title: Y_fr2

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

description:
processed data file: readcount.txt
processed data file: FPKM.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Genome_build: ASM168347v1
Supplementary_files_format_and_content: readcount.txt: Tab-delimited text file includes read counts.
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: transcript.fa: FASTA file

organism: Chenopodium quinoa

source_name: fruit

growth_protocol: The material for this experiment was planted in the experimental field of Chengdu University (Chengdu City, Sichuan, China) under the local natural temperature, humidity and circadian cycle. Two kinds of quinoa were sown in early March 2019. Samples of flowers were collected at the end of June, and mature fruit were collected in August. A total of 60 quinoa strains with the same growth rate were selected for sample collection (30 strains of white Chenopodium quinoa and 30 strains of yellow Chenopodium quinoa). A mixed sample containing 10 strains was regarded as a biological replicate, and three replicates were set for the two kinds of quinoa.

extract_protocol:
The flowers and fruits were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The flowers and fruits were collected from the same biological replicate for transcriptome sequencing samples. All of the above samples were collected from 60 plants, and the sample was thoroughly cleaned after collection, placed in liquid nitrogen and kept at -80°C.

tag: quinoa type

value: Yellow

value: Fruit


title: Y_fr3

status: Public on Sep 17 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: iKPC-5 ED U off dox

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

country: USA

institute: Rutgers University

data_processing:
BCL (raw output of Illumina HigSeq) files are processed using Illumina’s Consensus Assessment of sequence And Variation (CASAVA) tool (http://support.illumina.com/sequencing/sequencing_software/casava.html) for demultiplexing/conversion to FASTQ format, which is the standard input for most aligners and downstream analytic tools.
FASTQ files of RNA samples are processed using both STAR (Dobin et. al. 2012) following the two-step alignment procedure and TopHat (Kim and Salzberg 2011) and Cufflinks (Trapnell et. al. 2010).
Additional RNA quantification is conducted using HTSeq (Anders et. al. 2014) analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: pancreatic cancer cells

growth_protocol: 10% FBS + RPMI media

extract_protocol:
Cells cultured in Matrigel were collected by using cell revovery solution (Corning, cat # 354253). RNA were extracted by Qiagen Rneasy Micro kit (cat # 74004) according to provided manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Doxycycline treatment at 1 ug/ml (Sigma) to activate KRAS* expression.

tag: strain

value: pancreatic ductal adenocarcinoma

tag: genotype

value: Cre+ Tp53L/+ rtTA L/+ tetO-KRAS(G12D)+

tag: cell line

tag: overexpressing

value: enzyme-dead USP21

tag: treatment

value: off dox


title: Y_fr1


title: iKPC-1 WT U off dox

value: wildtype USP21


title: Y_fl3

source_name: flower

value: Flower


title: iKPC-3 WT U off dox


title: iKPC-5 GFP off dox

value: GFP


title: iKPC-3 GFP off dox


title: iKPC-1 GFP off dox


title: Y_fl2


title: iKPC-3 GFP on dox

value: on dox


title: iKPC-5 WT U off dox


title: W_fr2

value: White


title: iKPC-5 GFP on dox


title: Y_fl1


title: W_fl3


title: RNAPolII_Trim33-/-_12h

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

country: France

institute: cea

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

molecule: genomic DNA

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow cells were cultured in IMDM supplemented with 10% FCS (Invitrogen) 10μM thioglycerol (Sigma) and 25ng/ml mouse CSF1 (Milteny Biotech).

extract_protocol: ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).

treatment_protocol: On day 7, macrophages were treated for 4h, 12h and 24h  with 100ng/ml LPS (Sigma) in IMDM supplemented with 2.5% FCS. Cells were cross-linked with 1% formaldehyde for 10 min at 37°C, lysed in SDS lysis buffer [50 mM Tris pH8, 10 mM EDTA, 1% SDS, protease inhibitor cocktail (Roche)] and sonicated (cycle conditions: 15sec ON/30sec OFF, 15 min; Bioruptor, Diagenode) to obtain DNA fragments with an average length of 200-600 bp. Supernatant was diluted 10 times in IP dilution buffer [16.7 mM Tris pH8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X100, 0.01% SDS, protease inhibitor cocktail (Roche)] and immunoprecipitations were performed using 5μg of specific antibodies. Immunoprecipitated chromatin was collected using protein A agarose/Salmon Sperm DNA beads (Millipore) and, after washing and elution, reverse cross- linking was carried out with 0.2M NaCl at 65°C overnight. The chromatin was then digested by 20 μg of Proteinase K (Invitrogen) for 1h at 45°C and isolated by phenol- chloroform extraction.

tag: cell type

value: bone marrow derived macrophages

tag: chip antibody

value: RNA Pol II (sc-899X, Santa Cruz, lot:K0711)


title: RNAPolII_Trim33-/-_24h


title: iKPC-1 GFP on dox


title: RNAPolII_Trim33-/-_0h


title: W_fr1


title: W_fl1


title: RNAPolII_WT_24h

value: wild type


title: RNAPolII_Trim33-/-_4h


title: multiome_hft_dc2r2_r1

city: Stanford

first: Alex

middle: E

last: Trevino

state: California

address: 279 Campus Drive West

department: Genetics

institute: Enable Medicine

description: Multiome ATAC and RNA Data

data_processing:
Library strategy: Multiome (ATAC and RNA)
Raw sequencing data were converted to fastq format using cellranger atac mkfastq (10x Genomics, v.3.1.0). scRNA-seq reads were aligned to the GRCh38 (hg38) reference genome and quantified using cellranger count (10x Genomics, v.3.1.0). ‘Velocyto’ (v.0.17.17) [La Manno et al. 2018] was used to obtain splicing-specific count data for downstream RNA velocity analysis.
Genome_build: hg38

molecule: other

organism: Homo sapiens

source_name: Cerebral cortex

extract_protocol:
Samples were dissociated in papain and resuspended in ice-cold PBS + 0.02% BSA. For ATAC-seq, resuspension buffer (RSB) and lysis buffer (ALB) were prepared ice-cold. RSB: 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2. ALB: RSB + 0.1 % Tween-20 + 0.1% NP-40. Dissociated cells were counted and 100,000 cells were incubated for 5 minutes on ice in 100 uL ALB. ALB was diluted by adding 900 uL RSB, then samples were centrifuged at 500 x g for 5 minutes at 0 C. Nuclei were resuspended in 1X Nuclei Dilution Buffer (10X), checked for complete lysis, and counted. 4,000 cells per channel were loaded onto the Chromium 10X controller for ATAC, and 10,000 cells were loaded for RNA.
Libraries were constructed using the 10X Genomics ATAC and RNA Multiome Kit

value: Cerebral cortex

tag: age

tag: extraction

value: dissociation, whole cell


title: multiome_hft_dc2r2_r2

description: Multiome ATAC and RNA Data


title: RNAPolII_WT_12h


title: RNAPolII_WT_4h


title: RNAPolII_WT_0h


title: W_fr3


title: R8

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in GencodeV25 were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Dedifferentiated liposarcoma

extract_protocol:
Tissue RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using ribosomal RNA depletion RNA-seq protocols

tag: pathological types

value: Dedifferentiated liposarcoma

tag: gender

value: Male

tag: primary/recurrence

value: Primary

tag: tumor size (mm)


title: R7

value: Recurrence


title: R6

value: Female


title: R4

source_name: Well-differentiated liposarcoma

value: Well-differentiated liposarcoma


title: R5


title: 4FI

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

description:
6B1
6A-vs-6B_downregulated_genes.xlsx
6A-vs-6B_upregulated_genes.xlsx

data_processing:
Zebracall process Version 0.5.0.13875 used for basecalling.
The index of the reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000226075.1) was built using Bowtie v2.1.0.
Poor quality and to short reads (<30 nt) were removed from analysis.
Paired-end clean reads obtained for populations 17-5 and 17-6 were aligned to the reference genome using TopHat v2.0.9
Genome_build: GCF_000226075.1
Supplementary_files_format_and_content: xlsx files were generated using DESeq2 package
Supplementary_files_format_and_content: xlsx files, abundance measurements

organism: Solanum tuberosum

source_name: Tubers

growth_protocol: Potato tubers were planted in plastic pots filled with soil. Plants grew under tent from May to October.

extract_protocol:
Total RNA was isolated using TRIZol method as described Chomczyński and Sacchi (1987).
The mRNA was isolated using Dynabeads®mRNA Purification Kit for mRNA enrichment (Ambion, 61006), and cDNA libraries were prepared using using MGIEasy RNA Directional Library Prep Set (MGI, 1000006386). The established cDNA libraries were sequenced on the BGISEQ-500 sequencing platform (BGI Genomics, China) to generate 100-bp paired-end reads (PE100).

treatment_protocol: After harvest, tubers were ground in liquid nitrogen and freezed in -80°C untill use.

tag: population

value: Diploid hybrid 17-6

tag: developmental stage

value: Fully-developed tubers

tag: trait

value: Dark chip color

value: cold storage


title: 4FIII

description:
6B3
6A-vs-6B_downregulated_genes.xlsx
6A-vs-6B_upregulated_genes.xlsx


title: 4FII

description:
6B2
6A-vs-6B_downregulated_genes.xlsx
6A-vs-6B_upregulated_genes.xlsx


title: W_fl2

tag: quinoa type

tag: tissue

value: Flower


title: R3


title: R1


title: 4BIII

description:
17-5B3
17_5A-vs-17_5B_downregulated_genes.xlsx
17_5A-vs-17_5B_upregulated_genes.xlsx

value: Diploid hybrid 17-5


title: 4BII

description:
17-5B2
17_5A-vs-17_5B_downregulated_genes.xlsx
17_5A-vs-17_5B_upregulated_genes.xlsx


title: multiome_hft_dc1r3_r1

description: Multiome ATAC and RNA Data


title: 4EI

description:
6A1
6A-vs-6B_downregulated_genes.xlsx
6A-vs-6B_upregulated_genes.xlsx

value: Light chip color


title: Healthy PBMC & BAL Donor  2 GEX

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description:
mRNA + protein
HashTag1 : PBMC, HashTag2:BAL

data_processing:
The 10X Genomics Cellranger (v4.0.0) mkfastq was applied to demultiplex the Illumina BCL output into FASTQ files.
Cellranger count was applied to FASTQ file to align reads to pre-built GRCh38 reference genome downloaded from 10X Genomics website to generate barcode and UMI counts.
Cellranger vdj was applied to FASTQ files to align reads to the pre-built GRCh38 VDJ reference data to generate single-cell V(D)J sequences and annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: fastq file, hd5 file, csv files

source_name: PBMC and BAL

extract_protocol: Library were generated by following the instruction of 10X 5’ Library & Gel Bead Kit v1.1

treatment_protocol: CD3+ T cells were purified from PBMC and BAL cells with the StraightFrom® Whole Blood CD3 MicroBeads (Miltenyi Biotech).

tag: library preparation

value: 10x Genomics, Chromium Single Cell 5’

value: CD3+ T cell


title: Healthy BAL Donor  1 GEX

description: mRNA

source_name: BAL


title: 4BI

description:
17-5B1
17_5A-vs-17_5B_downregulated_genes.xlsx
17_5A-vs-17_5B_upregulated_genes.xlsx


title: 4AIII

description:
17-5A3
17_5A-vs-17_5B_downregulated_genes.xlsx
17_5A-vs-17_5B_upregulated_genes.xlsx


title: COVID-19 PBMC & BAL donor 7 TCR

description:
mRNA
HashTag1 : PBMC, HashTag2:BAL

value: 10x Genomics, Chromium Single Cell V(D)J


title: COVID-19 PBMC & BAL donor 6 TCR

description:
mRNA
HashTag1 : PBMC, HashTag2:BAL


title: COVID-19 PBMC & BAL donor 5 TCR

description:
mRNA
HashTag1 : PBMC, HashTag2:BAL


title: 4AI

description:
17-5A1
17_5A-vs-17_5B_downregulated_genes.xlsx
17_5A-vs-17_5B_upregulated_genes.xlsx


title: 4AII

description:
17-5A2
17_5A-vs-17_5B_downregulated_genes.xlsx
17_5A-vs-17_5B_upregulated_genes.xlsx


title: COVID-19 PBMC & BAL donor 4 TCR

description:
mRNA
HashTag1 : PBMC, HashTag2:BAL


title: 4EIII

description:
6A3
6A-vs-6B_downregulated_genes.xlsx
6A-vs-6B_upregulated_genes.xlsx


title: R2


title: 4EII

description:
6A2
6A-vs-6B_downregulated_genes.xlsx
6A-vs-6B_upregulated_genes.xlsx


title: COVID-19 PBMC & BAL donor 3 GEX


title: COVID-19 PBMC & BAL donor 4 GEX


title: COVID-19 PBMC & BAL donor 5 GEX


title: COVID-19 PBMC & BAL donor 3 TCR

description:
mRNA
HashTag1 : PBMC, HashTag2:BAL


title: COVID-19 PBMC & BAL donor 2 GEX


title: COVID-19 PBMC & BAL donor 2 TCR

description:
mRNA
HashTag1 : PBMC, HashTag2:BAL


title: COVID-19 PBMC & BAL donor 7 GEX


title: COVID-19 PBMC & BAL donor 6 GEX


title: Rat #322 skin at d14, post-treatment, XRT DMSO rep 1 of 3

type: RNA

city: Philadelphia

first: A

last: Linnenbach

state: NJ

address: 233 S 10th Streert

institute: Thomas Jefferson University

description: Gene expression data from 14d post-treatment rat skin.

hyb_protocol: Target denaturation was performed at 99°C for 5 min and then 45°C for 5 min, followed by hybridization with rotation at 60 rpm for 16 h at 45°C.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Gene set enrichment analysis (GSEA) was used to compare microarrays from experimental group time-points (XRT/RTA-408) or (XRT/DMSO) to baseline pre-treatment biopsies (day –10). Molecular Signatures Database (MSigDB) collections were used with GSEA9 to query microarray data derived from rat skin and soft tissue prior to any treatment (preTx baseline) compared to treatment with: (a) XRT/DMSO, (b) XRT/RTA-408, or (c) no XRT/DMSO. MSigDB collections totaling 9,599 gene sets, used in the present study, were GO biological process (C5BP), canonical pathways (C2CP), and the hallmark gene set described by Liberzon, et.al10. Supervised GSEA was then performed by query with a ROS gene set derived from the hallmark collection of well-curated 50 gene sets, either at individual time points, or all time points in aggregate.

label: Biotin

organism: Rattus norvegicus

source_name: Rat skin at d14, post-treatment, XRT DMSO

label_protocol: RNA (100 ng; mean RIN, 7.15) was used to prepare fragmented biotin-labeled cDNA by using the GeneChip WT Plus kit. Affymetrix gene chips (rat Clariom S) were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in hybridization cocktail (100 μl).

growth_protocol: Punch biopsies (5 mm) of abdominal skin were taken at baseline day –10, prior to the beginning of any drug or radiation treatment. These baseline samples were used throughout the transcriptome analysis as pretreatment baseline (preTx baseline) to which levels of gene expression are compared. DMSO vehicle or RTA-408 was administered on days –7, –5, –3 and 0. Experimental biopsies spanning 18 days were taken at mid-treatment day –4; and then post-treatment days 1, 3, 7, and 14 (

extract_protocol: Skin biopsies were flash-frozen in liquid nitrogen and stored at –70°C. Frozen tissue was diced in the presence of chilled RNAlater RNA stabilization reagent (500 ul) (Qiagen, Germantown, MD). Tissue fragments were then transferred to reinforced tubes containing 2.8-mm ceramic beads (Omni International, Kennesaw, GA) containing chilled, complete RLT lysis buffer (400 ul) (Qiagen). Tissue disruption was achieved using a Bead Ruptor Model 4 (Omni International); speed 5 m/sec. Three cycles of 15 sec milling/45 sec icing were performed. Homogenates were cleared at 10,000 xg for 3 min at 25°C, then processed as per the RNeasy Fibrous Tissue method (Qiagen). RNAs were quantified on a Nanodrop ND-100 spectrophotometer, followed by RIN-value determination on an Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Animals were radiated in a 6-MeV electron beam accelerator (Elekta). They received a cumulative dose of 40 Gy to the abdominal soft tissue, with radiation occurring every other day over 8 days in 4 total fractions of 10 Gy. To deliver the intended dose to the dermis/soft tissue/muscle without delivering toxic radiation to the alimentary tract, the steep part of the dosimetry curve was used, with a rapid fall to 2 Gy at 1 cm below the epidermis2. Animals received injection of vehicle control (DMSO) or RTA-408 on days of radiation or sham radiation.

tag: strain

value: Sprague-Dawley


title: Rat #324 skin at d14, post-treatment, XRT RTA408 DMSO rep 1 of 3

source_name: Rat skin at d14, post-treatment, XRT RTA408 DMSO


title: Rat #321 skin at d7, post-treatment, XRT DMSO rep 2 of 3

description: Gene expression data from 7d post-treatment rat skin.

source_name: Rat skin at d7, post-treatment, XRT DMSO


title: Rat #319 skin at d14, post-treatment, DMSO rep 1 of 2

source_name: Rat skin at d14, post-treatment, DMSO


title: Rat #320 skin at d14, post-treatment, XRT DMSO rep 3 of 3


title: Rat #322 skin at d7, post-treatment, XRT DMSO rep 1 of 3


title: Rat #324 skin at d7, post-treatment, XRT RTA408 DMSO rep 1 of 3

source_name: Rat skin at d7, post-treatment, XRT RTA408 DMSO


title: Rat #319 skin at d3, post-treatment, DMSO rep 1 of 2

description: Gene expression data from 3d post-treatment rat skin.

source_name: Rat skin at d3, post-treatment, DMSO


title: Rat #321 skin at d3, post-treatment, XRT DMSO rep 2 of 3

source_name: Rat skin at d3, post-treatment, XRT DMSO


title: Rat #320 skin at d3, post-treatment, XRT DMSO rep 3 of 3


title: Rat #319 skin at d7, post-treatment, DMSO rep 1 of 2

source_name: Rat skin at d7, post-treatment, DMSO


title: Rat #323 skin at d7, post-treatment, XRT RTA408 DMSO rep 2 of 3


title: Rat #323 skin at d14, post-treatment, XRT RTA408 DMSO rep 2 of 3


title: Rat #317 skin at d14, post-treatment, DMSO rep 2 of 2


title: Rat #320 skin at d7, post-treatment, XRT DMSO rep 3 of 3


title: Rat #322 skin at d3, post-treatment, XRT DMSO rep 1 of 3


title: Rat #303 skin at d14, post-treatment, XRT RTA408 DMSO rep 3 of 3


title: Rat #303 skin at d3, post-treatment, XRT RTA408 DMSO rep 3 of 3

source_name: Rat skin at d3, post-treatment, XRT RTA408 DMSO


title: Rat #323 skin at d3, post-treatment, XRT RTA408 DMSO rep 2 of 3


title: Rat #319 skin at d1, post-treatment, DMSO rep 1 of 2

description: Gene expression data from 1d post-treatment rat skin.

source_name: Rat skin at d1, post-treatment, DMSO


title: Rat #324 skin at d3, post-treatment, XRT RTA408 DMSO rep 1 of 3


title: NH16_677_SP1A [259165]

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

description:
processed data file:
ffpe_salmon_tpm_all_samples.xlsx
ffpe_star_counts_all_samples.xlsx

data_processing:
RNA-Seq quality and alignment:
Quality control was performed via FastQC and trimming of low quality reads and adapters was performed via TrimGalore v. 0.4.5-1 with default parameters. The pseudoalignment package Salmon v. 0.13.1 was used to obtain transcript per million (TPM) expression levels, normalized for library size and transcript length. Transcript to gene quantification was performed via biomaRt in R. For the purpose of identifying deregulated genes, gene counts were first estimated using the gapped alignment software STAR.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: RNA-Seq: read counts (xlsx) and TPM values (xlsx)

source_name: glioblastoma

growth_protocol: Patient consent and ethical approval was available for the study (08/H0716/16 Amendment 1 17/10/2014). GIC were isolated from bulk tumour following a previously described protocol (Pollard et al 2009; doi:10.1016/j.stem.2009.03.014). Fresh GBM tissue was sliced and triturated with razor blade, dissociated with Accumax (Sigma, A7089) at 37˚C for 10 mins then filtered through a 70μm cell strainer. Dissociated cells were plated on laminin-coated 6-well plate in NeuroCult NS-A Proliferation kit media (STEMCELL, 05751), heparin (2 μg/ml; Gibco 12587-010), mEGF (20ng/ml, Prepro Tech, 315-09) and hFGF (10ng/ml; Prepro tech, AF-100-18B). Established cells were passaged when 70% confluent, frozen in Stem Cell Banker (Ambsio ZENOAQ, 11890) and stored in liquid nitrogen. Cell lines used in this study are primary lines derived from human tumours, they have been characterised by transcriptomic profiling and cultured according to current practice, including contamination assessment. Fibroblasts cultures were established from small strips of dura mater, collected at surgery. Tissue was minced with a scalpel then spun down and resuspended in trypsin for 5 minutes at 37 degrees. To stop the reaction fresh fibroblast media (DMEM, Glutamax, 10% Foetal calf serum, 2% L-Glutamin and 1% penicillin-streptomycin) was added. Samples were centrifuged and resuspended in fresh media, then plated in 6 well plates (Corning #BC010). Media was topped up frequently during the first week then changed every other day.

extract_protocol:
RNA was extracted from cell pellets using the RNA/DNA/Protein Purification Plus kit (NORGEN, #47700), following the manufactured protocol.
Human RNA samples were sequenced on HiSeq4000, at 75 PE after polyA selection, by Oxford Genomics Centre

treatment_protocol: Fibroblasts reprogramming was performed following a previously described protocol (Yang et al. 2017; doi:10.1038/nature24052). Briefly, fibroblasts were electroporated with reprogramming vectors expressing Oct4, c-Myc, Klf4, Sox2 (OCKS 4F, 5µg) and Rarg, Lfh1 (RL 2F, 5.0 µg) using Amaxa Nucleofector (Lonza, Germany) then plated on SNL feeders with M15 media (Knockout DMEM Invitrogen, 15% Fetal Bovine Serum Hyclone, 1X Glutatamin-Penicillin-Streptomycin Invitrogen, 1X non-essential amino acids Invitrogen). Upon the appearance of colonies, media was replaced with EPSCM (DMEM/F12 Invitrogen, 20% Knockout Serum Replacement Invitrogen, 1X Glutamin-Penicillin-Streptomycin, 1X non-essential amino acids Invitrogen, 0.1 mM β Mercapto-ethanol Sigma, 106 U/ml hLIF Millipore supplemented with the following inhibitors: CHI99021 Tocris 1µM, JNK Inhibitor VIII Tocris 4 µM, SB203580 Tocris 10µM, A-419259 Santa Cruz 1µM and XAV939 Stratech 1µM). Colonies were picked and plated in 24 well SNL feeders’ plates for expansion and characterization. For embryoid bodies (EB) generation, EPSC lines were harvested and feeders removal was performed in T25 flasks for 30 minutes at 37 degrees to allow feeders to attach to the bottom and floating EPSC harvested were transferred in ultra-low attachment 96 well plates at different densities (60K, 45K, 35K and 20K) in EB media (DMEM/Knockout Invitrogen #10829-018, Fetal Bovine serum Gibco #16141061, non-essential amino acid Invitrogen #11140, glut-pen-strep Invitrogen #10378 and β mercapto-ethanol) changed every other days. After 7 days, they were transferred in 24 well plates on gelatine coated glass coverslips and after 10 to 14 days, cells were fixed with PFA 4%, 30 minutes at room temperature and immunocytochemistry was performed.   For iNSC induction, a commercially available kit was used following the manufacturer’s protocol (Gibco, #A1647801). Briefly, iPSC colonies were harvested, feeders removal was performed, as previously described for EB formation, and plated at density from 0.25 to 0.75 x106 per well of 6 well geltrex coated plates in EPSCM and Rock inhibitor 10μM (Stem cell technology #Y27632). The next day, the media was replaced with Gibco neural induction media (Neurobasal media #211030, pen-strep 1X and neural induction supplement 1X #A1647801, rock inhibitor 10μM), then changed every 2 days until day 7, cells were passaged at the density of 1x105/cm2 in Gibco neural expansion media (Neurobasal 0.5X, Advanced DMEMF/12 0.5X #12634, pen-strep 1X and neural induction supplement 1X, rock inhibitor 10μM), then media was changed every 2 days and 2-3 passages were performed with accutase (Millipore # SCR005) to establish the iNSC lines. Cells were frozen in synth-a-Freeze cryopreservation medium (Gibco #A12542). GIBCO® Human Neural Stem Cells (H9 hESC-Derived, #N7800-100) were used as control, cultured in StemPro® NSC SFM (Cat. no. A10509-01).

tag: patient

value: GBM

tag: sample type

value: FFPE


title: NH16_2806DEF3A1 [255184]

tag: cell type


title: NH16_616DEF1B [249112]


title: Rat #320 skin at d1, post-treatment, XRT DMSO rep 3 of 3

source_name: Rat skin at d1, post-treatment, XRT DMSO


title: NH16_270_DEF1Ereplacement [249112]


title: Rat #318 skin at d3, post-treatment, DMSO rep 2 of 2


title: Rat #321 skin at d1, post-treatment, XRT DMSO rep 2 of 3


title: Rat #323 skin at d1, post-treatment, XRT RTA408 DMSO rep 2 of 3

source_name: Rat skin at d1, post-treatment, XRT RTA408 DMSO


title: Rat #303 skin at d1, post-treatment, XRT RTA408 DMSO rep 3 of 3


title: Rat #318 skin at d-4, mid-treatment, DMSO rep 2 of 2

description: Gene expression data from mid-treatment rat skin.

source_name: Rat skin at d-4, mid-treatment, DMSO


title: Rat #318 skin at d1, post-treatment, DMSO rep 2 of 2


title: Rat #322 skin at d-4, mid-treatment, XRT DMSO rep 1 of 3

source_name: Rat skin at d-4, mid-treatment, XRT DMSO


title: Rat #322 skin at d1, post-treatment, XRT DMSO rep 1 of 3


title: Rat #319 skin at d-4, mid-treatment, DMSO rep 1 of 2


title: Rat #323 skin at d-4, mid-treatment, XRT RTA408 DMSO rep 2 of 3

source_name: Rat skin at d-4, mid-treatment, XRT RTA408 DMSO


title: Rat #303 skin at d7, post-treatment, XRT RTA408 DMSO rep 3 of 3


title: NH16_2214_DEF1A [256196]


title: Rat #324 skin at d-4, mid-treatment, XRT RTA408 DMSO rep 1 of 3


title: Rat #318 skin at d-10, untreated, rep 6 of 6

description: Gene expression data from untreated rat skin.

source_name: Rat skin, untreated, day -10


title: NH16_2063_DEF1Areplacement [251136]


title: Rat #321 skin at d-4, mid-treatment, XRT DMSO rep 2 of 3


title: Rat #319 skin at d-10, untreated, rep 5 of 6


title: Rat #324 skin at d1, post-treatment, XRT RTA408 DMSO rep 1 of 3


title: Rat #321 skin at d14, post-treatment, XRT DMSO rep 2 of 3

source_name: Rat skin at d14, post-treatment, XRT DMSO


title: Rat #320 skin at d-4, mid-treatment, XRT DMSO rep 3 of 3


title: Rat #317 skin at d7, post-treatment, DMSO rep 2 of 2


title: Rat #321 skin at d-10, untreated, rep 4 of 6


title: Rat #322 skin at d-10, untreated, rep 3 of 6


title: NH15_2101_DEF1A [231121]


title: NH15_1877_SP1C [211171]


title: NH15_1661DEF2C [250124]


title: GBM052_P6n7 [233187]

description:
processed data file:
cell_culture_salmon_tpm.xlsx
cell_culture_star_counts.xlsx

value: GIC

tag: passage


title: GBM054_P4 [229140]


title: GBM054_P6 [230128]


title: GBM061_P5 [232104]


title: GBM050_P9 [228152]


title: NH16_2255DEF1B2 [254172]


title: GBM052_P4n5 [234175]


title: GBM050_P7n8 [227164]


title: GBM061_P3 [231116]


title: GBM031_P7 [238127]


title: GBM031_P4 [205149]


title: Rat #323 skin at d-10, untreated, rep 2 of 6


title: Rat #324 skin at d-10, untreated, rep 1 of 6


title: GBM026_P8 [204137]


title: GBM019_P4 [202113]


title: GBM030_P5 [223117]


title: GBM030_P9n10 [237139]


title: GBM026_P3n4 [216106]


title: GBM018_P12 [217189]


title: GBM018_P10 [201101]


title: GBM017_P4 [243162]


title: DURA061_NSC_N4_P2 [241186]

source_name: dura mater

value: iNSC


title: GBM017_P3 [242174]


title: DURA061_NSC_N1_P3 [257196]


title: GBM019_P3n6 [239115]


title: Rat #303 skin at d-4, mid-treatment, XRT RTA408 DMSO rep 3 of 3


title: DURA061_FB_P7 [253137]

value: FB


title: DURA061_IPSC_N4_P5 [262136]

value: iPSC


title: DURA054_NSC_N3C_P2 [239115]


title: DURA054_NSC_N2E_P1 [240103]


title: RG867-T0

type: genomic

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

hyb_protocol: Samples were processed on the Illumina Human Methylation EPIC BeadChip following the Illumina Infinium HD Methylation Assay.

data_processing: Data were preprocessed with minfi, followed by normalisation with the SWAN method.

label: Cy5 and Cy3

source_name: Peripheral blood

extract_protocol: DNA was extracted from 500 µL of PBMC cryopreserved in DMSO/FCS using Qiagen Blood and Tissue kit (Qiagen, Germany) according to manufacturer’s protocols. For pre-processing, the samples were gently mixed and transferred into a new tube containing 500 µL of PBS. Samples were centrifuged at 1,000xg for 5 minutes and the supernatant was removed. 1mL of PBS was added to the pellet with gentle mixing. The pellet was resuspended in 200 µL of PBS before proceeding to the lysis step using the QIAGEN kit.

tag: crp highest level

tag: crp group

value: High

tag: age

tag: Sex

value: male

tag: timepoint

value: preoperative


title: DURA054_IPSC_N3C_P11 [261148]


title: RG860-POD

scan_protocol: Samples were processed on the Illumina Human Methylation EPIC BeadChip following the Illumina Infinium HD Methylation Assay.

value: female

value: postoperative


title: RG867-POD

label_protocol: Samples were processed on the Illumina Human Methylation EPIC BeadChip following the Illumina Infinium HD Methylation Assay.


title: DURA054_FB_P5 [252149]


title: RG866-T0


title: RG840-T0


title: RG849-POD

value: Low


title: DURA052_NSC_N5_P2 [244150]


title: RG860-T0


title: RG866-POD


title: RG831-POD


title: DURA052_FB_P6 [254125]


title: DURA050_NSC_N16_P4 [238127]


title: DURA052_NSC_N4_P3 [252149]


title: RG834-T0


title: DURA050_NSC_N12_P3 [237139]


title: RG847-POD


title: RG840-POD


title: RG818-POD


title: RG820-POD


title: RG831-T0


title: RG827-POD


title: RG827-T0


title: DURA050_IPSC_N12_P5 [264112]


title: DURA031_NSC_N44B_P2 [215174]


title: DURA050_FB_P7 [251161]


title: DURA031_NSC_N44_P3 [265195]


title: RG862-POD


title: RG813-T0


title: DURA030_NSC_N9_P2 [266183]


title: DURA031_IPSC_N44B_P10 [247114]


title: DURA031_FB_P7 [276158]


title: DURA030_NSC_N16B6_P1 [224105]


title: DURA030_IPSC_N16B6_P13 [248102]


title: DURA030_FB_P8 [277146]


title: RG813-POD


title: RG822-POD


title: DURA026_NSC_N31D_P5 [214162]


title: DURA026_FB_P8 [246126]


title: DURA019_NSC_N8C_P2 [212138]


title: RG809-T0


title: RG803-T0


title: RG809-POD


title: DURA019_IPSC_N8_P13 [245138]


title: DURA019_FB_P7 [275170]


title: RG849-T0


title: RG803-POD


title: DURA018_NSC_N4_P4 [222129]


title: RG862-T0


title: RG402-T0


title: DURA018_NSC_N2_P6 [211126]


title: RG408-POD


title: RG073-POD


title: DURA018_FB_P6 [244150]


title: RG408-T0


title: RG073-T0


title: DURA017_NSC_N3C5_P4 [244150]


title: DURA017_FB_P7 [255113]


title: RG834-POD


title: RG847-T0


title: TRNS_mec-8-_rep3

city: Riverside

first: Adam

middle: David

last: Norris

state: CA

address: 3401 Watkins Drive

institute: University of California, Riverside

data_processing:
Read alignment STAR, default parameters
Abundance measurement HTSeq, default parameters

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: sorted neurons from whole worm

growth_protocol: Staged via bleaching, L1s rescued onto OP50-seeded NGM plates, and grown to L4 stage

extract_protocol:
Cells dissociated according to Spencer et al. protocol (10.1371/journal.pone.0112102) and sorted for GFP+ cells on Sony SH800S
RNA extracted by Zymo direct-zol kit. Libraries prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina

value: touch receptor neuron


title: RG076-POD


title: TRNS_mec-8-_rep2


title: RG818-T0


title: DURA019_NSC_N5C1_P2 [267171]


title: RG067-T0


title: TRNS_mec-8-_rep1


title: TRNs_wt_rep2


title: TRNs_wt_rep3


title: RG801-POD


title: TRNs_wt_rep1


title: RG066-POD


title: JM03 rep3

first: Liu

last: Wenwen

address: 130 Meilong Road

institute: East China University of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment


title: RG071-POD


title: JM03 rep2


title: JM03 rep1


title: Ctrl rep3

value: control


title: RG071-T0


title: RG062-T0


title: RG067-POD


title: Ctrl rep2


title: Ctrl rep1


title: RG057-T0


title: EV_37_C

city: Athens

first: Paul

last: Briaud

state: OH

address: 107 Irvine Hall

institute: Ohio University

description:
total RNA, non-rRNA-depleted
24_S24

data_processing:
Raw data files (.fatsq) were imported into the CLC Genimics workbench (v11) software platform for analysis
Reads corresponding to RNA were filtered out and removed
Expression values were calculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped and noramlized using "quantile nornalization"
Normalized expression values were exported into excel files
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annaotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values for each gene were initially calculated as RPKM values. The RPKM values were then normalized and the "Normalized expression values"are presented in the excel files

organism: Staphylococcus aureus

source_name: Extracellular vesicles, pelleted

growth_protocol: Strains were grown in TSB medium at 34˚C or 37˚C with shaking for 15h

extract_protocol:
EVs were pelleted with ExoQuick-TC buffer and EV RNA was isolated utilizing the Aiagen miRNeasy kit ans contaminating DNA was removed by treatment with Ambion DNA-free
Libraries were created using the QIAseq FX Single Cell RNA Library kit

treatment_protocol: EVs were stored at -20˚C prior to RNA extraction

tag: genotype

value: wild-type

tag: growth medium

value: TSB

tag: growth time

tag: growth temperature


title: m5B2_RP_S4

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

description: Ribosome footprint profiling

data_processing:
library strategy: RIBO-seq
The raw reads were trimmed using FastX and rRNA removed using Bowtie v1.0.0
The trimmed reads were aligned to the Drosophila melanogaster reference genome (BDGP6.22) using TopHat v2.1.2 and Bowtie v1.0.0
The aligned reads were indexed using Samtools v0.1.19 and BigWig files were generated using BEDtools v2.26.0
Plastid was used to generate count tables
R package DESeq2 was used to run differential expression analysis
Genome_build: BDGP6.22
Supplementary_files_format_and_content: logCPM count table as a tab delimited txt file

organism: Drosophila melanogaster

source_name: mutant_D. melanogaster ovaries

growth_protocol: Flies were maintained at 25℃ on standard cornmeal-agar-yeast food. Ovaries from young control and mutant female flies were hand dissected 48 hours after eclosion and care was taken to remove any stage 10-14 egg chambers that were present in the control sample.

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher Scientific) followed the manufacture protocol.
For ribosome footprint libraries, 28-34mer footprints were selected on a 15% TBE-Urea gel. Dephosphorylation of the footprints were performed with shrimp alkaline phosphatase (rSAP, NEB) and ligated with 3' preadenylated adapter (rAppTGGAATTCTCGGGTGCCAAGG) by T4 RNA ligase 2, truncated (NEB). 49-55mer of ligated products were selected on a 10% TBE-Urea gel. Reverse transcription was performed with SuperScript III (company) using a primer (/5phos/GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGC/isp18/ CACTCA/isp18/CCTTGGCACCCGAGAATTCCA) following rRNA depletion. Samples are circularized by two sequential reactions with CircLigase (Epicentre) and amplified by 9-12 PCR cycles with primers compatible with Illumina flow cells.

treatment_protocol: Not applied.

tag: genotype/variation

value: RpS5b mutant

tag: tissue

value: ovaries


title: RG062-POD


title: RG054-T0


title: RG402-POD


title: RG066-T0


title: RG076-T0


title: EV_37_B

description:
total RNA, non-rRNA-depleted
23_S23

tag: strain


title: RG064-POD


title: RG822-T0


title: m5B1_RP_S3

description: Ribosome footprint profiling


title: RG052-POD


title: RG054-POD


title: RG801-T0


title: EV_37_A

description:
total RNA, non-rRNA-depleted
22_S22


title: RG820-T0


title: WT2_RP_S2

description: Ribosome footprint profiling

source_name: WT_D. melanogaster ovaries

value: wildtype


title: EV_34_C

description:
total RNA, non-rRNA-depleted
21_S21


title: EV_34_B

description:
total RNA, non-rRNA-depleted
20_S20


title: RG050-T0


title: WT1_RP_S1

description: Ribosome footprint profiling


title: WT521_Total_rep3

city: Puebla

first: Patricia

last: Sanchez-Alonso

state: Puebla

address: Av. San Claudio y 24 Sur, Col. San Manuel

department: Centro de Investigaciones en Ciencias Microbiologicas

country: Mexico

institute: Instituto de Ciencias, Benemerita Universidad Autonoma de Puebla

data_processing:
bcl2fastq2 v.2.20: To make call bases
FastQC v.0.11.9: To check quality reports
SortMeRNA v.4.2.0: To remove rRNA and mtRNA reads
Trimmomatic v.0.36: To remove adapters and poor quality reads
Trinity v.2.11.0: To build transcript assembly
RSEM v.1.3.3: To build counts table and generation of normalized abundance measurements
IDEAMEX: To analyze Differential Expression
Genome_build: Genome_build: Trinity.fasta
Supplementary_files_format_and_content: WT521_PolyA_vs_WT521_Total.txt: Tab-delimited text file with the following columns: logarithm base 2 of fold Change (logFC), logCoutPerMillon (logCPM), Pvalue, False Discovery Rate (FDR), columns for each sample with raw counts, columns with normalized counts for each sample, results of differential expression, and regulation.

organism: Mycosarcoma maydis

source_name: haploid cells

extract_protocol:
Extraction of nuclei from cultures in exponential phase was done based on the protocol described by Groner and Phillips (1975), for the extraction of total RNA the RNAeasy Mini kit (Qiagen) was used according to the manufacturer's instructions.
TruSeq Stranded mRNA Library Preparation kit was used for the preparation of the cDNA libraries of the polyA nuclear fraction, and the Truseq Stranded Total RNA Gold Prep Kit was used for the preparation of the total nuclear fraction libraries.

value: wild type


title: RG048-T0


title: RG064-T0


title: m5B1_WholeT_S3

data_processing:
The raw reads were trimmed using TrimGalore v0.4.1 and rRNA removed using Bowtie v1.0.0
The trimmed reads were aligned to the Drosophila melanogaster reference genome (BDGP6.22) using TopHat v2.1.2 and Bowtie v1.0.0
The aligned reads were indexed using Samtools v0.1.19 and BigWig files were generated using BEDtools v2.26.0
Plastid was used to generate count tables
R package DESeq2 was used to run differential expression analysis
Genome_build: BDGP6.22
Supplementary_files_format_and_content: logCPM count table as a tab delimited txt file

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher Scientific) followed the manufacture protocol.
mRNA-seq libraries were prepared with the TruSeq Stranded Total RNA (illumina).


title: EV_34_A

description:
total RNA, non-rRNA-depleted
19_S19


title: WT2_WholeT_S2


title: WT521_Total_rep2


title: RG049-POD


title: RG049-T0


title: WT1_WholeT_S1


title: WT521_Total_rep1


title: WT521_PolyA_rep3


title: C4

city: MILAN

first: Maria Rosaria

last: Sapienza

state: Italy

address: Via Ripamonti, 435

department: Division of Haematopathology

country: Italy

institute: IEO, European Institute of Oncology IRCCS

hyb_protocol: Nanostring nCounter Analysis System

scan_protocol: Nanostring nCounter Analysis System

data_processing: Normalization called through the NanoStringNorm package for R

label: Nanostring fluorophore barcode

source_name: Normal Plasmacytoid Dendritic Cell

label_protocol: Nanostring nCounter Analysis System

extract_protocol:
Trizol (Invitrogen, Life Technologies, Carlsbad, CA, USA)
RNA was extracted from FFPE and fresh/frozen samples of the discovery set with the RecoverAll Total Nucleic Acid Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA) and Trizol (Invitrogen, Life Technologies, Carlsbad, CA, USA), respectively

treatment_protocol: On average, 5 slides 10 um-thick were prepared for the extraction of total RNA from BPDCN FFPE samples

tag: disease state

value: Freshly isolated Normal Plasmacytoid Dendritic Cells


title: RG034-POD


title: RG037-T0


title: RG034-T0


title: C3


title: m5B2_WholeT_S4


title: RG037-POD


title: RG046-T0


title: RG046-POD


title: RG057-POD


title: WT521_PolyA_rep2


title: RG033-POD


title: RG056-POD


title: WT521_PolyA_rep1


title: C2


title: RG030-T0


title: RG033-T0


title: C1


title: BPDCN_25

source_name: Blastic Plasmacytoid Dendritic Cell Neoplasm

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: Cryopreserved skin biopsy


title: RG026-POD


title: RG031-POD

value: High


title: BPDCN_24


title: BPDCN_23


title: RG030-POD


title: BPDCN_22


title: RG056-T0


title: RG050-POD


title: RG019-T0

value: male


title: Kidney fibroblasts, Runx1_R3

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

description: bulk RNA-seq of human kidney fibroblasts with lentiviral RUNX1 overexpression

data_processing:
We use nf-core/rnaseq pipeline for analysis of RNA sequencing data.
Reads were aligned to hg38.
Transcript abundance were quantified by Salmon.
Differential expression analysis was performed by DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file estimated gene counts for each sample (abundance measurements)

source_name: Kidney

extract_protocol:
RNA was extracted using RNeasy Kit from Qiagen following the manufactor's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: fibroblasts

value: RUNX1 overexpression


title: BPDCN_21


title: RG023-POD

value: Low

value: female

value: postoperative


title: Kidney fibroblasts, Runx1_R2


title: RG012-T0

value: preoperative


title: RG019-POD


title: RG013-POD


title: RG013-T0


title: GBM_ffpe_52

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation850 BeadChip

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

data_processing: Raw array data were first pre-processed using the ChAMP package in R to remove failed detections and probes with known design flaws, before normalization using the SWAN algorithm

label: Cy3, Cy5

source_name: Glioblastoma

label_protocol: Standard Illumina Protocol

growth_protocol: Patient consent and ethical approval was available for the study (08/H0716/16 Amendment 1 17/10/2014). GIC were isolated from bulk tumor following a previously described protocol (Pollard et al 2009; doi:10.1016/j.stem.2009.03.014). Fresh GBM tissue was sliced and triturated with razor blade, dissociated with Accumax (Sigma, A7089) at 37˚C for 10 mins then filtered through a 70μm cell strainer. Dissociated cells were plated on laminin-coated 6-well plate in NeuroCult NS-A Proliferation kit media (STEMCELL, 05751), heparin (2 μg/ml; Gibco 12587-010), mEGF (20ng/ml, Prepro Tech, 315-09) and hFGF (10ng/ml; Prepro tech, AF-100-18B). Established cells were passaged when 70% confluent, frozen in Stem Cell Banker (Ambsio ZENOAQ, 11890) and stored in liquid nitrogen. Cell lines used in this study are primary lines derived from human tumors, they have been characterised by transcriptomic profiling and cultured according to current practice, including contamination assessment. Fibroblasts cultures were established from small strips of dura mater, collected at surgery. Tissue was minced with a scalpel then spun down and resuspended in trypsin for 5 minutes at 37 degrees. To stop the reaction fresh fibroblast media (DMEM, Glutamax, 10% Foetal calf serum, 2% L-Glutamin and 1% penicillin-streptomycin) was added. Samples were centrifuged and resuspended in fresh media, then plated in 6 well plates (Corning #BC010). Media was topped up frequently during the first week then changed every other day.

extract_protocol: DNA was extracted from cell pellets using the RNA/DNA/Protein Purification Plus kit (NORGEN, #47700), following the manufactured protocol.

tag: patient

tag: sample type

value: FFPE

value: GBM


title: RG012-POD


title: Kidney fibroblasts, Runx1_R1

tag: cell type


title: GBM_ffpe_54

tag: passage


title: GBM_ffpe_50


title: RG026-T0

tag: crp highest level

tag: crp group


title: BPDCN_20


title: Kidney fibroblasts, Control_R3

description: bulk RNA-seq of human kidney fibroblasts without lentiviral RUNX1 overexpression

value: control


title: RG052-T0

tag: age

tag: Sex


title: GBM_ffpe_26


title: BPDCN_19

extract_protocol:
RecoverAll Total Nucleic Acid Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA)
RNA was extracted from FFPE and fresh/frozen samples of the discovery set with the RecoverAll Total Nucleic Acid Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA) and Trizol (Invitrogen, Life Technologies, Carlsbad, CA, USA), respectively

value: FFPE skin biopsy


title: GBM_ffpe_31


title: RG048-POD

tag: timepoint


title: Kidney fibroblasts, Control_R2

tag: genotype


title: BPDCN_17


title: RG031-T0


title: RG003-T0


title: GBM_ffpe_61


title: Kidney fibroblasts, Control_R1


title: BPDCN_18


title: CTCL_P8_POST_B_3

first: Magdalena

last: Matusiak

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

data_processing:
Base calls from the NextSeq were de-multiplexed and converted to FASTQ format with bcl2fastq (Illumina)
The five-base unique molecular identifier (UMI) sequence and the G-overhang were extracted from FASTQ data, and A-tails were removed with umi_homopolymer.py (github.com/jwfoley/3SEQtools)
Reads were aligned and further processed to remove duplicates using STAR (github.com/alexdobin/STAR)
Genome_build: hg38
Supplementary_files_format_and_content: raw read counts

source_name: CTCL tumor

extract_protocol:
Two serial sections of the tissue microarray were taken at 7 µm thickness and mounted onto frame slides with polyethylene naphthalate membranes (Thermo Fisher Scientific, #LCM0521). Slides were immersed for 20 s each in xylene (three times), 100% ethanol (three times), 95% ethanol (two times), 70% ethanol (two times), water, hematoxylin (Dako, #S3309), water, bluing reagent (Thermo Fisher Scientific, #7301), water, 70% ethanol (two times), 95% ethanol (two times), 100% ethanol (three times), and xylene (three times). Immediately after staining, cells were dissected from every tissue microarray spot on an ArcturusXT LCM System (Thermo Fisher Scientific) using the ultraviolet laser to cut out the desired region and the infrared laser to adhere the membrane to a CapSure HS LCM Cap (Thermo Fisher Scientific, #LCM0215). A tissue area containing roughly 1000 mononuclear cells was captured from each spot, with cell numbers determined based on density estimates by cell counting in an adjacent H&E-stained section. If a core had more than 1000 mononuclear cells, a tissue fragment containing around 1000 mononuclear cells was dissected from that core. If a core had less than 1000 cells, tissue fragments from corresponding cores on the serial section membrane were combined in the same LCM cap to obtain approximately 1000 cells. After microdissection, the caps were sealed using 0.5-ml tubes (Thermo Fisher Scientific, #N8010611) and stored at -80 °C until cDNA library preparation.
Sequencing libraries were prepared according to the Smart-3SEQ protocol for LCM HS caps as previously described with slight modifications21. Briefly, 10 µl of lysis mix consisting of 40% (v/v) 5 M trimethylglycine solution (Sigma, #B0300), 20% (v/v) 10 mM nuclease-free dNTP mix (Thermo Fisher Scientific, #R0192), 10% (v/v) 20 µM first-strand primer in TE buffer (1S, /5Biosg/GT GAC TGG AGT TCA GAC GTG TGC TCT TCC GAT CTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TV; Integrated DNA Technologies), 10% (v/v) Triton-X 100 (Sigma #T8787; diluted to 0.5% v/v in molecular biology-grade water), and 20% (v/v) Proteinase K (New England Biolabs, #P8107S; diluted to 0.125 mg/ml in in molecular biology-grade water) was added to the center of each LCM cap. Caps were sealed with 0.2 ml low-retention PCR tubes (Corning, #PCR-02-L-C) and incubated on a pre-warmed metal CapSure incubation block (Thermo Fisher Scientific, #LCM0505) at 60 °C in an incubator. Then, tubes were briefly centrifuged, and 10 µl of template-switching reverse-transcription (TS-RT) FFPE LCM mix consisting of 40% (v/v) 5x SMARTScribe first-strand reaction buffer (Clontech, #639537), 20% (v/v) 20 mM DTT (Clontech, #639537), 10% (v/v) 20x RNase inhibitor (Thermo Fisher Scientific, #AM2694), 4% (v/v) 50 µM second-strand primer in TE buffer (2S, /5Biosg/CT ACA CGA CGC TCT TCC GAT CTN NNN NrGrG rG; Integrated DNA Technologies), 4% (v/v) 200 mM MgCl2 (Sigma, #63069), 2% 5 mM proteinase K inhibitor (EMD Millipore, #539470), and 20% (v/v) 100 U/µl SMARTScribe reverse transcriptase (Clontech, #639537) was added. Samples were incubated in a programmable thermal cycler (42 °C for 30 min, 70 °C for 10 min, 4 °C hold), and 1.25 µl of a unique P5 primer and 1.25 µl of a universal P7 primer (2 µM in TE buffer each; Integrated DNA Technologies; sequences available upon request) and HiFi HotStart ReadyMix (Kapa, #KK2601) were then added, followed by 22 cycles of PCR amplification (98 °C for 45 s; 22 cycles at 98 °C for 15 s, 60 °C for 30 s, 72 °C for 10 s; then 72 °C for 60 s, and 4 °C hold). Amplified cDNA was next purified with SPRI bead mix (Beckman Coulter, #B23317) and a magnetic separation block (V&P Scientific, #VP772F4). Finally, the samples were washed with 80% ethanol and resuspended in TE buffer to yield the sequencing-ready library.

value: cutaneous T cell lymphoma

tag: treatment

value: POST

tag: response

value: non-responders


title: GBM_ffpe_18


title: BPDCN_16

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)


title: RG003-POD


title: GIC_54_2

value: GIC


title: BPDCN_14


title: CTCL_P8_POST_B_1


title: CTCL_P8_POST_B_2


title: BPDCN_12


title: GBM_ffpe_17


title: GIC_61_2


title: GBM_ffpe_30


title: RG002-T0


title: BPDCN_13


title: GIC_52_2


title: GIC_54_1


title: RG023-T0


title: GBM_ffpe_19


title: BPDCN_10


title: GIC_61_1


title: BPDCN_8


title: CTCL_P6_POST_B_4


title: CTCL_P7_POST_B_2


title: RG002-POD


title: CTCL_P6_POST_B_3


title: GIC_52_1


title: GIC_30_2


title: GIC_50_2


title: GIC_31_1


title: BPDCN_3

value: FFPE lymph-node biopsy


title: CTCL_P6_POST_B_2


title: BPDCN_2


title: BPDCN_1


title: CTCL_P6_POST_B_1


title: GIC_18_1


title: CTCL_P4_POST_B_1


title: GIC_26_1


title: NSC_61_2

source_name: Dura mater fibroblasts

value: iNSC


title: CTCL_P3_POST_B_2


title: GIC_19_2


title: GIC_19_1


title: GIC_17_1


title: GIC_31_2


title: GIC_26_2


title: BPDCN_5


title: GIC_50_1


title: GIC_18_2


title: CTCL_P14_POST_B_8


title: mRNA and lncRNA expression for colorectal tumor tissue [907777C]

city: Beijing

first: Tianqi

last: Liu

address: Fucheng street

institute: Peking University

description: Biological replicate 9 of 9

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent 2100 Bioanalyzer Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and normalization. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) and of the red channel ,‘rProcessedSignal’ (rPS) to retrieve one resulting value per channel and unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5. For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula: normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i) Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 units. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.

source_name: tumor tissue

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

extract_protocol: Total RNA extracted using Ribozero toolkits following manufacturer's instructions

tag: gender

value: male

value: Sigmoid Colon


title: CTCL_P3_POST_B_1


title: GIC_30_1


title: NSC_52_1


title: CTCL_P7_POST_B_1


title: NSC_54_1


title: CTCL_P14_POST_B_7


title: NSC_54_2


title: NSC_61_1


title: GIC_17_2


title: mRNA and lncRNA expression for colorectal tumor tissue [838488C]

description: Biological replicate 8 of 9

value: Hepatic Flexure


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [648807N]

description: Biological replicate 7 of 9


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [838488N]

description: Biological replicate 8 of 9


title: CTCL_P14_POST_B_6


title: CTCL_P4_POST_B_2


title: NSC_52_2


title: CTCL_P14_POST_B_5


title: NSC_50_2


title: FB_52

value: FB


title: NSC_50_1


title: mRNA and lncRNA expression for colorectal tumor tissue [648807C]

description: Biological replicate 7 of 9


title: CTCL_P14_POST_B_3


title: FB_54


title: mRNA and lncRNA expression for colorectal tumor tissue [653747C]

description: Biological replicate 6 of 9


title: NSC_31_2


title: FB_50


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [653747N]

description: Biological replicate 6 of 9


title: IPSC_54

value: iPSC


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [907777N]

description: Biological replicate 9 of 9


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [598571N]

description: Biological replicate 5 of 9


title: IPSC_31


title: mRNA and lncRNA expression for colorectal tumor tissue [598571C]

description: Biological replicate 5 of 9


title: CTCL_P14_POST_B_2


title: CTCL_P12_POST_B_2


title: NSC_30_2


title: WM266-4_metastasis (rep3)

city: Ramat Gan,

first: Maya

middle: Ramot

last: Goshen

address: Derech Sheba 2,

department: Clinical Microbiology and Immunology

country: Israel

institute: Tel Aviv University

description: test

data_processing:
The amplification curves were analyzed using the LC480 software Fit Point algorithm. Cp values were exported for further analysis at the Genex-pro software version5 (MultiID). First the data was filtered to retain miRs with at least 2 Cp values in at least one of the cell lines. Cp values grater than 36 were considered negative. Missing data were interpulated based on the group average (115group or 266group). Finally, negative calls were given the value 40 in order to calculate the relative expression using the 2^-ΔΔCT method. miR-103 served as endogenous control.
the fold_change.txt reports the relative expression using the 2^-ΔΔCT method where WM115 is the control.

label: SYBR Green

source_name: skin melanoma

label_protocol: For miRNA expression 10ng of total RNA was reversed transcribed by the miRCURY LNA™ universal cDNA synthesis kit (Exiqon) according to the manufacturer’s instructions. cDNA was diluted 1:40 in Nuclease-free water, combined with 2x SYBR Green master mix (Exiqon) and 10ul were dispensed into each well of the panels. The amplification was carried in Lightcycler480 384-well instrument (Roche) according to the Exiqon panels instruction.

growth_protocol: cell lines WM115 and WM266-4 were obtained from the ATCC and were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1%NaP, 1%L-glu, 1%pen/strep and 1%non-essential amino acids all purchased from Biological-Industries, Israel

extract_protocol: Total RNA was isolated using Trizol reagent (Sigma-Aldrich), according to manufacturer’s instructions

tag: cell line

value: skin melanoma cell line

tag: tumor stage

value: skin metastasis


title: FB_31


title: CTCL_P12_POST_B_1


title: CTCL_P14_POST_B_1


title: FB_30


title: FB_26


title: WM115_primary (rep3)

description: control

value: skin primary tumor


title: NSC_19_2


title: CTCL_P8_PRE_B_3

value: PRE


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [598515N]

description: Biological replicate 4 of 9

value: female

tag: tissue

value: Transverse Colon


title: WM266-4_metastasis (rep1)

description: test


title: mRNA and lncRNA expression for colorectal tumor tissue [598515C]

description: Biological replicate 4 of 9


title: WM115_primary (rep1)

description: control


title: IPSC_19


title: NSC_19_1


title: CTCL_P8_PRE_B_2

tag: disease state

value: cutaneous T cell lymphoma


title: TBI-8

city: New York

last: Cohen

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
NovaSeq Control Software v.1.7.0 used to generate 50 base-pair paired-end reads
Sequencing reads were aligned and quantified using Salmon (v.0.8.2)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: subcutaneous adipose tissue

extract_protocol:
Biopsy of abdominal subcutaneous adipose was performed under local anesthesia through a small incision in the lower abdomen followed by aspiration of 2-3 g of tissue with a 4 mm blunt-end liposuction needle. Tissue was flash-frozen. RNA was extracted from frozen adipose tissue with Trizol (Invitrogen) and purified with RNAeasy columns (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment group

value: TBI


title: IPSC_50

tag: patient

tag: sample type


title: TBI-7


title: CTCL_P8_PRE_B_1

value: non-responders


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [512087N]

description: Biological replicate 2 of 9


title: TBI-6


title: NSC_17

tag: passage

tag: cell type


title: IPSC_30


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [9654856N]

description: Biological replicate 3 of 9


title: CTCL_P7_PRE_B_2


title: FB_19


title: NSC_30_1


title: CTCL_P14_POST_B_4

value: POST


title: TBI-4


title: NSC_18_1


title: CTCL_P6_PRE_B_2


title: TBI-3


title: WM266-4_metastasis (rep2)

description: test


title: FB_17


title: TBI-1


title: CTCL_P6_PRE_B_1


title: TBI-2


title: NSC_26


title: ABM-6

value: abdominal RT


title: ABM-7


title: CTCL_P4_PRE_B_2


title: NSC_31_1

value: iNSC


title: ABM-5


title: TBI-5


title: CTCL_P4_PRE_B_1


title: NSC_18_2


title: ATAC.Day1

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using cutadapt, then paired-end with min 36-bp reads length were aligned to mouse genome build GRCm38/mm10 using Bowtie2 v2.2.6 (PMID: 22388286) with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools. Then read positions were corrected for transposon insertion offset as described in (PMID:24097267).
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 146”,  “--qvalue 1E‐4”, "--nolambda" and "--keep-dup all" flags and arguments.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.narrowPeak (list of the peaks called by MACS2)  or *.bigwig (normalized signal tracks generated with bamCoverage)

source_name: Ex vivo samples from pancreas

extract_protocol: 50000-100000 cells were pelleted by centrifugation and re-suspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). After incubation on ice for five minutes, lysis was washed out by adding 1 mL of lysis buffer without NP40 and digitonin. Nuclei were pelleted by centrifugation for 10 min at 500g, 4 ºC.  The supernatant was discarded and nuclei were re-suspended in 50 µl of reaction buffer containing 1.5 µl of Tn5 transposase (Illumina), 10 ul of 5x transposase buffer (50mM Tris-HCl, pH 8.4 and 25mM MgCl2), 16.5 µl PBS, 0.5 µl of 1% digitonin, 0.5 µl of 10% Tween-20. The reaction was incubated at 37ºC for 30 minutes with 600 RPM mixing and cleaned up with PCR purification kit. The eluted DNA were then used for library preparation and sequenced on an Illumina Hiseq4000/HiseqX platform.

value: Primary pancreatic epithelial cells

tag: growth protocol

value: Ex vivo samples, no need to grow

value: Harvest at 1 day after Caerulein treatment


title: ABM-3


title: mRNA and lncRNA expression for histologically normal tissue adjacent to the tumor  [9635532N]

description: Biological replicate 1 of 9

tag: age

value: Sigmoid Colon


title: mRNA and lncRNA expression for colorectal tumor tissue [9635532C]

description: Biological replicate 1 of 9


title: ATAC.Day28

value: Harvest at 28 days after Caerulein treatment


title: ATAC.Day7

value: Harvest at 7 days after Caerulein treatment


title: mRNA and lncRNA expression for colorectal tumor tissue [512087C]

description: Biological replicate 2 of 9

value: male


title: ATAC.CTRL

value: Untreated


title: ABM-2


title: CTCL_P3_PRE_B_2

value: PRE


title: mRNA and lncRNA expression for colorectal tumor tissue [9654856C]

description: Biological replicate 3 of 9

value: Hepatic Flexure


title: FB_18

value: FB


title: ABM-4


title: SILP sample 5

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: hg19
Supplementary_files_format_and_content: raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: SILP_sorted ILC3s

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

tag: strain

value: Small intestinal lamina propria

value: Sorted ILC3s


title: CTCL_P3_PRE_B_1

value: cutaneous T cell lymphoma

value: non-responders


title: SILP sample 4


title: CNS sample 4

source_name: CNS_sorted ILC3s

value: Central nervous system


title: ABM-1

value: abdominal RT


title: CHM-1

value: chemo


title: CHM-3


title: CHM-4


title: CTL-8

value: controls


title: CTL-6


title: CNS sample 3


title: CTL-5


title: CNS sample 2


title: CTCL_P14_PRE_B_2


title: CTCL_P12_PRE_B_1


title: CNS sample 1


title: CTL-2


title: CTL-3


title: CTL-7


title: CTCL_P12_PRE_B_2


title: CLN sample 4

source_name: CLN_sorted ILC3s

value: Cervical lymph node


title: CTCL_P9_POST_A_3

value: POST

value: responders


title: D150 LCA7 retinal organoid with K88Q mutation

city: San Francisco

first: Deepak

middle: A

last: Lamba

address: 35 Medical Center Way

department: Ophthalmology

institute: University of California, San Francisco

data_processing:
CellRanger software (version 5.0.0) was used with default parameters for library demultiplexing, fastq file generation, read alignment, and UMI quantification
Further processing was carried out in Rstudio using Seurat 4.0.0 (Stuart et al., 2019). Seurat objects were crated to include genes expressed in at least 20 cells and cells with a minimum of 500 genes per cell. Data was further filtered to exclude cells with >2500 genes or >20% mitochondrial genes.
The data sets were merged and exported to Monocle 3
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Cellranger filtered output files, containing gene names, cellbarcodes, and expression matricies

source_name: iPSC derived form PBMCs of patient

growth_protocol: iPSCs were directed to generate retinal organoids using established protocols.

extract_protocol:
Oragnoids were dissociated using papain treatement to single cells and processed for 10x single cell rna seq analysis according to manufacturer's instructions (10X genomics).
10x libraries were prepared with the Chromium Next GEM Single Cell 3ʹ Dual Index Reagent Kits v3.1 [10X Genomics, PN-1000269] according to the manufacturer’s instructions.

tag: tissue/cell source

value: Retinal organoid

tag: subject status


title: CHM-2


title: CTL-4


title: CLN sample 3


title: D150 LCA7 retinal organoid with T155ins4 mutation


title: CTCL_P14_PRE_B_1

city: Stanford

tag: treatment


title: CTCL_P9_POST_A_4

tag: response


title: CTCL_P5_POST_A_2


title: RG867-T0

data_processing:
Illumina NovaSeq 6000 RTA3: v3.4.4 and basecalling with bcl2fastq: v2.20.
Skewer was used to remove poor quality bases from the 3’ end of reads with a minimum phred threshold of 10.
Reads were mapped to the human gencode v33 transcriptome using Kallisto version 0.46.1
Transcript quantifications were aggregated to gene level counts for analysis with DESeq2
Genome_build: gencode v33 transcriptome
Supplementary_files_format_and_content: matrix.tsv is a matrix of gene expression read counts in tab delimited format.

source_name: Peripheral blood

extract_protocol:
RNA was extracted from 500 µL of PBMC suspended in TRIzol (Thermo Fisher Scientific, USA) according to manufacturer’s protocols
For each sample, 120 ng of RNA (in a volume of 50 µL) was used to prepare the library using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) according to the manufacturer's protocol.

tag: crp highest level

tag: crp group

value: High

tag: Sex

value: male

tag: timepoint

value: preoperative


title: RG867-POD

value: female

value: postoperative


title: CLN sample 2

tag: tissue


title: RG866-T0


title: RG866-POD


title: CLN sample 1


title: CTL-1

tag: treatment group


title: CTCL_P5_POST_A_1

tag: disease state

tag: patient


title: CTCL_P9_POST_A_2


title: RG862-T0

value: Low


title: RG860-T0


title: RG860-POD


title: CTCL_P2_POST_A_2


title: iNSC 2, rep 3, Gibco protocol

data_processing:
RRBS-Seq quality and alignment: Quality was assessed via FastQC. Trimming of low quality reads and adapters was performed via TrimGalore v. 0.4.5-1 with “--rrbs” mode enabled. Subsequently, Bismark v. 0.22.1 was used for the alignment of reads, calling the subroutines “nucleotide-coverage” and “methylation-extractor”. Default settings were used, including the usage of Bowtie2 as background aligner.
RRBS-Seq post-processing: The coverage files were post-processed via edgeR. CpG sites with a total coverage – i.e. the sum of methylated (Me) and unmethylated (Un) reads – greater than 10 across all samples were retained as well as only those in chromosomes 1-19 and X. M-values were calculated as log2(Me+2)-log2(Un+2).
RNA-Seq quality and alignment: Quality was assessed via FastQC and trimming of low quality reads and adapters was performed via TrimGalore v. 0.4.5-1 with default parameters. The pseudoalignment package Salmon v. 0.13.1 was used to obtain transcript per million (TPM) expression levels, normalized for library size and transcript length.
RNA-Seq post-processing: Transcript to gene quantification was performed via biomaRt in R.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: RRBS-Seq: coverage files (cov.gz); RNA-Seq: TPM count table (csv)

source_name: Dura mater

growth_protocol: Primary endogenous NSC (eNSC) were isolated from the sub ventricular zone (SVZ) of 3 months old C57Black6/J mice following established protocols. Briefly, SVZ were dissected from the cerebral hemispheres and digested using Papain dissociation kit (PDS, Worthington #0031150 and #003153), plated at a density of 4x104 mL-1 and grown as Neurospheres (NS) for 4 days in DMEM/F12 (Invitrogen #31330), mouse recombinant EGF and human recombinant FGF (20ng/ml, Peprotech #31509 and #100-18B), 2% B27 (Invitrogen #12587) and Pen/Strep 1X (Invitrogen #15140), then media was changed every 4 days. After the first passage, cells were plated in adherent condition in geltrex (Gibco # A1413302) coated 6 well plates (corning # 3516) at a density of 0,5x10^6 cells. Dissociation between passages was performed enzymatically with accutase (Millipore #SCR005). After 2 passages, media was changed to neural expansion media (Gibco Advanced DMEM/F 12 0,5X #12634, Neurobasal medium 0,5X # 21103, 1% Pen-Strep and 2% neural induction supplement #A1647801). Dura mater was collected from C57Black6/J mice before dissection of the hemispheres for eNSC isolation.

extract_protocol:
RNA and DNA were extracted from cell pellets using the RNA/DNA/Protein Purification Plus kit (NORGEN, #47700), following the manufactured protocol.
RNA samples were sequenced on HiSeq4000, at 75 bp PE after polyA selection. For the RRBS library preparation, DNA samples were digested overnight with restriction enzyme Mssp1 (Agilent), then prepared following the manufactured protocol of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Biolab, E7645). Finally, bisulfite conversion following Zimo kit (Qiagen, D5001) run on NextSeq 500 Mid Output Run 150 cycles.

treatment_protocol: Fibroblasts cultures were established from small strips of dura mater, collected at surgery. Tissue was minced with a scalpel then spun down and resuspended in trypsin for 5 minutes at 37 degrees. To stop the reaction fresh fibroblast media (DMEM, Glutamax, 10% Foetal calf serum, 2% L-Glutamin and 1% penicillin-streptomycin) was added. Samples were centrifuged and resuspended in fresh media, then plated in 6 well plates (Corning #BC010). Media was topped up frequently during the first week then changed every other day.  Fibroblasts reprogramming was performed following a previously described protocol. Briefly, fibroblasts were electroporated with reprogramming vectors expressing Oct4, c-Myc, Klf4, Sox2 (OCKS 4F, 5µg) and Rarg, Lfh1 (RL 2F, 5.0 µg) using Amaxa Nucleofector (Lonza, Germany) then plated on SNL feeders with M15 media (Knockout DMEM Invitrogen, 15% Fetal Bovine Serum Hyclone, 1X Glutatamin-Penicillin-Streptomycin Invitrogen, 1X non-essential amino acids Invitrogen). Upon the appearance of colonies, media was replaced with EPSCM (DMEM/F12 Invitrogen, 20% Knockout Serum Replacement Invitrogen, 1X Glutamin-Penicillin-Streptomycin, 1X non-essential amino acids Invitrogen, 0.1 mM β Mercapto-ethanol Sigma, 106 U/ml hLIF Millipore supplemented with the following inhibitors: CHI99021 Tocris 1µM, JNK Inhibitor VIII Tocris 4 µM, SB203580 Tocris 10µM, A-419259 Santa Cruz 1µM and XAV939 Stratech 1µM). Colonies were picked and plated in 24 well SNL feeders’ plates for expansion and characterization. For embryoid bodies (EB) generation, EPSC lines were harvested and feeders removal was performed in T25 flasks for 30 minutes at 37 degrees to allow feeders to attach to the bottom and floating EPSC harvested were transferred in ultra-low attachment 96 well plates at different densities (60K, 45K, 35K and 20K) in EB media (DMEM/Knockout Invitrogen #10829-018, Fetal Bovine serum Gibco #16141061, non-essential amino acid Invitrogen #11140, glut-pen-strep Invitrogen #10378 and β mercapto-ethanol) changed every other days. After 7 days, they were transferred in 24 well plates on gelatine coated glass coverslips and after 10 to 14 days, cells were fixed with PFA 4%, 30 minutes at room temperature and immunocytochemistry was performed. EPSC were induced into iNSC following two protocols. The Gibco protocol (iNSCGibco) previously described and a bespoke protocol. For the latter, feeders were removed and EPSC colonies dissociated with accutase and plated in geltrex coated 6 well plates in EPSCM and rock inhibitor 10μM at density from 0.25 to 0.5x106 cells/well, media was changed the next day with N2B27 induction media (Neurobasal medium Gibco #12348017, DMEM/F21 Gibco #11330032, N2 supplement #17502048, B27 supplement 12587010, EGF and bFGF 10ng/ml peprotech and Pen-Strep-Glut Sigma) and afterwards every 4 days for a week. Cells were passaged with accutase and plated at density of 0.5x106 cells/well in geltrex coated 6 well plates and media was replaced by N2 expansion medium (DMEM/F21 Gibco #11330032, N2 supplement #17502048, EGF, bFDF and Pen-Strep-Glut) and changed every 2 days, passages were performed by enzymatic cells dissociation with accutase 2 to 3 times to establish iNSC N2B27 lines (iNSCN2B27). eNSC, iNSCGibco and iNSCN2B27 were frozen in synth-a-Freeze cryopreservation medium (Gibco #A12542).

value: Dura mater


title: WM115_primary (rep2)

description: control

tag: cell line

value: skin melanoma cell line

tag: tumor stage

value: skin primary tumor


title: RG849-T0


title: iNSC 2, rep 2, Gibco protocol


title: CTCL_P2_POST_A_1

value: cutaneous T cell lymphoma


title: D150 Control retinal organoid

source_name: Control iPSC

value: Control


title: RG849-POD


title: iNSC 2, rep 3, N2B27 protocol


title: RG862-POD


title: CTCL_P1_POST_A_2


title: iNSC 2, rep 2, N2B27 protocol


title: RG847-POD


title: RG847-T0


title: CTCL_P1_POST_A_1


title: RG840-T0


title: iNSC 3, rep 3, Gibco protocol


title: RG834-POD


title: CTCL_P13_POST_A_6


title: RG840-POD


title: RG834-T0


title: RG831-POD


title: iNSC 3, rep 2, Gibco protocol


title: iNSC 3, rep 3, N2B27 protocol


title: CTCL_P13_POST_A_4


title: RG827-T0


title: RG831-T0


title: RG827-POD


title: RG822-T0


title: CTCL_P13_POST_A_3


title: CTCL_P13_POST_A_2


title: RG822-POD


title: CTCL_P13_POST_A_1


title: RG818-POD


title: RG820-T0


title: CTCL_P11_POST_A_1


title: iNSC 1, rep 2, Gibco protocol


title: iNSC 1, rep 3, Gibco protocol


title: RG820-POD


title: RG813-POD


title: iNSC 1, rep 3, N2B27 protocol


title: iNSC 1, rep 2, N2B27 protocol


title: CTCL_P13_POST_A_5


title: CTCL_P9_PRE_A_1

value: PRE


title: RG818-T0


title: CTCL_P5_PRE_A_2


title: RG809-POD


title: iNSC 3, rep 1, Gibco protocol


title: RG803-POD


title: iNSC 2, rep 1, Gibco protocol


title: RG803-T0


title: CTCL_P5_PRE_A_1


title: RG801-T0


title: iNSC 1, rep 1, Gibco protocol


title: RG801-POD


title: iNSC 3, rep 1, N2B27 protocol


title: RG408-POD


title: CTCL_P2_PRE_A_2


title: CTCL_P1_PRE_A_2


title: iNSC 2, rep 1, N2B27 protocol


title: iNSC 1, rep 1, N2B27 protocol


title: CTCL_P1_PRE_A_1


title: RG402-T0


title: NC5

city: Changsha

first: Liya

last: LI

state: Hunan

address: Xiangya Road 87

department: Rheumatology and immunology

institute: Xiangya Hospital of Central South University

description:
lncRNA and miRNA respectively
DM_&_NC_neutrophil_exosome_lncRNA_profile.txt
DM_&_NC_neutrophil_exosome_miRNA_profile.txt

data_processing:
The Illumina HiSeq 3000 platform was used for paired-end sequencing (PE150) at Guangzhou RiboBio Co. (Guangzhou, China).
The sequencing reads were pre-processed with FastQC software and Trimmomatic tools (v 0.36) to obtain clean reads.
The mapped reads were obtained by mapping the clean reads to the human reference genome hg19; HISAT2 (v2.1.0) and HTSeq (v0.6.0) were used for lncRNAs, and Burrows-Wheeler Aligner (BWA; v0.7.12) was used for small RNAs.
The miRDeep2 database was used to identify known mature miRNAs based on miRBase (v21) (www.miRBase.org) and to predict novel miRNAs.
The DESeq2 was used to identify the significantly differentially expressed (DE) lncRNAs (adjusted p<0.05 and |log2(fold change)| > 1.5), while the R package edgeR was used to identify the significantly DE miRNAs (adjusted p<0.05 and |log2(fold change)| > 1).
Genome_build: Human reference genome hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab_delimited text files include FPKM or RPM value for every gene and every sample.

source_name: peripheral blood

extract_protocol:
We isolated EXOs from all of the cultured neutrophil supernatants (neutrophil EXOs) using an exoEasy Maxi Kit (Qiagen, Frederick, USA) according to the manufacturer’s instructions. The neutrophil EXOs were eluted using 600 μl Buffer XE and stored at −80 °C until analysis.
The total RNA of neutrophil EXOs was extracted with TRIzol (Invitrogen Life Technologies, California, USA) according to the manufacturer’s protocol. Small RNA and lncRNA libraries were created with an NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB, Ipswich, USA) and an NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB), respectively, according to the manufacturer’s instructions.

treatment_protocol: Peripheral whole blood samples were collected in EDTA anticoagulant-coated tubes and processed within 2 h. Neutrophils were isolated by density gradient equilibrium centrifugation using Histopaque-1077 and Histopaque-1119 (Sigma-Aldrich, St. Louis, USA) according to the manufacturer’s instructions. The neutrophils were incubated for 2 h at 37 °C in a humidified atmosphere containing 5% CO2.

tag: diagnosis

value: Normal control

tag: cell type

value: Exosomes from the supernatants of neutrophils


title: NC4


title: CTCL_P13_PRE_A_2


title: RG402-POD

tag: age


title: CTCL_P13_PRE_A_1


title: eNSC 2. rep 2

last: Marino

address: 4, Newark St

institute: Queen Mary University of London

source_name: Sub ventricular zone

tag: strain

value: Sub ventricular zone


title: NC2


title: CTCL_P11_PRE_A_2

value: responders


title: NC1


title: RG076-T0

last: Ziemann

address: 85 Commercial Rd

institute: Burnet Institute


title: eNSC 1, rep 2


title: eNSC 3, rep 2


title: CTCL_P11_PRE_A_1


title: RG076-POD


title: RG809-T0


title: RG408-T0


title: RG073-T0


title: eNSC 3, rep 1


title: DM5

value: Dermatomyositis


title: DM4


title: CTCL_P10_PRE_A_1


title: eNSC 2, rep 1


title: RG071-T0

value: High


title: eNSC 1, rep 1


title: DM3


title: DM2


title: iNSC 3, rep 2, N2B27 protocol


title: RG071-POD


title: intracellular P. gingivalis [S_3_Pg]

city: CHENGDU

first: CHENGCHENG

last: LIU

state: SICHUAN

address: No. 14, Section 3, Renminnan Road

institute: Sichuan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: raw gene count

organism: Porphyromonas gingivalis ATCC 33277

source_name: intracellular P. gingivalis

extract_protocol:
Total RNA was isolated from the samples using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocols. Further, genomic DNA was removed using the commercially available DNase I system (Qiagen, Germantown, PA, USA), and RNA concentration was realized by determining the A260/A280 ratio using a Nanodrop 2000 system (ThermoFisher, Waltham, MA, USA). RNA integrity was verified via 1.5% agarose gel electrophoresis, and qualified RNAs were quantified using a Qubit 3.0 fluorometer with a QubitTM RNA Broad Range Assay Kit (ThermoFisher, Waltham, MA). Furthermore, the RNA samples were analyzed at the Huayin Genome Research Facility (Huayin Health Medical Group Co, Wuhan, China) to determine ribosomal RNA (rRNA) depletion and subsequent RNA sequencing, and rRNA was removed using a Ribo-off rRNA Depletion Kit (Vazyme Biotech Co., Nanjing, China) for humans (Catalog No. N406) and/or bacteria (catalog NO. N407). Additionally, cDNA libraries for Illumina® sequencing were generated using the KC-DigitalTM Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). The library products corresponding to 200–250 bps were then enriched, quantified, and sequenced using a Nova-seq 6000 sequencer (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: infection


title: RG067-T0

value: preoperative


title: RG066-T0

value: male


title: NSCLC 21

city: Saint Louis

first: Robert

last: Schreiber

state: MO

address: 425 South Euclid

department: Department of Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Read-mapping was performed with TopHat (version 2.0.14) using Hg19 as the reference genome.
Transcriptome reconstruction and expression quantification into FPKM was performed.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: NSCLC tissue

extract_protocol:
RNA was extracted from tumor tissue using an RNeasy Mini Kit (Qiagen).
After quality assessment with an Agilent 2100 Bioanalyzer (Agilent Technologies), polyadenylated RNA libraries were generated with a TruSeq Stranded mRNA Sample Prep Kit (Illumina) on an Agilent XT-Auto System (Agilent Technologies), and they were sequenced with a HiSeq SBS Kit v4-HS (Illumina) on a HiSeq2500 system (Illumina).

value: tumor

tag: group

value: C


title: RG067-POD

first: Mark

value: Low

value: female

value: postoperative


title: intracellular P. gingivalis [S_1_Pg]

tag: treatment


title: P. gingivalis cultured in medium [J_3]

source_name: P. gingivalis cultured in medium

value: untreated


title: NSCLC 22


title: Ageing_rep2_control

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

data_processing:
Adapter seqeucnes were trimmed by using trim_galore
fastuniq is used to remove PCR duplication. Then use seqtk trimfq '-e 10' or '-b 6 -e 10' remove random sequences added in library construction
Clean reads were mapped to genome by using HISAT2; with parameter "--mp 4,2 --rna-strandness RF --no-softclip --no-mixed --no-discordant".
Peak detection within genes. To search for enriched peaks in the treated samples, we scanned each gene using sliding windows of 100 nt with 50 nt overlaps. The total number of reads per window was calculated for each dataset. The number of reads for each window in treated and control was determined using HTSeq 0.12.4(-s no -m union --nonunique all parameters)
A custom python script was used to parse the pileup format into a tabular format summarizing the mutation at each position.
Genome_build: hg38 and mm10

source_name: mouse brain tissue

extract_protocol:
Total RNA was isolated from cell lines or mouse tissues with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25(NEB) and gDNA was removed by TURBO DNase (Invitrogen). Purified polyadenylated RNA was fragmented using RNA fragmentation reagents (Ambion) at 70 °C for 10 min. Fragmented RNA was incubated with freshly prepared 50 mM NaIO4 at 25°C for 30 min in the dark.The RNA cleave assays were performed using Endonuclease V (NEB) with standard reaction buffer (10mM Tris-HCl pH 7.5, 0.5mM MnCl2, 50mM KCl, 1mM dithiothreitol and 5% glycerol)  and then perform next-generation sequencing (NGS).
Fragmented RNA was first subjected to end repair by T4 PNK. For the treated sample, the RNA was treated with periodate followed by Endonuclease V cleavage.3′-adapter ligation (3′ adapter, /5rApp/NNNNNNTGGAATTCTCGGGTGCCAAGG/3ddC/) followed by the 3′ adapter removing by 5′-deadenylase and RecJf digestion. After purification, SuperScript III was used to perform RT (RT primer, /ACACGACGCTCTTCCGATCT). After cDNA synthesis, 5′ adapter (5′ adapter, /5Phos/NNNNNNNNNNAGATCGGAAGAGCACACGTCTG/3ddC/) ligation were performed. After purification, qPCR was performed to evaluate the cycle numbers of each samples to avoid over-amplification. Library PCR amplification was performed using the NEB primers. The products were purified by NEBNext Sample Purification Beads or low melting point agarose gel and used for sequencing.

value: Ageing

value: brain

tag: phenotype

value: Dull eyes, Hair shedding, Abdomen with white hair-bands


title: RG073-POD

city: Melbourne

tag: crp highest level


title: NSCLC 19


title: RG066-POD

tag: crp group


title: NSCLC 20


title: DM1

value: Exosomes from the supernatants of neutrophils


title: P. gingivalis cultured in medium [J_2]


title: Ageing_rep2_treated


title: Ageing_rep1_control


title: RG064-T0

tag: Sex


title: E14Tg2a_WT_FCSL_rep2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

description: rRNA depleted strand-specific library

data_processing:
for quantifications reads were aligned with STAR; for assambly with Hisat2
gene expression estimates were obtained using RSEM
transcript models were built with Stringtie
Genome_build: mm10
Supplementary_files_format_and_content: txt file of TPM values for each sample (TF depletions; poly-A RNA-seq)
Supplementary_files_format_and_content: strand-specific bigwig files for undifferentiated ES cells (Ribo-depleted RNA-seq)

source_name: wild-type ES cell

growth_protocol: ES cells were cultured on 0.1% gelatine in DMEM-FCS10%-LIF

extract_protocol:
Extraction with Trizol (Invitrogen, 15596026) according to the manufacture’s protocol
poly-A enriched strand-specific (SR)  or rRNA depleted strand-specific library (PE)

treatment_protocol: Doxycycline treatment (1µg/mL) for 24h

value: undifferentiated


title: NSCLC 18


title: NC3

value: Normal control


title: intracellular P. gingivalis [S_2_Pg]


title: Ageing_rep1_treated


title: NSCLC 17


title: Normal_rep2_control

value: Control

value: Normal phenotype


title: RG064-POD

value: High

tag: timepoint


title: E14Tg2a_WT_FCSL_rep1

description: rRNA depleted strand-specific library


title: NSCLC 16

tag: tissue

value: B


title: RG057-T0

value: male

value: preoperative


title: Zhbtc4_mDox_2

description:
gene_tpm.txt
Sample 7
poly-A enriched strand-specific library

source_name: E14Tg2a ES cell derivative

value: No Doxycycline treatment


title: NSCLC 14

value: tumor


title: NSCLC 15


title: Zhbtc4_pDox_2

description:
gene_tpm.txt
Sample 8
poly-A enriched strand-specific library

value: 24h Doxycycline treatment


title: Normal_rep1_control


title: NSCLC 13


title: Normal_rep1_treated


title: P. gingivalis cultured in medium [J_1]


title: Epilepsy_rep2_control

value: Epilepsy

value: Epilepsy in grade 5


title: Normal_rep2_treated


title: Zhbtc4_pDox_1

description:
gene_tpm.txt
Sample 6
poly-A enriched strand-specific library


title: NSCLC 11


title: RG062-POD

value: Low

value: female

value: postoperative


title: RG813-T0


title: RG057-POD


title: NSCLC 10


title: Epilepsy_rep2_treated

value: brain


title: EKOiE_pDox_2

description:
gene_tpm.txt
Sample 4
poly-A enriched strand-specific library


title: EKOiE_mDox_2

description:
gene_tpm.txt
Sample 3
poly-A enriched strand-specific library


title: RG056-POD


title: EKOiE_pDox_1

description:
gene_tpm.txt
Sample 2
poly-A enriched strand-specific library


title: Epilepsy_rep1_treated


title: NSCLC 9


title: RG062-T0


title: Zhbtc4_mDox_1

description:
gene_tpm.txt
Sample 5
poly-A enriched strand-specific library


title: RG054-POD


title: EKOiE_mDox_1

description:
gene_tpm.txt
Sample 1
poly-A enriched strand-specific library


title: NSCLC 12


title: RG056-T0


title: AD_rep2_control

value: Alzheimer's disease

value: Dull eyes, Hair shedding, Abdomen with white hair-bands


title: RG052-T0


title: NSCLC 8


title: Epilepsy_rep1_control


title: AD_rep1_control


title: RG054-T0


title: NSCLC 6

value: A


title: AD_rep2_treated


title: NSCLC 5


title: RG052-POD


title: RG050-T0


title: NSCLC 7


title: AD_rep1_treated


title: RG049-T0


title: NSCLC 4


title: ATAC.Day28.DCLK1

value: Primary pancreatic epithelial cells

tag: growth protocol

value: Ex vivo samples, no need to grow

value: Harvest at 28 days after Caerulein treatment


title: ATAC.Day1.DCLK1

value: Harvest at 1 day after Caerulein treatment


title: NSCLC 3


title: RG049-POD

value: High

value: male


title: wt_female_E12.5 rep1

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

data_processing:
The quality control with the software FastQC v0.11.9
Clean reads were aligned to the mouse mm10 genome with the STAR 2.5.3a software
The normalized FPKM were calculated with the software cufflinks-2.2.1.Linux_x86_64

source_name: primordial germ cells

extract_protocol:
1000 cells per sample were resuspended in PBS with 0.1% BSA and transferred to the bottom of a PCR tube consisting of 3 μl lysis buffer, and cDNA was synthesized in the tube containing mRNA,and then the libraries were prepared by using TruePrep DNA Library Prep Kit V2
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primordial germ cells

value: wt


title: wt_female_E12.5 rep2


title: NSCLC 2

value: tumor


title: wt_female_E12.5 rep3


title: Terc-/-_female_E12.5 rep3

value: Terc-/-


title: Terc-/-_female_E12.5 rep1


title: RG048-T0

value: Low

value: preoperative


title: Terc-/-_female_E12.5 rep2


title: NSCLC 1


title: Terc-/-_male_E12.5 rep3


title: RG050-POD

value: female

value: postoperative


title: RG048-POD


title: Terc-/-_male_E12.5 rep2


title: Terc-/-_male_E12.5 rep1


title: WT_Total_Rep1

city: Bethesda

first: Kumaran

last: Ramamurthi

state: MD

address: 37 Convent Drive

institute: National Cancer Institute

data_processing:
Illumina Hiseq 2500 System was used for sequencing.
The Illumina reads in FASTQ format were first trimmed by Trimmomtaic version 0.36 to remove the adaptor sequences and low quality reads.
The RNAseq pipeline READemption version 0.4.5. was then used to process those trimmed reads. Those longer than 12 nt were aligned to the Escherichia coli str. K-12 substr. MG1665 reference sequence (NC_000913.3) download from the NCBI ftp website by using segemehl version 0.2.0.
To find differentially expressed genes, the “deseq” subcommand in READemption executing   DESeq2 version 1.20.0 was used with the fold-change of 2.0 or higher and the adjusted p-value below 0.1.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include rawcount for each Sample.

organism: Escherichia coli K-12

source_name: E.coli K12 MG1655

growth_protocol: All strains used in this study were grown at 37 oC under aerobic conditions in LB. Wherever required, the liquid and solid media was supplemented with Ampicillin (100 mg/ml). The bacteria used for the RNA Seq experiment were grown to OD600 =1 in LB.

extract_protocol:
Polyclonal antibodies to Hfq were generated previously by immunizing rabbits with purified Hfq protein (Covance). RNAs that co-IP with Hfq were isolated as described previously(Zhang, A., et al., Mol Cell, 9, 11-22) with the following modifications. Overnight cultures of strains KK2440 (WT) and KK2448 (Hfq65) cells were grown to OD600 ~ 1.0 in LB medium. Cells corresponding to the  equivalent of 40 OD600 were collected, and 2 ml cell lysates were prepared by vortexing with 212-300 μm glass beads (Sigma) in a final volume of 2 ml lysis buffer (20 mM Tris-HCl/pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT). Co-IPs were carried out either using 200 μl of α-Hfq, 240 mg of protein A-Sepharose CL-4B (GE Healthcare), and 1.9 ml of cell lysate. Co-IP RNA was isolated from protein A-Sepharose beads by extraction with phenol: chloroform:isoamyl alcohol (25:24:1), followed by ethanol precipitation. Total RNA was isolated from 100 μl of cell lysate by Trizol (Thermo Fisher Scientific) extraction followed by chloroform extraction and isopropanol precipitation. Total and co-IP RNA samples were resuspended in 30 μl and 50 μl of DEPC H2O.  The integrity of RNA was checked on 1% agarose gel. The RNA were treated with DNAase I(100 μl) followed by phenol: Chloroform: IAA based purification and ethanol precipitation. The gDNA contamination was checked by PCR amplification.  The DNA free RNA samples were then subjected to rRNA depletion using Ribo-zero kit and purified by using (2.5X)RNAClean XP Beads and isopropanol (1.5X). isopropanol ratio(1.5X) is critical to keeping short RNAs (>70 nt) om the RMA [pp;. The isopropanol and RNAClean XP bead ratios were both optimized in orger to remove nonligated adaptors while saving short RNA fragments.
The RNAs (400 ng) were used for cDNA library preparation.  Library construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al. 2015, Nat Methods, 12, 323-325), which was adapted to capture (optimized amount of isopropanol and RNAClean XP for short sRNA) bacterial sRNA (Melamed, S et al.,  2018, Nat Protoc, 13, 1-33).   To enrich the libraries, 12 cycles of PCR were carried out at the end step of enrichment. Bead purification was performed twice at the last step to ensure high purity of the library from the adaptor dimer.

tag: genotype

value: Wild Type

tag: anti-hfq antibody


title: WT_Total_Rep2


title: RG046-T0


title: RG046-POD


title: RG037-T0


title: wt_male_E12.5 rep3


title: Hfq65_Total_Rep2

value: Hfq65 mutant


title: RG037-POD


title: ATAC.CTRL.DCLK1

source_name: Ex vivo samples from pancreas

value: Untreated