title: Sample 253 (Lung, Normal)

description:
D7_253-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 662 (Lung, Normal)

status: Public on Jun 15 2021

type: RNA

city: London

first: William

last: Cookson

address: Dovehouse Street

country: United Kingdom

institute: Imperial College London

description:
D5_662_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.

hyb_protocol: Hybridization was performed for 16 h on GeneTitanTM Instrument.

scan_protocol: GeneChips were scanned on a GeneTitan system (Affymetrix Ltd.).

data_processing: Raw expression data for these 237 samples were RMA-treated using Oligo (1.38.0) as part of a larger study and filtered. Specifically, transcript cluster intensity was required to exceed the data set median in 1 or more sample (genefilter 1.56.0), and be designated within the Affymetrix annotation (netaffx build 36) with a cross-hybridisation potential of 1 (unique), a non-missing mRNA assignment and as part of the main design probe set category.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lung

label_protocol: Total RNA was converted to labelled cDNA for hybridization onto the gene expression chips using the AmbionTM WT Expression Kit. The single-stranded DNA was fragmented and labelled using Affymetrix GeneChipTM WT Terminal Labelling Kit.

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit (Qiagen, Crawley, UK).

tag: diagnosis

value: Lung cancer

tag: gender

value: Female

tag: tissue

value: Normal

tag: patient id


title: Sample 00013 (Lung, Normal)

description:
D7_00013_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.

value: Male


title: Sample 23 (Lung, Normal)

description:
D5_23-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 941 (Lung, Normal)

description:
D5_D5_941_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1279 (Lung, Normal)

description:
D7_1279_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 937 (Lung, Tumor)

description:
C9_937_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.

value: Tumor


title: Sample 00362 (Lung, Tumor)

description:
C9_00362_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 634 (Lung, Tumor)

description:
C9_634_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 696 (Lung, Normal)

description:
D5_696_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1023 (Lung, Normal)

description:
D5_1023_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00449 (Lung, Normal)

description:
D5_00449_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 413 (Lung, Tumor)

description:
C9_413_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00306 (Lung, Normal)

description:
D5_00306_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1289 (Lung, Normal)

description:
D5_1289_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1011 (Lung, Tumor)

description:
C9_1011_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 834 (Lung, Normal)

description:
D5_834_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 806 (Lung, Tumor)

description:
C7_806_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1270 (Lung, Tumor)

description:
C9_1270_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 615 (Lung, Tumor)

description:
C7_615_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 878 (Lung, Tumor)

description:
C7_878_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 490 (Lung, Normal)

description:
D5_490_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 988 (Lung, Tumor)

description:
C7_988_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 470 (Lung, Tumor)

description:
C7_470_T_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 826 (Lung, Normal)

description:
C7_C7_826_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 925 (Lung, Tumor)

description:
C7_925_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 380 (Lung, Tumor)

description:
C7_380_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1241 (Lung, Tumor)

description:
C7_1241_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1279 (Lung, Tumor)

description:
C7_1279_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 631 (Lung, Normal)

description:
B9_631_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 687 (Lung, Tumor)

description:
C5_687_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 941 (Lung, Tumor)

description:
C5_C5_941_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 889 (Lung, Normal)

description:
B7_889_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00449 (Lung, Tumor)

description:
C5_00449_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 826 (Lung, Tumor)

description:
B7_B7_826_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00408 (Lung, Normal)

description:
B9_00408_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1289 (Lung, Tumor)

description:
C5_1289_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 696 (Lung, Tumor)

description:
C5_696_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1023 (Lung, Tumor)

description:
C5_1023_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00356 (Lung, Normal)

description:
B9_00356_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 983 (Lung, Normal)

description:
B7_983_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 835 (Lung, Normal)

description:
B7_835_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 490 (Lung, Tumor)

description:
C5_490_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 253 (Lung, Tumor)

description:
C7_253-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 965 (Lung, Normal)

description:
B9_965_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 23 (Lung, Tumor)

description:
C5_23-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00306 (Lung, Tumor)

description:
C5_00306_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 73 (Lung, Normal)

description:
B7_73-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 606 (Lung, Normal)

description:
B7_606_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 662 (Lung, Tumor)

description:
C5_662_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00345 (Lung, Tumor)

description:
C7_00345_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 388 (Lung, Normal)

description:
B9_388_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 379 (Lung, Normal)

description:
B7_379_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 250 (Lung, Normal)

description:
B7_250_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1259 (Lung, Tumor)

description:
B9_1259_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1303 (Lung, Normal)

description:
B7_1303_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1276 (Lung, Normal)

description:
B7_1276_N2
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 851 (Lung, Normal)

description:
B5_B5_851_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1306 (Lung, Normal)

description:
H7_1306_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00328 (Lung, Normal)

description:
B7_00328_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00443 (Lung, Normal)

description:
B5_00443_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 885 (Lung, Normal)

description:
B5_885_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 954 (Lung, Normal)

description:
B5_954_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 832 (Lung, Normal)

description:
B5_832_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00304 (Lung, Normal)

description:
B5_00304_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 64 (Lung, Normal)

description:
B5_64-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 631 (Lung, Tumor)

description:
A9_631_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 983 (Lung, Tumor)

description:
A7_983_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1288 (Lung, Normal)

description:
B5_1288_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 222 (Lung, Normal)

description:
B5_222-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 476 (Lung, Normal)

description:
B5_476_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1008 (Lung, Normal)

description:
B5_1008_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 388 (Lung, Tumor)

description:
A9_388_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 250 (Lung, Tumor)

description:
A7_250_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 677 (Lung, Normal)

description:
B5_677_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 379 (Lung, Tumor)

description:
A7_379_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00408 (Lung, Tumor)

description:
A9_00408_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1303 (Lung, Tumor)

description:
A7_1303_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 965 (Lung, Tumor)

description:
A9_965_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 73 (Lung, Tumor)

description:
A7_73-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1276 (Lung, Tumor)

description:
A7_1276_T2_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00356 (Lung, Tumor)

description:
A9_00356_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 835 (Lung, Tumor)

description:
A7_835_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 469 (Lung, Tumor)

description:
A7_469_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 954 (Lung, Tumor)

description:
A5_954_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 885 (Lung, Tumor)

description:
A5_885_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 832 (Lung, Tumor)

description:
A5_832_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00328 (Lung, Tumor)

description:
A7_00328_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 851 (Lung, Tumor)

description:
A5_A5_851_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: RNA-seq of planktonic P. aeruginosa - R1

status: Public on Jun 08 2021

type: SRA

city: Pittsburgh

first: Charles

middle: Joel

last: McManus

state: Pennsylvania

address: 4400 Fifth Ave

department: Biological Sciences

country: USA

institute: Carnegie Mellon University

description: rRNA-depleted with RiboZero

library_source: transcriptomic

data_processing:
Reads were first trimmed with a custom perl script (5p-trimmer.pl), which removed 15-17 nucleotides preceeding “CAG”
Reads were adapter trimmed using cutadapt (v. 1.9.1; parameters -a AGATCGGAAGAGC -m 25)
Reads were aligned to the UCBP-PA14 reference genome using Bowtie2 (v 2.1.0, default parameters) to obtain the genomic coordinates for the 3’-ends of reads
Significant peaks were called using a custom Perl script, Map3p-seq-peaks.pl, to compare aligned 3’-end locations to an expected Poisson distribution of random 3’-ends in 50 nucleotide windows. Candidate peaks required a raw p-value < 5 x 10^-5, > 5-fold more reads than the average within the window, and a minimum of 5 total reads per peak.
Strand specific peak files for each replicate were combined and RNA 3’-peaks that are present in at least two of three sample replicates were identified using bedtools functions.
Genome_build: UCBP-PA14
Supplementary_files_format_and_content: Tab-delimited file contains significant peaks mapped to genes, BedGraph files contain aligned 3' ends of reads from the raw data.

organism: Pseudomonas aeruginosa PA14

source_name: microbial culture

growth_protocol: Populations from freezer stock were revived by culturing overnight in LB broth at 37oC with shaking at 300 RPM to an optical density (OD600) of 1.0. For planktonic cells, this culture was diluted to OD600 0.1 in 5 mL LB broth and grown to a final OD600 of 0.47 (approximately 3 hours shaking at 37oC). For biofilms, a mid-log phase PA14 culture was diluted to an optical density of 0.05 into six-well plates (one plate per culture) incubated at 37oC for 24 hours.

extract_protocol:
For planktonic, one volume of RNA stabilization solution (5.3M ammonium sulfate, 20 mM EDTA, 25 mM sodium citrate, pH 5.2) was added and the cells were pelleted by centrifugation at 2,500g for 10 minutes. The supernatants were discarded and the pellets were frozen at -20oC for RNA extraction. For biofilm, The media was removed and 750 ul RNA stabilization solution was added to each well. The biofilms were scraped from the wells and the cells were pelleted by centrifugation at 2500xG for 10 minutes. The supernatants were discarded and samples were saved at -20oC until RNA extraction. Total RNA was extracted using the Quick-RNA™ Fungal/Bacterial Miniprep kit (Zymo Research R2010) according to the manufacturer’s instructions, followed by extensive DNase treatment.
The RNA was ligated to the universal miRNA 3-cloning linker (New England Biolabs S1315S). rRNA was subtracted using the Ribo-Zero rRNA removal kit for bacteria (Illumina MRZMB126). Strand-specific 3pMap libraries were prepared using the QuantSeq Flex Targeted RNA-seq kit (Lexogen SKU:035.24). A custom primer complementary to the 3' linker was used for first strand synthesis, and custom random primers were used for second strand synthesis as described in the kit manual

treatment_protocol: For planktonic, a subinhibitory concentration of AZM (0.5 µg/ml final concentration) was added to treated cultures and left out of negative controls. The cultures were incubated for an additional 20 minutes at 37oC. For biofilms, the media was removed and replaced with or without AZM (0.5 µg/ml) and incubated at 37oC for 3 hours.

tag: strain

tag: treatment

value: Untreated


title: RNA-seq of planktonic P. aeruginosa - R2

description: rRNA-depleted with RiboZero


title: Sample 677 (Lung, Tumor)

description:
A5_677_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: RNA-seq of planktonic P. aeruginosa treated with AZM - R1

description: rRNA-depleted with RiboZero

value: AZM


title: RNA-seq of P. aeruginosa biofilm - R2

description: rRNA-depleted with RiboZero


title: Sample 64 (Lung, Tumor)

description:
A5_64-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: RNA-seq of planktonic P. aeruginosa treated with AZM - R2

description: rRNA-depleted with RiboZero


title: RNA-seq of P. aeruginosa biofilm - R3

description: rRNA-depleted with RiboZero


title: Sample 1288 (Lung, Tumor)

description:
A5_1288_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1008 (Lung, Tumor)

description:
A5_1008_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00304 (Lung, Tumor)

description:
A5_00304_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00443 (Lung, Tumor)

description:
A5_00443_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 222 (Lung, Tumor)

description:
A5_222-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: RNA-seq of planktonic P. aeruginosa treated with AZM - R3

description: rRNA-depleted with RiboZero


title: RNA-seq of P. aeruginosa biofilm treated with AZM- R1

description: rRNA-depleted with RiboZero


title: RNA-seq of P. aeruginosa biofilm - R1

description: rRNA-depleted with RiboZero


title: RNA-seq of P. aeruginosa biofilm treated with AZM- R3

description: rRNA-depleted with RiboZero


title: RNA-seq of P. aeruginosa biofilm treated with AZM- R2

description: rRNA-depleted with RiboZero


title: DRG_rep10_scRNA-seq

status: Public on Jun 01 2021

city: Baltimore

first: Rejji

last: Kuruvilla

state: MD

address: 3400 N. Charles St.

department: Biology

institute: Johns Hopkins University

data_processing:
Reads were demultiplexed with Illumina bcl2fastq2 v2.20
Reads were aligned to the mouse genome (mm10) and digital gene expression matrices were generated using the Drop-Seq Tools 2.0.0 pipeline (https://github.com/broadinstitute/Drop-seq/releases).
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrices for all genes/cells separated by sample (.txt.gz format).
Supplementary_files_format_and_content: Single cell metadata including cluster assignments and QC for each cell barcode (.csv format).

molecule: polyA RNA

organism: Mus musculus

source_name: Dorsal root ganglion

extract_protocol:
Multiple sympathetic (SGC) or sensory (DRG) ganglia were pooled together for each round of Drop-Seq. Each SCG library was generated from 4 SCGs collected from two animals, and each DRG library was generated from 6 lower lumbar DRGs collected from two animals. In total, we generated 5 SCG libraries and 11 DRG libraries. SCGs and DRGs were not collected from the same animal because of time considerations related to ganglia isolation and dissociation. Ganglia were incubated in 50units Papain diluted in HBSS plus HEPES for 20 min at 37°C then washed with HBSS plus HEPES and incubated for an additional 20 min at 37°C with 1.5mg/mL collagenase in HBSS plus HEPES. Following the second incubation, ganglia were washed again and then suspended and triturated in DMEM AIR (DMEM F12 supplemented with 12.5mM glucose and 1U/ml penicillin/streptomycin). Cells were centrifuged and resuspended in fresh DMEM AIR. Single cell suspensions were diluted to a concentration of 100cells/ul and processed with the Drop-Seq protocol as previously described (Macosko et al., 2015) including the following modifications. Flow rates for cells, beads, and oil were optimized for aquapel-treated PDMS devices purchased from FlowJem (cells and beads: 2,300ul/hour, oil: 13,000ul/hour). Up to two samples were processed in series, with single cell suspensions and stable emulsions held on ice until all collections were completed (no more than 1 hour) before proceeding immediately with reverse transcription. cDNA amplification was performed using 4000 beads/reaction with a total of 15 cycles of PCR.
Sequencing libraries were prepared from amplified cDNA using the Illumina Nextera XT library prep kit

treatment_protocol: Mice were housed in a 12 h light:12 h dark light cycle at a temperature of 22--25°C with food and water ad libitum. Dissections and single cell collections were performed between 9a.m-2p.m.

tag: age

value: Dorsal root ganglion


title: Sample 476 (Lung, Tumor)

description:
A5_476_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: DRG_rep9_scRNA-seq


title: Sample 480 (Lung, Normal)

description:
D7_480_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: DRG_rep6_scRNA-seq


title: DRG_rep7_scRNA-seq


title: DRG_rep4_scRNA-seq


title: DRG_rep5_scRNA-seq


title: DRG_rep11_scRNA-seq


title: DRG_rep3_scRNA-seq


title: SCG_rep5_scRNA-seq

source_name: Superior cervical ganglion

value: Superior cervical ganglion


title: DRG_rep2_scRNA-seq


title: KIR3DL3- CD8 TEMRA Donor WH

status: Public on May 27 2021

city: Bronx

first: Yao

last: Wei

state: New York

address: 1300 Morris Park Ave F411

institute: Albert Einstein college of medicine

data_processing:
Alignment was done using STAR (version 2.6.1b)
Htseq (version 0.6.1) was used to quanitfy the number of RNA-seq fragements mapped to each gene
differntial expression analysis prformed using DESeq2 (version 3.11)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: CD8 T cell from PBMCs

extract_protocol:
10,000 to 20,000 KIR3DL3+ and KIR3DL3- CD8 TEMRA, defined as CD3+CD8+CD45RA+CCR7- were sorted by the BD FACSAria directly into RNA lysis buffer. RNA was then extracted with the RNeasy Micro Kit (Qiagen).
SMARTer Stranded Total RNA Pico Kit.
Library preparation (by SMARTer Stranded Total RNA Pico Kit) and sequencing (at 40M paired-end reads per sample) was performed by Admera Health.

tag: cell type

tag: genotype/variation

value: CD8+ T Cells


title: KIR3DL3- CD8 TEMRA Donor 341


title: KIR3DL3+ CD8 TEMRA Donor WH


title: SCG_rep3_scRNA-seq


title: SCG_rep4_scRNA-seq


title: KIR3DL3+ CD8 TEMRA Donor 641


title: KIR3DL3- CD8 TEMRA Donor 641


title: KIR3DL3+ CD8 TEMRA Donor 341


title: KO1 RPF

status: Public on May 18 2021

city: Chicago

first: Caraline

last: Sepich

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

description: Sepich-Poore_METTL5.TE.rpkm.with.foldchange.txt

data_processing:
Base calling was performed with Illumina bcl2fastq software.
Fastq files from different flowcells were combined using the command "cat".
Quality of sequenced reads was assessed with FastQC v0.11.5
Adapters were trimmed and quality filtering was performed with BBDuk (https://sourceforge.net/projects/bbmap/) from BBTools version 38.84 using a reference fasta file of the NEBNext adapter sequences and settings ktrim = 4, qtrim = rl, trimq = 20, k = 31, mink = 11, hdist = 1, entropy = 0.5, entropywindow = 30, entropyk = 5, minlen = 25 and maxlen = 34 (for RPFs), and minlen = 15 (for inputs) (BBtools: sourceforge.net/projects/bbmap/).
For input files, alignment to human genome hg38 was performed using STAR 2.7.3a  in quantMode TranscriptomeSAM. Bam files were sorted and uniquely mapped reads extracted with samtools, followed by featureCounts v1.6.0  to create a counts table from mapped reads with options -s 1, -g gene_id, and -t exon.
rRNA reads were removed from RPF Fasta files using BBDuk with a reference fasta file of human rRNA sequences. Analysis was then performed on the RiboToolkit server (http://rnabioinfor.tch.harvard.edu/RiboToolkit/). First, RPF files were uploaded for single-case submission in collapsed fasta format with the following options: species = homo sapiens (hg38), RPF interval = 25-34, allowed mismatch = 2, max multiple-mapping = 1, no duplicate removal, offsets to infer P-sites - calculate by RiboToolkit, min coverage for pause sites = 10, fold change for pause sites = 20, ORF p-value = 0.05. Input counts table and single case Job IDs were then used as inputs for group case analysis with F value = 2 and P-value = 0.05.
genome build: hg38
processed data files format and content: (For inputs): tab-delimited text file includes information about gene location and transcript counts in each sample. (For RPFs): tab-delimited text file includes information about geneID, gene name, transcript counts and RPF counts for each sample, log2FoldChange, and p-values.

source_name: METTL5 KO HepG2

growth_protocol: HepG2 cells were obtained from ATTCC (cat# HB-8065). METTL5 knockout was performed using CRISPR/Cas9 technology with guide RNAs designed for excision of exons 2-3. All cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum, sodium pyruvate, and penicillin/streptomycin.

extract_protocol:
Plates were washed with 10mL of ice-cold PBS with 100μg/mL cycloheximide twice, then cells were collected in ice-cold PBS and centrifuged at 500g for 5 minutes. Each pellet was resuspended in 3 pellet volumes of lysis buffer (20mM HEPES pH 7.6, 100mM KCl, 5mM MgCl2, 1% Triton x-100, 100μg/mL cycloheximide, 1% v/v SUPERaseIN inhibitor in nuclease-free water) and cells were lysed with rotation at 4ºC for 20 minutes before being centrifuged at 16,000 g for 15 minutes.
To the clarified lysate, 4μL of Turbo DNase (Thermo Fisher) was added and samples were incubated at room temperature 15 minutes then centrifuged again to clear the lysate. About 20% of the sample was saved as input with 3 volumes of Trizol added, while the other 80% was treated with 3μL MNase (NEB) in 1x MNase buffer for 15 minutes at room temperature to digest RNA not covered by ribosomes. Additional SUPERaseIN (Invitrogen) was added to a final concentration of 0.5mM to quench the reaction. Then, samples were loaded on 5-50% w/v sucrose gradients and fractionated by Gradient Station (BioComp) equipped with an ECONO UV monitor (BioRad) and fraction collector (Gilson).
Fractions containing the digested monosomes were collected and pooled, and three volumes of Trizol (Invitrogen) was added to each sample. RNA purification was performed for both input and ribosome-protected fragment (RPF) samples by chloroform extraction followed by isopropanol precipitation, and one round of rRNA depletion was performed (see “RNA purification” section of Methods). Input RNA was fragmented by combining 20μL RNA with 7.5 uL PNK buffer A (Thermo Fisher) and incubating at 94ºC for 25 minutes, then end repaired by diluting in 37.5μL nuclease-free water, adding 10μL T4 PNK (Thermo Fisher) and incubating at 37ºC for 30 minutes. Then, 12μL 10mM ATP (EMD Millipore), 2μL 10x PNK buffer A, and 6μL T4 PNK were added to incubate at 37ºC for 30 minutes. These samples were purified using the RNA clean and concentrator-5 kit (Zymo Research).
Purified RPF RNA was run in 1x Novex TBU sample buffer (Thermo Fisher) on a 10% TBE-urea gel (Thermo Fisher) in 1x RNase-free TBE buffer (Thermo Fisher) with an IDT 10/60 loading control (IDT) for 1 hour at 180V. The gel was stained 15 minutes in 1x SYBR gold in TBE with gentle shaking and visualized using a Biorad Gel Doc EZ Imager. Fragments between 26-34 nucleotides were excised and purified by Small-RNA PAGE recovery kit (Zymo Research) per manufacturer’s instructions. RPFs were end repaired similarly to inputs with T4 PNK. Input and RPF RNA samples were used to prepare libraries for sequencing using the NEBNext Small RNA Library Prep Kit (NEB) per manufacturer’s instructions, and were sequenced by Illumina NovaSeq6000 with 100bp single-end reads.

treatment_protocol: Each plate was treated with cycloheximide at a final concentration of 100μg/mL in antibiotic-free medium and incubated at 37ºC for 7 minutes.

tag: cell line

tag: genotype

value: METTL5 KO

value: cycloheximide (CHX)

tag: condition

value: ribosome-protected-fragments (RPFs)


title: DRG_rep8_scRNA-seq


title: DRG_rep1_scRNA-seq


title: WT2 RPF

value: WT


title: KO2 input

description:
Sepich-Poore_METTL5.TE.rpkm.with.foldchange.txt
Sepich-Poore_METTL5.riboseq.input.merged.featurecount.txt

value: input


title: WT2 input


title: KO1 input


title: mES S9.6 CUT&Tag Rep1 Batch2

status: Public on Apr 27 2021

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: genomic

data_processing:
Library strategy: CUT&Tag
[read alignment]  reads were aligned with bowtie2 (v.2.3.5.1) using --fast-local and samtools (v1.10).
[deduplication]  BAM files were deduplicated with picard (v2.23.4) MarkDuplicates
[blacklist]  Blacklisted regions were removed from the BAM file with bedtools (v2.29.2) intersect using ENCODE blacklist bed files for mm9 or hg19
[genome coverage]  Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 5 --normalizeUsing RPGC
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Normalized Ggenomic tracks in bigwig format

molecule: genomic DNA

source_name: mES

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated flasks (Sigma, G1890) under standard conditions (10% CO2, 90% humidity, 37 °C) in KnockOut DMEM (LifeTechnologies, 10829018), 2 mM Alanyl-glutamine (Sigma, G8541), 0.1 mM non-essential amino acids (Sigma, M7145) 15% fetal bovine serum (FBS) (Sigma, F7524), 0.1 mM β-mercaptoethanol (Sigma, M3148), ESGRO Leukemia Inhibitory Factor (LIF) (Millipore, ESG1107), Penicillin-Streptomycin (Sigma, P4333).

extract_protocol:
CUT&Tag experiment was performed as described previously (Kaya-Okur et al. 2019) with minor modifications Briefly, 1x10e5 cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Bangs Laboratories, BP531) with incubation at room temperature for 10min. The beads-bound cells were incubated in 200μl of primary antibody buffer (wash buffer with 2mM EDTA and 0.05% digitonin) with 1:100 BG4 antibody or S9.6 (Millipore, MABE1095) antibody dilution at 4℃ by rotating overnight. The next day, the primary antibody buffer was removed and cells were washed with 800μl of dig-wash buffer (wash buffer with 0.05% digitonin) three times. After washing, BG4 antibody-incubated cells were resuspended with 200ul of dig-wash buffer with 1:100 dilution of anti-FLAG antibody (Sigma, F1804) and incubated at room temperature for 1 hour by rotating. Cells were washed with 800μl of dig-wash buffer briefly three times to remove unbound antibodies. S9.6-treated or anti-FLAG treated cells were incubated with 1:100 dilution of anti-mouse antibody (Sigma, M7023) in 200μl of dig-wash buffer at room temperature for 1 hour by rotating. After brief wash with dig-wash buffer, cells were resuspended in 200ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:200 dilution of pA-Tn5 adapter complex and incubated at room temperature for 1 hour by rotating. pA-Tn5-bound cells were washed with 800ul of dig-300 buffer three times, followed by tagmentation in 200ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 15mM EDTA, 500μg/ml proteinase K and 0.1% SDS were added and further incubated at 63℃ for another 1 hour to stop tagmentation and digest protein.
Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (BeckmaGenomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) and sequenced with Illumina Nextseq 500 instrument.

value: mouse embryonic stem cells

tag: antibody


title: RNA-seq of planktonic P. aeruginosa - R3

description: rRNA-depleted with RiboZero


title: mES S9.6 CUT&Tag Rep1 Batch1


title: mES H3K27me3 CnT Rep1 Batch1

data_processing:
Library strategy: CUT&Tag
[read alignment] reads were aligned with bowtie2 (v.2.3.5.1) using --fast-local and samtools (v1.10).
[deduplication] BAM files were deduplicated with picard (v2.23.4) MarkDuplicates
[blacklist] Blacklisted regions were removed from the BAM file with bedtools (v2.29.2) intersect using ENCODE blacklist bed files for mm9 or hg19
[genome coverage] Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 5 --normalizeUsing RPGC
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Normalized Ggenomic tracks in bigwig format

extract_protocol:
CUT&Tag experiment was performed as described previously (Kaya-Okur et al. 2019) with minor modifications" Briefly, 1x10e5 cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Bangs Laboratories, BP531) with incubation at room temperature for 10min. The beads-bound cells were incubated in 200μl of primary antibody buffer (wash buffer with 2mM EDTA and 0.05% digitonin) with 1:100 BG4 antibody or S9.6 (Millipore, MABE1095) antibody dilution at 4℃ by rotating overnight. The next day, the primary antibody buffer was removed and cells were washed with 800μl of dig-wash buffer (wash buffer with 0.05% digitonin) three times. After washing, BG4 antibody-incubated cells were resuspended with 200ul of dig-wash buffer with 1:100 dilution of anti-FLAG antibody (Sigma, F1804) and incubated at room temperature for 1 hour by rotating. Cells were washed with 800μl of dig-wash buffer briefly three times to remove unbound antibodies. S9.6-treated or anti-FLAG treated cells were incubated with 1:100 dilution of anti-mouse antibody (Sigma, M7023) in 200μl of dig-wash buffer at room temperature for 1 hour by rotating. After brief wash with dig-wash buffer, cells were resuspended in 200ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:200 dilution of pA-Tn5 adapter complex and incubated at room temperature for 1 hour by rotating. pA-Tn5-bound cells were washed with 800ul of dig-300 buffer three times, followed by tagmentation in 200ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 15mM  EDTA, 500μg/ml proteinase K and 0.1% SDS were added and further incubated at 63℃ for another 1 hour to stop tagmentation and digest protein.
Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) and sequenced with Illumina Nextseq 500 instrument.

value: H3K27me3 (Millipore 07-449)


title: mES G4 CUT&Tag Rep3 Batch1


title: mES G4 CUT&Tag Rep1 Batch1


title: mES G4 CUT&Tag mock Rep1 Batch3

extract_protocol:
CUT&Tag experiment was performed as described previously (Kaya-Okur et al. 2019) with minor modifications Briefly, 1x10e5 cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Bangs Laboratories, BP531) with incubation at room temperature for 10min. The beads-bound cells were incubated in 200μl of primary antibody buffer (wash buffer with 2mM EDTA and 0.05% digitonin) with 1:100 BG4 antibody or S9.6 (Millipore, MABE1095) antibody dilution at 4℃ by rotating overnight. The next day, the primary antibody buffer was removed and cells were washed with 800μl of dig-wash buffer (wash buffer with 0.05% digitonin) three times. After washing, BG4 antibody-incubated cells were resuspended with 200ul of dig-wash buffer with 1:100 dilution of anti-FLAG antibody (Sigma, F1804) and incubated at room temperature for 1 hour by rotating. Cells were washed with 800μl of dig-wash buffer briefly three times to remove unbound antibodies. S9.6-treated or anti-FLAG treated cells were incubated with 1:100 dilution of anti-mouse antibody (Sigma, M7023) in 200μl of dig-wash buffer at room temperature for 1 hour by rotating. After brief wash with dig-wash buffer, cells were resuspended in 200ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:200 dilution of pA-Tn5 adapter complex and incubated at room temperature for 1 hour by rotating. pA-Tn5-bound cells were washed with 800ul of dig-300 buffer three times, followed by tagmentation in 200ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 15mM EDTA, 500μg/ml proteinase K and 0.1% SDS were added and further incubated at 63℃ for another 1 hour to stop tagmentation and digest protein.
Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckma

value: Cells were mock treated with nuclease digestion buffer at 30C for 30min before BG4 antibody incubation


title: HEK293T G4 CUT&Tag

growth_protocol: HEK293T and HaCaT cells were cultured in DMEM high glucose, GlutaMAX™ Supplement, pyruvate (LifeTechnologies, 10569010), 10% fetal bovine serum (Sigma, F7524) under standard conditions (10% CO2, 90% humidity, 37 °C).

extract_protocol:
CUT&Tag experiment was performed as described previously (Kaya-Okur et al. 2019) with minor modifications" Briefly, 1x10e5 cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Bangs Laboratories, BP531) with incubation at room temperature for 10min. The beads-bound cells were incubated in 200μl of primary antibody buffer (wash buffer with 2mM EDTA and 0.05% digitonin) with 1:100 BG4 antibody or S9.6 (Millipore, MABE1095) antibody dilution at 4℃ by rotating overnight. The next day, the primary antibody buffer was removed and cells were washed with 800μl of dig-wash buffer (wash buffer with 0.05% digitonin) three times. After washing, BG4 antibody-incubated cells were resuspended with 200ul of dig-wash buffer with 1:100 dilution of anti-FLAG antibody (Sigma, F1804) and incubated at room temperature for 1 hour by rotating. Cells were washed with 800μl of dig-wash buffer briefly three times to remove unbound antibodies. S9.6-treated or anti-FLAG treated cells were incubated with 1:100 dilution of anti-mouse antibody (Sigma, M7023) in 200μl of dig-wash buffer at room temperature for 1 hour by rotating. After brief wash with dig-wash buffer, cells were resuspended in 200ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:200 dilution of pA-Tn5 adapter complex and incubated at room temperature for 1 hour by rotating. pA-Tn5-bound cells were washed with 800ul of dig-300 buffer three times, followed by tagmentation in 200ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 15mM EDTA, 500μg/ml proteinase K and 0.1% SDS were added and further incubated at 63℃ for another 1 hour to stop tagmentation and digest protein.
Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) and sequenced with Illumina Nextseq 500 instrument.Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) and sequenced with Illumina Nextseq 500 instrument.

value: embryonic kidney


title: HaCaT G4 CUT&Tag

source_name: HaCaT

value: HaCaT

value: immortalized keratinocytes


title: SCG_rep2_scRNA-seq


title: PBMC_HC_polyIC_3

status: Public on Apr 22 2021

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

description:
single-cell RNA
868_P

data_processing:
Dropseq-derived sequencing reads were aligned to Genome Reference Consortium Human Build 38 (GRCh38) and then binned onto the cell barcodes corresponding to individual beads using Drop-Seq tools [23]. We filtered out cells containing less than 200 genes and genes not detected in at least three cells to ensure qualifying genes and cells. Library-size normalization was performed with a global scaling method by Seurat v 3.1.1 [24]; briefly, the UMI-collapsed gene expression values for each cell barcode were scaled by the total number of transcripts and multiplied by 10,000. Data was then natural log-transformed before any further downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv/

source_name: Peripheral blood mononuclear cells

growth_protocol: One vial of frozen PBMCs (approximately 3 million cells) was removed from liquid nitrogen and quickly thawed in a 37°C water bath. Cells were then transferred into 10 mL pre-warmed cell culture medium and centrifuged at 400 g for 10 minutes to wash away DMSO. The supernatant was discarded after centrifugation. The cell pellet was resuspended with 3 mL 1x BD Pharm Lyse™ (BD Biosciences, Franklin Lakes, NJ) to remove red blood cells, incubated at room temperature for 3 minutes, then quenched with 7 mL PBS. An aliquot of cells was removed for cell counting before centrifuging at 400 g for 10 minutes. After centrifugation was completed, the supernatant was removed. Cells were resuspended with medium pre-warmed to achieve a concentration of 2 x 106 cells/mL.

extract_protocol: After 24 hours of incubation, cells were harvested into Eppendorf tubes and centrifuged for 10 min at 400g. Cells were washed once with 1 mL PBS with 0.01% BSA (PBS-BSA) to remove remaining FBS, then centrifuged for 8 min at 400g. After discarding the supernatant, cells were then resuspended with 1 mL plain PBS. An aliquot of cells was removed for cell counting and viability recording with a hemocytometer using the trypan blue exclusion method to select samples with cell viability greater than 90%. Cells were adjusted to 140-160 live cells/µL using PBS-BSA as Drop-Seq input. The Drop-Seq experiment was carried out with the version 3.1 protocol from the McCarroll Lab

treatment_protocol: Cells were then plated into 96-well plates at 100 µL/well and incubated at 37°C, 5% CO2 100% humidity for 30 min. After incubation, cells were quenched with either 100 µL cell culture medium or 10 µg/mL poly I:C working solutions. The final concentrations were plain medium and 5 µg/mL poly I:C. Cells were cultured at 37°C, 5% CO2 100% humidity for 24 hours.

tag: Sex

value: F

tag: stimulation

value: Poly (I:C)

tag: disease state

value: Healthy control

value: Peripheral blood mononuclear cells


title: PBMC_HC_polyIC_2

description:
single-cell RNA
851_P


title: PBMC_SA_polyIC_5

description:
single-cell RNA
868_C

value: Media


title: KO2 RPF


title: WT1 RPF


title: PBMC_HC_polyIC_1

description:
single-cell RNA
459_P

value: M


title: WT1 input


title: PBMC_SA_polyIC_3

description:
single-cell RNA
459_C


title: mES H3K4me3 CnT Rep1 Batch1

value: H3K4me3 (MC315) mAb (Millipore 04-745)


title: SCG_rep1_scRNA-seq

value: Superior cervical ganglion


title: PBMC_SA_polyIC_4

description:
single-cell RNA
851_C


title: PBMC_SA_polyIC_2

description:
single-cell RNA
A311_P

value: Asthma


title: PBMC_HC_Baseline_1

description:
single-cell RNA
350_P


title: PBMC_SA_polyIC_1

description:
single-cell RNA
A307_P


title: PBMC_HC_Baseline_2

description:
single-cell RNA
865_P


title: PBMC_SA_Baseline_5

description:
single-cell RNA
A311_C


title: mES G4 CUT&Tag Mungbean-100U Rep1 Batch3

value: Cells were treated with 100 units Mung Bean nuclease at 30C for 30min before BG4 antibody incubation


title: PBMC_SA_Baseline_4

description:
single-cell RNA
A307_C


title: PBMC_SA_Baseline_2

description:
single-cell RNA
865_C


title: PBMC_SA_Baseline_1

description:
single-cell RNA
350_C


title: 12E_mmu-miR-6944-3p

status: Public on Apr 06 2021

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
counts.txt
Sample 29

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

source_name: NMUMG cells, clone E9

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen).
200ng RNA was used to generate sequencing libraries with the TruSeq Stranded RNA LT kit (Illumina). Sequencing was performed on an Illumina HiSeq 2500 with the HiSeq SBS kit v4 from Illumina.

treatment_protocol: NMuMG/E9 cells were transfected with 20nM miRNA construct.  After two days, TGFbeta was added and one day later, cells were retransfected in the presence of TGFbeta to ensure proper downregulation until the end of the experiment (4d TGFb). 0d TGFbeta cells were transfected for three days in the absence of TGFbeta.

value: NMUMG

tag: subclone

value: clone E9

tag: tgfbeta treatment

tag: miRNA transfected

tag: replicate

value: E


title: 20A_mmu-miR-31-3p

description:
counts.txt
Sample 27

value: A


title: 2D_mmu-miR-Ctr_1_4d

description:
GSM2290764
counts.txt
Sample 30

value: D


title: 11E_mmu-miR-1199-5p

description:
GSM2290767
counts.txt
Sample 28


title: 22D_mmu-miR-101b-3p

description:
counts.txt
Sample 24


title: PBMC_HC_Baseline_3

description:
single-cell RNA
866_P


title: 64D_mmu-miR-Ctr_1_0d

description:
GSM2290762
counts.txt
Sample 26


title: 13E_mmu-miR-200a-3p

description:
counts.txt
Sample 22


title: 62A_mmu-miR-1247-3p

description:
counts.txt
Sample 19


title: 19D_mmu-miR-181b-2-3p

description:
counts.txt
Sample 18


title: 16E_mmu-miR-429-3p

description:
GSM2290771
counts.txt
Sample 20


title: 11D_mmu-miR-1199-5p

description:
GSM2290766
counts.txt
Sample 21


title: 15D_mmu-miR-200c-3p

description:
counts.txt
Sample 15


title: 13D_mmu-miR-200a-3p

description:
counts.txt
Sample 16


title: 17C_mmu-miR-96-5p

description:
counts.txt
Sample 17

value: C


title: 64E_mmu-miR-Ctr_1_0d

description:
GSM2290763
counts.txt
Sample 13


title: PBMC_SA_Baseline_3

description:
single-cell RNA
866_C


title: 22E_mmu-miR-101b-3p

description:
counts.txt
Sample 14


title: 14D_mmu-miR-200b-3p

description:
GSM2290768
counts.txt
Sample 11


title: 21E_mmu-miR-101a-3p

description:
counts.txt
Sample 10


title: 20C_mmu-miR-31-3p

description:
counts.txt
Sample 7


title: 15E_mmu-miR-200c-3p

description:
counts.txt
Sample 9


title: 18D_mmu-miR-125b-5p

description:
counts.txt
Sample 6


title: 21D_mmu-miR-101a-3p

description:
counts.txt
Sample 25


title: 12D_mmu-miR-6944-3p

description:
counts.txt
Sample 23


title: 17A_mmu-miR-96-5p

description:
counts.txt
Sample 8


title: 16D_mmu-miR-429-3p

description:
GSM2290770
counts.txt
Sample 4


title: 62E_mmu-miR-1247-3p

description:
counts.txt
Sample 2


title: 35B_Hdac4

description:
counts.txt
Sample 90

treatment_protocol: NMuMG/E9 cells were transfected with 20nM siRNA. After two days, TGFbeta was added and one day later, cells were retransfected in the presence of TGFbeta to ensure proper downregulation until the end of the experiment (4d TGFb). 0d TGFbeta cells were transfected for three days in the absence of TGFbeta.

tag: tgfb treatment

tag: sirna transfected

value: B


title: 31C_Fosl2

description:
counts.txt
Sample 94


title: 19E_mmu-miR-181b-2-3p

description:
counts.txt
Sample 12


title: 18E_mmu-miR-125b-5p

description:
counts.txt
Sample 1


title: 10C_Maml2

description:
counts.txt
Sample 93


title: 14E_mmu-miR-200b-3p

description:
GSM2290769
counts.txt
Sample 3


title: 55C_Sp1

description:
counts.txt
Sample 92


title: 42A_Ncoa2

description:
counts.txt
Sample 89


title: 38C_Klf8

description:
counts.txt
Sample 95


title: 2E_mmu-miR-Ctr_1_4d

description:
GSM2290765
counts.txt
Sample 5


title: 4C_Zeb1

description:
counts.txt
Sample 96


title: 52A_Rybp

description:
counts.txt
Sample 87

value: Rybp


title: 34B_Gtf2i

description:
counts.txt
Sample 86


title: 41B_Mnt

description:
counts.txt
Sample 85

value: Mnt


title: 59A_Tcfe2a

description:
counts.txt
Sample 84


title: 49A_Pou2f1

description:
counts.txt
Sample 83


title: mES G4 CUT&Tag Mungbean-150U Rep1 Batch3

tag: strain

value: mouse embryonic stem cells

tag: treatment

value: Cells were treated with 150 units Mung Bean nuclease at 30C for 30min before BG4 antibody incubation


title: 63C_siCtr_0d

description:
GSM3083812
counts.txt
Sample 91

value: siCtr


title: 39A_Mef2b

description:
counts.txt
Sample 88


title: 8A_Irf2bp2

description:
counts.txt
Sample 80


title: 57A_Taf5l

description:
counts.txt
Sample 79


title: 58B_Taf6l

description:
counts.txt
Sample 82


title: 42B_Ncoa2

description:
counts.txt
Sample 78


title: 6A_Sox4

description:
counts.txt
Sample 77


title: 1A_siCtr_4d

description:
GSM3083813
counts.txt
Sample 74


title: 46A_Pawr

description:
counts.txt
Sample 73

value: Pawr


title: 61A_Trank1

description:
counts.txt
Sample 71


title: Sample 1254 (Lung, Tumor)

description:
A9_1254_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.

tag: diagnosis

value: Lung cancer

tag: gender

value: Male

tag: tissue

value: Tumor

tag: patient id


title: 41A_Mnt

description:
counts.txt
Sample 72

tag: cell line


title: 51B_Rxrb

description:
counts.txt
Sample 67

value: Rxrb


title: 60A_Tead2

description:
counts.txt
Sample 68

value: NMUMG


title: 47B_Pbx3

description:
counts.txt
Sample 63

value: clone E9


title: 55A_Sp1

description:
counts.txt
Sample 69


title: 59B_Tcfe2a

description:
counts.txt
Sample 64


title: 25B_Zbtb7a

description:
counts.txt
Sample 70


title: 43B_Nfat5

description:
counts.txt
Sample 60


title: 45B_Nrip2

description:
counts.txt
Sample 58


title: 5B_Zeb2

description:
counts.txt
Sample 59


title: 9A_Irf9

description:
counts.txt
Sample 56


title: 35A_Hdac4

description:
counts.txt
Sample 55


title: 33A_Foxf2

description:
GSM3083815
counts.txt
Sample 66


title: 36B_Hoxb6

description:
counts.txt
Sample 76


title: 56A_Sub1

description:
counts.txt
Sample 61


title: 33B_Foxf2

description:
GSM3083816
counts.txt
Sample 57


title: 23A_Smad7

description:
counts.txt
Sample 81


title: 52B_Rybp

description:
counts.txt
Sample 54


title: 26B_Cnbp

description:
counts.txt
Sample 51

value: Cnbp


title: 32B_Foxc1

description:
counts.txt
Sample 52


title: 51A_Rxrb

description:
counts.txt
Sample 53

value: A


title: 29B_Fosb

description:
counts.txt
Sample 50

value: Fosb


title: 29A_Fosb

description:
counts.txt
Sample 75


title: 54B_Snail

description:
counts.txt
Sample 49

value: Snail


title: 54A_Snail

description:
counts.txt
Sample 65


title: 8B_Irf2bp2

description:
counts.txt
Sample 62

value: B


title: 48A_Pml

description:
counts.txt
Sample 47

value: Pml


title: 50B_Rexo1

description:
counts.txt
Sample 48


title: 30A_Fosl1

description:
counts.txt
Sample 46


title: 49B_Pou2f1

description:
counts.txt
Sample 44


title: 7B_Irf1

description:
counts.txt
Sample 45


title: 25A_Zbtb7a

description:
counts.txt
Sample 43


title: 57B_Taf5l

description:
counts.txt
Sample 36


title: 5A_Zeb2

description:
counts.txt
Sample 37


title: 26A_Cnbp

description:
counts.txt
Sample 41


title: 58A_Taf6l

description:
counts.txt
Sample 38


title: 3B_Smad4

description:
counts.txt
Sample 42


title: 3A_Smad4

description:
counts.txt
Sample 32


title: 37B_Junb

description:
counts.txt
Sample 33

value: Junb


title: 24A_Trip4

description:
counts.txt
Sample 31


title: 39B_Mef2b

description:
counts.txt
Sample 29


title: 1B_siCtr_4d

description:
GSM3083814
counts.txt
Sample 30


title: 30B_Fosl1

description:
counts.txt
Sample 27


title: 53A_Smarce1

description:
counts.txt
Sample 28


title: 32A_Foxc1

description:
counts.txt
Sample 24


title: 31A_Fosl2

description:
counts.txt
Sample 34


title: 27A_Ctbp1

description:
counts.txt
Sample 26


title: 10A_Maml2

description:
counts.txt
Sample 25


title: 38B_Klf8

description:
counts.txt
Sample 23


title: 44B_Nfkbib

description:
counts.txt
Sample 39

value: Nfkbib


title: 44A_Nfkbib

description:
counts.txt
Sample 22


title: 46B_Pawr

description:
counts.txt
Sample 21


title: 28A_Elf4

description:
counts.txt
Sample 20


title: 24B_Trip4

description:
counts.txt
Sample 40


title: 37A_Junb

description:
counts.txt
Sample 18


title: 9B_Irf9

description:
counts.txt
Sample 16


title: 23B_Smad7

description:
counts.txt
Sample 19


title: 53B_Smarce1

description:
counts.txt
Sample 35


title: 48B_Pml

description:
counts.txt
Sample 10


title: 28B_Elf4

description:
counts.txt
Sample 9


title: 27B_Ctbp1

description:
counts.txt
Sample 7


title: 36A_Hoxb6

description:
counts.txt
Sample 12


title: 61B_Trank1

description:
counts.txt
Sample 8


title: 63A_siCtr_0d

description:
GSM3083811
counts.txt
Sample 13


title: 7A_Irf1

description:
counts.txt
Sample 6


title: 60B_Tead2

description:
counts.txt
Sample 4


title: 43A_Nfat5

description:
counts.txt
Sample 2


title: 34A_Gtf2i

description:
counts.txt
Sample 1


title: 6B_Sox4

description:
counts.txt
Sample 5


title: 4B_Zeb1

description:
counts.txt
Sample 3


title: Sp1_55C

data_processing:
Sequencing adapters were removed from obtained single-end miRNA-seq reads (51-mers).
Preprocessed reads were mapped to mouse genome assembly, version mm10, with Bowtie (included in R/Bioconductor package QuasR, version 1.0.9.) allowing up 50 hits in the genome.
miRNA coordinates from miRBase (http://www.mirbase.org/, version 21) were extented by 3bp on each side and miRNA expression levels were quantified as the number of reads that started within any extended mature miRNA.
The differentially expressed miRNAs were identified using the edgeR package (version 3.2.4).
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for miRNAs, 1.column is miRNA id, 2. and remaining columns contain raw counts

extract_protocol:
Total RNA was isolated with the miRNeasy Mini Kit (Qiagen). 1µg total RNA was electrophoresed to isolate the miRNA fraction from 17 to 29 nct. After extraction from the PAGE gel and precipitation, RNA was resuspended in 4ul Rnase-free water
MicroRNAs were ligated with 3’ adapters, RT primers annealed, then 5' adapters ligated followed by reverse transcription and amplification including one of 48 different reverse primers. The amplified cDNA constructs were gel purified using QIAEX II Gel Extraction Kit (Qiagen) and eluted in 25µl water. Libraries were quality-checked on the Fragment Analyzer and samples pooled by batches of of 48, 40 and 42 libraries respectively in equal molarity. Each pool was further quantified with Pico-Green. 11pM and used for clustering on the cBot2 (Illumina). Samples were sequenced Single-Read over 51 cycles on HiSeq2500 using the HiSeq Flow Cell v4 (Illumina) and the HiSeq SBS Kit v4 (Illumina). Primary data analysis was performed with the Illumina RTA version 1.18.64 and bcl2fastq-2.16.0.10.

value: NMUMG cells, clone E9


title: Fosb_29A

value: siFosb


title: Taf5l_57A


title: Mnt_41B

value: siMnt


title: 50A_Rexo1

description:
counts.txt
Sample 17


title: Foxf2_33A


title: Rybp_52A

value: siRybp


title: 6944-3p_12E


title: Smad7_23A


title: 101a-3p_21D


title: 56B_Sub1

description:
counts.txt
Sample 15


title: 45A_Nrip2

description:
counts.txt
Sample 14


title: Taf6l_58B


title: Hoxb6_36B


title: 47A_Pbx3

description:
counts.txt
Sample 11


title: Gtf2i_34B


title: Maml2_10C


title: Zbtb7a_25B


title: 1199-5p_11E


title: 0dmiCtr_64D

value: miCtr


title: 200a-3p_13E


title: 31-3p_20A


title: Sub1_56A


title: Pou2f1_49A


title: Trank1_61A


title: Tcf3_59B


title: 4dmiCtr_2D


title: Tead2_60A


title: Zeb1_4C


title: Snai1_54A


title: mES G4 CUT&Tag Rep2 Batch1

tag: cell type

value: mouse embryonic stem cells

tag: antibody


title: Tcf3_59A


title: Ncoa2_42B


title: 4dCtr_1A

value: siCtr


title: Irf2bp2_8A


title: 0dCtr_63C


title: Mnt_41A


title: Rxrb_51B

value: siRxrb


title: Pbx3_47B


title: Nfat5_43B


title: Fosl2_31C


title: Sox4_6A


title: Irf2bp2_8B


title: Klf8_38C


title: 96-5p_17C


title: Fosl2_31A


title: Smad4_3B


title: Ncoa2_42A


title: 1199-5p_11D


title: Cbnp_26A

value: siCbnp


title: Pou2f1_49B


title: Irf9_9A


title: Nfkbib_44B

value: siNfkbib


title: 200a-3p_13D


title: Pawr_46A

value: siPawr


title: Junb_37B

value: siJunb


title: Sp1_55A


title: Taf5l_57B


title: Zbtb7a_25A


title: Hdac4_35B


title: Rxrb_51A


title: Hdac4_35A


title: Snai1_54B


title: 1247-3p_62A


title: Nrip2_45B


title: 429-3p_16E


title: 181b-2-3p_19D


title: Fosl1_30A


title: Zeb2_5B


title: 101b-3p_22D


title: Foxf2_33B


title: Zeb2_5A


title: 200c-3p_15D


title: Fosb_29B


title: Smarce1_53B


title: Trip4_24B


title: Pml_48A

value: siPml


title: Cnbp_26B

value: siCnbp


title: Irf1_7B


title: Taf6l_58A


title: Foxc1_32B


title: Rexo1_50B


title: 96-5p_17A


title: Elf4_28A


title: Mef2b_39A


title: 101b-3p_22E


title: 31-3p_20C


title: Nrip2_45A


title: Irf1_7A


title: 6944-3p_12D


title: Junb_37A


title: 4dCtr_1B


title: Fosl1_30B


title: 0dmiCtr_64E


title: 4dmiCtr_2E


title: 101a-3p_21E


title: Gtf2i_34A


title: Klf8_38B


title: Smad4_3A


title: Tead2_60B


title: Sox4_6B


title: Elf4_28B


title: Rybp_52B


title: 200c-3p_15E


title: 125b-5p_18D


title: Maml2_10A


title: Pawr_46B


title: Smarce1_53A


title: Smad7_23B


title: Zeb1_4B


title: Trank1_61B


title: 200b-3p_14D


title: Nfkbib_44A


title: Mef2b_39B


title: 200b-3p_14E


title: Hoxb6_36A


title: 429-3p_16D


title: Pml_48B


title: Foxc1_32A


title: Ctbp1_27A


title: 125b-5p_18E


title: Rexo1_50A


title: Trip4_24A


title: 0dCtr_63A

value: miR-Ctr


title: Pbx3_47A


title: 1247-3p_62E


title: Ctbp1_27B


title: Sub1_56B


title: Irf9_9B


title: Nfat5_43A


title: Subject TS5 at timepoint B

status: Public on Apr 05 2021

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

description: single-cell RNAseq

data_processing:
Raw sequencing reads were demultiplexed using Cell Ranger mkfastq pipeline to create FASTQ files.
Cell Ranger count pipeline (v3.1) was employed in order to perform alignment (using STAR), filtering, barcode counting, and UMI counting.
Seurat v3.1 pre-processing standard protocol as defined by Satija lab.
10x cellranger count filtered output data of PBMCs from thirteen healthy controls were added to that of the eighteen Covid-19 samples. Seurat package (v3.1) was used for all downstream analysis. 10x gene expression matrices for each sample were converted and combined into one Seurat object.
Cells that had mitochondrial gene percentages higher than 12% and cells with less than 200 genes were excluded from the study to filter out dead and dying cells.
Genome_build: GRCh38 (Ensembl 93)
Supplementary_files_format_and_content: Cell Ranger filtered_gene_matrix, seurat objects

source_name: PBMC

extract_protocol:
PBMCs were isolated from whole blood using density gradient centrifugation, and immediately cryopreserved. They were later thawed, DMSO was removed, cells were filtered and loaded to the 10x chromium platform
Libraries were prepared using the 10X Genomics Chromium Next GEM Chip G, according to the manufacturer’s user guide (document number CG000208, revision E, February 2020)

value: PBMC

tag: disease severity

value: Stable

tag: tocilizumab treatment

value: Yes

tag: age

tag: Sex

value: M

tag: race

value: white

tag: bmi

tag: weight-kg

tag: height-m

value: Tocilizumab

tag: time-point

value: B

tag: chronic htn

tag: htn

tag: lung disease

value: No

tag: hospital admission

tag: icu admission

tag: outcome

value: Discharged

tag: tocilizumab dose (mg/kg)

tag: time difference between samples a and b (d)


title: Subject TS5 at timepoint A

description: single-cell RNAseq

tag: cell type

tag: diagnosis

tag: disease severity

tag: treatment

value: A


title: Subject TS4 at timepoint B

description: single-cell RNAseq

tag: tocilizumab treatment

tag: age

tag: Sex

tag: race


title: Subject TS4 at timepoint A

description: single-cell RNAseq

tag: bmi

tag: weight-kg

tag: height-m

tag: time-point


title: Subject TP9 at timepoint B

description: single-cell RNAseq

value: Progressive

value: hispanic

value: B (only 1 time-point available for this patient)

tag: chronic htn

tag: htn

tag: lung disease

tag: hospital admission

value: Expired


title: Subject TP8 at timepoint B

description: single-cell RNAseq

tag: icu admission

tag: outcome

tag: tocilizumab dose (mg/kg)

tag: time difference between samples a and b (d)


title: Subject TS2 at timepoint B

description: single-cell RNAseq

tag: cell type

tag: diagnosis

tag: disease severity

value: black

tag: treatment


title: Subject TS2 at timepoint A

description: single-cell RNAseq

tag: tocilizumab treatment

tag: age

tag: Sex

tag: race


title: Subject TS3 at timepoint B

description: single-cell RNAseq

value: F

tag: bmi

tag: weight-kg

tag: height-m

tag: time-point


title: Subject TP7 at timepoint B

description: single-cell RNAseq

tag: chronic htn

tag: htn

tag: lung disease

tag: hospital admission


title: Subject TP6 at timepoint A

description: single-cell RNAseq

tag: icu admission

tag: outcome

tag: tocilizumab dose (mg/kg)

tag: time difference between samples a and b (d)


title: Subject TP6 at timepoint B

description: single-cell RNAseq

tag: cell type

tag: diagnosis

tag: disease severity

tag: treatment


title: Subject NS1 at timepoint B

description: single-cell RNAseq

tag: tocilizumab treatment

tag: age

tag: Sex

tag: race

value: No Tocilizumab


title: Subject TP7 at timepoint A

description: single-cell RNAseq

value: PBMC

tag: bmi

tag: weight-kg

tag: height-m

tag: time-point


title: Subject NS1 at timepoint A

description: single-cell RNAseq

value: Stable

tag: chronic htn

tag: htn

tag: lung disease

tag: hospital admission


title: 181b-2-3p_19E

tag: tissue

value: NMUMG cells, clone E9

tag: tgfb treatment

tag: sirna transfected


title: Subject TS3 at timepoint A

description: single-cell RNAseq

tag: cell type

tag: diagnosis

tag: disease severity

value: Yes

tag: icu admission

tag: outcome

tag: tocilizumab dose (mg/kg)

tag: time difference between samples a and b (d)


title: CITE3_Samples NS0A, NS0B, TS2A, TS2B, TP6A

description:
single-cell RNAseq + CITEseq
Detailed sample metadata are included in the tar archive with the processed data.

data_processing:
Library strategy: CITE-seq
Raw sequencing reads were demultiplexed using Cell Ranger mkfastq pipeline to create FASTQ files.
Cell Ranger count pipeline (v3.1) was employed in order to perform alignment (using STAR), filtering, barcode counting, and UMI counting.
CITE-seq samples were demultiplexed and attributed to a biological sample
Seurat v3.1 pre-processing standard protocol as defined by Satija lab
Genome_build: GRCh38 (Ensembl 93)
Supplementary_files_format_and_content: Cell Ranger filtered_gene_matrix, seurat objects

extract_protocol:
PBMCs were isolated from whole blood using density gradient centrifugation, and immediately cryopreserved. They were later thawed, DMSO was removed, cells were filtered, antibodies were applied, and cells were loaded to the 10x chromium platform
Libraries were prepared using the 10X Genomics Chromium Next GEM Chip G, according to the manufacturer’s user guide (document number CG000208, revision E, February 2020)


title: CITE5_Samples TS3A, TS3B, TS4A, TS4B, TP9B


title: CITE2_Samples NS1A, NS1B, TS5A, TS5B, TP7A, TP7B


title: Subject NS0 at timepoint B

description: single-cell RNAseq

tag: tocilizumab treatment

tag: age

tag: Sex

value: M

tag: race

value: white

tag: bmi

tag: weight-kg

tag: treatment


title: CITE6_Samples TS3A, TS3B, TS4A, TS4B, TP9B


title: CITE4_Samples NS0A, NS0B, TS2A, TS2B, TP6A, TP6B


title: CITE1_Samples NS1A, NS1B, TS5A, TS5B, TP7A, TP7B


title: Subject NS0 at timepoint A

description: single-cell RNAseq

tag: height-m

tag: time-point

tag: chronic htn

tag: htn

tag: lung disease

tag: hospital admission


title: IMR90 control RNA-seq #1

status: Public on Mar 25 2021

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

institute: Lund University

data_processing:
RNA-seq datasets were aligned to the hg38 human genome using STAR v2.5.2b  with the parameter outFilterMultimapNmax set to 1.
Bioconductor package DESeq2  was used to analyze differential gene expression.
rMAT v4.0.2 was used to identify alternative splicing events
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: IMR90 cells

growth_protocol: IMR90 human primary cells cultured in EMEM+10%FBS+1%Penicilin/Streptomycin under standard conditions (5% CO2 humified chamber).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MicroPrep (Zymo Research Corporation) according to manufacturer's protocol. DNAse in column treatment was performed according to guidelines of the producer. Quality and quantity of the resulting RNA was confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 300 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with  Ribo-Zero Gold treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq 500 High Output v2 kit (300 cycles) Illumina platform.

treatment_protocol: Cells were subjected to subsequent lentiviral transduction with doxycycline (dox) inducible c-MYC oncogene vector and short hairpin RNA against SF3A3 splicing factor. After selection for pure populations of transduced cells, MYC was induced by 1 ug/ml dox and cells were harvested 24 hours afterwards into Trizol reagent.

tag: cell line

tag: overexpression

value: Control

tag: knockdown


title: IMR90 MYC RNA-seq #1

value: MYC


title: IMR90 MYC RNA-seq #2


title: IMR90 control RNA-seq #2


title: WT-High_input

status: Public on Mar 18 2021

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed ChIP-seq reads were aligned using bowtie 1.1.2
Aligned ChIP-seq reads that overlapped ENCODE blacklist regions were removed
ChIP-seq reads were extended to 250bp
ChIP-seq samples were normalized to sequencing depth and normalized input was subtracted
ChIP-seq samples were converted to BigWig format
RNA-seq trimmed reads were quantified using Salmon v1.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format
Supplementary_files_format_and_content: Quantified RNA-seq transcripts in text

source_name: Bone-marrow derived monocytes

extract_protocol:
Samples containing 1M cells were centrifuged at 1600 g for 5 minutes at 4°C. Each sample was washed twice with cold 1 mL PBS and resuspended in 9.375mL of PBS. Then, 0.625 mL of 16% formaldehyde was added and the samples were incubated on a shaker for 5 minutes at room temperature. The samples were then quenched with 0.667 mL of 2M glycine and incubated for 5 minutes at room temperature on a rotator. The cells were then centrifuged at 1600 g for 5 minutes and washed twice with 1 mL cold PBS. The pellet was resuspended in 130 µL of Covaris sonication buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.1% SDS and 1x protease inhibitor cocktail (PIC)) and sonicated with a Covaris S220 sonicator using 75 W peak incident power, 5% duty factor, and 200 cycles per burst for 16 minutes at 4°C. Sonicated samples were centrifuged at 16,100 g for 10 minutes at 4°C before the supernatant containing sheared chromatin was removed to a fresh tube. 2.4 µL of sheared chromatin was then mixed with 46.6 µL of IP buffer (20mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100, 1% freshly added PMSF and PIC) to generate a 50µL sample containing chromatin from 20,000 cells for MOWChIP-seq.
Libraries for sequencing were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift-Bio).

treatment_protocol: Cells were cultured in RPMI complete media (RPMI 1640 with 10% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin) along with M-CSF (10 ng/mL) and either PBS, low-dose LPS (100 pg/mL), or high-dose LPS (1 µg/mL). Fresh LPS was added every two days and the cells were harvested after 5 days.

tag: strain

tag: genotype

value: WT

tag: cell type

value: BMDMs

value: high-dose LPS

tag: chip antibody


title: IMR90 MYC RNA-seq #3


title: IMR90 control RNA-seq #3


title: WT-Low_input

value: low-dose LPS


title: 78 hpf liver from transgenics overexpressing nAtf6 - Clutch 1

status: Public on Mar 10 2021

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

country: United Arab Emirates

institute: New York University Abu Dhabi

description: For library preparation, high quality of total RNA was QCed using a bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). The samples collected at 120 hpf were rRNA depleted by Ribo Zero Gold treatment. Further, mRNA library of all samples was prepared using Illumina TruSeq V2 RNA sample Prep Kit (San Diego, CA) according to the manufacturer’s protocol. Briefly, 100 ng of total mRNA was poly-A purified, fragmented, and first-strand cDNA reverse transcribed using random primers. Following second-strand cDNA synthesis, end repair, addition of a single A base, TrueSeq adapter-index was ligated to cDNA libraries, and PCR amplification of 12 cycles was done for enrichment, producing a 350-400 bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 (Agilent Technologies). The quantities of the libraries required for RNA-seq were determined by real-time qPCR using a KAPA library quantification kit for the Illumina platform (Kapa Bio systems).

data_processing:
Illumina Casava  software used for basecalling.
Sequencing quality was assessed by using MultiQC v1.7
Alignment by HISTA2 with default parameters, only paired reads are aligned and multiple alignments are kept
Gene expression is counted in the exon of  ensemble gene annotation with HTseq, in union mode
Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V4.0.2
Genome_build: GRCz10
Supplementary_files_format_and_content: csv files for raw reads count of genes

organism: Danio rerio

source_name: Liver

growth_protocol: This experiment was conducted by natural spawnings between tg:(fabp10:nAtf6-cherry; cmlc2:GFP)-C   and tg(fabp10a:CAAX-EGFP ) . Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection, embryos were divided into 30 mL plates, 60 embryos per plate in embryo medium (Zebrafish Information Network). Plates were cleaned daily to remove unfertilized or dead embryos.

extract_protocol: 20 livers were microdissected and immediately placed into 500 uL of TRIzol (Thermo Fisher, 15596026). RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water (Thermo Fisher Scientifc).RNA was quantified by Qubit flurometer.(Thermo Scientific) The 120 hpf samples were DNAseI treated for 30 minutes at 37°C followed by RNA purification (RapidOut DNA Removal Kit–Thermo Fisher Scientific).

treatment_protocol: At approximately 78 hpf/3 dpf - 3 PM  and at 120 hpf/  5  dpf- 9 AM,  plates were treated with 500 uM tricaine (Ethyl 3- aminobenzoate methanesulfonate, Sigma-Aldrich, USA) and  were first sorted for green liver positive as all fish needed to have marked livers to proceed. Next, green liver positive fish were spilt between siblings without green hearts (larvae that don't express nAtf6 - Sample name- Sibs) and with green hearts (larvae that express nAtf6- Sample name : Natf6). These fish were dissected in 3% methyl-cellulose.

tag: pool

tag: rna qbit concentration(ng/ul)


title: 78 hpf liver from transgenics overexpressing nAtf6 - Clutch 2


title: WT-PBS_input

value: PBS


title: SF1_CD41-plus_3

status: Public on Mar 03 2021

data_processing:
Reads were aligned to the mouse genome (UCSC version mm10) with STAR (version 2.5.2a) using the multi-map settings '--outFilterMultimapNmax 10 --outSAMmultNmax 1'
Read and alignment quality was evaluated using the qQCReport function of the R/Bioconductor package QuasR (R version 3.4.2, Bioconductor version 3.6)
Assignment of reads to genes employed the UCSC refGene annotation (downloaded 2015-Dec-18)
QuasR function qCount was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model
Differential expression analysis was based on transformed expression values applying limma voom with quantile normalization to the count data.
Genome_build: mm10
Supplementary_files_format_and_content: counts.csv.gz; tab-seperated values text file with columns: 1.Entrez gene ID, 1. gene symbol, 3. gene name, 4. length (exon-union model), 5.-27. read counts

source_name: bone marrow

extract_protocol:
Indicated HSPC subsets from SclCre;V617F and Wildtype mice were isolated by FACS sorting. Total RNA was prepared using Acturus PicoPure RNA isloation kit (Applied biosystems).
RNA was reverse transcribed and cDNA amplified with SMART-Seq v2 or v4 (Takara). Libraries were prepared with Nextera XT (Illumina) according to manufacturer's instructions.

treatment_protocol: SclCre;V617F and Wild type mice were treated with tamoxifen for 5 consequtive days. 12 weeks post-tamoxifen injections, indicated HSPC subsets were isolated by FACS sorting

tag: Sex

value: Female

tag: tissue

value: bone marrow

tag: cell population

value: SclCre;V617F (SF1; Transgenic mice)

tag: protocol


title: 78 hpf liver from sibling of transgenics overexpressing nAtf6 - Clutch 1

growth_protocol: Zebrafish larvae were kept in petri dish at a density of 60 larvae/plate in a 10:14 light/dark cycle.

extract_protocol: 20 livers were microdissected and immediately placed into 500 uL of TRIzol (Thermo Fisher, 15596026). RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water (Thermo Fisher Scientifc).RNA was quantified by Qubit flurometer.(Thermo Scientific). The 120 hpf samples were DNAseI treated for 30 minutes at 37°C followed by RNA purification (RapidOut DNA Removal Kit–Thermo Fisher Scientific).


title: SF1_CD41-plus_2

value: Male


title: SF1_CD41-plus_1


title: SF1_CD41-minus_2


title: WT_CD41-plus_4

value: Wildtype (WT)


title: WT_CD41-plus_3


title: WT_CD41-minus_1


title: SF1_CD41-minus_1


title: MKP_WT_31

value: MKP


title: SF1_CD41-minus_3


title: WT_CD41-minus_4


title: MKP_WT_32


title: WT_CD41-minus_3


title: MKP_WT_30


title: LTHSC_WT_30

value: LTHSC


title: LTHSC_WT_32


title: LTHSC_WT_31


title: MKP_SF1_3


title: LTHSC_SF1_6


title: LTHSC_SF1_7


title: MKP_SF1_1


title: WT-3

status: Public on Jan 28 2021

city: Suzhou

first: xiaoliang

last: yu

state: Jiangsu

address: Chongwen Road

country: China

institute: Suzhou Institute of Systems Medicine

data_processing:
RTA2 software used for basecalling.
Trimmomatic was used to remove illumina sequencing adapters within raw reads of every sample, trim low quality bases of both read ends
Clean reads were mapped to mouse mm10 reference genome with STAR
The alignment bam files were used as htseq-sount（command of python package HTSeq）
DESeq2 was used to identify DEGs (p<=0.05, FC>=2) based on raw reads counts.
Genome_build: mouse mm10
Supplementary_files_format_and_content: txt files include reads counts for each Sample

source_name: small intestine

extract_protocol:
Small intestine were removed, stored in RNAlater buffer, and RNA was harvested using TRIzol（Cat no. 15596018, invitrogen, Thermo Fisher Scientific）. Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat)(Illumina, MRZG12324)  and NEBNext Ultra Directional RNA Libra（NEB, E7420L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s guideline.

value: small intestine

tag: age

value: post natal week 8

value: wild type


title: 78 hpf liver from sibling of transgenics overexpressing nAtf6 - Clutch 2

source_name: dissected liver


title: Vil-1

value: Villin-cre. RIPK3fl/fl


title: Vil-2


title: WT-2


title: WT-1


title: Medulla-pons-2 scRNA-seq

status: Public on Jan 26 2021

city: La Jolla

first: Richard

last: Daneman

state: California

address: 9500 Gilman Dr

institute: UCSD

data_processing:
FASTQ files were run through the 10X Genomics CellRanger pipeline to generate gene counts data using CellRanger version 6.0.1
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, a folder containing the filtered counts matrix, cell barcodes, and feature (gene) names is provided

source_name: Brain

extract_protocol:
Dissectied brain regions were dissociated using both chemical and mechanical dissociation methods and single, tdTomato+ cells were sorted using FACS sorting
RNA libraries were prepared for sequencing using the 10x Genomics v2 standard protocols

treatment_protocol: 1 week before endothelial cells purification, mice were injected I.P. with 20mg/mL Tamoxifen for 3 consecutive days (100 µL/day) to induce tdTomato expression in endothelial cells

value: Tdt-Tomato VeCreERT2; C57/BL6 background

value: Medulla + pons


title: H3K27ac-NHP-LvE-5-17871

status: Public on Jan 27 2021

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
ChIP-seq: After reads mapping to the RheMac reference genome using BWA, peak calling was conducted using MACS2 at default settings. Bigwig files were generated using bamCoverage.
Genome_build: RheMac10
Supplementary_files_format_and_content: bigwig

organism: Macaca mulatta

source_name: PBMCs

extract_protocol:
Cell pellets were dissolved in PBS and crosslinked in solution by using formaldehyde (1% final volume, shaking 10 min at room temperature). Glycine (0.125 M) was added to quench the reaction. Cells were then washed two times with cold PBS. Cell pellets were lysed in a volume of 110µl using lysis buffer (20 mM HEPES pH 7.6, 1% SDS, 1×Protease Inhibitor Cocktails). Samples were sonicated using the Biorupter Pico (Diagenode) with eight cycles (30 s on/30 s off). Afterward, the samples were spun at 16,000×g for 5 min at room temperature and the supernatant was stored at -80°C. Chromatin from 100,000 cells was used for ChIPmentation. ChIPmentation was performed as described by Schmidl et al (*), with several modifications. In short, The chromatin was incubated overnight at 4°C rotating in dilution buffer (1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8, 167 mM NaCl), 1×Protease Inhibitor Cocktail (Roche) and 1µg of antibody [H3K27ac (C15410196, Diagenode)] in a total volume of 300 µl. The next day per ChIP 10µl protein A Dynabeads and 10µl protein G Dynabeads  (both Invitrogen) were added. Beads were washed before use with dilution buffer (+0.15% SDS,+0.1% BSA) and incubated with the chromatin and antibody mix for 60 min at 4°C rotating. Afterward, the beads were washed at 4°C once with ChIP wash buffer 1 (2 mM EDTA, 20 mM Tris pH 8, 1%Triton X-100, 0.1% SDS, 150 mM NaCl), twice with ChIP washbuffer 2 (2 mM EDTA, 20 mM Tris pH 8, 1% Triton X-100, 0.1%SDS, 500 mM NaCl), and twice with TE (1 mM EDTA, 10 mM TrispH 8). Beads were resuspended in 24 µl Tagment DNA buffer ( Nextera) and 1µl Tn5 enzyme (produced in-house) and incubated for 10 min at 37°C with 550 rpm shaking. Afterward, the beads were washed twice with WBI (20 mM HEPES, 150 mM NaCl, 0.1% SDS, 0.1% DOC,1% Triton X-100, 1 mM EDTA, 0.5 mM EGTA) and twice with WBIV (20 mM HEPES, 1 mM EDTA, 0.5 mM EGTA) with 5 min rotating at room temperature in between. Samples were decrosslinked for 1 h at 55°C 1,000 rpm shaking followed by an overnight incubation at 65°C using elution buffer (0.5% SDS, 300 mM NaCl,5 mM EDTA, 10 mM Tris pH 8) and proteinase K. Samples were incubated one additional hour the next day with elution buffer and proteinase K for 1 h at 55°C. The samples were purified using 2×SPRI AMPureXP beads. qPCR was used to determine the sufficient amount of PCR cycles needed to amplify the library. The libraries were amplified using the KAPA HiFi Hotstart Ready Mix (KAPA Biosystems) and Nextera Index Kit 1 (i7) and 2 (i5) primers (Illumina). Amplified libraries were purified using a 0.65× SPRI AMPureXP beads incubation followed by a 1.8× SPRI AMPureXP beads incubation. Library concentration was measured using the KAPA Library Quantification Kit (KAPA Biosystems); library size  was determined using the BioAnalyzer High Sensitivity DNA Kit (Agilent). Sequencing was performed using an Illumina HiSeq 2000, and 50-bp paired-end reads were generated.
ChIP-seq libraries were prepared from precipitated DNA of  1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the HiSeq 2000 or NextSeq (Illumina). RNA-seq: Total RNA was isolated with the RNeasy RNA extraction kit with on-column DNaseI treatment (Qiagen), and the concentration was measured with a Qubit fluorometer (Invitrogen). Ribosomal RNA was removed by Ribo-Zero rRNA Removal Kit (Epicentre) according to manufacturer instructions. 16 µl of purified RNA was fragmented by addition of 4 µl 5× fragmentation buffer (200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and incubated at 94℃ for exactly 90 s. After ethanol precipitation, fragmented RNA was mixed with 5 µg random hexamers, followed by incubation at 70℃ for 10 min and chilling on ice. We synthesized the first-strand cDNA with this RNA primer mix by adding 4 µl 5× first-strand buffer, 2 µl 100 mM DTT, 1 µl 10 mM dNTPs, 132 ng of actinomycin D, 200 U SuperScript III, followed by 2 h incubation at 48℃. First strand cDNA was purified by Qiagen mini elute column to remove dNTPs and eluted in 34 µl elution buffer. Second-strand cDNA was synthesized by adding 91.8 µl, 5 µg random hexamers, 4 µl of 5× first-strand buffer, 2 µl of 100 mM DTT, 4 µl of 10 mM dNTPs with dTTP replaced by dUTP, 30 µl of 5× second-strand buffer, 40 U of Escherichia coli DNA polymer¬ase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubated at 16℃ for 2 h followed by incubation with 10 U T4 polymerase at 16℃ for 10 minutes. Double-stranded cDNA was purified by Qiagen mini elute column and used for library preparation as described in the KAPA HyperPrep protocol.

treatment_protocol: Animals immunized with Bacillus Calmette-Guérin (BCG) strain Sofia (InterVax Ltd.) received a single standard adult human dose of 1.5 - 6.0 × 10^5 CFU.  Vaccines were delivered in a volume of 10 mL intravenously. PBMCs were obtained by density gradient centrifugation with Lymphoprep lymphocyte separation medium (Axis-Shield) and resuspended in RPMI 10% serum for further analysis.

value: H3K27ac (Diagenode C15410196)

tag: treatment

value: Post vaccination BCGiv

value: PBMCs


title: Striatum-2 scRNA-seq

value: Striatum


title: Hypothalamus-2 scRNA-seq

value: Hypothalamus


title: Hypothalamus-1 scRNA-seq


title: H3K27ac-NHP-LvE-4-17870


title: Thalamus-1 scRNA-seq

value: Thalamus


title: MKP_SF1_2

value: Female

value: bone marrow

value: SclCre;V617F (SF1; Transgenic mice)


title: H3K27ac-NHP-LvE-3-17869

value: Pre vaccination


title: H3K27ac-NHP-LvE-1-17867


title: H3K27ac-NHP-LvE-6-17872


title: Striatum-1 scRNA-seq


title: Hippocampus-1 scRNA-seq

value: Hippocampus


title: Spinal-cord-1 scRNA-seq

value: Spinal


title: Medulla-pons-1 scRNA-seq

status: Public on Feb 03 2021

value: Medulla


title: Cortex-1 scRNA-seq

value: Cortex


title: Cerebellum-1 scRNA-seq

value: Cerebellum


title: Vil-3

value: small intestine

value: post natal week 8

value: Villin-cre. RIPK3fl/fl


title: CMML patient classical monocytes [CMML_2086 RNA-Seq]

status: Public on Jan 23 2021

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

data_processing:
Read were trimmed using CUTADAPT
Trimmed reads were mapped to hg19 using star
gene expression data were analyzed using QoRTs
differentail expressed genes  were calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw count txt file

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were sorted using density centrifugation Pancoll (Pan-Biotech, Dutscher, Brumath, France) and CD14+ monocytes through negative selection with magnetic beads and the AutoMacs system (Miltenyi Biotech, Paris, France).
Total DNA AND RNA were extracted using RNA/DNA/Protein Purification Plus Kit (Cat. 47700) (Norgen Biotek Corp.)
libraries were prepared for sequencing using standard Illumina protocols

tag: apoptosis


title: CMML patient classical monocytes [CMML_2108 RNA-Seq]

value: defective


title: CMML patient classical monocytes [CMML_2025 RNA-Seq]


title: CMML patient classical monocytes [CMML_2059 RNA-Seq]


title: LTHSC_SF1_8

value: Male

value: LTHSC


title: CMML patient classical monocytes [CMML_1989 RNA-Seq]


title: CMML patient classical monocytes [CMML_2056 RNA-Seq]


title: CMML patient classical monocytes [CMML_2050 RNA-Seq]


title: CMML patient classical monocytes [CMML_1964 RNA-Seq]


title: H3K27ac-NHP-LvE-2-17868

value: H3K27ac (Diagenode C15410196)

value: PBMCs


title: Thalamus-2 scRNA-seq

value: Tdt-Tomato VeCreERT2; C57/BL6 background

value: Thalamus


title: Midbrain-1 scRNA-seq

value: midbrain


title: CMML patient classical monocytes [CMML_1944 RNA-Seq]


title: CMML patient classical monocytes [CMML_1660 RNA-Seq]


title: CMML patient classical monocytes [CMML_1740 RNA-Seq]


title: CMML patient classical monocytes [CMML_1714 RNA-Seq]


title: CMML patient classical monocytes [CMML_1637 RNA-Seq]


title: CMML patient classical monocytes [CMML_1750 RNA-Seq]


title: CMML patient classical monocytes [CMML_1900 RNA-Seq]


title: CMML patient classical monocytes [CMML_1603 RNA-Seq]


title: CMML patient classical monocytes [CMML_1529 RNA-Seq]


title: CMML patient classical monocytes [CMML_1541 RNA-Seq]


title: CMML patient classical monocytes [CMML_1550 RNA-Seq]


title: 5 dpf  larvae_control (sibling)_RRBS with 50 ng

status: Public on Dec 01 2020

description: DNA quantitiy and quality was assesed by Qbit and Bioanalyzer. 50-250ng of DNA was used for library prep. Libraries were prepared according to Garrett-Bakelman et al., 2015, with the exception that the adaptors used for multiplexing were purchased separately (Next Multiplex Methylated Adaptors–New England Biolabs). Libraries were size selected by dual-step purification with Ampure XP Magnetic Beads (Beckman Coulter, Agencourt) to specifically select a region of fragments from 175 to 670 bp to enrich the intergenomic fraction. Bisulfite conversion was performed with Lightning Methylation Kit (ZYMO Research) by following the manufacturer’s instructions. Libraries were amplified using KAPA HiFi HotStart Uracil+ Taq polymerase (Roche) and purified with Ampure XP Magnetic Beads (Beckman Coulter, Agencourt) before sequencing. RRBS was perfomed using 50 ng of DNA (RBSS-Mut50 and RBSS-Sib50) or 250 ng of DNA (RBSS-Mut250 and RBSS-Sib250).

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed read were mapped to reference GRCz10 with Bismark-0.22.3/bismark bowtie2
bismark_methylation_extractor --gzip --bedGraph input.bam
Genome_build: GRCz10
Supplementary_files_format_and_content: Methylation coverage and percent .txt file in bedgraph format

source_name: 5 dpf whole larvae

growth_protocol: Zebrafish larvae derivied from incross of uhrf1 (hi272) heterozygous adults were kept in 10 cm petri dish at a density of 60 larvae/plate (30ml) in a 10:14 light/dark cycle.

extract_protocol: Genomic DNA was extracted from 10 larvae by using a DNA extraction buffer (10mM Tris-HCl pH9, 10mM EDTA, 200mM NaCl, 0.5% DSD, 200µg/ml proteinase K) as previously described (Chernyavskaya et al., 2017). DNA was resuspended in water and quantified by Qubit dsDNA High Sensitivity kit.

treatment_protocol: Zebrafish larvae were anethetized in tricaine and collected between 120 and 122 hpf.

tag: developmental stage

value: 5 dpf whole larvae

value: sibling


title: 5 dpf  larvae_control (sibling)_RRBS with 250 ng


title: FTS-B

status: Public on Nov 25 2020

city: Houston

first: Yulin

last: Li

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

data_processing:
Library strategy: CRISPR screen
Computational analysis of the libraries was performed using MAGeCK (version 0.5.9.2)
First, cutadapt (version 2.6) was used to trim primer and other technical sequences from paired-end FASTQ files with the specified options: -j 0 --maximum-length 30 --pair-filter=both -e 0.3 -g GCTTTATATATCTTGTGGAAAGGACGAAACACC...GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGT -G CCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAAC...GGTGTTTCGTCCTTTCCACAAGATATATAAAGC
Second, the command, mageck count, was run under default options with the trimmed paired-end FASTQ files supplied in the arguments --fastq and --fastq-2 to collect read counts
Genome_build: Brie mouse sgRNA library (Addgene #73633)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts for each sgRNA

source_name: pancreatic ductal adenocarcinoma cells

growth_protocol: The 4292 pancreatic ductal adenocarcinoma cell line, which has KRAS expressed controlled by the Tet-ON system, was cultured in RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin, containing 1μg/ml doxycycline.

extract_protocol:
Genomic DNA was isolated using the Zymo-Spin V column (Zymo Research).
HiSeq libraries were constructed by one-step PCR amplification following reported protocols (Joung J et al., Nat Protoc. 2017, 12(4):828-863. PMID: 28333914).

treatment_protocol: The 4292 pancreatic ductal adenocarcinoma cells with stable Cas9 expression were infected at low viral titers with the CRISPR lentiviral library so that approximately 10% of the cells were infected, and the infected cells were selected with puromycin (1µg/ml) for two days.

tag: cell line

value: pancreatic ductal adenocarcinoma

value: 100μM farnesylthiosalicylic acid

tag: doxycycline induction


title: RAS-ON-B

value: Untreated


title: NFATc3_rep1

status: Public on Dec 04 2020

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Zhongshan School of Medicine, Sun Yat-Sen University

hyb_protocol: 1.5 ug of Cy5-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent Agilent  Microarray Scanner (G2505C).

data_processing: Rosetta Biosoftware was used to preprocess the small RNA expression data, inlcude normalization and differentially expression analysis.

source_name: human monocyte-derived macrophages

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human peripheral blood mononuclear cells were isolated from healthy volunteer donors by Percoll density gradient centrifugation, and were then differentiated into HMDMs in RPMI-1640 medium supplemented with 10% fetal calf serum, 1% HEPES, 1% penicillin/streptomycin, and 100 ng/ml of macrophage colony-stimulating factor.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: HMDMs were treated with Lacz adenovirus (negative control [NC]) or NFATc3 adenovirus at multiplicity of infection 40 for 24 h.

value: human monocyte-derived macrophages


title: NFATc3_rep2


title: 5 dpf larvae uhrf1-hi272 mutants_RRBS with 50 ng

value: uhrf1 (hi272) mutant


title: RAS-ON-A


title: 5 dpf larvae uhrf1-hi272 mutants_RRBS with 250 ng


title: FTS-A


title: Negative control_rep2


title: Negative control_rep1


title: OR19

status: Public on Oct 14 2020

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Genome_build: Mouse: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: total RNA extracted from mice lung

growth_protocol: Female CD-1 mice weighing 27-32 g were obtained from Charles River Laboratories Ltd. U.K. Prior to exposure, animals were habituated for 5 days. All mice were housed in filter-top cages in an enviromentally controled room and maintained at 21°C and 55% humidity. Lighting was set to mimic a 12/12 h dawn to dusk cycle. Animals had acess to food and water ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Mice were anesthetized by an interperitoneal injection of ketamine (1.9 mg/mouse) and xylazine (0.19 mg/mouse), and were intranasally (50 µl/nostril) intoxicated with crude ricin.

value: NO TREATMENT

value: lung