth Medium (Lonza)

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

treatment_protocol: Tofacitinib 50 nm in the treated group. Saline in the control group

value: untreated


title: 20087P01A02_01


title: Hp infection_2

description:
Hp_6.5 months_2
Mouse 2

source_name: Hp infection (6.5 months)

extract_protocol: The day after the final vehicle/HD-Tam injection (or after 6.5 months of Hp infection), mouse stomachs were harvested, and the gastric corpora were removed and snap-frozen in liquid nitrogen and stored at -80°C until further use. RNA was isolated from tissue sections using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Wild-type C57BL/6 cagemate/littermate mice were treated intra-peritoneally injected once with either vehicle (10% ethanol in sunflower seed oil), two daily injections with HD-Tam (5 mg tamoxifen/20 g body weight), or infected with Hp (~1 x 108 cfu/mouse) for 6.5 months.

value: Gastric corpus

value: Hp infection


title: HD-Tam_1

description:
HD-Tam_48 hours_1
Mouse 1

source_name: HD-Tam treatment (48 hours)


title: HD-Tam_2

description:
HD-Tam_48 hours_2
Mouse 2


title: Hp infection_1

description:
Hp_6.5 months_1
Mouse 1


title: UN_436


title: 20087P01H01_01

value: Astro


title: tetO-Clock/Bmal1DN pHes7-luc iPSM #19 with dox

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: iPSM_KnownCanonical2020_genebody_rpkm_readCounts.txt.gz

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Trimmotatic (Version 0.39) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads mapped to ribosomal DNA (GenBank: BK000964.1) were filtered out and the remaining reads were mapped to mouse genome mm10 with STAR (2.7.2a and 2.7.4a for ESCs and iPSM, respectively) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools (1.7) (Li et al. 2009).
The known canonical genes from GENCODE VM23 was used for annotation, and the reads mapped to the genebody were quantified using Homer (Heinz et al. 2010).
The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands. In  the bigWigs for iPSM colonies, the reads mapped in the promoter (chr11:69115096-69120473) and 3’UTR (chr11:69122995-69123324) sequence of Hes7 were filtered out to eliminated transcripts from the pHes7-luc reporter transgene.
Fragments Per Kilobase per Million mapped reads (FPKM) were calculated using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and tab-delimited text files containing gene read counts and FPKM values for each sample.

growth_protocol: TetO-Clock/Bmal1 or tetO-Clock/Bmal1DN  KY1.1 ESCs (Yagita et al. PNAS 2010) were maintained as described previously (Umemura, Koike et al. PNAS 2017). TetO-Clock/Bmal1 or tetO-Clock/Bmal1DN  pHes7-luc ESCs were established from E14TG2a ESCs carrying Hes7-promoter driven luciferase reporters (Matsumiya et al.Development  2018), which were maintained without feeder cells in DMEM medium (Nacalai) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM L-glutamine (Nacalai), 1 mM non-essential amino acids (Nacalai), 100 µM StemSure® 2-Mercaptoethanol solution (Wako), 1 mM sodium pyruvate (Nacalai), 100 units/mL penicillin and streptomycin (Nacalai), 1000 units/ml leukemia inhibitory factor (LIF, Wako), 3 µM CHIRON99021 (Wako), and 1 µM PD0325901 (Wako) with 5% CO2 at 37°C. The iPSM colonies were differentiated from the pHes7-luc ESCs as described previously (Matumiya et al., Development 2018).

extract_protocol:
RNA was extracted by using QIAGEN miRNeasy Mini Kit as per manufacturer’s protocol.
The library constructions using TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) and the sequencing was carried out by Macrogen Japan on Illumina NovaSeq 6000 with 101-bp paired-end reads.

treatment_protocol: The tetO-Clock/Bmal1  or tetO-Clock/Bmal1DN ESCs lines were treated with/without 500 ng/mL doxycycline for 6 hours. The tetO-Clock/Bmal1  or tetO-Clock/Bmal1DN iPSM colonies were treated with 1000 ng/mL doxycycline for 2 hours.

tag: cell type

value: iPSM colonies

value: 1000 ng/mL doxycycline for 2 hours


title: Vehicle_2

description:
Vehicle_24 hours_2
Mouse 2

source_name: Vehicle treatment (24 hours)

value: Vehicle


title: HB_T106_1c

city: New York

first: Tom

middle: Samuel

last: Carroll

state: New York

address: 1230 York Avenue

department: Bioinformatics

institute: The Rockefeller University

data_processing:
Illumina's bcl2fastq2 Conversion Software v2.19 was used for basecalling.
Salmon quantifications were derived using Salmon (version 0.8.2) from raw FastQ against the hg19 transcriptome sequences retrieved in the Bioconductor TxDb.Hsapiens.UCSC.hg19.knownGene package (version 3.2.2)
Differential expression analysis was performed directly from Salmon quantifications using Tximport (version 1.8.0 ) and DESeq2 (version 1.20.0)
Genome_build: hg19 - (From Bioconductor package - BSgenome.Hsapiens.UCSC.hg19 version 1.4.0)
Supplementary_files_format_and_content: Salmon transcript quantifications against the hg19 transcriptome sequences.

source_name: ATOH1+ progenitor cells - IP

growth_protocol: hPSCs (RUES2 cell line) were maintained in HUESM medium conditioned by mouse embryonic fibroblasts (MEF-CM) and supplemented with 20ng/mL bFGF. Patterning of a single cells seeded at 900 cells/ml on transwell polyester membranes (Corning™3450) were carried out in DMEM/F12 containing N2/B27 and puromycin, with dual smad inhibition (SB431542+LDN-193189) at days 0-7, CHIR99021 (Stemgent, 04-0004-02) at days 1-11, FGF2 at days 1-28, BDNF at days 11-28, BMP7 at days 7-15.

extract_protocol:
TRAP was performed as previously reported by M. Heiman et al. Nat. Protoc. 9, 1282–1291 (2014). Briefly, polysomes were stabilized by adding 100 µg/ml cycloheximide to cell culture media for 10 minutes prior to homogenization with polysome extraction buffer. Following clearing by centrifugation, supernatants were incubated at 4˚C with end-over-end rotation for 16-18 hours with biotinylated Streptavidin T1 Dynabeads (ThermoFisher, 65601) previously conjugated with GFP antibodies (Sloan Kettering Institute Antibody Core, HtzGFP-19C8 and HtzGFP-19F7). The beads were collected on a magnetic rack, washed, and resuspended in lysis buffer with β-mercaptoethanol (Agilent, 400753) to extract bound RNA from polysomes. RNA was purified using the RNeasy micro kit (Qiagen, 74004). RNA quantity and quality was measured using an Agilent 2100 Bioanalyzer with the 6000 Pico Kit (Agilent, 5067-1513).
Full length cDNA was prepared using Clontech’s SMART-Seq v4 Ultra Low Input RNA Kit (Cat # 634888). 1 ng of cDNA was then used to prepare libraries using Illumina Nextera XT DNA sample preparation kit (Cat # FC-131-1024). Libraries with unique barcodes were pooled at equal molar ratios and sequenced on Illumina NextSeq 500 sequencer to generate 75 bp single reads, following manufactures protocol

value: hPSC-derived neural progenitor cells

tag: trap antibody

value: 19C8 and 19F7, GFP monoclonal antibodies


title: UN_431


title: Vehicle_1

description:
Vehicle_24 hours_1
Mouse 1


title: HB_T106_1b


title: UN_428


title: tetO-Clock/Bmal1DN pHes7-luc iPSM #19 without dox


title: 20087P01G01_01

value: Diffuse glioma


title: tetO-Clock/Bmal1DN pHes7-luc iPSM #7 with dox


title: UN_427


title: UN_324


title: 20087P01F01I2_01

value: Glioma


title: UN_323


title: tetO-Clock/Bmal1 pHes7-luc iPSM #20 with dox


title: tetO-Clock/Bmal1DN pHes7-luc iPSM #7 without dox


title: KO GL 8 GFP

library_source: genomic

data_processing:
Raw sequence reads were aligned to the mm10 genome using Rsubread (version 1.30.6) in paired end mode.
Bigwigs were created from properly paired reads (fragments between 0 -5000 bp) using rtracklayer package (version 1.40.6) and normalised to total mapped and properly paired reads.
Peak calls were made using Macs2 (2.2.6) in BAMPE mode
Signals in peaks were counted using featureCounts in Rsubread package (version 1.30.6)  and differential ATAC-seq signal analysis was performed with DESeq2 (version 1.20.0)
Genome_build: Mm10-UCSC (Genome sequence from Bioconductor package BSgenome.Mmusculus.UCSC.mm10 v1.4.0, Transcript models from  Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene Version = 3.4.0)
Supplementary_files_format_and_content: bigWig files contain ATAC-seq signal normalised to total mapped and properly paired reads

molecule: genomic DNA

source_name: hippocampus

extract_protocol: Illumina Nextera, Buenrostro et al., 2015

value: hippocampus

tag: markers

value: GAD2 cells

value: SMARCA3 cKO

value: interneurons


title: KO GL 7 GFP


title: 20087P01C01_01

value: Glio

value: Untreated


title: 20087P01D01I2_01


title: HB_T106_T113

source_name: ATOH1+ progenitor cells - input

value: input


title: 20087P01B01_01


title: KO GL 6 GFP


title: tetO-Clock/Bmal1 pHes7-luc iPSM #12 without dox

value: untreated


title: KO GL 5 GFP


title: UN_307


title: 20087P01A01_01


title: KO GL 4 GFP


title: HB_T106_1a


title: pHes7-luc iPSM with dox

value: control


title: pHes7-luc iPSM without dox


title: HRT18-P12-2

city: Cheongju

first: Jiyeong

last: Noh

address: Chungdae-ro 1

country: South Korea

institute: Chungbuk National University

data_processing:
Raw sequences were checked the quality of the data  with FastQCv0.11.7 program before proceeding.
The adapter sequence was removed with Trimmomatic 0.38 program. Trimmed data was generated by removing base qulity less than 3 from reads ends and base unsatisfied with window size =4, mean quality =15 using the sliding window trim method.
cDNA fragment were mapped ASM985889v2 genomic reference with Bowtie 2 2.3.4.1 aligner.
The amount of abundance of the transcript was normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value considering read count, transcript length and depth of coverage.
Genome_build: ASM985889v2

growth_protocol: Vero, A549, Caco-2, and HRT18 cell lines were used for the SARS-CoV2 passages. Vero cells were cultured in DMEM with 2% FBS and 1% penicillin-streptomycin (10,000 IU/ml each) at 37°C in a 5% CO2 incubator, while Caco-2 cells were done in MEM with 2% FBS and 1% penicillin-streptomycin. For the A549 and HRT18 cells, RPMI 1640 with 2% FBS ans 1% penicillin-streptomycin was used.

extract_protocol:
In case of the first passage, the infected cell pellets were resuspended to 250µl with fresh medium, to extract RNA for the high-throughput sequencing. The serial passage of SARS-CoV-2 on A549, CaCO2, and HRT18 cell lines were continued to passage 12 and the cultured cell supernatant of the infected cells in passage 12 was centrifuged at 3,000g for 10 min, and used to extract RNA for the high-throughput sequencing.
The RNA libraries were prepared with illumine TruSeq Strand Total RNA LT kit and illumine NovaSeq6000 plaform form Macrogen, Inc (Seoul, Korea) for high throughput sequencing accroding to the manufacturer's instruction.

treatment_protocol: The 8×104 PFU of SARS-CoV2 stocks passaged on vero cells were inoculated to the monolayer of A549, Caco-2, and HRT-18 cell lines in 75T flask  for 1hour at 37℃ in a 5% CO2 incubator with gentle shaking of 15 minutes interval.  After that, the infected cells were washed two times with DPBS and incubated with the fresh maintenance medium for 3 days. The virus inoculation was performed in triplicate for each cell lines. The cultured cell supernatant of the virus-infected A549, CaCO2, and HRT18 cells was centrifuged at 3,000g for 10min to use for the next passage, and stored at -80℃.

value: Colon

value: Epithelial cells

value: infected with SARS-CoV2 p11


title: KO GL 3 GFP


title: T50_436

value: in vitro treated with Tofacitinib


title: HRT18-P12-3


title: KO GL 5 c

value: non GAD2 cells


title: tetO-Clock/Bmal1 pHes7-luc iPSM #12 with dox

value: iPSM colonies

value: 1000 ng/mL doxycycline for 2 hours


title: UN_317


title: tetO-Clock/Bmal1DN ESC #6 without dox

description: ESCs_KnownCanonical2020_genebody_rpkm_readCounts.txt.gz

value: ESCs


title: KO GL 2 GFP

value: hippocampus


title: HRT18-P12-1


title: tetO-Clock/Bmal1DN ESC #5 with dox

value: 500 ng/mL doxycycline for 6 hours


title: T50_431


title: UN_313


title: T50_428


title: T50_427


title: HRT18-P1-2

value: infected with SARS-CoV2 stock


title: KO GL 5 b

value: SMARCA3 cKO

value: interneurons


title: KO GL 1 GFP

value: GAD2 cells


title: HRT18-P1-3


title: T50_324


title: T50_476


title: tetO-Clock/Bmal1 ESC #7 with dox


title: CaCO2-P12-3


title: KO GL 5 a


title: T50_323


title: tetO-Clock/Bmal1DN ESC #6 with dox


title: control GL 9 GFP


title: tetO-Clock/Bmal1  ESC #7 without dox


title: T50_317


title: tetO-Clock/Bmal1 ESC #1 with dox


title: CaCO2-P12-2


title: CaCO2-P12-1


title: control GL 8 GFP


title: T50_313


title: control GL 5


title: T50_307


title: tetO-Clock/Bmal1DN ESC #5 without dox


title: CaCO2-P1-2


title: HRT18-P1-1


title: S9_Healthy_4

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

data_processing:
Trimmomatic (v0.39)42 was used to remove adaptors and trim low-quality bases. The quality of the processed reads was checked using FastQC before and after preprocessing.
Remove reads containing adaptors; Remove reads containing N > 10% (N represents base that could not be determined); The Qscore (Quality value) of over 50% bases of the read is <= 5.
STAR (v2.7) was performed using the default parameters to build the indexes of the reference genome and align the paired-end clean reads to the reference genome.
Genome_build: GRCh37
Supplementary_files_format_and_content: abundance measurements

source_name: monocyte

extract_protocol:
Human primary monocytes were enriched by negative selection using a Pan Monocyte Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Next, the isolated monocytes were further enriched by positive selection using CD14 MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions. Total RNA was extracted from the purified monocytes with the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

value: monocyte

tag: group

value: Healthy

tag: hiv-1 infection status

value: not infected


title: ESC with dox

value: control


title: CaCO2-P1-3

value: Colon

value: Epithelial cells


title: control GL 7 GFP


title: CaCO2-P1-1


title: ESC without dox

value: untreated


title: EB065

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
count_data.tsv
normalized_data.tsv
neurexin_isoform_data.tsv

data_processing:
Base calling was done using Illumina RTA3
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned using STAR aligner to GRCm38 version 91 to get gene counts (count_data.tsv)
Cells that passed quality control were normalized using edgeR (normalized_data.tsv)
Alternative splicing and Neurexin isoforms for cells that passed quality control were calculated from STAR output using custom code (neurexin_isoform_data.tsv)
Genome_build: GRCm38 version 91
Supplementary_files_format_and_content: count_data.tsv contains raw read counts, normalized_data.tsv contains normalized read counts, and neurexin_isoform_data.tsv contains isoform and alternative splicing level data. All 3 datasets are in tab-separated text file formats

source_name: PV cells from ventral subiculum

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT DNA Library Preparation Kit (Illumina)

value: Female

tag: quality control

value: Pass

tag: vrest

tag: rm

tag: cm


title: control GL 6 GFP

tag: genotype


title: A549-P12-3

value: Lung

tag: treatment

value: infected with SARS-CoV2 p11


title: S69_ART_12

value: ART

value: infected with HIV


title: EB064

tag: age


title: control GL 5 GFP

value: hippocampus


title: S8_Healthy_3


title: tetO-Clock/Bmal1 ESC #1 without dox

value: ESCs


title: A549-P12-2


title: A549-P12-1


title: S67_ART-naïve_11

value: ART-naive


title: S68_ART_11

value: PBMC


title: EB063


title: control GL 3

value: non GAD2 cells

value: interneurons


title: EB062


title: S66_ECs_10

value: monocyte

value: Ecs


title: A549-P1-3

value: infected with SARS-CoV2 stock


title: control GL 4 GFP

value: GAD2 cells

value: control


title: control GL 3 GFP


title: S65_ECs

value: ECs


title: control GL 4


title: EB061

value: Female

value: Pass


title: A549-P1-1

value: Lung

value: Epithelial cells


title: A549-P1-2


title: S64_ECs

value: infected with HIV


title: EB060


title: EB059


title: control GL 1 GFP

value: hippocampus


title: EB058


title: S62_ART-naïve_10


title: S60_ART-naïve


title: EB057


title: control GL 2


title: S59_ART-naïve


title: Activated PTBP1 cKO RNAseq 4

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Reads were trimmed with Trim Galore (v0.6.1) to remove adapters and poor quality base calls
Trimmed reads were mapped to the GRCm38 mouse genome using HISAT2 (v2.1.0), suppressing unpaired or discordant alignments and taking into account known splice sites from the Ensembl Mus_musculus.GRCm38.90 annotation.
BAM files were imported into Seqmonk (v1.45.0), and raw read counts generated over mRNA features with merged isoforms, using the Ensembl Mus_musculus.GRCm38.96 annotation, assuming unstranded, paired reads.
FPKMs were calculated using the same annotation, using cuffnorm from Cufflinks (v2.2.1), with geometric normalisation.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNAseq_raw_counts.tsv: tab-delimited text file containing gene names and IDs together with raw counts for all RNAseq samples, generated with Seqmonk.
Supplementary_files_format_and_content: RNAseq_FPKM.tsv: tab-delimited text file containing gene names and IDs together with FPKM values for all RNAseq samples, generated with cuffnorm from Cufflinks.
Supplementary_files_format_and_content: iCLIP processed data files: bedgraph files for each replicate containing significant xlink-binding sites (FDR<0.05) identified with iCOUNT

source_name: Activated CD8 T cells

growth_protocol: Single cell suspensions were prepared from spleen and lymph nodes by passing the organs through 70 and 40 mm cell strainers consecutively. Negative naïve CD8 T cell isolation was achieved by depletion of cells bound by biotinylated antibodies: CD4 (GK1.5), CD11b (M1/70), CD11c (N418), CD19 (1D3), B220 (A3-6B3), CD105 (MJ7/18), TER-119, gamma/delta TCR (GL3), Gr1 (RB6-8C5), NK1.1 (PK136), F4/80 (BM8), CD44 (1M7) and magnetic Dynabeads™ M-280 Streptavidin (Thermofisher cat#:11206D), except for iCLIP experiments where the anti-CD44 antibody was omitted.

extract_protocol:
RNA was extracted from naïve and activated CD8 T cells using the RNeasy Micro Kit (cat# 74004, Qiagen).
10 ng RNA were used and 7 PCR cycles were carried out to synthesise cDNA with the SMART-Seq® v4 Ultra® Low Input RNA Kit (cat # 634891, Takara). RNAseq libraries were prepared with the Nextera XT DNA Library Preparation Kit (cat# FC-131–1096, Illumina) and carrying out 8 PCR cycles. mRNA-seq libraries were run across two lanes of a HiSeq 2500 RapidRun, generating 125bp paired end reads.

treatment_protocol: Naïve cells were either used unstimulated, or were activated ex vivo for 24h by culturing in RPMI 1640 Medium (Dutch modification) with 20 mM HEPES (ThermoFisher cat#:22409-015), 50 μM b-Mercaptoethanol, 100 units/ml penicillin and streptomycin, GlutaMAX and 10% FCS on 96 flat-bottom well plates precoated with 5μg/ml anti-CD3 (2C11) and 1μg/ml anti-CD28 (37.51) antibodies, in the presence of 20ng/ml murine IL2.

value: Spleen + LN

value: 24h activation, anti-CD3 + anti-CD28 + IL2

value: CD4-CreTg Ptbp1-fl/fl

value: 9 weeks


title: EB055


title: S58_Healthy_11

value: PBMC

value: Healthy

value: not infected


title: control GL 2 GFP

value: interneurons


title: Activated PTBP1 cKO RNAseq 3


title: Activated PTBP1 cKO RNAseq 2

value: 13 weeks


title: EB054


title: EB053


title: S57_Healthy_10

value: monocyte


title: EB052


title: S56_Healthy


title: S53_ART_10

value: ART


title: S55_Healthy


title: Activated PTBP1 cKO RNAseq 1

value: Female

value: 10 weeks


title: Activated Ctrl RNAseq 4


title: EB051

value: Pass


title: S51_ART


title: EB049


title: Activated Ctrl RNAseq 3


title: EB050


title: S5_ART_2


title: S52_ART


title: Activated Ctrl RNAseq 2


title: EB056


title: Naïve PTBP1 cKO RNAseq 4

source_name: Naïve CD8 T cells

value: Unstimulated


title: control GL 1

value: non GAD2 cells

value: control


title: EB048


title: EB047


title: Activated Ctrl RNAseq 1

value: Spleen + LN

value: 11 weeks


title: S46_ECs

value: ECs

value: infected with HIV


title: S49_ART

value: PBMC


title: Naïve PTBP1 cKO RNAseq 3

value: CD4-CreTg Ptbp1-fl/fl

value: 9 weeks


title: EB046

value: Fail


title: S44_ECs_5


title: Naïve PTBP1 cKO RNAseq 1


title: Naïve Ctrl RNAseq 4


title: EB044


title: S43_ECs_4


title: EB045


title: EB042


title: Naïve Ctrl RNAseq 2

value: 13 weeks


title: Naïve Ctrl RNAseq 3


title: EB041


title: EB040


title: EB039


title: S40_ECs_2

value: monocyte


title: EB038


title: Sort-purified (CD8/Thy1.1/CD44+)  TCR SV40-I CD8 TIL N4 rep2, RNA-seq

first: Andrea

last: Schietinger

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
DNA sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M17) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Differentially expressed genes (DEG) were determined with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: Mouse MCA 205-N4 tumor-infiltrating T cells

extract_protocol:
CD8 T cells were FACS-sorted straight into Trizol tube and stored at -80°C until all samples were collected. RNA from sorted cells was extracted using RNeasy mini kit (Qiagen) according to instructions provided by the manufacturer. After ribogreen quantification and quality control of Agilent BioAnalyzer, 6-15 ng of total RNA underwent amplification (12 cycles) using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing. 10ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 51 million paired reads were generated per sample and the percent of mRNA bases was 62.5% on average.
10ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).

value: TCR SV40-I transgenic CD8 T cells

tag: biological context

value: MCA205-N4 tumor


title: S39_ECs_1


title: Sort-purified (CD8/Thy1.1/CD44+)  TCR SV40-I CD8 TIL N4 rep1, RNA-seq


title: S33_ART-naïve

value: ART-naive


title: Naïve PTBP1 cKO RNAseq 2

value: Female


title: S31_ART-naïve_6


title: EB036

value: Pass


title: S4_ART_1

value: ART


title: EB037


title: S45_ECs_6


title: S30_ART-naïve_5


title: Sort-purified (CD8/Thy1.1/CD44+)  TCR SV40-I CD8 TIL F6 rep1, RNA-seq

source_name: Mouse MCA 205-F6 tumor-infiltrating T cells

value: MCA205-F6 tumor


title: S26_ART-naïve_4


title: Sort-purified (CD8/Thy1.1/CD44+)  TCR SV40-I CD8 TIL D4 rep3, RNA-seq

source_name: Mouse MCA 205-D4 tumor-infiltrating T cells

value: MCA205-D4 tumor


title: EB034

value: Male


title: Sort-purified (CD8/Thy1.1/CD44+)  TCR SV40-I CD8 TIL F6 rep2, RNA-seq


title: Sort-purified (CD8/Thy1.1/CD44+)  TCR SV40-I CD8 TIL D4 rep2, RNA-seq


title: S25_ART-naïve_3


title: EB035


title: EB032


title: EB031


title: Sort-purified (CD8/Thy1.1/CD44+) day 4 effector TCR SV40-I CD8 T cells rep2, RNA-seq

source_name: mouse effector T cells from lymph nodes

value: acute Listeria infection (lymph node)


title: Sort-purified (CD8/Thy1.1/CD44+)  TCR SV40-I CD8 TIL D4 rep1, RNA-seq


title: S23_ART-naïve_1

value: infected with HIV


title: Sort-purified (CD8/Thy1.1/CD44+) day 4 effector TCR SV40-I CD8 T cells rep1, RNA-seq


title: EB028


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells from dLN of D4 tumors rep2, RNA-seq

source_name: mouse T cells from MCA 205-D4 tumor draining lymph nodes

value: MCA205-D4 tumor-draining lymph nodes


title: EB027


title: S2_Healthy_2

value: PBMC

value: Healthy

value: not infected


title: EB030


title: EB025


title: S22_ART_6


title: S19_ART_5


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells from dLN of D4 tumors rep1, RNA-seq


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells from dLN of N4 tumors rep1, RNA-seq

source_name: mouse T cells from MCA 205-N4 tumor draining lymph nodes

value: MCA205-N4 tumor-draining lymph nodes


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells from dLN of N4 tumors rep2, RNA-seq


title: EB021


title: S18_ART_4

value: monocyte


title: S15_ART_3


title: EB026


title: S13_Healthy


title: EB020


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells from dLN of F6 tumors rep2, RNA-seq

source_name: mouse T cells from MCA 205-F6 tumor draining lymph nodes

value: TCR SV40-I transgenic CD8 T cells

value: MCA205-F6 tumor-draining lymph nodes


title: S10_Healthy_5


title: EB018


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells from dLN of F6 tumors rep1, RNA-seq


title: S1_Healthy_1


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells rep3, RNA-seq

source_name: mouse splenocytes

value: spleens


title: EB016


title: S24_ART-naïve_2

value: ART-naive


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells from dLN of N4 tumors rep3, RNA-seq


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells rep1, RNA-seq


title: DNJ4 hydroxyurea rep2 [DNJ4HU02]

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
illumina hiseq was used for basecalling
Sequenced reads were trimmed for adapter content using BBDuk and parameters ktrim=r k=23 mink=11
Trimmed sequences were then aligned (and genes counted) to the cryptococcus neoformans genome CNA3 via STAR version 2.7.6a with parameters   --runMode alignReads --twopassMode Basic --quantMode GeneCounts --outSAMtype BAM Unsorted --outSAMunmapped Within
Counts were normalized during differential expression analysis via DESeq2’s median of ratios from Anders, S., & Huber, W. (2010).
Genome_build: CNA3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized expression (DESeq2) information for each gene and every sample

organism: Cryptococcus neoformans H99

source_name: DNJ4 hydroxyurea

growth_protocol: Overnight YPD grown cultures were diluted 1 in 10 in fresh YPD and grown for 3 hours at 30°C to reach log phase.

extract_protocol:
Cells were flash frozen with liquid nitrogen and RNA was extracted using the Qiagen Rneasy protocol for yeast (mechanical disruption)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were harvested and resuspended in either fresh YPD for the control, or YPD supplemented with 25 mM hydroxyurea and incubated for one hour at 30°C

tag: genotype/variation

value: mutant (dnj4{delta})

value: 25mM Hydroxyurea for 1 hour


title: TOP1cc cross-CAD-seq DOX ETO MG132 rep 1

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

institute: Karolinska Institute

data_processing:
library strategy: Covalent Adduct Detection coupled to ChIP-seq
FastQC and MultiQC were used for quality control of the .fastq-files
Adapter and poor quality read trimming was performed with cutadapt
The ChIP-seq data was mapped using bowtie2.
Aligned files were sorted, deduplicated and indexes using SortSam, MarkDuplicates and BuildBamIndex from Picard package.
BigWig files were generated with bamCoverage from Deeptools package.
Merging of duplicates for visualization was performed using MergeSamFiles from Picard package.
Genome_build: hg38
Supplementary_files_format_and_content: Bam coverage BigWig files generated from merged replicas, normalized to RPM.

growth_protocol: The bone osteosarcoma epithelial cells U2OS expressing a doxycycline inducible lentivirus- MYC-EGFP (wild type) were grown in DMEM containing 10% Tet approved FBS (Takara, 631103), MEM Nonessential Amino Acids (Corning cellgro, 25-025-Cl), 50 U/ml penicillin G and 50 μg/ml streptomycin sulfate (Gibco, 15070-063)

extract_protocol:
Cells were lysed with 10 ml of STE buffer (2% SDS, 0.5 M Tris-HCl pH 8.1, 10 mM EDTA) and were disrupted using a Dounce homogenizer tight pestle shearing apparatus. Samples were extracted with Phenol: chloroform and was precipitated by adding 2.5 volume ethanol 100% and 1/10 volume sodium acetate (3M, pH 5.2). Pellet was washed by ethanol 70%, dried and finally dissolved in elution buffer (Tris pH 8.5). samples were sonicated with a Bandelin probe sonicator to produce chromatin fragments <1 kb on average, were further purified through QIAquick PCR purification kit (QIAGEN) using columns (provided in the kit) such that the total DNA bound per column was not exceeded 10 mg (each sample were divided into 3 columns) and was eluted in elution buffer (Tris-HCl pH 8.5). 2 µg of anti-TOP1 antibody (ab109374) were mixed with 40 ml Protein A/G magnetic beads (Pierce, 88803) and incubated at 40C for 6 hrs with controlled rotation. Preeluted CAD samples from 1×107 cells were added to the Protein A/G-antibody complexes and incubated with rotation overnight at 40C. Washing was performed as described for the ChIP protocol but twice with every buffer and always in presence of 0.1% SDS. The beads were then resuspended in 100 μl TE plus 0.25% SDS supplemented with proteinase K (500 μg/ml, Roche) and incubated for 4 hrs at 650C. Samples were then either purified by PCR purification Kit (QIAGEN) or extracted with Phenol: Chloroform and precipitated with EtOH (1/10 volume of NaoAc 3M, 2.5xVolume 100% EtOH, 1.5μl Glycogen).
DNA from the Cross-CAD CHIP samples quantified with the Qubit dsDNA HS Assay Kit. To cleave off covalently bound tyrosyl residues from cross-CAD samples, the samples were additionally treated with ExoVII (0.5-1U per 10 ng of DNA) and purified by PCR purification Kit (QIAGEN). Cross-CAD libraries were prepared with Swift Bioscience AccelNGS 2S Plus DNA kit, pooled together and sequenced on NovaSeq in Single End mode with 101 bp reads.

treatment_protocol: To induce MYC, Cells (U2OS-EGFP-MYC) were treated with doxycycline (final concentration 0.6 μg/ml in the growth media) for 7 hrs. Cells were treated with 10 µM MG132 for 30 min before addition of 25 µM ETO or 10 µM CPT and further incubation for 15 min to trap TOP2cc or TOP1cc respectively.

value: Human Bone Osteosarcoma Epithelial Cells

tag: chip antibody

value: MYC-EGFP

value: 0.6 μg/ml DOX, 10 µM MG132 and 25 µM ETO


title: DNJ4 hydroxyurea rep3 [DNJ4HU03]


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from high-affinity MCA205-F6 tumor rep6, ATAC-seq

data_processing:
Alignment and identification of open chromatin regions The data was processed following the recommendations of the ENCODE consortium (The ENCODE Consortium, n.d.): Reads were aligned to the mouse reference genome (version GRCm38) with BWA-backtrack (Heng Li and Durbin 2009). Post-alignment filtering was done with samtools and Picard tools (Li et al. 2009, Broad Institute (2015)) to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates. To identify regions of open chromatin represented by enrichments of reads, peak calling was performed with MACS2 (Liu 2014). For every replicate, the narrowpeak results of MACS2 were used after filtering for adjusted p-values smaller than 0.01.
Differentially accessible regions Regions where the chromatin accessibility changed between different conditions were identified with diffBind (Stark and Brown 2011).
Coverage files Individual coverage files per replicate normalized for differences in sequencing depths between the different samples were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --blackListFileName mm10.blacklist --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40 -p 1. To create merged coverage files of replicates of the same condition, we used multiBigwigSummary to obtain the sequencing-depth-normalized coverage values for 10 bp bins along the entire genome, i.e. for every condition, we obtained a table with the coverage values in every replicate within the same bin. Subsequently, we chose the mean value for every bin to represent the coverage in the resulting “merged” file.
Genome_build: mm10 for mus musculus data
Supplementary_files_format_and_content: BigWig files for each sample

extract_protocol:
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition happened at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Illumina Hiseq 2500in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47x106 paired reads were generated per sample.

tag: strain

value: MCA205-F6 tumors


title: EB014

tag: Sex

value: Male

value: Pass


title: S11_Healthy_6

tag: tissue

value: PBMC

tag: cell type


title: EB013


title: EB019


title: DNJ4 hydroxyurea rep1 [DNJ4HU01]


title: TOP1cc cross-CAD-seq DOX MG132 rep 1

value: 0.6 μg/ml DOX and 10 µM MG132


title: DNJ4 untreated rep2 [DNJ402]

source_name: DNJ4 untreated

value: Untreated


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from high-affinity MCA205-F6 tumor rep4, ATAC-seq


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells rep2, RNA-seq


title: TOP1cc cross-CAD-seq DOX ETO MG132 rep 2


title: EB011


title: EB010


title: DNJ4 untreated rep1 [DNJ401]


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from high-affinity MCA205-F6 tumor rep3, ATAC-seq


title: EB015


title: TOP1cc cross-CAD-seq DOX MG132 rep 2


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from high-affinity MCA205-F6 tumor rep2, ATAC-seq


title: WT hydroxyurea rep3 [WTHU03]

source_name: WT hydroxyurea

value: wild type


title: DNJ4 untreated rep3 [DNJ403]


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from high-affinity MCA205-F6 tumor rep1, ATAC-seq


title: EB012


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from high-affinity MCA205-F6 tumor rep5, ATAC-seq


title: TOP1cc cross-CAD-seq untr ETO MG132 rep 2

value: 10 µM MG132 and 25 µM ETO


title: WT hydroxyurea rep2 [WTHU02]


title: TOP1cc cross-CAD-seq untr MG132 rep 2


title: TOP1cc cross-CAD-seq DOX rep 2

value: 0.6 μg/ml DOX


title: EB009


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from low-affinity MCA205-D4 tumor rep5, ATAC-seq

value: TCR SV40-I transgenic CD8 T cells

value: MCA205-D4 tumors


title: EB007


title: TOP1cc cross-CAD-seq DOX rep 1


title: TOP1cc cross-CAD-seq untr ETO MG132 rep 1


title: TOP1cc cross-CAD-seq untr MG132 rep 1


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from low-affinity MCA205-D4 tumor rep4, ATAC-seq


title: TOP1cc cross-CAD-seq untr rep 2


title: EB006


title: WT untreated rep3 [WT03]

source_name: WT untreated


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from low-affinity MCA205-D4 tumor rep3, ATAC-seq


title: WT untreated rep2 [WT02]


title: EB005


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from low-affinity MCA205-D4 tumor rep2, ATAC-seq


title: EB008


title: WT untreated rep1 [WT01]


title: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated Day 14 from low-affinity MCA205-D4 tumor rep1, ATAC-seq


title: WT hydroxyurea rep1  [WTHU01]


title: Ori-3

organism: Chlorocebus aethiops

source_name: Vero

value: kidney

value: Epithelial cells

tag: cell line

value: Vero

value: infected with SARS-CoV2 stock


title: TOP1cc cross-CAD-seq untr rep 1

value: Human Bone Osteosarcoma Epithelial Cells

value: MYC-EGFP


title: TOP1cc cross-CAD-seq input


title: Ori-2


title: EB002


title: EB003

value: Fail


title: Ori-1


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells rep2, ATAC-seq

value: spleens


title: EB001

value: Male

value: Pass


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells rep1, ATAC-seq


title: EB004


title: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells rep3, ATAC-seq


title: S42_ECs_3

source_name: monocyte

value: PBMC

value: monocyte

tag: group

value: ECs

value: infected with HIV


title: Naïve Ctrl RNAseq 1

value: Spleen + LN

value: Unstimulated

value: Female

value: 11 weeks


title: 20087P01E01_01

data_processing:
Read quality of RNA-seq data in FASTQ files was assessed using ngs-bits (v.2020_06), to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR v2.7.3a (Dobin et al., 2013) to the GRCh37 and alignment quality was analyzed using ngs-bits and visually inspected in the Integrative Genome Viewer (v2.7.2).
Normalized read counts for all genes were obtained using Subread (v2.0.0).
The distribution of logarithmized cpm-normalized expression values shows similar characteristics over all samples. Based on the filtered data set, samples were investigated with respect to their pairwise similarity. Spearman’s rank correlation coefficient was calculated for each pair of samples.
A hierarchical clustering was performed on the resulting similarity values. Differential gene expression analysis was conducted based on the filtered gene expression data set. A statistical model incorporating the group property of samples was tested by fitting a negative binomial distribution using a generalized linear model (GLM) approach.
Genome_build: GRCh37
Supplementary_files_format_and_content: The full processed and annotated gene expression values are given in the file "Processed_Data_Spreadsheet_Glioma_Study.xlsx". Simple boxplots between genes and groups of interest were used for the publication.

source_name: glioma tissue

extract_protocol:
Tissue collection: Archival tumor samples were available after tissue acquisition according to a standardized routine bio banking procedures. In brief, after removal of tumor tissue from the resection cavity in the operating room, samples were immediately frozen in liquid nitrogen, the tumor content was assessed on a cryo-slide by a neuropathologist, and only tissue samples with sufficient tumor content (> 70-80%) were stored as bio samples in the biobank at -80°C.
Tissue homogenization: Tissue samples were cryogenically pulverized (Covaris CryoPREP CP02) and aliquots of 5 mg used for RNA analysis.
RNA was purified from lyophilized tissue using the QIAsymphony RNA kit (Qiagen). More precisely, tissue was thawed at room temperature and 800 µl of Buffer RTL Plus was added to the tissue. Homogenization was performed twice for 2 minutes at 25 Hz using the TissueLyser II (Qiagen). Resulting homogenates were centrifuged for 3 minutes at maximum speed in a microcentrifuge and 400 µl of the resulting lysate was loaded on the QIAsymphony SP (Qiagen) using the RNA CT 400 protocol. At the end of the protocol, the RNA was eluted in 35 µl of RNase-free water.
For library preparation, mRNA fraction was enriched using polyA capture from 200ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) using the liquid handler Biomek i7 (Beckman). Next, mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. Library molarity was determined by measuring the library size (approximately 400 bp) using the Fragment Analyzer with the High NGS Fragment 1-6000bp assay (Agilent) and the library concentration (approximately 5 ng/µl) using the Infinite 200Pro (Tecan) and the Quant-iT HS Assay Kit (Thermo Fisher Scientific).
The libraries were denatured, diluted to 270 pM and sequenced as paired-end 100bp reads on an Illumina NovaSeq6000 (Illumina, San Diego, CA, USA) with a sequencing depth of approximately 25 million clusters per sample.

tag: diagnosis

value: Diffuse glioma

value: Glioma

tag: histology

value: Glio

value: Untreated


title: tetO-Clock/Bmal1 pHes7-luc iPSM #20 without dox

value: iPSM colonies

value: untreated


title: study_dataset_49

status: Public on Dec 08 2021

type: genomic

city: Berlin

first: Maximilian

last: Leitheiser

address: Charitéplatz 1

department: Institute of Pathology

institute: Charité - University Hospital Berlin

hyb_protocol: The EpiTect Fast DNA Bisulfite Kit (Qiagen) was used to perform DNA bisulfite conversion. Following DNA restoration for FFPE samples (Infinium HD FFPE DNA Restore Kit, Illumina), DNA methylation analysis was done using the Illumina Infinium MethylationEPIC BeadChip, according to the manufacturer’s instructions.

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings.

data_processing: Statistical analysis was performed using the minfi package (version 1.32.0) running on R (version 3.6.1).

label: Cy5 and Cy3

source_name: cervical squamous cell lymph node metastasis

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega) on a Maxwell RSC 16 instrument (Promega) according to protocols supplied by the manufacturer.

value: m

value: neg

tag: region of origin

value: hypopharynx

tag: organ of origin

tag: tumor purity


title: study_dataset_42

value: pos

value: oropharynx

value: tongue


title: study_dataset_39

value: sex

value: oral cavity


title: study_dataset_37

value: tonsil


title: study_dataset_40


title: study_dataset_26

value: larynx


title: study_dataset_33

value: oral mucosa


title: study_dataset_46

value: f


title: study_dataset_35


title: study_dataset_31


title: study_dataset_38


title: study_dataset_32


title: study_dataset_48


title: study_dataset_22


title: study_dataset_30


title: study_dataset_36


title: study_dataset_24


title: study_dataset_28


title: study_dataset_43


title: study_dataset_47


title: study_dataset_45


title: study_dataset_25


title: study_dataset_41


title: BPDCN712_TCR-Seq

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

data_processing:
Demultiplexing using Illumina bcl2fastq2 v2.20.0
Alignment using STAR 2.7.2a or CellRanger version 3.1.0 or CellRanger-Arc
Generate single-cell expression matrix using custom scripts or CellRanger version 3.1.0 or CellRanger-Arc
MAESTER: generate single-cell variant call matrix using maegatk version 0.0.2
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrices, metadata, maegatk rds output with variant counts

source_name: Bone marrow hematopoietic cells

extract_protocol:
mRNA and mitochondrial mRNA was extracted by hybridization to polyT oligos on Seq-Well or 10x beads. DNA for ATAC-seq was extracted using the 10x multiome protocol with adaptations as described in DOGMA-Seq (Mimitou et al., Nat Biotech 2021).
Seq-Well S3 and 10x 3' v3 single-cell RNA-sequencing library construction methods were utilized for mRNA libraries. MAESTER was used to enrich and sequence mitochondrial mRNA. The 10x Genomics multiome protocol was used for the multiome samples.

tag: technology

value: TCR-Seq


title: study_dataset_23


title: study_dataset_21


title: 1HR2_5mM_RNaseR2h

city: Los Angeles

first: Minjie

last: Zhang

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

description: crosslinked in vitro RNA

data_processing:
Sequencing data were preprocessed to remove adapters form the 5'end and 3’end using Trimmomatic software; PCR duplicates are removed using splitFastqLibrary (in the icSHAPE pipeline)
Reads were mapped to 1HR2 genome using STAR program.
The primary mapping alignments were filtered to remove low-confidence segments, rearranged and classified into six different types using gaptypes.py (https://github.com/zhipenglu/CRSSANT).
Filtering alignments were assembled to DGs and NGs using the crssant.py script (https://github.com/zhipenglu/CRSSANT).
Bedtools v2.25.0 was used to annotate gapped and chimeric alignments.
Genome_build: 1HR2
Supplementary_files_format_and_content: bam files contain RNA structures and interactions; BEDPE file contains disjoint RNA structures and interaction.

organism: synthetic construct

source_name: In vitro transcription

growth_protocol: 1HR2 was in vitro transcripted using T7 RNA Polymerase (M0251, NEB).

extract_protocol:
Crosslinked RNAs were purified using alcohol precipitation.
Library was prepared using optimized PARIS protocol (Lu. et al. Cell, 2016).

treatment_protocol: 5mM SHARC in vitro crosslinking; RNaseR (E049, ABM) were used to trim 3'end of RNA fragments.

tag: crosslinker

value: 5mM SHARC


title: ms_Pancreas3

city: Campbelltown

first: Mugdha

middle: V.

last: Joglekar

state: NSW

address: Cnr Goldsmith and David Pilgrim Ave

department: School of Medicine

country: Australia

institute: Western Sydney University

description: Two pancreas pooled

data_processing:
Strand Next-generation sequencing (NGS) version 2.5 software was used to analyse the RNA-Seq data
Alignment: Reads from mouse samples were aligned to the mouse mm10 transcriptome and genome using the Ensembl genes and transcript (2013.04.03) model. While for human samples were aligned to the human hg38 transcriptome and genome using the Ensembl genes and transcript (2016.12.01) model. All alignments were processed with novel splices.
Alignment: Raw reads were aligned with a minimum of 90 percent identity, maximum five percent gaps and a minimum match length of 25 base pairs.
Alignment trimming: The read pairs output with more than five valid matches were not reported. Quality trimming was applied to trim 3’ end with an average quality less than 10 and on poorly aligned portion at 3’ end post alignment.
Filtering: Raw reads with an average base quality below 20 and reads which have failed quality control (QC) were removed.
Generation of normalized abundance: Normalized values were calculated using the Deseq algorithm, with the threshold normalized count set at 1 and no baseline transformation.
Genome_build: mm10 (for mouse samples) and hg38 (for human samples)
Supplementary_files_format_and_content: excel (Note: for Hg38_islets and GB-Deseq.xlsx ; the six human islets samples used for analysis are taken from our GSE152111 study and included in this series.)

source_name: Adult mouse pancreas

extract_protocol:
RNA was extracted using TRIzol® RNA Isolation (Thermo Fisher Scientific, Waltham, MA) protocol with minor modification  (Joglekar et al. 2012). For mouse RNA samples, poly(A) mRNA extraction was performed for RNA-sequencing on the Ion Torrent (Thermo Fisher Scientific, Waltham, MA)  platform, using the MicroPoly(A)Purist™ Kit (Thermo Fisher Scientific, Waltham, MA) following the manufacturer instructions.
For mouse samples: cDNA libraries were generated using the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, Waltham, MA) following manufacturer's protocol. For human samples: libraries were generated through using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) through following manufacturer’s protocol.

value: Pancreas


title: ms_Pancreas2

description: Two pancreas pooled


title: ms_Pancreas1

description: Two pancreas pooled


title: study_dataset_29


title: ms_GB2

description: Three gallbladder pooled

source_name: Adult mouse gallbladder

value: Gallbladder


title: study_dataset_44


title: study_dataset_27


title: 3998787146_I

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data was quantile normalized and log2 transformed using the Bioconductor package lumi v2.40 in R. The probes accounting for the bottom 50% in each measurement were overlapped, and those probes that fell in the bottom 50% of all measurements (n=20,147) were removed from further analysis, leaving a final set of 27,960 probes of the initial 48,107 probes. Batch effects were removed using the Combat function from the Bioconductor package sva v3.36 in R

source_name: blood

label_protocol: Biotinylated cRNA were prepared with the TotalPrep RNA Amplification Kit (Illumina) according to the manufacturer’s instruction. Quality was assessed using the Agilent bioanalyser.

growth_protocol: No in vitro stimulation

extract_protocol: Total intracellular RNA was extracted from PAXgene® samples using the Blood RNA Kit (Qiagen) according to the manufacturer’s instructions. Bound RNA was treated with DNase I to remove trace amounts of bound DNA and after further washes the RNA was eluted in elution buffer and heat-denatured. The purity and quantity of the isolated total RNA was assessed spectrophotometrically prior to storage at -20oC until required for microarray analysis.

value: blood

tag: cohort

value: Control

tag: timepoint

value: pre-treatment


title: 3998787146_H


title: ms_GB1

description: Three gallbladder pooled


title: study_dataset_34

value: m


title: 3998787146_J


title: 3998787146_L


title: 3998787146_F

value: Latent TB


title: 3998787146_K


title: study_dataset_20

value: neg


title: 3998787146_E

value: post-treatment


title: 1HR2_5mM_RNaseR0h

description: crosslinked in vitro RNA


title: 3998787146_D


title: 3998787146_G


title: 3998787142_L


title: 3998787146_B


title: 3998787146_A


title: 3998787146_C


title: 3998787142_K


title: 3998787142_I


title: study_dataset_19

value: hypopharynx


title: 3998787142_G


title: 3998787142_F


title: 3998787142_E


title: study_dataset_13

value: pos

value: oropharynx


title: study_dataset_14

value: oral cavity


title: 3998787142_B


title: study_dataset_12

value: tonsil


title: 3998787142_H


title: study_dataset_15


title: 3998787142_C


title: 3998787142_A


title: study_dataset_11

value: larynx


title: 3998787105_L


title: 3998787105_G

value: Active TB


title: 3998787105_I


title: 3998787105_H


title: 3998787105_E


title: 3998787105_B


title: 3998787105_C


title: study_dataset_7

value: oral mucosa


title: 3998787105_K


title: 3998787142_J


title: study_dataset_6

value: f


title: 3998755031_H


title: 3998755031_G


title: 3998755031_J


title: 3998787105_D


title: 3998755031_L


title: study_dataset_5

value: tongue


title: study_dataset_1


title: study_dataset_2


title: study_dataset_10


title: 3998755031_I

value: blood


title: 3998755031_E


title: study_dataset_4


title: 3998755031_K


title: study_dataset_3


title: study_dataset_16


title: study_dataset_9


title: 3998755031_B


title: 3998755028_K


title: 3998755028_D


title: 3998755016_L


title: 3998755031_F


title: 3998755028_L


title: 3998755028_E


title: 3998787142_D


title: 3998755028_A


title: 3998755028_J


title: 3998755028_I


title: 3998755016_K


title: study_dataset_8


title: 3998755028_H


title: 3998755031_C


title: 3998755028_C


title: 3998755016_I


title: 3998755016_H


title: 3998755016_J


title: 3998755028_B


title: 3998755031_D


title: 3998755016_G


title: 3998787105_F


title: 3998755028_G


title: 3998755031_A


title: 3998755016_B


title: study_dataset_17


title: study_dataset_18


title: 3998755015_E


title: 3998755016_D


title: 3998755016_C


title: 3998755015_I


title: 3998755015_K


title: 3998755015_G


title: 3998755015_F


title: 3998755015_J


title: 3998755015_L


title: 3998755015_C


title: 3998405155_H

value: Control


title: 3998755016_E

value: pre-treatment


title: 3998755015_A


title: 3998405155_J


title: 3998405155_F


title: 3998755016_A


title: 3998755028_F


title: 3998405155_I


title: 3998405155_D


title: 3998405155_B


title: 3998405155_E


title: 3998405152_L


title: 3998405155_G


title: 3998405155_C


title: 3998405152_K


title: 3998405152_H


title: 3998405152_C


title: 3998405155_A


title: 3998405152_J


title: 3998405152_G


title: 3998405152_I


title: 3998405152_B


title: 3998405022_K


title: 3998405152_E


title: 3998405152_A


title: 3998405022_L


title: 3998405152_F


title: 3998405022_F


title: 3998405022_G


title: 3998405022_I


title: 3998405022_D


title: 3998405022_E


title: 3998405021_L


title: 3998405021_J


title: 3998405022_H


title: 3998405022_A


title: 3998405022_B


title: 3998405021_I


title: 3998405021_H


title: 3998405022_J


title: 3998405022_C


title: 3998405021_K


title: LUT library

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

data_processing:
Sequencing reads were parsed to generate a table of barcode-tag counts using a custom Python script.
Enhancer barcode-tag pairs were compared to expected barcode-tag pairs obtained by Sanger sequencing during library cloning to define true positive pairs. Additional tags with comparable read counts were defined as positive for individual enhancer barcodes.
A fasta file was generated from the resulting list of positive pairs and used to build a bowtie index for mapping reads from the subsequent QeFS experiment.
Genome_build: n/a
Supplementary_files_format_and_content: LUT_counts_Simple.tsv file contains barcode-tag pair read counts.
Supplementary_files_format_and_content: Simplified_Sorted_RC.txt file contains barcode-tag pairs passing empirical criteria for inclusion in the mapping library.
Supplementary_files_format_and_content: fasta file contains recovered degenerate tag sequences with enhancer element names for informative mapping

organism: unidentified plasmid

source_name: plasmid library

growth_protocol: Reporter plasmids were grown in E. coli and purified in parallel.

extract_protocol:
The reporter library was subjected to restriction digestion and intramolecular ligation to juxtapose the barcodes and sequence tags.
Custom primers were used to amplify barcode-tag pairs and add standard Illumina sequencing and cluster generation primer sequences.

treatment_protocol: Plasmids were pooled at equal concentrations to produce a reporter library.

tag: sample type

value: amplicon from digested and religated reporter plasmid library


title: 3998405021_E

value: Latent TB


title: 3998405021_F


title: 3998405021_G


title: 3998405021_D


title: 3998405009_L


title: 3998405009_F


title: 3998405009_K


title: 3998405009_E


title: 3998405009_B


title: 3998405006_L


title: 3998405021_C


title: 3998405006_I


title: 3998405009_A


title: 3998405006_K


title: 3998405006_H


title: 3998405009_G


title: 3998405021_A


title: 3998405009_D


title: 3998405006_J


title: 3998405009_H


title: 3998405009_C


title: Huh-7_gap-P13_20nM_2

city: Kawasaki

first: Takao

last: Inoue

state: Kanagawa

address: 3-25-26, Tonomachi

department: Division of Molecular Target and Gene Therapy Products

institute: National Institute of Health Sciences

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome U133 Plus 2.0 Array　using the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The scanned data were processed for signal values using Microarray Suite 5.0 software  .

source_name: The Huh-7 cells transfected with gap-P13 at 20 nM using Lipofectamine 2000 for 24hr.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: The Huh-7 cells were maintained at 37 °C and 5% CO2 in Dulbecco’s Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics.

extract_protocol: Total RNA was isolated using a Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The Huh-7 cells transfected with the gapmer ASOs using Lipofectamine 2000 (Invitrogen, Gaithersburg, MD, USA) according to the manufacturer’s protocol. The cells treated with transfection reagent in the absence of ASO were used as a control.

value: Liver


title: Huh-7_gap-P13_20nM_3


title: Huh-7_gap-P13_20nM_1


title: Huh-7_gap-A13_20nM_4

source_name: The Huh-7 cells transfected with gap-A13 at 20 nM using Lipofectamine 2000 for 24hr.


title: Huh-7_gap-P13_20nM_4


title: LD_myonuc_3

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

description: Late Dox

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Genome_build: A custom genome assembly to interrogate both nuclear and rDNA methylation was generated by adding the consensus rDNA repeat sequences, BK000964.3, as a separate chromosome to the GRCm39 (GCA_000001635.9) mouse reference genome assembly.
Supplementary_files_format_and_content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome

source_name: plantaris

extract_protocol:
DNA was isolated from the plantaris myonuclei or interstitial nuclei using the Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) as specified in the protocol.
“Classic” RRBS library preparation was performed by digesting genomic DNA with 30 units of MspI enzyme (New England BioLabs, R0106), and fragments were ligated to pre-annealed adapters containing 5’-methyl-cyotosine. Adapter-ligated fragments ≥50 base pairs were recovered using the DNA Clean & Concentrator Kit (Zymo Research, D4003) and bisulfite-converted using the EZ DNA Methylation-Lightning KitTM (Zymo Research, D5030) following the standard protocol. Preparative-scale PCR was performed, and the products were purified again using the Clean and Concentrator kit.

treatment_protocol: Plantaris myonuclei and interstitial nuclei were isolated by FACS and DNA were extracted and reduced representation bisulfite sequencing (RRBS) for whole-genome and ribosomal DNA-specific analysis.

value: Skeletal Muscle

tag: conditions

value: Exercise

tag: age


title: LD_myonuc_2

description: Late Dox


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 5

city: St. Louis

first: Barak

middle: A

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University School of Medicine

data_processing:
Library strategy: Sort-seq
All raw reads were processed regardless of quality score.
grep -o CTAGC.*.CTCGAG
sort "$i" | uniq -c > "$i"sorted.txt
Barcode sequences that exactly matched the design were used for downstream analysis
Barcode counts were used to create a probability mass function for the abundance of each AD in each bin. Thie PMF and the fluorescence of each bin was used to calculate the activity of the each AD. See paper methods for details
Genome_build: N/A
Supplementary_files_format_and_content: Barcode counts and sequences

growth_protocol: We derived clonal derivatives of K562 cells (ATCC CCL-243) after transfecting out GFP reporter and integrating it at the AAVS1 locus. We integrated libraries of synthetic transcription factors into the LP3 landing pad with G418 selection for 14 days. We enriched for live cells with MACS magnetic separation We then cultured lines in IMDM supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% non-essential amino acids at 37C.

extract_protocol:
We sorted 1e6 cells into each pool. We extracted genomic DNA from these cells with the  Qiamp DNA Mini kit (Qiagen).
 We performed 8 PCRs on each sample. The sequencing libraries were prepared in 2 batches: Batch 1 contained biological replicates 1-3 and Batch 2 contained biological replicate 4 and the 8 bin sort. We did 25 cycles with NEB Q5 polymerase using CP36.P10 and LP_019 primers. We pooled the PCRs, cleaned up the DNA (NEB Monarch), quantified it, digested the entire sample with NheI and EcoRI-HF (NEB) for 90 minutes and then ligated sequencing adaptors with T4 ligase (NEB) for 30 min. These adaptors contained sample barcodes in Read1 and Index1 We used 4 ng of this ligation for a 20 cycle enrichment PCR with Q5 and the EPCR_P1_short and EPCR_PE2_short primers. We sequenced each Batch on a NextSeq 500 1x75 High Output run.

treatment_protocol: We treated cells with ß-estradiol for 48hrs before cell sorting/

tag: cell type used for experiment

value: Immortalized lymphoblast

tag: genotype

value: AAVS1:UAS GFP (pmvs184) LP3::AD library

tag: treatment

value: Beta-estradiol


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 4

tag: cell line


title: 3998405006_E

tag: tissue


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 6


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 7


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 3


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 8


title: 3998405006_F


title: Huh-7_gap-A13_20nM_3

tag: cell type


title: 3998405006_G


title: Huh-7_Control_4

source_name: The Huh-7 cells treated with transfection reagent in the absence of ASO.


title: 3998405006_C


title: Huh-7_Control_1


title: Huh-7_gap-A13_20nM_2


title: Huh-7_Control_3


title: 3998405006_D

value: post-treatment


title: LD_myonuc_1

description: Late Dox


title: 3998405006_A


title: 3998755015_D


title: 3998405006_B


title: Huh-7_Control_2


title: mRNAs associated in eIF4E and CBP80 in polysome, replicate 1

city: Seoul

first: Yoon Ki

last: Kim

address: Anam-ro 145, Seongbuk-gu

institute: Korea University

description:
80_vs_4E_IP_rep_1
Biological replicate 1 of 2

hyb_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent's Low RNA Input Linear Amplification kit (Agilent Technology, USA) according to manufacturer's instructions.

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner

data_processing: Quantification was performed by Feature Extraction Software (Agilent Technology, Palo Alto, CA), and analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: CBP80-associated mRNAs in polysome

growth_protocol: 293FT cells were grown with Dulbecco’s Modified Eagles Medium (HyClone) supplemented with 10% (vol/vol) fetal bovine serum (HyClone) and 1% (vol/vol) penicillin/streptomycin (HyClone)

extract_protocol: mRNAs associated with CBP80 or eIF4E in polysome fractions were extracted using Trizol by manufacturer's recommendations

treatment_protocol: Cytosolic fractions obtained from 293FT cells were fractionated using 10-50% (vol/vol) sucrose gradient. Polysome fractions containing more than three ribosomes were pooled and then RNA immunoprecipitations were performed using either α-CBP80 or α-eIF4E antibodies.

tag: immunoprecipitated with

value: α-CBP80 antibody

source_name: eIF4E-associated mRNAs in polysome

tag: cell lines

value: α-eIF4E antibody


title: Huh-7_gap-A13_20nM_1


title: h+ spx1∆::kanMX rep3

first: Angad

last: Garg

department: Molecular Biology

data_processing:
Base calls from Illumina NovaSeq 6000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts; DESeq2 output

organism: Schizosaccharomyces pombe

source_name: S. pombe

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: mRNAs associated in eIF4E and CBP80 in polysome, replicate 2

description:
80_vs_4E_IP_rep_2
Biological replicate 2 of 2

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent's Low RNA Input Linear Amplification kit (Agilent Technology, USA) according to manufacturer's instructions.


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 2


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 3 Bin 1


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 2 Bin 2


title: h+ spx1∆::kanMX rep1


title: h+ spx1∆::kanMX rep2


title: Untreated replicate 1

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

data_processing:
Reads were aligned using STAR aligner to human genome reference (hg19)
Quantitation of gene expressions was performed suing Rsubread package in R
Low expressed features were removed and library size and vsn normalization was performed
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene counts

source_name: hepatoma cell line

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: HepaRG hepatocyte

value: bipotent hepatic progenitors actively proliferating

value: Untreated


title: Untreated replicate 2


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 2 Bin 4


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 2 Bin 1


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 1 Bin 3


title: Untreated replicate 3


title: h+ rep3

city: New York


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 1 Bin 4


title: ActA treatment 3 replicate

value: ActA treatment


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 1 Bin 2


title: ActA treatment 2 replicate


title: h+ rep2


title: Predicted ADs Sort Seq Replicate 3 Bin 4


title: ActA treatment 1 replicate


title: A1456_coloncancer

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Methylation profiles were generated from 750 ng DNA using the Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

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

data_processing:
Raw data was processed and normalised using the Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC (ChAMP) package in R [PMID: 24336642; PMID: 28961746]. This package contains functions for filtering low-quality probes, adjustment for Infinium I and Infinium II probe design, batch effect correction, and data normalisation. In short, bad quality probes (detection p value >0.01), probes containing SNPs, probes mapping to multiple locations, and probes mapping to chromosomes X and Y were removed, resulting in 429705 probes for further analysis. Data were normalised by Beta-Mixture Quantile (BMIQ) normalisation to correct for bias between type I and type II probe chemistry and potential batch effects were removed using Combat. The returned Beta values per probe represent the percentage of methylation for that particular CpG dinucleotide.
Processed file includes BMIQ-normalised Beta-values

label: Cy3 and Cy5

source_name: colon cancer, CMS2

extract_protocol: Genomic DNA was isolated from 30 µm frozen tissue sections using the Nucleospin Tissue kit according to the manufacturer’s instructions.

value: colon cancer

tag: cms class

tag: tumor stage

tag: gender

value: female

tag: t

tag: n

tag: m

tag: differentiation grade

value: good

tag: tumor location

value: Left

tag: adjuvant treatment

value: no


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 2 Bin 3

tag: cell line

tag: cell type used for experiment

value: Immortalized lymphoblast

tag: genotype

tag: treatment


title: h+ rep1


title: Predicted ADs Sort Seq Replicate 3 Bin 1

value: AAVS1:UAS GFP (pmvs184) LP3::AD library


title: Untreated 3

tag: cell type


title: Predicted ADs Sort Seq Replicate 2 Bin 4

value: Beta-estradiol