title: High-Dose-IL2-1

description: rawdata.Malek.high-dose.filtrcpms.csv


title: High-Dose-PBS-2

status: Public on Feb 16 2022

type: SRA

city: Miami

first: Thomas

last: Malek

state: Florida

address: 1600 N.W. 10th Avenue

department: Department of Microbiology and Immunology

country: USA

institute: University of Miami Miller School of Medicine

description: rawdata.Malek.high-dose.filtrcpms.csv

library_source: transcriptomic

data_processing:
Reads from RNA-seq were mapped to the Mus musculus genome GRCm38 using STAR (ver.2.5.0) aligner. Raw counts were generated on Ensembl gene (GENCODE M13) with featureCounts (ver.1.5.0). Differential expressed genes in Tregs between the mIL-2 or mIL-2/CD25 and PBS injected mice were identified using DESeq2, and determined according to threshold of false discovery rate (FDR) <0.01
Genome_build: GRCm38

molecule: total RNA

organism: Mus musculus

source_name: regulatory T cells

extract_protocol:
RNA was isolated from sorted Tregs using TRIzol Reagent (Thermo Fisher) and column purified using miRNeasy Micro Kit (Qiagen). RNA quality was assessed using an Agilent 2100 BioAnalyzer and was quantified using Qubit RNA assay
RNA-seq libraries were prepared from 25 ng of total RNA using the KAPA’s RNA Hyperprep with RiboErase protocol and quantified using Qubit DNA and  Kapa qPCR Library Quantification kit for Illumina (KapaBiosystems).

treatment_protocol: RFP-FoxP3+ BL6 mice were injected with 20 ug of FP or 100 uL of control PBS. 1.5 hr post injection splenic Tregs were sorted out.

tag: strain

tag: tissue

value: Spleen

tag: injected molecule

value: control PBS

tag: treatment

value: High-Dose-PBS


title: SAARLK

city: Chapel Hill

first: Federico

last: Innocenti

state: North Carolina

address: 120 Mason Farm  Road, CB7361

department: Eshelman School of Pharmacy

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-seq reads were aligned to ribosomal RNA sequences to remove ribosomal reads
Remaining reads were aligned to the human reference genome using GSNAP4,5 version '2013-10-10' allowing maximum of two mismatches per 75 base sequence
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated in a strand-specific manner using the functionality provided by the R package GenomicAlignments13
Genome_build: NCBI Build 38
Supplementary_files_format_and_content: CALGB 80405 RNAseq Processed data.csv - gene read counts

organism: Homo sapiens

source_name: primary tumor

extract_protocol: Illumina TruSeq RNA Access

tag: tumor type

value: metastatic colorectal cancer

tag: age

tag: Sex

value: Male

tag: race

value: White

tag: treatment group

value: Bevacizumab


title: High-Dose-PBS-1

description: rawdata.Malek.high-dose.filtrcpms.csv


title: SAARLI

value: Bevacizumab/Cetuximab


title: SAARLM

value: Female


title: Restimulate-1.5h-FP-2

description: rawdata.Malak_Restimulate_mouse.filtrcpms.csv

value: mIL-2/CD25 and 2nd mIL-2/CD25

tag: sample id


title: In-Vitro-1.5h-IL2-3-2nd-run

description: rawdata.Malak_invitro_1.5h_mouse.filtercpm.csv


title: In-Vitro-1.5h-IL2-2-2nd-run


title: SAARLE


title: In-Vitro-1.5h-IL2-1-2nd-run


title: SAARLB

value: Black or African American

value: Cetuximab


title: SAARLC


title: In-Vitro-1.5h-PBS-2-2nd-run


title: High-Dose-PBS-3

description: rawdata.Malek.high-dose.filtrcpms.csv


title: SAARLF


title: SAARLG


title: SAARJZ


title: SAARKG


title: In-Vitro-1.5h-IL2-1-1st-run


title: In-Vitro-1.5h-PBS-3-1st-run


title: SAARJX


title: In-Vitro-1.5h-PBS-3-2nd-run


title: In-Vitro-1.5h-PBS-2-1st-run


title: In-Vitro-1.5h-PBS-1-1st-run


title: SAARJY


title: SAARJW


title: 168h-FP-3


title: In-Vitro-1.5h-IL2-2-1st-run


title: SAARJS


title: 168h-FP-2


title: SAARKK


title: SAARJL


title: SAARJJ


title: 168h-PBS-3


title: In-Vitro-1.5h-IL2-3-1st-run


title: SAARJH


title: SAARKN


title: 168h-PBS-1


title: 72h-FP-4-2nd-run


title: SAARJG


title: 168h-PBS-2


title: SAARJT


title: In-Vitro-1.5h-PBS-1-2nd-run


title: SAARIY


title: 72h-FP-3-2nd-run


title: 168h-FP-1


title: SAARIZ


title: 72h-FP-2-2nd-run


title: SAARIV


title: ILC3 MRE rep2

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

library_source: genomic

data_processing:
The reads for MeDIP-seq, MRE-seq, and hmC-Seal were trimmed using cutAdapt and aligned to the mm10 reference genome with BWA and then processed by methylQA. The signal for MeDIP-seq, MRE-seq, and hmC-Seal at each CpG was the number of reads aligned to that location divided by total reads (million). The average signal for MeDIP-seq, MRE-seq, and hmC-Seal in each window was the mean of signal at all bases in that window.
After processing by methylQA, de-duplicated reads from hmC-seal samples were used to call broad peaks using MACS2 with a FDR threshold of 0.01. hmC peaks were then used for differential enrichment analysis with DiffBind and DHMRs were called using a q value of 1e-15 and an absolute log2FoldChange cutoff >= 194. De-duplicated reads from MeDIP-seq and MRE-seq samples were then used to identify 500bp differentially methylated regions using MethylM&M35. Briefly, M&M computes a probability score for a given genomic window based on observed MeDIP-Seq and MRE-seq measurements using the null hypothesis that there is an equal amount of methylation between two samples for the given region. An empirical FDR was estimated using intrareplicate comparisons and a q threshold for NK vs. ILC2 and NK vs. ILC3 DMRs were called using a cutoff of q = 1e-5 whereas ILC2 vs. ILC3 DMRs were called using q = 0.05. ENCODE blacklisted regions, chrM, chrX, and chrY regions were removed from our DHMR and DMR sets.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing RPKM for MeDIP, MRE, and hmC-Seal

molecule: genomic DNA

source_name: ILC3 MRE

extract_protocol:
For sorting, spleens were dissociated and washed through 70um cell strainers and enriched with DX5+ MACS positive selection columns. For immune phenotyping and cell stimulation, spleens were dissociated and washed through 70um cell strainers. Lysates were lysed for red blood cells and resuspended in medium. Small intestinal ILC2 and ILC3 were isolated as previously described. Briefly, small intestines were dissected and washed with Peyer’s patches and mesenteric fat removed. Intestines were opened lengthwise; gently agitated for 20 min in Hanks’ balanced salt solution (HBSS) containing HEPES, bovine calf serum, and EDTA; and then vortexed. Small intestines were subjected to a second round of gentle agitation and vortexing in EDTA. The tissue was then rinsed with HBSS before digestion with collagenase IV (Sigma-Aldrich) in complete RPMI 1640 for 40 min at 37°C under agitation. Digests were filtered through 100-um mesh and subjected to density gradient centrifugation using 40 and 70% Percoll solutions.
MeDIP-seq libraries were generated as previously described with few modifications. One hundred nanograms of sheared DNA was ligated with Illumina adapters, and methylation-enriched adapter-ligated DNA fragments were immunoprecipitated with 0.1 ug of anti-methylcytidine antibody (Eurogentec, BI-MECY-0100). MeDIP DNA fragments were amplified with Illumina barcodes with NEBNext High-Fidelity 2× PCR Master Mix (polymerase chain reaction) master mix (NEB, M0541). MeDIP-seq libraries were sequenced on Illumina NextSeq 500 platform. MRE-seq libraries were generated as previously described with few modifications. In brief, 20 ng of genomic DNA was digested by four restriction enzymes (HpaII, HinP1I, AciI, and HpyCH4IV) that generate a CG overhang. Adapter ligation was performed with custom Illumina adapters (5'-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3' and 5'-P-CGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3'). Adapter-ligated DNA fragments were amplified with Illumina barcodes with NEBNext High-Fidelity 2× PCR Master Mix master mix (NEB, M0541) and sequenced on Illumina NextSeq 500 platform. To identify 5hmC-enriched regions, we performed hmC-Seal on cell samples. In brief, 275 ng of sheared DNA was ligated with Illumina adapters. Hydroxymethylation-enriched adapter-ligated DNA fragments were glucosylated by incubating in a 50-ul solution containing 1× glucosylation buffer, 200 uM UDP-azide-glucose (Active Motif, 55020), and 5 U of T4 B-glucosyltransferase (Thermo Fisher Scientific, EO0831) at 37°C for 1 hour. After glucosylation, the DBCO-PEG4-biotin reaction and streptavidin C1 bead pull-down were same as the Nano-hmC-Seal. The beads were washed 10 times with 1× binding-washing buffer and twice with double-distilled water (ddH2O) and were resuspended in 15 ul of ddH2O. The captured DNA fragments were amplified and barcoded with Illumina barcodes with the NEBNext High-Fidelity 2× PCR Master Mix (NEB, M0541). hmC-Seal libraries were sequenced on Illumina NextSeq 500 platform.

value: small intestine lamina propria

tag: cell type/genotype


title: 72h-FP-1-2nd-run


title: SAARIS


title: 72h-IL2-3-2nd-run


title: SAARIU


title: SAARIR


title: 72h-IL2-2-2nd-run


title: SAARIL


title: 72h-IL2-1-2nd-run


title: 72h-PBS-3-2nd-run


title: SAARIJ


title: SAARIG


title: SAARIF


title: 72h-PBS-2-2nd-run


title: SAARIB


title: 72h-PBS-1-2nd-run


title: 72h-FP-3-1st-run


title: 72h-FP-4-1st-run


title: SAARIE


title: 72h-FP-2-1st-run


title: 72h-FP-1-1st-run


title: SAARHR


title: SAARHY


title: 72h-IL2-3-1st-run


title: 72h-PBS-3-1st-run


title: 72h-PBS-2-1st-run


title: 72h-PBS-1-1st-run


title: SAARHD


title: SAARHI


title: SAARHF


title: 16h-FP-4


title: 72h-IL2-1-1st-run


title: SAARHM


title: SAARHK


title: SAARHZ


title: SAARHU


title: SAARHC


title: 16h-FP-3


title: SAARGU


title: 16h-FP-1


title: SAARGM


title: SAARHP


title: SAARHA


title: SAARGV


title: 16h-FP-2


title: SAARGG


title: 16h-IL2-3


title: 16h-IL2-1


title: 72h-IL2-2-1st-run


title: 16h-IL2-4


title: SAARFZ


title: 16h-PBS-2


title: SAARGB


title: 16h-PBS-3


title: SAARFV


title: 16h-PBS-1


title: SAARFT


title: 16h-PBS-4


title: SAARFM

value: Unknown


title: SAARFS


title: 16h-IL2-2


title: 4h-FP-4


title: SAARFH


title: SAARFK


title: 4h-FP-3


title: 4h-FP-2


title: 168h-FP-4


title: SAARFD


title: SAARFA


title: 4h-FP-1


title: 4h-IL2-3


title: SAAREX


title: 4h-IL2-4


title: 4h-PBS-4


title: SAAREW


title: SAAREU


title: 4h-PBS-3


title: 4h-IL2-2


title: SAARET


title: SAARES


title: 4h-PBS-1


title: SAAREN


title: SAARFE


title: 1.5h-FP-3


title: 4h-IL2-1


title: 1.5h-FP-4


title: 1.5h-FP-2


title: RB-VCaP-Veh

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description:
VRbMinus4.bw
VRbMinus4_peaks.narrowPeak.gz

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Genome_build: hg19
Supplementary_files_format_and_content: bw, narrowPeak

source_name: VCaP cell

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

tag: cell type

value: prostate cancer cell line

tag: medium condition

value: In DMEM medium with 5% charcoal-stripped FBS (CSS)

tag: cell line

value: VCaP

value: untreated

tag: chip antibody

value: anti-RB (cell signaling)


title: SAAREB


title: SAAREH


title: SAARER


title: SAARDB


title: SAARDH


title: 1.5h-IL2-3

value: Spleen


title: SAARCV

value: metastatic colorectal cancer


title: SAAREV


title: SAARCS

value: Male


title: 1.5h-IL2-4


title: 1.5h-IL2-2


title: SAAPVN

value: White


title: SAARCL


title: 4h-PBS-2

value: control PBS


title: 1.5h-IL2-1


title: 1.5h-PBS-3


title: 1.5h-PBS-4


title: 1.5h-PBS-2


title: 1.5h-FP-1


title: SAAPUZ

value: Bevacizumab/Cetuximab


title: 168h_FP-4-2runs

data_processing:
The ATAC-seq data were preprocessed (trimmed, aligned, filtered, and quality controlled) and analyzed using the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/, accessed on 2019-05-26) (Stowers et al., 2019).
Reads were mapped to the GRCm38 (mm10) mouse reference sequence using bwa-mem (Li and Durbin, 2009) and MACS (version 2.1.2) (Zhang et al., 2008) was used to identify the peak regions.
The Irreproducible Discovery Rate (IDR) method (Li et al., 2011) was used to identify reproducible peaks between two pseudo-replicates that were generated for each sample. Only reproducible peaks (IDR > 0.1) were retained for downstream analyses.
peaks overlapping with blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/, Oct 2016 version). removed by ENCODE ATAC-seq pipeline
Peaks obtained from samples in the same treatment and at the same time point were merged together.
Genome_build: mm10

extract_protocol:
50,000 unfixed nuclei were tagged using Tn5 transposase  for 30 min at 37°C.
Libraries were generated using the Ad1_noMX and Ad2.1-24 barcoded primers and amplified for 10-12 cycles. Resulting library fragments were purified using a DNA Clean & Concentrator-5 kit (Zymo Research). Size-selection was performed using the Agencourt AMPure XP PCR purification system (Beckman Coulter) to remove large fragments > 1 kb and primers to maintain high library complexity. Libraries qualities were assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit and sequenced on an Illumina NextSeq500 with a read length of 75 bp to a minimum depth of 40 million reads per sample using the NextSeq 500 High-Output Kit (150-Cycle, 400 M Flow Cell). Two technical replicates were processed per biological sample.

treatment_protocol: RFP-FoxP3+ BL6 mice were injected with 5 µg of mIL-2 or 20 µg of FP or 100 µL of control PBS. 0.75 hr post injection, spleen Tregs were sorted out.

value: regulatory T cells

value: FusionProtein-treaed-Treg


title: SAAPUH

value: Female


title: 1.5h-PBS-1


title: SAAPVM


title: 168h_FP-1-2runs


title: SAAPUE

value: Asian


title: SAAPUC

value: Cetuximab


title: SAAPUP

value: Bevacizumab


title: 168h_FP-3-2runs


title: SAAPUA


title: SAAPTW


title: SAAPVL

value: Black or African American


title: SAAPTV


title: SAAPTY


title: 168h_PBS-1-2runs

value: PBS-treaed-Treg


title: 72h_FP_1


title: SAAPTR


title: 72h_FP_3


title: SAAPTN


title: 168h_FP-2-2runs


title: SAAPTL


title: SAAPTJ


title: 72h_PBS_2


title: SAAPTH


title: 72h_PBS_1


title: 168h_PBS-2-2runs


title: 16h_FP_6


title: 16h_FP_9


title: SAAPTT


title: SAAPTB


title: SAAPST


title: 168h_PBS-4-2runs


title: 72h_FP_2


title: 16h_IL2_8


title: SAAPSM


title: 16h_IL2_2


title: 16h_IL2_5


title: 16h_PBS_7


title: 16h_PBS_4


title: SAAPSC


title: 0.75h_FP_3


title: SAAPSD


title: SAAPSB


title: SAAPSA


title: 16h_PBS_1


title: 0.75h_FP_1


title: SAAPRP


title: SAAPRK


title: 0.75h_IL2_3


title: 16h_FP_3


title: SAAPPZ


title: SAAPSU


title: 0.75h_FP_2


title: SAAPPJ


title: SAAPPU


title: 0.75h_IL2_2


title: SAAPPK


title: SAAPPI


title: 0.75h_PBS_2


title: 0.75h_IL2_1


title: 0.75h_PBS_3


title: 0.75h_PBS_1


title: SAAPPH


title: SAAPPC


title: SAAPNY


title: SAAPRX


title: SAAPKA


title: SAAPJB


title: SAAPJC


title: KYSE-30_ctrl_Ribo-seq

city: Guangzhou

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

country: China

institute: The First Affliliated Hospital, Sun Yat-sen University

description:
polyA RNA
esophageal epithelial
ctrl_Ribo-seq
mRNA_expression_for_ribo-seq.txt

data_processing:
Library strategy: Ribo-seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Fragments per kilo base per million mapped reads (FPKM) using edegR.
For Ribo-Seq data analysis, adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases, respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files

source_name: esophagus

growth_protocol: KYSE-30 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol:
KYSE-30 cells were transfected with shRNA for stable knockdown of METTL1. KYSE-30 cells with normal expression of METTL1 were used as control.
To immobilize initiating ribosomes, harringtonine was added to cell culture medium to a final concentration of 2 µg/ml. Cells were Incubated for 120 s with harringtonine in the incubator. Next, to block translational elongation, cycloheximide was added to cell culture medium to a final concentration of 100 µg/ml. Cells were mixed well and proceeded immediately to cell lysis.

value: esophageal squamous cell carcinoma cell line

tag: genotype

value: normal

value: harringtonine; cycloheximide

tag: sample type

value: Ribo-seq


title: KYSE-30_M1_KD_RNA-seq

description:
polyA RNA
esophageal epithelial
M1_KD_RNA-seq
mRNA_expression_for_ribo-seq.txt

treatment_protocol: KYSE-30 cells were transfected with shRNA for stable knockdown of METTL1. KYSE-30 cells with normal expression of METTL1 were used as control.


title: SAAPIV

value: metastatic colorectal cancer


title: SAAPJS

value: Male


title: KYSE-30_M1_KD_Ribo-seq

description:
polyA RNA
esophageal epithelial
M1_KD_Ribo-seq
mRNA_expression_for_ribo-seq.txt


title: SAAPMZ

value: White


title: SAAPIU


title: KYSE-30_ctrl_RNA-seq

description:
polyA RNA
esophageal epithelial
ctrl_RNA-seq
mRNA_expression_for_ribo-seq.txt


title: Patient 2 [scRNA-seq]

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Single-cell sequencing FASTQ files were processed using Kallisto (v0.46.0) and BUStools (v0.39.2) for sample demultiplexing, barcode processing, pseudo-alignment to human transcriptome (Ensembl release 96) and UMI counting. The unfiltered output of Kallisto and BUStools is provided for each sample (genes.barcodes.txt, genes.genes.txt and genes.mtx files)
Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes, based on the distribution observed across cells. Low-abundance genes were filtered out. After quality filtering, the resulting dataset consisted of 17,869 genes and 7,498 cells derived from patient 1, 905 cells from patient 2, and 550 cells from patient 3. The filtered UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the dropletUtils (version 1.5.4), scran (v1.14.5) and scatter (v1.14.5) Bioconductor packages, mostly following the steps of the simpleSingleCell  Bioconductor workflow (https://osca.bioconductor.org/).
Genome_build: hg38
Supplementary_files_format_and_content:
TSV file (tab separated values) with UMI counts for ensembl release 96 gene models (after filtering out genes with low average expression level); columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-Patient_X")
gene-barcode matrix (.mtx) output of bustools count in Matrix Market Exchange format (https://bustools.github.io/manual)
list of barcodes (*barcodes.txt) represented in the patient_7_genes.mtx file
list of genes (Ensembl IDs) represented in the patient_7_genes.mtx file

source_name: Basal-like cells from peripheral lung tissue of IPF patient

growth_protocol: For the culture of basal-like cells, lung tissue was cut into small pieces and placed into flasks containing DMEM with 10% FCS, 25 mM HEPES and 2 mM l-glutamine, 1× (vol/vol) MEM vitamin-mix, 100 U/l penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin B and maintained in a humified atmosphere of 5% CO2 at 37°C. After five days, tissue pieces were removed and cells were harvested for down-stream analysis.

extract_protocol:
Basal-like cells were grown in 2 batches (patient 1 on April 8th 2019, and patients 2 and 3 on May 27th 2019) for an expected recovery of 10,000 cells.
Cell suspensions from each patient were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed at the Genomics Facility Basel of the ETH Zurich, Basel, with a Single Cell 3’ v3 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: No treatment

tag: subject status

value: idiopathic pulmonary fibrosis (IPF) patient

value: female

value: mixed; Basal-like cells cultured from peripheral lung tissue


title: SAAPGH

value: Bevacizumab/Cetuximab


title: Pdzk1ip1-in vivo-3-ImmB-5TR

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and read counting performed using HT-seq to make count tables
BAM to bedgraph performed using bedtools bedgraph to bigwig performed using bedGraphToBigWig v4
FlipJump-seq reads were trimmed using cutadapt and mapped using bowtie2, all the BAM files were merged to find all the peaks on all files and count tables were made for each BAM files using BEDTools
For FlipJump: bowtie2 -x ${Ref_DIR} -1 ${R1} -2 ${R2} --end-to-end -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 -X 1000 | samtools view -Sb - > BAMs/${File_Name}.bam
For FlipJump: bedtools coverage -counts -b BAMtoBED.bed -a Peaks.bed > CounTable.bed
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw), count tables (.txt)

extract_protocol:
Bulk RNA-Seq: RNA from sorted cells was extracted using TRIzol Plus purification kit (ThermoFisher) and cDNA libraries were prepared with the Low input Clontech SMART-seq HT with Nxt HT.  Flip-Jump-Seq (MiSeq): Genomic DNA was extracted by NucleoSpin Tissue XS (Takara) (< 15,000 cells) or QIAamp Mini  kit (> 15,000 cells). Extracted DNA was further amplified with REPLI-g Mini Kit (Qiagen) for whole genome amplification (WGA).Three-arm LM-PCR-based method was optimized and adapted to clone FlipJump transposon integration sites from both 3TR and 5TR ends. Amplified DNA was quantified using Qubit 2.0 fluorometer (Thermo Fisher), and 1 ug was digested separately with MspI, HindIII or HaeIII for 5TR cloning, and MspI, DpnII or HaeIII for 3TR cloning. The digested DNA was purified using QIAquick PCR Purification Kit. To prepare the individual LM-PCR linker mix, the equal volume of 50 uM linker common (long strand)(5’ GACCCGGGAGATCTGAATTCAGTGGCACAGCAGTTAGGGGGCTGGTCG 3’) and 50 uM restriction enzyme (RE)-digested end-specific linker (Blunt end linker /5Phos/CGACCAGCCC/3AmMO/ for HaeIII or CG end linker /5Phos/CGCGACCAGCCC/3AmMO/ for MspI or GATC end linker/5Phos/GATCCGACCAGCCC/3AmMO/ for DpnII or AGCT end linker/5Phos/AGCTCGACCAGCCC/3AmMO/ for HindIII were mixed in a PCR tube. The linker mix was then denatured and annealed by heating it to 95° C for 5 mins and cooling slowly to room temperature. One third of purified digested DNA was ligated with the individual LM-PCR linker mix using PfuTurbo Hotstart DNA Polymerase (Agilent Technologies). The ligation reaction was then digested with EcoRV (internal RE site of PB at 5TR direction) or MluI (internal RE site of PB at 3TR direction) to remove any linker that has ligated onto the 5TR or 3TR end of DNA, respectively. The remaining DNA containing MspI, HindIII and HaeIII linkers were pooled for 5TR sampling and the remaining DNA containing MspI, DpnII and HaeIII were pooled for 3TR processing. The pooled DNA was set up for PCR amplification using linker primer 1 (5’ GACCCGGGAGATCTGAATTC3’) and TR-specific biotinylated primers (LM_5TR_inver_A2: /5Biosg/AGATAATCATGCGTCATTTTGACTCAC or LM_3TR_inverA: /5Biosg/TCGATATACAGACCGATAAAACACATG). Biotinylated PCR products were pulled down using Dynabeads kilobaseBINDER kit at room temperature for 4 hours. Further nested PCR amplification was conducted using a primer that was specific for 5TR (LM_5TR_inver_B2: AGCGGCGACTGAGATGTCC) or 3TR (LM_3TR_inverB: ATGCGTCAATTTTACGCATGATTATC), and a Miseq sequencing index primer (Supplementary Table 5) containing individual sample barcode. The PCR products were tagged with modified P5 and P7 primers for sequencing.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

tag: tissue

value: Bone marrow

value: Immature B cell


title: Patient 3 [scRNA-seq]

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Single-cell sequencing FASTQ files were processed using Kallisto (v0.46.0) and BUStools (v0.39.2) for sample demultiplexing, barcode processing, pseudo-alignment to human transcriptome (Ensembl release 96) and UMI counting. The unfiltered output of Kallisto and BUStools is provided for each sample (genes.barcodes.txt, genes.genes.txt and genes.mtx files)
Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes, based on the distribution observed across cells. Low-abundance genes were filtered out. After quality filtering, the resulting dataset consisted of 17,869 genes and 7,498 cells derived from patient 1, 905 cells from patient 2, and 550 cells from patient 3. The filtered UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the dropletUtils (version 1.5.4), scran (v1.14.5) and scatter (v1.14.5) Bioconductor packages, mostly following the steps of the simpleSingleCell  Bioconductor workflow (https://osca.bioconductor.org/).
Genome_build: hg38
Supplementary_files_format_and_content:
TSV file (tab separated values) with UMI counts for ensembl release 96 gene models (after filtering out genes with low average expression level); columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-Patient_X")
gene-barcode matrix (.mtx) output of bustools count in Matrix Market Exchange format (https://bustools.github.io/manual)
list of barcodes (*barcodes.txt) represented in the patient_8_genes.mtx file
list of genes (Ensembl IDs) represented in the patient_8_genes.mtx file

value: male

value: mixed; basal-like cells cultured from peripheral lung tissue


title: SAAPII

value: Female

value: Bevacizumab


title: Pdzk1ip1-in vivo-2-ImmB-5TR


title: Patient 1 [scRNA-seq]

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Single-cell sequencing FASTQ files were processed using Kallisto (v0.46.0) and BUStools (v0.39.2) for sample demultiplexing, barcode processing, pseudo-alignment to human transcriptome (Ensembl release 96) and UMI counting. The unfiltered output of Kallisto and BUStools is provided for each sample (genes.barcodes.txt, genes.genes.txt and genes.mtx files)
Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes, based on the distribution observed across cells. Low-abundance genes were filtered out. After quality filtering, the resulting dataset consisted of 17,869 genes and 7,498 cells derived from patient 1, 905 cells from patient 2, and 550 cells from patient 3. The filtered UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the dropletUtils (version 1.5.4), scran (v1.14.5) and scatter (v1.14.5) Bioconductor packages, mostly following the steps of the simpleSingleCell  Bioconductor workflow (https://osca.bioconductor.org/).
Genome_build: hg38
Supplementary_files_format_and_content:
TSV file (tab separated values) with UMI counts for ensembl release 96 gene models (after filtering out genes with low average expression level); columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-Patient_X")
gene-barcode matrix (.mtx) output of bustools count in Matrix Market Exchange format (https://bustools.github.io/manual)
list of barcodes (*barcodes.txt) represented in the patient_6_genes.mtx file
list of genes (Ensembl IDs) represented in the patient_6_genes.mtx file


title: SAAPIL


title: SAAPGF

value: Cetuximab


title: SAAPPF


title: SAAPFT


title: Pdzk1ip1-in vivo-3-ImmB-3TR


title: Pdzk1ip1-in vivo-2-ImmB-3TR


title: SAAPES


title: SAAPFC


title: Pdzk1ip1-in vivo-1-ImmB-3TR


title: SAAPEM


title: B6-in vitro-pDC-5TR

value: pDC


title: SAANZG


title: SAANYV


title: SAAPAJ


title: B6-in vitro-cDC 1-3TR


title: B6-in vitro-pDC-3TR


title: B6-in vitro-cDC 1-5TR


title: SAAPIM

value: More then one race


title: Pdzk1ip1-in vivo-1-ImmB-5TR


title: B6-BM-2-5TR

value: total cells


title: B6-in vitro-cDC 2-3TR


title: SAANRU

value: metastatic colorectal cancer


title: SAANSH


title: B6-BM-1-5TR


title: Pdzk1ip1-in vivo-3-pDC-5TR

value: Spleen


title: SAANSK

value: Male

value: Black or African American


title: SAANRL

value: White


title: SAANNE


title: SAANXP


title: Pdzk1ip1-in vivo-3-cDC2-5TR


title: Pdzk1ip1-in vivo-3-HSC-5TR

value: HSC


title: SAANMW


title: SAANMN


title: Pdzk1ip1-in vivo-3-cDC1-5TR


title: Pdzk1ip1-in vivo-2-pDC-5TR


title: SAANMJ


title: SAANMY


title: SAANXW

value: Bevacizumab/Cetuximab


title: Pdzk1ip1-in vivo-2-HSC-5TR

value: Bone marrow


title: Pdzk1ip1-in vivo-2-cDC2-5TR


title: SAANZS


title: B6-in vitro-cDC 2-5TR


title: SAANPN


title: SAANMC


title: SAANKE


title: SAANLY


title: Pdzk1ip1-in vivo-1-pDC-5TR


title: SAANJU


title: SAANJN


title: Pdzk1ip1-in vivo-1-HSC-5TR


title: SAANJL


title: Cx3cr1-in vivo-6-cDC2-5TR


title: SAANIS


title: SAANMB


title: Pdzk1ip1-in vivo-2-cDC1-5TR


title: Cx3cr1-in vivo-5-cDC2-5TR


title: Pdzk1ip1-in vivo-1-cDC2-5TR


title: SAANLT


title: SAANKD


title: Cx3cr1-in vivo-5-cDC1-5TR


title: Pdzk1ip1-in vivo-1-cDC1-5TR


title: Cx3cr1-in vivo-7-pDC-5TR


title: Cx3cr1-in vivo-4-pDC-5TR


title: Cx3cr1-in vivo-6-pDC-5TR


title: SAANEI


title: Cx3cr1-in vivo-7-cDC1-5TR


title: Cx3cr1-in vivo-4-cDC1-5TR


title: Cx3cr1-in vivo-6-cDC1-5TR


title: SAANJH


title: Cx3cr1-in vivo-5-pDC-5TR


title: PitNET27-24h

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

data_processing:
The FASTQ files from NGS were analysed using CLC Genomics Workbench (v20.0.4). During read trimming any reads with Q (Phred score) < 30 were discarded. Reads also underwent trimming by length and any reads that did not fall into 15 - 55 nt length category were discarded. Trimmed reads were aligned to miRBase (V22) with the following settings: additional upstream / downstream bases = 2, missing upstream / downstream bases = 2, maximum mismatches = 2, sequence length = 15 to 28, minimum supporting count = 1. The counts were compiled and exported into DESeq2 compatible counts matrix format.
miRNA differential expression analysis was done in DESeq2 (v1.30.1) in R (v 4.0.3).
Genome_build: miRBase V22 for miRNA annotation and counting
Supplementary_files_format_and_content: counts table

source_name: Plasma

extract_protocol:
Total RNA from plasma samples was extracted using exoRNeasy Midi kit (Qiagen, Germany) according to manufacturer's instructions. Total RNA from tumor tissue samples was extracted using AllPrep DNA/RNA/miRNA Universal kit (Qiagen Germany) according to manufacturer's instructions
miRNA-seq libraries were prepared using Lexogen Small RNA-seq Library prep Kit according to manufacturer's instructions

tag: pitnet type

value: NF PitNET

tag: sample/tissue

value: Plasma


title: SAANIK

tag: tumor type

tag: age


title: SAANHX

tag: Sex

tag: race


title: PitNET26-24h


title: PitNET24-24h


title: SAANEC

tag: treatment group


title: Cx3cr1-in vivo-3-cDC2-5TR


title: SAANFT


title: PitNET21-24h

value: GH secreting


title: Cx3cr1-in vivo-3-cDC1-5TR


title: Cx3cr1-in vivo-7-cDC2-5TR


title: SAANEK

value: Female


title: Cx3cr1-in vivo-4-cDC2-5TR


title: PitNET36-24h


title: Cx3cr1-in vivo-2-pDC-5TR


title: PitNET33-24h


title: PitNET34-24h


title: PitNET16-24h


title: Cx3cr1-in vivo-3-pDC-5TR


title: PitNET14-24h

value: PRL secreting


title: SAANBM

value: Cetuximab


title: PitNET13-24h


title: SAANEH

value: Unknown

value: Bevacizumab


title: SAAMZH


title: PitNET25-24h


title: SAANEG


title: PitNET22-24h


title: PitNET19-24h


title: PitNET8-24h

value: ACTH secreting


title: SAAMJN

value: metastatic colorectal cancer


title: PitNET18-24h


title: SAANCT


title: PitNET3-24h


title: Cx3cr1-in vivo-2-cDC2-5TR

value: Spleen


title: PitNET9-24h


title: B6-BM-2-3TR

value: total cells


title: PitNET7-24h


title: Cx3cr1-in vivo-1-cDC2-5TR


title: PitNET5-24h


title: SAAKZP

value: Male


title: PitNET33-x


title: SAAMGP

value: White


title: PitNET10-24h


title: 72h_PBS_3

tag: strain

value: regulatory T cells

tag: injected molecule

value: control PBS

tag: treatment

value: PBS-treaed-Treg


title: SAAKZI

value: Bevacizumab/Cetuximab


title: Pdzk1ip1-in vivo-3HSC-3TR

value: Bone marrow

tag: cell type

value: HSC


title: Cx3cr1-in vivo-1-cDC1-5TR


title: PitNET24-x

value: NF PitNET

value: Plasma


title: PitNET2-24h


title: SAAMGM

value: Female


title: PitNET1-24h


title: PitNET36-x

value: GH secreting


title: SAAKVJ

value: Bevacizumab


title: B6-BM-1-3TR


title: SAAMGL


title: PitNET34-x


title: Cx3cr1-in vivo-2-cDC1-5TR


title: Pdzk1ip1-in vivo-3-pDC-3TR

value: pDC


title: Pdzk1ip1-in vivo-3-cDC1-3TR


title: Cx3cr1-in vivo-1-pDC-5TR


title: SAAKVC

value: metastatic colorectal cancer

value: Black or African American


title: PitNET18-x

value: PRL secreting


title: SAAKUE


title: PitNET14-x


title: PitNET26-x


title: PitNET19-x


title: SAAKTZ

value: Male

value: Cetuximab


title: PitNET25-x


title: Pdzk1ip1-in vivo-2-pDC-3TR

value: Spleen


title: PitNET22-x


title: PitNET13-x


title: Pdzk1ip1-in vivo-2-HSC-3TR


title: PitNET21-x


title: Pdzk1ip1-in vivo-2-cDC2-3TR


title: PitNET27-x


title: Pdzk1ip1-in vivo-3-cDC2-3TR


title: PitNET16-x


title: PitNET8-x

value: ACTH secreting


title: SAAKTY

value: White


title: PitNET9-x


title: SAAKLY


title: PitNET7-x


title: Pdzk1ip1-in vivo-2-cDC1-3TR


title: PitNET5-x


title: PitNET3-x


title: Pdzk1ip1-in vivo-1-pDC-3TR


title: SAAKGR

value: Bevacizumab/Cetuximab


title: PitNET2-x


title: PitNET1-x


title: Pdzk1ip1-in vivo-1-HSC-3TR

value: Bone marrow


title: PitNET10-x


title: SAAKFW


title: Pdzk1ip1-in vivo-1-cDC2-3TR


title: SAAKFL


title: L_Sham_rep10_batchB

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to rat genome using STAR (Dobin et al., 2013)  v2.7.2b with default parameters based on RefSeq annotation version 106 for GCF_000001895.5/Rnor_6.0
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 106 for GCF_000001895.5/Rnor_6.0) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
Genome_build: GCF_000001895.5/Rnor_6.0 (primary assembly and mitochondrion)
Supplementary_files_format_and_content: Character (TAB) separated value file containing mRNA abundance measurements

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Livers were removed and frozen in Eppendorf tubes using liquid nitrogen immediately. Tissue was homogenized using QIAGEN Tissue Lyser II (85300; QIAGEN) and further purified using Proteinase K (PK) Solution (MC5005; Promega). Prior to extraction, RNA integrity and concentration were tested using NanoDrop™ 2000c spectrophotometer (Thermo Fisher Scientific). In the following step, mRNA was extracted using Promega’s “Maxwell SimplyRNA Tissue Kit” (AS1340).
RNA quality was checked using RNA 6000 Nano kits on a 2100 Bioanalyzer (Agilent Technologies). Afterwards, cDNA libraries were prepared from total RNA with oligo-dT capture beads for poly(A)-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions. After 15 cycles of PCR amplification, barcoded cDNA libraries were quantified via Qubit 2.0 Fluorometer using dsDNA HS Assay Kits (ThermoFisher). Quality and size distribution (average size: 290 bp) was checked with a 2100 Bioanalyzer using DNA 1000 kits (Agilent).

tag: group

value: Sham

value: Wistar rat

tag: batch

value: B

value: Liver


title: L_Sham_rep11_batchB


title: L_Sham_rep09_batchB


title: L_Sham_rep12_batchB


title: L_Sham_rep08_batchB


title: SAAHWN


title: L_Sham_rep07_batchA

value: A


title: SAAHLZ


title: Cx3cr1-in vivo-7-cDC2-3TR


title: Cx3cr1-in vivo-7-pDC-3TR


title: L_Sham_rep05_batchA


title: L_Sham_rep04_batchA


title: L_Sham_rep06_batchA


title: SAAHCH

value: Female


title: L_Sham_rep03_batchA


title: Cx3cr1-in vivo-7-cDC1-3TR


title: L_Sham_rep02_batchA


title: SAAKLS

value: Bevacizumab


title: SAAHBW

value: metastatic colorectal cancer

value: Asian


title: L_Sham_rep01_batchA


title: Cx3cr1-in vivo-6-pDC-3TR

value: pDC


title: Cx3cr1-in vivo-6-cDC2-3TR


title: L_Saline_rep09_batchB

value: Saline


title: L_Saline_rep08_batchB


title: L_Saline_rep06_batchB


title: Cx3cr1-in vivo-6-cDC1-3TR


title: L_Saline_rep04_batchA


title: L_Saline_rep07_batchB


title: SAAGMX

value: Male

value: Cetuximab


title: Cx3cr1-in vivo-5-pDC-3TR

value: Spleen


title: Pdzk1ip1-in vivo-1-cDC1-3TR


title: L_Saline_rep02_batchA


title: L_PYY_rep05_batchB

value: PYY


title: SAAGRU

value: Black or African American

value: Bevacizumab/Cetuximab


title: Cx3cr1-in vivo-5-cDC1-3TR


title: L_Saline_rep03_batchA


title: SAAFWB

value: White


title: L_Saline_rep05_batchB

value: Wistar rat


title: SAAGLZ


title: Cx3cr1-in vivo-4-pDC-3TR


title: SAAHAB


title: Cx3cr1-in vivo-5-cDC2-3TR


title: L_PYY_rep03_batchB

value: B


title: L_PYY_Lira_rep11_batchB

value: Liver


title: L_PYY_rep04_batchB


title: L_PYY_rep01_batchB


title: L_PYY_rep02_batchB


title: SAAFPG


title: SAAFPV


title: Cx3cr1-in vivo-4-cDC2-3TR


title: L_PYY_Lira_rep10_batchB


title: SAAFLW

value: American Indian or Alaska Native


title: SAAGJE


title: L_PYY_Lira_rep07_batchB


title: L_PYY_Lira_rep08_batchB


title: L_PYY_Lira_rep06_batchA

value: A


title: L_PYY_Lira_rep09_batchB


title: L_PYY_Lira_rep05_batchA


title: Cx3cr1-in vivo-3-pDC-3TR


title: SAAFDH

value: Female


title: Cx3cr1-in vivo-3-cDC2-3TR


title: Cx3cr1-in vivo-3-cDC1-3TR


title: SAAETU

value: metastatic colorectal cancer


title: L_PYY_Lira_rep03_batchA


title: L_Lira_rep05_batchB

value: Lira


title: L_Lira_rep04_batchB


title: L_PYY_Lira_rep02_batchA


title: L_PYY_Lira_rep01_batchA


title: Cx3cr1-in vivo-4-cDC1-3TR


title: SAAFCC


title: SAAEMY

value: Bevacizumab


title: L_Lira_rep03_batchB


title: L_Lira_rep02_batchB


title: Cx3cr1-in vivo-2-cDC2-3TR


title: Cx3cr1-in vivo-2-cDC1-3TR


title: L_Lean_rep06_batchA

value: Lean


title: L_Lira_rep01_batchB


title: SAAELU

value: Male


title: L_Lean_rep05_batchA


title: SAAELS


title: L_PYY_Lira_rep04_batchA


title: Cx3cr1-in vivo-1-pDC-3TR

value: pDC


title: L_Lean_rep02_batchA


title: L_Lean_rep03_batchA


title: Cx3cr1-in vivo-1-cDC2-3TR

value: Spleen


title: SAAEPR


title: SAAEKL


title: SAAELG

value: Cetuximab


title: L_Bypass_rep14_batchB

value: Bypass


title: Cx3cr1-in vivo-2-pDC-3TR


title: L_Bypass_rep13_batchB


title: Cx3cr1-in vitro-3-pDC-5TR


title: SAAEKD


title: L_Bypass_rep12_batchB


title: L_Bypass_rep11_batchA


title: SAAEIW

value: Bevacizumab/Cetuximab


title: L_Bypass_rep10_batchA


title: Cx3cr1-in vitro-3-pDC-3TR


title: Cx3cr1-in vitro-3-cDC1-5TR


title: SAAEIT

value: White


title: L_Bypass_rep09_batchA

value: Wistar rat


title: L_Bypass_rep07_batchA


title: SAAEIR


title: L_Lean_rep04_batchA


title: L_Bypass_rep08_batchA


title: Cx3cr1-in vivo-1-cDC1-3TR


title: L_Lean_rep01_batchA


title: L_Bypass_rep05_batchA


title: L_Bypass_rep04_batchA


title: Cx3cr1-in vitro-3-cDC2-3TR


title: L_Bypass_rep03_batchA


title: SAAEIA


title: SAAEID


title: L_Bypass_rep06_batchA


title: L_Bypass_rep01_batchA


title: Cx3cr1-in vitro-2-pDC-5TR


title: L_Bypass_rep02_batchA


title: L_BWM_rep08_batchA

value: BWM


title: L_BWM_rep07_batchA

value: Liver


title: SAAEGX


title: SAAEFT

value: Asian


title: Cx3cr1-in vitro-3-cDC1-3TR


title: Cx3cr1-in vitro-2-pDC-3TR


title: L_BWM_rep06_batchA

value: A


title: L_BWM_rep05_batchA


title: Cx3cr1-in vitro-2-cDC1-5TR


title: L_BWM_rep03_batchA


title: Cx3cr1-in vitro-2-cDC1-3TR


title: Cx3cr1-in vitro-3-cDC2-5TR


title: Cx3cr1-in vitro-2-cDC2-5TR


title: SAAEFA


title: SAAEFB


title: L_BWM_rep02_batchA


title: L_BWM_rep04_batchA


title: SAADTK

value: Unknown


title: Cx3cr1-in viitro-2-cDC2-3TR


title: MM468_DMSO3_D147

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

data_processing:
Library strategy: WES
The WES sequencing files were mapped using bwa-mem to the human genome (hg19)
Reads falling in the targeted regions were then filtered based on their mapping quality and PCR duplicates were removed
Local Indel Realignment and Base Score Recalibration was applied to deduplicated reads using GATK
Somatic variants were called with Mutect2 using early passage 16 (initial population) as constitutional sample
Genome_build: hg19
Supplementary_files_format_and_content: BigWig binary file of coverage and compared coverage

source_name: MDA-MB-468 cell line

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). HCC38 cell lines were cultured in RPMI 1640 (Gibco-BRL, Ref: 11875085), supplemented with 10% heat-inactivated fetal calf serum.

extract_protocol:
Samples were extracted with NucleoSpin Tissue, Mini kit for DNA from cells and tissue (Macherey Nagel, Ref: 740952.50) and sequenced on a NovaSeq 6000 (Illumina) with a 100X depth.
Sureselect Agilent XT2

treatment_protocol: All cell lines were cultured in a humidified 5% CO2 atmosphere at 37 °C, and were tested as mycoplasma negative. Cells were treated with 5 ?M of 5-FU (Sigma, Ref: F6627).

value: DMSO

tag: day


title: SAADBE

value: metastatic colorectal cancer


title: MM468_DMSO6_D131


title: Cx3cr1-in vitro-1-pDC-5TR


title: Cx3cr1-in vitro-1-pDC-3TR


title: MM468_5FU2_D153


title: SAACYN

value: Not Reported

value: Bevacizumab


title: SAACYX

value: Female


title: MM468_5FU2_D67


title: MMA468_DMSO5_D171


title: MM468_5FU6_D131


title: Cx3cr1-in vitro-1-cDC1-5TR


title: MM468_5FU3_D50


title: MM468_5FU3_D147


title: SAACXT

value: Male


title: MM468_initial_population


title: L_BWM_rep01_batchA


title: SAACXP


title: SAACWM


title: PC3

city: New York

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and then aligned to human assembly hg19 with STAR v2.6 using default parameters to generate BAM alignment files.
Normalized using counts(dds, normalized=T) from DESeq2, then logged
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: comma delimited text file containing log normalized counts of genes

source_name: prostate cancer cell line

growth_protocol:
Prostate cancer organoids were maintained in human organoid media as described previously (PMID: 25201529, 26797458).
PDX: 8 week old NSG mice (Jackson labs) were implanted s.c. on the flank with patient tumor fragments mixed with matrigel (Corning) in 1:1 ratio. Mice were then monitored once/weekly for tumor growth.
All cell lines except for H660 were maintained in RPMI supplemented with 10% Fetal bovine serum and 1% pen/strep. H660 was grown in RPMI-1640 with 0.005mg/mL insulin, 0.01 mg/mL transferrin, 30nM sodium selenite, 10nM hydrocortisone, 10nM B-estradiol, 2mL L-glutamine, 5% FBS and 1% pen/strep.

extract_protocol:
prostate cancer organoid and cell line: RNA extraction was performed according to manufacture's instuction using RNeasy Plus Mini Kit (Qiagen #74134)
PDX: Tissue was coarsely pulverized on dry ice, and RNA extraction was performed per tissue protocol using the RNeasy Plus Mini Kit (Qiagen 74134).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA kit, with 8 cycles of PCR amplification, starting from 500 ng of total RNA, at the Integrative Genomics Operation (IGO) at MSKCC

tag: primary site

value: Prostate

tag: biopsy site

value: bone


title: PDX34a

source_name: prostate cancer PDX

value: Circulating tumor cells


title: SAACVW


title: PDX16a

value: femur left


title: Cx3cr1-in vitro-1-cDC2-3TR

tag: genotype/variation

tag: tissue

value: Spleen


title: Cx3cr1-in vitro-1-cDC1-3TR


title: PDX16b

value: ilium right


title: Cx3cr1-in vitro-1-cDC2-5TR


title: PDX10a

value: Brain


title: 4113-7

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

data_processing:
Reads were trimmed for quality and adapters using Cutadapt (v1.16).
These quality trimmed reads were later mapped against the Ensembl human reference genome (GRCh38) using Hisat2 mapper (v2.0.4).
Counts for genes were generated using HT-Seq (v0.9.1) on the mapped files. edgeR (v3.22.3), a bioconductor R (v3.5.0) package was used to differentially expressed genes.
Genome_build: GRCh38

source_name: PBMC

extract_protocol:
PBMCs were isolated from serum drawn into CPT™ mononuclear cell preparation tubes with sodium citrate additive (BD 362761) following the manufacturer’s protocol. After isolation, PBMCs were lysed in RLT buffer (Qiagen) and stored at -80° C for RNA isolation using RNeasy kit (Qiagen). Total RNA from PBMCs was isolated from collections at Days 0, 3 and 7 post-vaccination; ribosomal RNA was depleted (Ribo-zero Gold) and sequenced using the Illumina TruSeq platform.
Reads per sample were collected and mapped to the Human Ensembl reference genome GRCh38 using the fast alignment tool HISAT2 v2.1.0.

treatment_protocol: All participants received an intramuscular injection of either the high dose or standard dose seasonal 2017-2018 inactivated influenza vaccine. The trivalent high dose vaccine contained the A/H1N1/Michigan/45/2015-pdm09-like virus, A/H3N2/Hong Kong/4801/2014-like virus and B/Brisbane/60/2008-like influenza virus. The quadrivalent standard dose vaccine also contained the B/Phuket/3073/2013-like virus.

tag: sample timing

value: 7 days post-vaccination

tag: frailty status

value: non-frail


title: 0107-7

tag: age


title: WCM1262

source_name: prostate cancer organoid

value: soft tissue


title: 0316-7


title: SAACVD

tag: tumor type

tag: Sex

value: White


title: SAACRR

tag: race

tag: treatment group


title: BPDCN5_TREKseq

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

description: BPDCN sample 5 had very few T-cells, so while we performed the procedure (and generated raw data), there weren’t enough cells to proceed with the processing pipeline WARPT, and therefore there is no processed file.

data_processing:
Library strategy: TREK-seq
Demultiplexing  and FASTQ generation using CellRanger version 5.0.0
Generate single-cell expression matrix using CellRanger version 5.0.0
Ambient RNA removal using SoupX version 1.5.2
Quality control and filtering using R 4.1.0
Normalization using Seurat 4.0.2
Control samples: Clustering and Integration using Seurat 4.0.2
BPDCN samples: Classification using cellHarmony in AltAnalyze 2.0
TREK-seq: Demultiplexing with bcl2fastq version 2.20.0
TREK-seq: TCR sequence extraction and scRNAseq pairing using WARPT
R1 — UMI and barcode
I1 — T-cell receptor sequence
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrices (scRNAseq), metadata (scRNAseq), WARPT output (TREK-seq)

molecule: polyA RNA

source_name: Bone marrow hematopoietic cells

extract_protocol:
mRNA was extracted by 10x 3' sequencing technology
10x 3' v3 or v3.1 single-cell RNA-sequencing library construction methods were utilized for mRNA libraries. TREK-seq was used to enrich and sequence T-cell receptors.

tag: technology

value: TREK-seq

tag: disease state

value: BPDCN


title: PDX09a

value: Pleural Fluid


title: 4163-7

value: frail


title: 4110-7


title: WCM1078

value: lymph node


title: SAACVU

value: metastatic colorectal cancer

value: Male

value: Bevacizumab


title: PDX01a

value: Prostate


title: BPDCN3_TREKseq


title: 4026-7


title: BPDCN4_TREKseq


title: BPDCN2_TREKseq


title: MM468_5FU5_D171

tag: treatment


title: SAACNN

value: Bevacizumab/Cetuximab


title: SAACJP

value: Female

value: Cetuximab


title: BM4_TREKseq

value: control


title: BM3_TREKseq


title: 4108-7

value: 7 days post-vaccination


title: BPDCN1_TREKseq


title: BM5_TREKseq


title: SAACUK


title: WCM154

value: sternum


title: WCM155

value: liver


title: BM2_TREKseq


title: 0147-7


title: 1235-7

value: non-frail


title: SAACDL

value: White


title: BPDCN5-3_10x_scRNAseq

description:
BPDCN5_10x_scRNAseq_Expression.txt
BPDCN5_10x_scRNAseq_MetaData.txt

data_processing:
Demultiplexing  and FASTQ generation using CellRanger version 5.0.0
Generate single-cell expression matrix using CellRanger version 5.0.0
Ambient RNA removal using SoupX version 1.5.2
Quality control and filtering using R 4.1.0
Normalization using Seurat 4.0.2
Control samples: Clustering and Integration using Seurat 4.0.2
BPDCN samples: Classification using cellHarmony in AltAnalyze 2.0
TREK-seq: Demultiplexing with bcl2fastq version 2.20.0
TREK-seq: TCR sequence extraction and scRNAseq pairing using WARPT
R1 — UMI and barcode
I1 — T-cell receptor sequence
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrices (scRNAseq), metadata (scRNAseq), WARPT output (TREK-seq)

value: 10x 3' v3.1 scRNA-seq

value: BPDCN


title: shM1_RPTOR_3_RNC

description:
RPTOR-rescued polyribosome-bound-RNA-seq
gene_expression_for RPTOR-rescued_polyribosome_bound_mRNA_sequencing.txt

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Genome_build: hg19,hg38
Supplementary_files_format_and_content: fpkm, tpm, readcount

growth_protocol: KYSE-30 and KYSE-150 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: KYSE-30 and KYSE-150 cells were  transfected with shRNA for stable knockdown of METTL1. KYSE-30 or KYSE-150 cells with normal expression of METTL1 were used as control. For RPTOR-rescued polyribosome-bound-RNA-seq, the METTL1-depleted KYSE150 cells were transfected with RPTOR-expressed plasmid.

tag: cell type

value: esophageal epithelial

value: The polyribosome-bound-mRNAs were isolated from total RNA by ultra-centrifugation

tag: genotype

value: METTL6-knockdown;RPTOR overexpression


title: BPDCN5-2_10x_scRNAseq


title: shM1_RPTOR_3_input

value: METTL5-knockdown;RPTOR overexpression


title: 0104-7


title: BPDCN5-1_10x_scRNAseq


title: SAABWS

data_processing:
RNA-seq reads were aligned to ribosomal RNA sequences to remove ribosomal reads
Remaining reads were aligned to the human reference genome using GSNAP4,5 version '2013-10-10' allowing maximum of two mismatches per 75 base sequence
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated in a strand-specific manner using the functionality provided by the R package GenomicAlignments13
Genome_build: NCBI Build 38
Supplementary_files_format_and_content: CALGB 80405 RNAseq Processed data.csv - gene read counts

value: metastatic colorectal cancer

value: Bevacizumab


title: BM1_TREKseq

value: TREK-seq


title: 3414-7


title: SAABZB

value: Male


title: BPDCN4-3_10x_scRNAseq

description:
BPDCN4_10x_scRNAseq_Expression.txt
BPDCN4_10x_scRNAseq_MetaData.txt


title: 4149-7

value: frail


title: shM1_RPTOR_2_RNC

value: METTL4-knockdown;RPTOR overexpression


title: 1116-7

value: 7 days post-vaccination


title: SAACKS


title: SAABPT

value: American Indian or Alaska Native

value: Cetuximab


title: 4050-7


title: BPDCN4-1_10x_scRNAseq


title: BPDCN4-2_10x_scRNAseq


title: SAABPK


title: shM1_RPTOR_1_RNC

value: METTL2-knockdown;RPTOR overexpression


title: shM1_RPTOR_1_input

value: METTL1-knockdown;RPTOR overexpression


title: SAABZC

value: White


title: 1130-7


title: 0258-7

value: non-frail


title: BPDCN3-2_10x_scRNAseq

description:
BPDCN3_10x_scRNAseq_Expression.txt
BPDCN3_10x_scRNAseq_MetaData.txt

value: 10x 3' v3.1 scRNA-seq

value: BPDCN


title: shM1_3_RNC

value: esophageal epithelial

value: The polyribosome-bound-mRNAs were isolated from total RNA by ultra-centrifugation


title: SAABNE

value: metastatic colorectal cancer


title: 4153-7


title: 4162-7


title: SAABNG

value: Female

value: Bevacizumab


title: shM1_3_input


title: SAABND


title: shM1_RPTOR_2_input

value: METTL3-knockdown;RPTOR overexpression


title: BPDCN2-2_10x_scRNAseq

description:
BPDCN2_10x_scRNAseq_Expression.txt
BPDCN2_10x_scRNAseq_MetaData.txt


title: shM1_2_RNC


title: shM1_2_input


title: BPDCN2-1_10x_scRNAseq


title: SAABMZ


title: 0225-7


title: SAABMW


title: SAABPR

value: Male


title: 4007-7


title: BPDCN1-1_10x_scRNAseq

description:
BPDCN1_10x_scRNAseq_Expression.txt
BPDCN1_10x_scRNAseq_MetaData.txt


title: SAABLZ


title: 0226-7

value: frail


title: shM1_1_RNC


title: BPDCN3-1_10x_scRNAseq


title: SAABLP

value: Black or African American


title: BM5-2_10x_scRNAseq

description:
BM5_10x_scRNAseq_Expression.txt
BM5_10x_scRNAseq_MetaData.txt

value: control


title: shGFP_3_RNC

value: normal


title: SAABKS


title: shM1_1_input


title: BM5-1_10x_scRNAseq


title: shGFP_3_input


title: 0148-7

value: 7 days post-vaccination


title: 0029-7


title: BM4-3_10x_scRNAseq

description:
BM4_10x_scRNAseq_Expression.txt
BM4_10x_scRNAseq_MetaData.txt


title: 4025-7


title: BPDCN1-2_10x_scRNAseq


title: SAABFT


title: BM4-2_10x_scRNAseq


title: SAABDD


title: shGFP_2_input


title: SAABDC


title: 4053-7


title: BM4-1_10x_scRNAseq


title: SAABDB


title: 1135-7


title: shGFP_1_input


title: SAABBJ


title: SAABBH

value: Cetuximab


title: KYSE-30_M1_KD_input

description:
polyA RNA
esophageal epithelial
M1_KD_input
mRNA_expression_for_polyribosome-bound-mRNA-seq.txt

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Fragments per kilo base per million mapped reads (FPKM) using edegR.
For Ribo-Seq data analysis, adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases, respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files

tag: cell line

value: esophageal squamous cell carcinoma cell line

tag: sample type

value: Polyribosome-bound-RNA-seq


title: SAABAZ

value: White


title: 4113-3

value: 3 days post-vaccination

value: non-frail


title: 4115-7


title: 1125-7


title: 0316-3


title: 0107-3


title: KYSE-30_ctrl_input

description:
polyA RNA
esophageal epithelial
ctrl_input
mRNA_expression_for_polyribosome-bound-mRNA-seq.txt


title: SAAAYX


title: KYSE-30_ctrl_rnc

description:
polyA RNA
esophageal epithelial
ctrl_polyribosome-bound-mRNA
mRNA_expression_for_polyribosome-bound-mRNA-seq.txt

treatment_protocol:
KYSE-30 cells were transfected with shRNA for stable knockdown of METTL1. KYSE-30 cells with normal expression of METTL1 were used as control.
The polyribosome-bound-mRNAs were isolated from total RNA by ultra-centrifugation.

value: polyribosome-bound-mRNAs isolated


title: SAAAYU

value: metastatic colorectal cancer


title: shGFP_2_RNC

value: esophageal epithelial

value: The polyribosome-bound-mRNAs were isolated from total RNA by ultra-centrifugation


title: SAAAYT

value: Bevacizumab


title: 4110-3


title: SAAAYC

value: Male


title: 4163-3

value: frail


title: shGFP_1_RNC


title: 3414-3


title: SAAAXA

value: Female


title: KYSE-30_M1_KD_rnc

description:
polyA RNA
esophageal epithelial
M1_KD_polyribosome-bound-mRNA
mRNA_expression_for_polyribosome-bound-mRNA-seq.txt


title: SAAAUS


title: 4108-3


title: SAAAUR


title: LPS_72h_1

city: Beijing

first: Fuliang

last: Zong

address: Feitai region Dongda road

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%.
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set， then expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung tissue cells

extract_protocol:
extracted from lung tissue using Trizol
mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads, mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction  a certain period in proper temperture. First-strand cDNA was generated using random hexamer-primed reverse transcription,  followed by a second-strand cDNA synthesis.

value: lung

tag: strain

value: BALB/c

tag: time point

value: LPS


title: 1235-3


title: LPS_48h_4

tag: tissue


title: LPS_72h_3


title: LPS_72h_2


title: 0147-3

tag: sample timing


title: LPS_48h_3


title: LPS_48h_2


title: LPS_72h_4


title: SAAAKR


title: LPS_48h_1


title: SAAAME

value: Cetuximab


title: SAAAUD


title: SAAAKP

value: Black or African American


title: 0104-3

tag: frailty status


title: 4050-3

tag: age


title: SAAAGV

tag: tumor type


title: 1116-3


title: LPS_24h_4


title: LPS_24h_3


title: 4026-3


title: 4149-3


title: LPS_24h_2


title: SAAAFV

tag: Sex


title: SAAAGP

tag: race


title: 1130-3


title: 0258-3


title: LPS_24h_1


title: LPS_12h_4


title: 4153-3


title: LPS_12h_3


title: LPS_12h_2


title: 4162-3


title: 4007-3


title: LPS_12h_1


title: U87MG-Gami 5uM-72h-2

city: Durham

first: Gao

last: Zhang

state: NC

address: 203 Research Dr | MSRB1, Rm 179

department: The Preston Robert Tisch Brain Tumor Center

institute: Duke University School of Medicine

data_processing:
Quality control using fastqc version 0.11.5
Sequenced reads were trimmed for adaptor sequence using Trim Galore version 0.6.5 with command: trim_galore --illumina --paired --fastqc --clip_R1 15 --clip_R2 15 --three_prime_clip_R1 5 --three_prime_clip_R2 5 R1.fq.gz R2.fq.gz
Mapped to GRCh38 whole genome using STAR2.7.6a with default parameters
Count how many reads map to each gene using featureCount-2.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: A172 or U87MG cells are cultured with DMEM and 10% Fetal Bovine Serum

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A172 or U87MG cells are treated with 5uM Gamitrinib or DMSO for 72h

value: Patient-derived cell line

value: treatment


title: U87MG-Ctrl-72h-2

value: untreatment


title: LPS_6h_4


title: U87MG-Ctrl-72h-1


title: U87MG-Gami 5uM-72h-1


title: LPS_6h_3


title: LPS_6h_2


title: 0226-3

value: 3 days post-vaccination


title: LPS_6h_1


title: A172-Ctrl-72h-2


title: 4025-3


title: A172-Gami 5uM-72h-2


title: SEB_LPS_72h_4

value: SEB and LPS


title: A172-Ctrl-72h-1


title: 1135-3

value: non-frail


title: SAAAEL

value: metastatic colorectal cancer

value: White

tag: treatment group


title: SEB_LPS_72h_2


title: SEB_LPS_72h_3


title: 4053-3


title: DY-LN229-Gami 5uM-48h-2

data_processing:
Quality control using fastqc version 0.11.5
Sequenced reads were trimmed for adaptor sequence using Trim Galore version 0.6.5
Mapped to GRCh38 whole genome using STAR2.7.6a with parameters --runThreadN 6 --sjdbOverhang 149
Count how many reads map to each gene using htseq-count version 0.12.4
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: M059K or LN229 cells are cultured with DMEM and 10% Fetal Bovine Serum

treatment_protocol: M059K or LN229 cells are treated with 5uM 6-thio-dG or DMSO for 72h

value: Gami 5uM-48h


title: 4115-3


title: DY-LN229-Ctrl-48h-2

value: untreated


title: 0148-3


title: 1125-3


title: SEB_LPS_48h_4


title: DY-LN229-Gami 5uM-48h-1


title: 0029-3

value: frail


title: SEB_LPS_48h_3


title: DY-LN229-Ctrl-48h-1


title: BPH, 10X Chromium platform, v3.1 [052100_1652-all-cells_CSP]

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

description:
052100_1652-all-cells
052100_1652_CSP_S5

data_processing:
FastQC v.0.11.3 was used to observe read quality
Cellranger v.3.0.0 was used to do initial quality control, alignment, and counting
Seurat was used to normalize, cluster, identify marker genes and perform DE analysis.
Genome_build: Ensembl Genome Reference Consortium Human Build 38 (GRCh38.p3)
Supplementary_files_format_and_content: raw measurements for 10x Genomics data (filtered to contain only detected cellular barcodes)

source_name: whole cell

extract_protocol:
Human BPH tissue was minced and then digested in 1000 U/mL Collagenase I + 1 mg/mL DNAse in HBSS while shaking at 37 degrees C for 4 hours. Digested samples were further incubated with TrypLE Express for 5 min while shaking at 37 degrees C. Samples were washed, red blood cells lysed, and debris removal completed with Miltenyi kit prior to loading onto the 10X Chromium.
Libraries were prepared following the protocol for mRNA sequencing (10x Chromium), v3.0 or v3.1.
RNA sequencing on an Illumina NovaSeq 6000 next generation sequencer

tag: tissue id

value: antibody derived tag

value: all BPH associated cells


title: DY-M059K-Gami 5uM-48h-2


title: 4113-0

value: pre-vaccination


title: BPH, 10X Chromium platform, v3.1 [047563_1562-all-cells_cDNA]

description:
047563_1562-all-cells
047563_1562_cDNA_S2

value: mRNA from whole cell


title: SEB_LPS_72h_1

value: lung

value: BALB/c


title: 0316-0


title: DY-M059K-Gami 5uM-48h-1

value: Patient-derived cell line


title: BPH, 10X Chromium platform, v3.1 [052097_1595-all-cells_cDNA]

description:
052097_1595-all-cells
052097_1595_cDNA_S9


title: 0107-0


title: A172-Gami 5uM-72h-1

value: treatment


title: BPH, 10X Chromium platform, v3.1 [052098_1595-all-cells_CSP]

description:
052098_1595-all-cells
052098_1595_CSP_S4


title: 4163-0


title: BPH, 10X Chromium platform, v3.1 [052096_1628-all-cells_CSP]

description:
052096_1628-all-cells
052096_1628_CSP_S3


title: DY-M059K-Ctrl-48h-2


title: SEB_LPS_48h_1


title: SEB_LPS_48h_2


title: BPH, 10X Chromium platform, v3.1 [052095_1628-all-cells_cDNA]

description:
052095_1628-all-cells
052095_1628_cDNA_S8


title: 4110-0


title: BPH, 10X Chromium platform, v3.1 [052099_1652-all-cells_cDNA]

description:
052099_1652-all-cells
052099_1652_cDNA_S10


title: SEB_LPS_24h_3


title: DY-M059K-Ctrl-48h-1


title: SEB_LPS_24h_2


title: SEB_LPS_24h_4


title: Chordoma associated with tuberous sclerosis complex (TSC) patient

type: genomic

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

hyb_protocol: Hybridization was performed using OncoScan™ CNV Assay Array Kit according to the manufacturer's protocol.

scan_protocol: GeneChip was scanned using the GeneChip™ Scanner 3000 7G.

data_processing: Computational analysis of the microarray data files was performed using Chromosome Analysis Suite software.

label: biotin

source_name: FFPE tumor tissues of chordoma

label_protocol: As per manufacturer for OncoScan™ CNV Assay

extract_protocol: DNA was extracted from FFPE tumor tissues of chordoma from one patient with tuberous sclerosis complex by using GeneRead DNA FFPE kit (Qiagen, cat. № 180134).

value: Male

value: 1 yr


title: BPH, 10X Chromium platform, v3.0 [048752_1579-all-cells_cDNA]

description:
048752_1579-all-cells
048752_1579_cDNA_S5


title: BPH, 10X Chromium platform, v3.0 [048753_1579-all-cells_CSP]

description:
048753_1579-all-cells
048753_1579_CSP_S6


title: 3414-0


title: 4026-0


title: C10_I72_2

first: Kyungku

last: Jang

address: 430 East 29th Street

department: Microbiology

institute: New York University

data_processing:
RNA-seq results were processed using the R package “DESeq2” to obtain variance stabilized count reads, fold changes relative to specific condition, and statistical P-value
Genome_build: NCBI36

source_name: Colonic monolayers

growth_protocol: To generate monolayers, mature human small intestinal colonic organoids grown with the expansion media were digested into single cells using TrypLE Express (ThermoFisher) and seeded into Matrigel-coated 96-well culture plate (Corning) in Y-27632-supplemented expansion medium at 150,000 cells/well for the first 2 days. The culture media were changed every day.

extract_protocol:
Total RNA were extracted using RNeasy mini kti (Qiagen)
CEL-seq2 libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The organoid monolayers grown with the differentiation media for 7 days were infected with icSARS-CoV-2-mNG at a MOI of 4 for 1 hr at 37°C. Following incubation, organoids were washed 4 times with phosphate buffered saline (PBS) and differentiation media was added for the indicated time.

tag: organoid line

tag: primary tissues

value: Non-inflamed ascending colon

tag: disease status

value: Ulcerative colitis

tag: culture condition

value: Differentiated colonic monolayers

tag: infection status

value: Infected

tag: time post infection (h)


title: SEB_LPS_24h_1

tag: strain

tag: treatment

value: SEB and LPS


title: 4108-0

value: non-frail


title: C10_I72_1


title: 1235-0


title: SEB_LPS_12h_3

tag: tissue

tag: time point


title: SEB_LPS_12h_2


title: 0147-0

tag: sample timing

tag: frailty status

value: frail


title: SEB_LPS_12h_4


title: C10_UI72_2

value: Uninfected


title: C10_UI72_1


title: 0104-0

tag: age


title: 4149-0


title: C10_I24_2


title: SEB_LPS_6h_3


title: SEB_LPS_6h_4


title: 4050-0


title: 1116-0


title: Pancreatic cancer xenograft [Taco-7]

type: RNA

city: Tokyo

first: Masayuki

last: Komatsu

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression data of pancreatic tumor

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring version 12.6 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

source_name: Pancreatic cancer

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: Cell lines were maintained in RPMI1640 medium supplemented with 10% FCS (Biowest, Riverside, MO, USA), 100 IU/mL penicillin G sodium, and 100 μg/mL streptomycin sulfate in 5% CO2/95% air, at 37°C.

extract_protocol: Both cultured cells and xenografted tumors was resuspended by ISOGEN solution. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: RNAs of the samples were isolated using an ISOGEN lysis buffer (Nippon Gene, Toyama, Japan) followed by precipitation with isopropanol.

tag: sample type

value: xenografted tumor


title: SEB_LPS_6h_2


title: C10_I24_1


title: C10_UI0_1


title: Pancreatic cancer xenograft [Taco-23]


title: Pancreatic cancer xenograft [Taco-6]


title: SEB_LPS_6h_1


title: 1130-0

value: pre-vaccination


title: SEB_LPS_12h_1


title: 0258-0


title: 4153-0


title: CTRL_4

value: untreated


title: C9_I72_1


title: C9_UI72_2


title: Pancreatic cancer xenograft-SC [Taco-16-SC]


title: Pancreatic cancer xenograft [Taco-5]


title: 4162-0


title: Pancreatic cancer xenograft [Taco-22]


title: C9_UI72_1


title: Pancreatic cancer xenograft-OR [Taco-16-OR]


title: Pancreatic cancer xenograft [Taco-4]


title: Pancreatic cancer xenograft [Taco-15]


title: C10_UI0_2


title: 4007-0


title: Pancreatic cancer xenograft [Taco-2]


title: C9_I24_2


title: 0225-0


title: C9_I72_2


title: Pancreatic cancer xenograft [Taco-21]


title: CTRL_1

value: lung


title: C9_I24_1


title: CTRL_3

value: BALB/c


title: Pancreatic cancer xenograft [Taco-13]


title: C9_UI0_2


title: Dnmt3a KO naïve

city: Houston

first: Katherine

middle: Yudeh

last: King

state: Texas

address: 1102 Bates Ave., Ste.1150

department: Pediatrics and Infectious diseases

institute: Baylor College of Medicine

data_processing:
Quality control was conducted using FastQC and CGmapTools
Adaptor and quality trimmed reads, processed using trim_galore, were aligned to GRCm38 reference genome using Bismark ver. 0.22.3
Duplicate reads were removed using MarkDuplicates from the Picard tool set
Raw methylation calls were extracted from pre-processed reads using bismark_methylation_extractor and converted to CGmap format using bismark2cgmap
Differentially methylated regions (DMRs) were identified with CGmapTools (ver. 0.1.2), using all CG sites with a minimum of 4x and maximum of 100x coverage. Benjamini & Hochberg correction for multiple testing was used in all tests.
Genome_build: GRCm38
Supplementary_files_format_and_content: CGmap file provides sequence context and estimated DNA methylation level of any covered cytosines on the reference genome; DMR positions - contains genomic coordinates of differentially methylated regions

source_name: Hematopoietic stem cells LK CD150+ CD48-

extract_protocol:
Cells were either left naïve or infected, and were WT or Dnmt3a KO cells (four possible combinations)
All prep DNA/RNA mini kit
NEBnext Ultra II prep kit/EZ methylation lightning kit

treatment_protocol: in vivo growth, isolation via FACS

tag: cell type

value: murine Hematpoietic stem cells

value: naïve

tag: genotype

value: Dnmt3a KO


title: C9_UI0_1


title: 0148-0


title: WT naïve

value: WT


title: Dnmt3a KO infected

value: 1 month M. avium infection


title: WT infected


title: 0029-0


title: CTRL_2


title: ESCs, R3 -- S/L + 1 hr dTAG

city: Ithaca

first: Charles

middle: G

last: Danko

address: Hungerford Hill Rd

institute: Baker Institute

description:
Merged processed data files:
Abood22.23.24_spikeIn_plus.bw
Abood22.23.24_spikeIn_minus.bw

data_processing:
Library strategy: PRO-seq
FASTQ data was aligned and processed using the proseq2.0 pipeline developed by Danko lab (https://github.com/Danko-Lab/proseq2.0).
All data was competitively aligned to a merged genome assembly of mm10 and dm3. Merging the two genome builds was performed using fastq merge.
PRO-seq libraries were competitively aligned to a genome resulted by merging mm10 assembly with D.melanogaster dm3 genome assembly. Alignment was performed using the proseq2.0 pipeline developed by the Danko lab (https://github.com/Danko-Lab/proseq2.0) using the parameters -PE --RNA5=R2_5prime --UMI1=6. Downstream analysis was performed in R, using Genomic Ranges (Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan M, Carey V (2013). “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology, 9. doi: 10.1371/journal.) and BRgenomics1.1.3 (https://mdeber.github.io/index.html).
Genome_build: mm10 and dm3
Supplementary_files_format_and_content: bigwig

source_name: Mouse mESCs

extract_protocol:
RNA extraction, run-on, and library preparation were executed according to “Mahat, D. B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat. Protoc. 11, 1455–1476 (2016).” (PMID: 27442863).
Library prep was performed using Illumina custom adapters: Reverse 3' RNA adapter (/5Phos/NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT) and Reverse 5' RNA Adapter (5'-CCUUGGCACCCGAGAAUUCCA-3').

value: mESCs

tag: assay

value: PRO-seq

value: 60min dTAG-13

tag: time point from differentiation

tag: replicate

tag: growth medium

value: serum lift (S/L)

tag: spike-in

value: Drosophila S2 nuclei


title: C8_I72_2

tag: organoid line

tag: primary tissues

value: Non-inflamed ascending colon

tag: disease status

value: Healtyh donor

tag: culture condition

value: Differentiated colonic monolayers

tag: infection status

value: Infected


title: 4025-0

value: pre-vaccination

value: frail


title: Taco-23-derived cell lines [Sui77]

description: Gene expression data of pancreatic cancer cell line

value: Cell line


title: ESCs, R2 -- S/L + 1 hr dTAG

tag: treatment


title: Pancreatic cancer xenograft [Taco-12]

value: xenografted tumor


title: Pancreatic cancer xenograft [Taco-1]


title: Taco-21-derived cell lines [Sui75]


title: Taco-22-derived cell lines [Sui76]


title: 4053-0

tag: sample timing


title: 1135-0

tag: frailty status

value: non-frail


title: 0226-0

tag: age


title: C8_UI72_2

value: Uninfected

tag: time post infection (h)


title: C8_UI72_1


title: ESCs, R3 -- S/L (19.20.21)

description:
Merged processed data files:
Abood19.20.21_spikeIn_plus.bw
Abood19.20.21_spikeIn_minus.bw

tag: cell type

value: untreated


title: C8_I24_2


title: ESCs, R1 -- S/L + 1 hr dTAG


title: ESCs, R2 -- S/L (19.20.21)


title: 1125-0


title: C8_I24_1


title: C8_I72_1


title: 4115-0


title: Taco-16-derived cell lines [Sui74]

tag: sample type


title: 0225-3

value: 3 days post-vaccination


title: ESCs, R1 -- S/L (19.20.21)

value: mESCs

tag: assay


title: C8_UI0_2


title: Taco-13-derived cell lines [Sui72]


title: Taco-7-derived cell lines [Sui70]


title: ESCs, R2 -- S/L + 30 mins dTAG

description:
Merged processed data files:
Abood78_spikeIn_plus.bw
Abood78_spikeIn_minus.bw

value: PRO-seq

value: 30min dTAG-13

tag: time point from differentiation


title: Taco-15-derived cell lines [Sui73]


title: Taco-12-derived cell lines [Sui71]


title: ESCs, R1 -- S/L + 30 mins dTAG

tag: replicate

value: serum lift (S/L)


title: MTX_P97

city: le kremlin bicetre

first: audrey

last: paoletti

address: 78 rue du general Leclerc

institute: inserm U1184

data_processing:
STAR 2.7.1a
STAR --genomeDir [/path/to/genome/STAR/index] --sjdbGTFfile [/path/to/genome/annotations/file] --runThreadN 10 --readFilesIn $fq1 $fq2 --outFileNamePrefix $prefix --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
RSEM v1.3.1
rsem-calculate-expression -p 14 --paired-end --bam --no-bam-output [/path/to/alignedToTransciptomeBamFile/by/sample] [/path/to/genome/RSEM/index] $sample_name
Genome_build: Homo_sapiens.GRCh38; Ensembl release 96
Supplementary_files_format_and_content: RSEM count file: result of the rsem-calculate-expression command

source_name: blood MDM

growth_protocol: extraction of PBMCs from blood and monocytes negative selection following by human serum AB culture for polarization in macrophages

extract_protocol: extraction by GeneJet RNA extraction kit

tag: tissue

value: Blood

value: monocytes derived macrophages

tag: disease

value: Rheumatoid arthritis

value: Rhumatoid arthritis patient under MTX treatment


title: MTX_P43


title: Taco-5-derived cell lines [Sui68]


title: ESCs, R3 -- 2i

description: Merged processed data files:

tag: growth medium

tag: spike-in

value: Drosophila S2 nuclei


title: EFS_946

value: Healthy

value: Healthy  donor


title: ESCs, R3 -- S/L (123)

description:
Merged processed data files:
Abood123_spikeIn_plus.bw
Abood123_spikeIn_minus.bw


title: C7_UI72_2

tag: organoid line

tag: primary tissues

value: Non-inflamed ascending colon

tag: disease status

value: Ulcerative colitis

value: Differentiated colonic monolayers


title: C7_I72_2

tag: culture condition

tag: infection status

value: Infected


title: C7_I72_1


title: C7_I72_3


title: ESCs, R2 -- 2i

description: Merged processed data files:

tag: treatment

value: untreated


title: C8_UI0_1

value: Healtyh donor

value: Uninfected


title: MTX_P85


title: C7_UI72_1


title: EFS_683


title: C7_I24_3


title: ESCs, R2 -- S/L (123)

value: mESCs

value: PRO-seq


title: EFS_448


title: MTX_P102


title: ESCs, R1 -- S/L (123)

value: serum lift (S/L)


title: MTX_P41

value: Blood


title: EFS_112

value: monocytes derived macrophages


title: ESCs, R1 -- 2i

description: Merged processed data files:


title: 72 hr EpiLC, dTAG-13 30 mins wash, R3

description:
Merged processed data files:
AA_72h.dTAG30_spikeIn_plus.bw
AA_72h.dTAG30_spikeIn_minus.bw

source_name: Mouse EpiLC

value: EpiLC

value: 30min dTAG-13


title: ADA_P53

value: Rheumatoid arthritis

value: Rhumatoid arthritis patient under adalumumab treatment


title: ADA_P44


title: 72 hr EpiLC, dTAG-13 30 mins wash, R2

value: Drosophila S2 nuclei


title: 72 hr EpiLC, dTAG-13 30 mins wash, R1


title: ADA_P42


title: ADA_P100


title: C7_I24_2

value: Non-inflamed ascending colon


title: Taco-6-derived cell lines [Sui69]

value: Cell line


title: PitNET46-t

data_processing:
The FASTQ files from NGS were analysed using CLC Genomics Workbench (v20.0.4). During read trimming any reads with Q (Phred score) < 30 were discarded. Reads also underwent trimming by length and any reads that did not fall into 15 - 55 nt length category were discarded. Trimmed reads were aligned to miRBase (V22) with the following settings: additional upstream / downstream bases = 2, missing upstream / downstream bases = 2, maximum mismatches = 2, sequence length = 15 to 28, minimum supporting count = 1. The counts were compiled and exported into DESeq2 compatible counts matrix format.
miRNA differential expression analysis was done in DESeq2 (v1.30.1) in R (v 4.0.3).
Genome_build: miRBase V22 for miRNA annotation and counting
Supplementary_files_format_and_content: counts table

source_name: Tumor tissue

tag: pitnet type

value: GH secreting

tag: sample/tissue

value: Tumor tissue


title: C2_I72_3

value: Ulcerative colitis

value: Differentiated colonic monolayers

value: Infected

tag: time post infection (h)


title: C7_UI0_2

value: Uninfected


title: C7_UI0_1


title: 72 hr EpiLC, ctl, R1

description:
Merged processed data files:
AA_72h.ctrl_spikeIn_plus.bw
AA_72h.ctrl_spikeIn_minus.bw

tag: cell type

value: PRO-seq

value: untreated


title: C2_I72_2


title: PitNET44-t

value: NF PitNET


title: C7_I24_1


title: 48 hr EpiLC, dTAG-13 30 mins wash, R2

description:
Merged processed data files:
AA_48h.dTAG30_spikeIn_plus.bw
AA_48h.dTAG30_spikeIn_minus.bw

tag: assay


title: C2_I72_1


title: 72 hr EpiLC, ctl, R2

tag: time point from differentiation


title: PitNET43-t


title: Taco-2-derived cell lines [Sui66]

tag: sample type


title: Sui74-derived CDX-SC [CDX74-SC]

value: xenografted tumor


title: C2_UI72_2


title: Sui73-derived CDX [CDX73]


title: Taco-1-derived cell lines [Sui65]


title: Sui70-derived CDX [CDX70]


title: Sui75-derived CDX [CDX75]


title: Taco-4-derived cell lines [Sui67]


title: Sui74-derived CDX-OR [CDX74-OR]


title: Sui76-derived CDX [CDX76]


title: Sui69-derived CDX [CDX69]


title: Sui71-derived CDX [CDX71]


title: PitNET42-t


title: C2_UI72_1


title: C2_I24_3


title: 48 hr EpiLC, dTAG-13 30 mins wash, R1

value: EpiLC

tag: replicate


title: Sui68-derived CDX [CDX68]


title: Sui67-derived CDX [CDX67]


title: 48 hr EpiLC, ctl, R3

description:
Merged processed data files:
AA_48h.ctrl_spikeIn_plus.bw
AA_48h.ctrl_spikeIn_minus.bw


title: PitNET41-t


title: Sui72-derived CDX [CDX72]


title: 48 hr EpiLC, dTAG-13 30 mins wash, R3

value: 30min dTAG-13


title: 48 hr EpiLC, ctl, R2


title: PitNET40-t


title: 48 hr EpiLC, ctl, R1


title: C2_I24_1


title: C2_I24_2


title: 28 hr EpiLC, dTAG-13 30 mins wash, R3

description:
Merged processed data files:
AA_28h.dTAG30_spikeIn_plus.bw
AA_28h.dTAG30_spikeIn_minus.bw


title: PitNET39-t


title: PitNET38-t


title: Sui66-derived CDX [CDX66]


title: 28 hr EpiLC, dTAG-13 30 mins wash, R2


title: PitNET37-t


title: 28 hr EpiLC, dTAG-13 30 mins wash, R1


title: C2_UI0_2


title: LC27_N

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

description: small RNA

data_processing:
Sequenced reads were trimmed by the sequencing quality and/or adopter contaminations using Cutadapt (Martin et al. EMBnet.Journal 2011) with the following parameters: --overlap=6 -f fastq -a TGGAATTCTCGGGTGCCAAGG -m 18 -M 26.
The sequencing quality of trimmed reads were checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimmed reads were aligned to the reference human genome using the mapper (mapper.pl; the following parameters were used: -e -h -j -m -s) function of miRDeep2 (Friedländer et al. Nucleic Acids Res. 2012) with Bowtie (Langmead et al. Genome Biol. 2009).
Expression levels of all known miRNAs were estimated using the quantifier (quantifier.pl; the following parameters were used: -t has -g 2 -e 2 -f 5) function of miRDeep2.
Differentially expressed miRNAs between lung adenocarcinoma and adjacent normal tissues were identified using DESeq2 (Love et al. Genome Biol. 2014).
Genome_build: hg38

source_name: fresh tissue

extract_protocol:
The patients with untreated, primary, non-metastatic lung tumors, who underwent lung lobe resection with curative intent and provided informed consent, were included in this study. Following surgical resection, paired tumor and normal tissues were isolated and immediately transported to the research facility. The tumor and normal tissues were macroscopically examined for tumor positioning. Ten paired normal and cancer samples from lung adenocarcinoma patients were placed in RNAlater solution (Thermo Scientific, Cat.#AM7020) at 4°C within a few minutes of collection and left overnight to ensure RNA sefety. For further analysis, samples were stored at −20 °C with the RNAlater removed.
The integrity and amount of RNA was measured using the Agilent Bioanalyzer 2100. Approximately 1 μg total RNA was used to prepare a small RNA library, according to the protocol of the TruSeq Small RNA RNA library prep kit (Illumina, San Diego, CA). The libraries were quantified using KAPA Library Quantification kits for Illumina sequencing platforms, according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854), and were sequenced (single-end; 51 bp) using the Illumina HiSeq 2500 system (LC Sciences, Houston, TX) by the Macrogen Inc (Seoul).

tag: tissue

value: Adjacent normal cells

tag: disease state

value: lung adenocarcinoma


title: LC27_T

description: small RNA

value: Lung adenocarcinoma cells


title: C1_I72_2

value: Non-inflamed ascending colon

value: Healtyh donor


title: PitNET35-t

extract_protocol:
Total RNA from plasma samples was extracted using exoRNeasy Midi kit (Qiagen, Germany) according to manufacturer's instructions. Total RNA from tumor tissue samples was extracted using AllPrep DNA/RNA/miRNA Universal kit (Qiagen Germany) according to manufacturer's instructions
miRNA-seq libraries were prepared using Lexogen Small RNA-seq Library prep Kit according to manufacturer's instructions


title: Sui65-derived CDX-SC [CDX65-SC]


title: C2_UI0_1


title: LC28_N

description: small RNA


title: PitNET36-t

value: GH secreting


title: 28 hr EpiLC, ctl, R2

description:
Merged processed data files:
AA_28h.ctrl_spikeIn_plus.bw
AA_28h.ctrl_spikeIn_minus.bw

tag: growth medium

tag: spike-in

value: Drosophila S2 nuclei


title: 28 hr EpiLC, ctl, R3


title: Sui65-derived CDX-OR [CDX65-OR]


title: LC25_T

description: small RNA


title: C1_I72_1

tag: organoid line

tag: primary tissues


title: LC16_T

description: small RNA


title: C1_UI72_2

tag: disease status

tag: culture condition


title: 28 hr EpiLC, ctl, R1

tag: treatment


title: C1_UI72_1

tag: infection status


title: C2_UI0_3

value: Ulcerative colitis


title: LC37_T

description: small RNA


title: PitNET33-t

tag: pitnet type

tag: sample/tissue

value: Tumor tissue


title: PitNET46-24h

source_name: Plasma

value: Plasma


title: 24 hr EpiLC, dTAG-13 30 mins wash, R3

description:
Merged processed data files:
AA_24h.dTAG30_spikeIn_plus.bw
AA_24h.dTAG30_spikeIn_minus.bw

tag: cell type


title: LC25_N

description: small RNA


title: LC16_N

description: small RNA


title: C1_I24_2

value: Differentiated colonic monolayers

value: Infected

tag: time post infection (h)


title: LC37_N

description: small RNA


title: PitNET45-24h

value: PRL secreting


title: 24 hr EpiLC, dTAG-13 30 mins wash, R1

tag: assay

value: PRO-seq

tag: time point from differentiation


title: 24 hr EpiLC, dTAG-13 30 mins wash, R2

tag: replicate


title: PitNET34-t

value: NF PitNET


title: PitNET44-24h


title: C1_I24_1


title: PitNET42-24h


title: 24 hr EpiLC, ctl, R1

description:
Merged processed data files:
AA_24h.ctrl_spikeIn_plus.bw
AA_24h.ctrl_spikeIn_minus.bw

value: EpiLC

value: untreated


title: C1_UI0_2

value: Uninfected


title: LC36_T

description: small RNA

tag: tissue

value: lung adenocarcinoma


title: LC17_T

description: small RNA

value: Lung adenocarcinoma cells

tag: disease state


title: LC36_N

description: small RNA

value: Adjacent normal cells


title: 24 hr EpiLC, ctl, R2

tag: growth medium


title: C1_UI0_1

value: Non-inflamed ascending colon

value: Healtyh donor


title: PitNET41-24h

value: GH secreting


title: LC1_T

description: small RNA


title: Sample65_SUP-B15_BR2

city: Solna

first: Rozbeh

last: Jafari

address: Tomtebodavägen 23B

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description:
total RNA (ribosomal depleted)
SH-2290-SUP-B15-R2_S83

data_processing:
The sequenced reads were preprocessed  for adapter and quality-based trimming using cutadapt  v2.4 and then mapped to the human reference genome GRCh38 (gencode.v31.p12 primary assembly) using STAR aligner v2.7.1a (DOI: 10.1093/bioinformatics/bts635) with enabled chimeric reads detection.
The mapped reads were quantified at the gene level using featureCount.
The raw counts were processed to remove any techinical variation due to different RNA-seq library prepartion times using ComBat-seq method in sva R package (DOI: 10.1093/nargab/lqaa078).
The batch-corrected raw counts are provided in the processed data files
Genome_build: gencode.v31.p12 primary assembly
Supplementary_files_format_and_content: raw counts at gene level

source_name: Blood

growth_protocol: RPMI 1640 Media with 10% or 20% FBS

extract_protocol:
QIAGEN RNeasy Mini Kit with DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina protocols using Ribo-Zero and/or Ribo-Zero Gold Kit

tag: disease

value: childhood acute lymohoblastic leukemia

value: BCP-ALL

value: B-cells


title: Sample66_TMD5_BR2

description:
total RNA (ribosomal depleted)
SH-2290-TMD5-R2_S84


title: LC1_N

description: small RNA


title: PitNET38-24h

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

institute: Latvian Biomedical Research and Study Centre

value: Plasma


title: LC17_N

description: small RNA


title: PitNET43-24h


title: Lnc956 KO-rep3

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Illumina Casava2.19 software used for basecalling.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.8 with default parameter.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel with raw FPKM for every gene and every sample

source_name: embryo

extract_protocol:
E12.5 embryos was used for RNA extraction using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: developmental stage

tag: genotype

value: lnc956 knockout

value: embryo


title: Lnc956 KO-rep2


title: PitNET40-24h

city: Riga


title: 24 hr EpiLC, ctl, R3

value: PRO-seq

tag: spike-in

value: Drosophila S2 nuclei


title: PitNET39-24h

value: NF PitNET


title: Lnc956 KO-rep1


title: Sample64_KOPN-8_BR2

description:
total RNA (ribosomal depleted)
SH-2290-KOPN-8-R2_S85

tag: treatment

value: untreated


title: Sample63_RCH-ACV_BR2

description:
total RNA (ribosomal depleted)
SD-2137-RCH-ACV-R2_S17


title: B170906001GTV_T

description: small RNA


title: PitNET32-24h


title: B170406001GTV_N

description: small RNA


title: Sample62_P30-OHKUBO_BR2

description:
total RNA (ribosomal depleted)
SD-2137-P30-OHKUBO-R2_S16


title: B170906001GTV_N

description: small RNA


title: PitNET37-24h


title: PitNET35-24h


title: wild type-rep2

value: wild type


title: Sample61_NALL-1_BR2

description:
total RNA (ribosomal depleted)
SD-2137-NALL-1-R2_S15


title: B170406001GTV_T

description: small RNA

value: lung adenocarcinoma


title: OE ERRg-3 in hiPSC-CMs (RNA-seq)

city: Philadelphia

first: Tomoya

last: Sakamoto

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

institute: University of Pennsylvania

description:
Gene Expression Data
ERR-G-3

data_processing:
Transcript-level gene expression was quantified using Salmon (Nat Methods. 2017 Apr;14(4):417-419. PMID: 28263959)
Transcript data was aggregated to produce gene-level quantifications, and tests for differential expression were performed using DESeq2 (Genome Biol. 2014;15(12):550. PMID: 25516281)
We considered genes with FDR < 0.05 and fold change at least 1.5 in any direction for further analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file contains significantly regulated gene name, log2 fold change (ERRg/GFP), and adjusted p-values.

source_name: hiPSC-CMs overexpressed with ERRg

growth_protocol: hiPSC were cultured in TeSR-E8 (StemCell Technologies) and differentiated toward cardiomyocytes with the method published by Dr. Joseph Wu (Nat Methods. 2014 Aug;11(8):855-60. PMID: 24930130).

extract_protocol:
RNA was harvested using Qiazol (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). 1ug of Total RNA was used as starting material to construct RNA Seq library using Illumina's Truseq Stranded Total RNA Library preparation kit as per the instructions. First the total RNA is Ribo depleted to remove rRNA from total RNA. The remaining non-rRNA is fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR.
The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR. Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 2500.

treatment_protocol: At D22, OE GFP or ERRg was performed using adenovirus expressing each gene. Two days after the infection, RNA samples were harvested.

value: hiPSC-derived cardioyocytes

tag: differentiation

value: overexpressed ERRg


title: wild type-rep3


title: PitNET46-x

tag: pitnet type


title: Sample59_MOLT-14

description:
total RNA (ribosomal depleted)
SD-2137-MOLT-14_S13

value: T-ALL

value: T-cells