title: GS_L1D_H06


title: GS_L1D_H01

status: Public on Jun 29 2021

type: SRA

city: Natal

first: Diego

middle: Marques

last: Coelho

state: RN

address: Av. Nascimento de Castro, 2155

department: Bioinformatics

country: Brazil

institute: UFRN

description: Single cell RNA-Seq library from FACS sorted CAG-mRFP;Hes5p-GFP E13.5 mouse brain

library_source: transcriptomic

data_processing:
Illumina Hiseq 2500 default software for basecalling.
Paired-end reads were aligned to the mouse reference genome (mm10) using hisat2 (Kim et al, 2015) with the default parameters except: -p 6.
Quantified against a modified reference transcriptome (GENCODE vM15; (Frankish et al., 2018)) with cuffquant.
Data were analyzed using Seurat R package v2 (Butler et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited with log-normalized count reads for every gene and sample
Supplementary_files_format_and_content: Tab-delimeted with raw gene counts for every gene and sample

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Fluorescence-activated cell sorting (FACS) to separate single-labeled CAG+ cells (only CAG promoter active, mRFP+GFP- cells) and double-labeled CAG+/Hes5+ cells (both promoters active, mRFP+GFP+ cells)
Viable sorted cells of both types collected individually were lysed and libraries were generated using a modified Smart-seq 2 protocol for subsequent scRNA sequencing as described (Chevée et al., 2018).

treatment_protocol: In utero electroporation with a dual promoter plasmid containing two fluorescent proteins under the control of two different promoters: the CAG promoter driving mRFP and the Hes5 promoter driving GFP

tag: strain

tag: tissue

value: cerebral cortex

tag: age

value: embrionic day 13.5

tag: genotype

tag: marker

value: pCAG-mRFP


title: GS_L1D_G09


title: GS_L1D_H04


title: GS_L1D_H03


title: GS_L1D_G08


title: GS_L1D_G07


title: GS_L1D_G04


title: GS_L1D_G02


title: GS_L1D_G05


title: GS_L1D_G03


title: GS_L1D_G01


title: GS_L2C_A01


title: GS_L1D_F12


title: GS_L1D_F11


title: GS_L1D_G12


title: GS_L1D_F10


title: GS_L1D_F07


title: GS_L1D_F04


title: GS_L1D_F08


title: GS_L1D_F02


title: GS_L1D_F05


title: GS_L1D_F03


title: GS_L1D_F01


title: GS_L1D_E06


title: GS_L1D_E08


title: GS_L1D_E07


title: GS_L1D_E12


title: GS_L1D_E10


title: GS_L1D_E02


title: GS_L1D_E11


title: GS_L1D_D12


title: GS_L1D_E09


title: GS_L1D_E01


title: GS_L1D_D11


title: GS_L1D_E04


title: GS_L1D_D10


title: GS_L1D_D09


title: GS_L1D_D08


title: GS_L1D_D06


title: GS_L1D_D07


title: GS_L1D_F09


title: GS_L1D_D03


title: GS_L1D_D05


title: GS_L1D_D02


title: GS_L1D_E03


title: GS_L1D_E05


title: GS_L1D_C07


title: GS_L1D_C09


title: GS_L1D_D01


title: GS_L1D_C12


title: GS_L1D_C06


title: GS_L1D_C08


title: GS_L1D_B12


title: GS_L1D_B11


title: GS_L1D_C02


title: GS_L1D_C01


title: GS_L1D_B07


title: GS_L1D_C03


title: GS_L1D_C04


title: GS_L1D_C05


title: GS_L1D_B03


title: GS_L1D_B02


title: GS_L1D_B09


title: GS_L1D_B06


title: GS_L1D_B01


title: GS_L1D_B08


title: GS_L1D_A12


title: GS_L1D_A11


title: GS_L1D_A10


title: GS_L1D_C11


title: GS_L1D_A09


title: GS_L1D_A08


title: GS_L1D_A07


title: GS_L1D_A06


title: GS_L1D_A03


title: GS_L1D_A04


title: GS_L1A_H12


title: GS_L1A_H11


title: GS_L1D_A01


title: GS_L1A_H10


title: GS_L1A_H09


title: GS_L1A_H05


title: GS_L1A_H07


title: GS_L1A_H08


title: GS_L1A_H06


title: GS_L1A_H04


title: GS_L1A_G11


title: GS_L1A_G12


title: GS_L1A_H02


title: GS_L1A_G09


title: GS_L1A_G10


title: GS_L1A_G08


title: GS_L1A_G07


title: GS_L1A_G03


title: GS_L1A_G05


title: GS_L1A_G04


title: GS_L1A_G06


title: GS_L1A_F10


title: GS_L1A_F12


title: GS_L1A_F09


title: GS_L1D_A02


title: GS_L1A_F08


title: GS_L1D_A05


title: GS_L1A_F06


title: GS_L1A_F05


title: GS_L1A_F02


title: GS_L1A_F07


title: GS_L1A_F01


title: GS_L1A_F04


title: GS_L1A_E11


title: GS_L1A_E10


title: GS_L1A_E09


title: GS_L1A_E08


title: GS_L1A_E05


title: GS_L1A_E04


title: GS_L1A_E07


title: GS_L1A_D10


title: GS_L1A_D12


title: GS_L1A_D11


title: GS_L1A_D03


title: GS_L1A_D09


title: GS_L1A_D07


title: GS_L1A_D08


title: GS_L1A_D05


title: GS_L1A_D01


title: GS_L1A_D06


title: GS_L1A_C11


title: GS_L1A_D02


title: GS_L1A_C12


title: GS_L1A_C09


title: GS_L1A_E12


title: GS_L1A_C08


title: GS_L1A_C02


title: GS_L1A_C03


title: GS_L1A_C04


title: GS_L1A_E02


title: GS_L1A_B08


title: GS_L1A_B11


title: GS_L1A_B10


title: GS_L1A_E03


title: GS_L1A_B07


title: GS_L1A_B05


title: GS_L1A_A12


title: GS_L1A_A11


title: GS_L1A_B02


title: GS_L1A_A07


title: GS_L1A_A08


title: GS_L1A_A06


title: GS_L1A_A09


title: GS_L1A_A05


title: GS_04_C12


title: GS_L1A_B12


title: GS_L1A_A02


title: GS_L1A_B09


title: GS_L1A_A03


title: GS_04_C10


title: GS_L1A_B04


title: GS_04_C11


title: GS_04_C09


title: GS_04_C05


title: GS_04_C07


title: GS_04_B12


title: GS_L1A_B03


title: GS_L1A_B01


title: GS_04_B10


title: GS_04_C02


title: GS_04_B09


title: GS_04_B08


title: GS_L1A_A10


title: GS_L1A_A04


title: GS_04_C06


title: GS_04_B11


title: GS_04_B07


title: GS_04_B06


title: GS_04_B05


title: GS_04_A06


title: GS_04_B04


title: GS_04_A08


title: GS_04_A07


title: GS_04_C08


title: GS_04_A03


title: GS_04_A04


title: GS_03_H12


title: GS_03_H04


title: GS_01_H09


title: GS_01_H11


title: GS_01_H08


title: GS_01_H07


title: GS_01_H05


title: GS_01_H04


title: GS_01_H03


title: GS_01_H02


title: GS_01_G12


title: GS_01_H01


title: GS_01_G11


title: GS_01_G10


title: GS_01_G09


title: GS_01_G07


title: GS_01_G04


title: GS_01_G08


title: GS_01_G05


title: GS_01_G03


title: GS_01_G02


title: GS_01_F11


title: GS_01_F05


title: GS_L3D_H08


title: GS_L3D_H11


title: GS_01_F09


title: GS_L3D_H06


title: GS_L3D_H07


title: GS_01_H06


title: GS_L3D_H05


title: GS_L3D_H01


title: GS_L3D_H03


title: GS_L3D_H02


title: GS_L3D_G11


title: GS_L3D_G12


title: GS_L3D_G10


title: GS_L3D_G09


title: GS_L3D_G08


title: GS_L3D_G07


title: GS_L3D_G05


title: GS_01_G01


title: GS_L3D_G04


title: GS_L3D_G02


title: GS_L3D_G06


title: GS_L3D_F12


title: GS_L3D_H12


title: GS_L3D_F10


title: GS_L3D_F07


title: GS_L3D_F08


title: GS_L3D_F06


title: GS_L3D_H04


title: GS_L3D_F03


title: GS_L3D_F11


title: GS_L3D_F02


title: GS_L3D_F09


title: GS_L3D_F04


title: GS_L3D_E12


title: GS_L3D_G01


title: GS_L3D_F01


title: GS_L3D_F05


title: GS_L3D_E11


title: GS_L3D_E07


title: GS_L3D_E03


title: GS_L3D_E08


title: GS_L3D_E10


title: GS_L3D_E02


title: GS_L3D_E09


title: GS_L3D_E04


title: GS_L3D_D12


title: GS_L3D_D09


title: GS_L3D_D03


title: GS_L3D_D07


title: GS_L3D_D05


title: GS_L3D_C12


title: GS_L3D_D01


title: GS_L3D_D06


title: GS_L3D_C10


title: GS_L3D_C05


title: GS_L3D_E05


title: GS_L3D_C11


title: GS_L3D_C04


title: GS_L3D_C07


title: GS_L3D_C09


title: GS_L3D_C06


title: GS_L3D_C01


title: GS_L3D_C03


title: GS_L3D_B07


title: GS_L3D_B05


title: GS_L3D_B09


title: GS_L3D_D08


title: GS_L3D_E01


title: GS_L3D_B08


title: GS_L3D_B04


title: GS_L3D_D11


title: GS_L3D_C08


title: GS_L3D_B03


title: GS_L3D_D02


title: GS_L3D_B02


title: GS_L3D_B01


title: GS_L3D_A12


title: GS_L3D_A11


title: GS_L3D_A10


title: GS_L3D_A07


title: GS_L3D_A09


title: GS_L3D_A06


title: GS_L3D_A05


title: GS_L3D_A01


title: GS_L3D_A04


title: GS_L3D_A02


title: GS_L3D_A03


title: GS_L3A_H12


title: GS_L3D_B11


title: GS_L3D_B10


title: GS_L3A_H11


title: GS_L3A_H08


title: GS_L3A_H09


title: GS_L3A_H07


title: GS_L3A_H05


title: GS_L3A_H01


title: GS_L3A_H03


title: GS_L3A_H04


title: GS_L3A_G11


title: GS_L3A_G08


title: GS_L3A_G09


title: GS_L3A_H10


title: GS_L3A_G05


title: GS_L3A_G12


title: GS_L3A_G03


title: GS_L3A_H06


title: GS_L3A_G01


title: GS_L3A_F11


title: GS_L3A_F09


title: GS_L3A_F07


title: GS_L3A_F12


title: GS_L3A_F03


title: GS_L3A_H02


title: GS_L3A_E10


title: GS_L3A_E12


title: GS_L3A_E09


title: GS_L3A_F05


title: GS_L3A_E05


title: GS_L3A_E02


title: GS_L3A_F04


title: GS_L3A_F02


title: GS_L3A_E01


title: GS_L3A_E08


title: GS_L3A_D07


title: GS_L3A_D05


title: GS_L3A_E06


title: GS_L3A_D03


title: GS_L3A_C12


title: GS_L3A_C09


title: GS_L3A_E03


title: GS_L3A_G07


title: GS_L3A_D11


title: GS_L3A_C07


title: GS_L3A_C05


title: GS_L3A_D10


title: GS_L3A_D08


title: GS_L3A_C02


title: GS_L3A_C10


title: GS_L3A_F08


title: GS_L3A_C11


title: GS_L3A_B11


title: GS_L3A_C06


title: GS_L3A_C04


title: GS_L3A_B04


title: GS_L3A_B03


title: GS_L3A_C03


title: GS_L3A_B02


title: GS_L3A_A12


title: GS_L3A_B12


title: GS_L3A_A11


title: GS_L3A_B10


title: GS_L3A_B08


title: GS_L3A_B05


title: GS_L3A_B06


title: GS_L3A_A06


title: GS_L3A_A08


title: GS_L3A_A04


title: GS_L3A_A02


title: GS_L3A_A10


title: GS_L3A_A07


title: GS_L3A_A03


title: GS_L3A_A09


title: GS_L3A_A01


title: GS_L2B_H12


title: GS_L2B_H04


title: GS_L2B_H05


title: GS_L2B_H03


title: GS_L2B_H06


title: GS_L2B_H11


title: GS_L2B_H02


title: GS_L2B_H08


title: GS_L2B_H07


title: GS_L2B_G11


title: GS_L2B_G09


title: GS_L2B_G07


title: GS_L2B_G12


title: GS_L2B_G05


title: GS_L2B_G02


title: GS_L2B_H01


title: GS_L2B_G06


title: GS_L3A_B09


title: GS_L2B_G04


title: GS_L2B_F12


title: GS_L2B_H09


title: GS_L2B_F11


title: GS_L2B_F06


title: GS_L2B_F07


title: GS_L2B_F09


title: GS_L2B_F08


title: GS_L2B_E12


title: GS_L2B_E08


title: GS_L2B_E05


title: GS_L2B_G01


title: GS_L2B_F05


title: GS_L2B_D09


title: GS_L2B_D11


title: GS_L2B_F04


title: GS_L2B_F03


title: GS_L2B_D01


title: GS_L2B_F02


title: GS_L2B_E09


title: GS_L2B_E11


title: GS_L2B_C07


title: GS_L2B_C02


title: GS_L2B_B12


title: GS_L2B_E07


title: GS_L2B_C03


title: GS_L2B_E04


title: GS_L2B_B11


title: GS_L2B_D08


title: GS_L2B_D12


title: GS_L2B_D03


title: GS_L2B_D07


title: GS_L2B_C12


title: GS_L2B_C09


title: GS_L2B_C11


title: GS_L2B_C05


title: GS_L2B_C08


title: GS_L2B_E03


title: GS_L2B_B06


title: GS_L2B_C04


title: GS_L2B_B05


title: GS_L2B_B02


title: GS_L2B_B04


title: GS_L2B_B03


title: GS_L2B_B09


title: GS_L2B_B08


title: GS_L2B_B01


title: GS_L2B_D05


title: GS_L2B_A11


title: GS_L2B_A09


title: GS_L2B_A08


title: GS_L2B_A12


title: GS_L2B_A07


title: GS_L2B_A05


title: GS_L2B_A06


title: GS_L2B_A02


title: GS_L2B_A01


title: GS_L2B_B07


title: GS_L1C_H12


title: GS_L2B_A03


title: GS_L1C_H08


title: GS_L3A_C08


title: GS_L1C_H09


title: GS_L3A_G04


title: GS_L1C_H06


title: GS_L1C_H07


title: GS_L1C_H04


title: GS_L1C_H03


title: GS_L1C_G12


title: GS_L1C_G11


title: GS_L1C_G10


title: GS_L1C_G09


title: GS_L1C_G07


title: GS_L1C_G05


title: GS_L1C_G04


title: GS_L1C_G01


title: GS_L1C_G02


title: GS_L1C_G03


title: GS_L1C_H10


title: GS_L1C_F10


title: GS_L1C_F11


title: GS_L1C_F09


title: GS_L1C_F12


title: GS_L2B_A04


title: GS_L1C_F08


title: GS_L1C_F07


title: GS_L1C_F06


title: GS_L1C_H02


title: GS_L1C_H01


title: GS_L1C_F02


title: GS_L1C_F01


title: GS_L1C_E12


title: GS_L1C_E11


title: GS_L1C_G06


title: GS_L1C_E09


title: GS_L1C_E10


title: GS_L1C_E08


title: GS_L1C_E07


title: GS_L1C_E04


title: GS_L1C_E03


title: GS_L1C_F05


title: GS_L1C_E01


title: GS_L1C_D11


title: GS_L1C_D10


title: GS_L1C_D09


title: GS_L1C_F03


title: GS_L1C_E02


title: GS_L1C_D12


title: GS_L1C_D03


title: GS_L1C_D05


title: GS_L1C_D07


title: GS_L1C_F04


title: GS_L1C_D01


title: GS_L1C_C12


title: GS_L1C_D02


title: GS_L1C_C08


title: GS_L1C_C10


title: GS_L1C_C06


title: GS_L1C_E05


title: GS_L1C_E06


title: GS_L1C_C11


title: GS_L1C_C05


title: GS_L1C_C09


title: GS_L1C_C04


title: GS_L1C_C02


title: GS_L1C_D08


title: GS_L1C_B12


title: GS_L1C_B06


title: GS_L1C_B10


title: GS_L1C_B04


title: GS_L1C_C01


title: GS_L3A_B01


title: GS_L1C_B05


title: GS_L1C_A12


title: GS_L1C_B08


title: GS_L1C_A11


title: GS_L1C_B03


title: GS_L1C_A10


title: GS_L1C_B09


title: GS_L1C_A09


title: GS_L1C_B11


title: GS_L1C_C07


title: GS_L1C_A08


title: GS_L1C_A07


title: GS_L1C_A05


title: GS_L1C_A06


title: GS_L1C_A04


title: GS_L1C_A03


title: GS_L1C_A01


title: GS_04_G12


title: GS_L1C_A02


title: GS_L1C_C03


title: GS_04_G11


title: GS_04_G10


title: GS_04_G09


title: GS_04_G07


title: GS_04_G06


title: GS_04_G05


title: GS_04_G03


title: GS_04_F12


title: GS_04_G02


title: GS_04_F09


title: GS_04_F04


title: GS_04_F01


title: GS_04_F10


title: GS_04_F08


title: GS_04_F07


title: GS_04_F02


title: GS_04_E12


title: GS_04_F03


title: GS_04_E09


title: GS_04_E11


title: GS_04_E05


title: GS_04_E10


title: GS_04_E06


title: GS_02_C12


title: GS_01_D12


title: GS_01_D10


title: GS_01_D09


title: GS_04_G04


title: GS_01_D07


title: GS_04_F11


title: GS_01_D06


title: GS_01_D03


title: GS_01_D02


title: GS_01_C11


title: GS_01_C10


title: GS_01_C05


title: GS_01_D11


title: GS_01_C06


title: GS_01_C03


title: GS_01_B05


title: GS_01_B07


title: GS_01_B09


title: GS_01_B10


title: kidney - input

city: Shenzhen

first: Yunjun

last: Xiao

address: Zhenyuan Road 628

country: China

institute: Sun Yat-sen University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: peak excel files

molecule: genomic DNA

source_name: kidney

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: chip antibody

value: none (input)

tag: treatment

value: untreated


title: kidney - H3K27me3_ctrl

value: H3K27me3 (Cell Signaling Technology)


title: GS_01_B06


title: GS_01_D08


title: GS_01_B08


title: kidney - H3K27me3_ADA

value: ADA-treated


title: GS_01_B03


title: Egan_SB_Lane_27

city: Toronto

first: Sean

last: Egan

state: ON

address: 555 University Ave

country: Canada

institute: Hospital for Sick Children

description:
primary_combined_insertions.txt
sample_information.txt

data_processing:
Library strategy: Shear-SPLINK
Samples were demultiplexed using fastx_barcode_splitter with parameters ' --bol --mismatches 2' . Sample barcodes and genotypes found in the "sample_information.txt" file.
Read 1 Adaptors were trimmed with cutadapt (v1.8) using parameters ‘-m 5 --no-indels --discard-untrimmed -g R1_5prime=^NNNNNNNNTGTATGTAAACTTCCGACTTCAACTG’
Only the reads starting with a TA were kept for downstream steps
R1 reads were then paired with their respective paired reads (R2)
alignment with novoalign (v3.05.01) using parameters ‘-r ALL 1 -R 0 -c 8 -o SAM’ on paired reads
insertion location and orientation was parsed from sam files and annotated
19493_NICD-49_IRL sample did not pass quality control
Genome_build: mm9
Supplementary_files_format_and_content: Final processed files contain insertion locations. Each insertion is annotated (where possible) and has a corresponding read count. All insertions are found in the primary_combined_insertions.txt file.

extract_protocol:
DNA was purified by DNeasy Blood and Tissue Kit, Qiagen, Cat # 69506
DNA was sheared and then ligated with adaptors. SB insertion junctions were selected amplfied using nested PCR and sent for sequencing.

tag: disease

value: breast cancer


title: GS_01_D05


title: Egan_SB_Lane_24


title: Egan_SB_Lane_26


title: Egan_SB_Lane_25


title: GS_01_D04


title: Egan_SB_Lane_23


title: GS_01_C07


title: Egan_SB_Lane_22


title: Egan_SB_Lane_21


title: Egan_SB_Lane_20


title: GS_01_C04


title: GS_01_B04


title: Egan_SB_Lane_17


title: Egan_SB_Lane_18


title: Egan_SB_Lane_19


title: Egan_SB_Lane_15


title: Egan_SB_Lane_16


title: Egan_SB_Lane_14


title: Egan_SB_Lane_8


title: Egan_SB_Lane_10


title: Egan_SB_Lane_11


title: Egan_SB_Lane_6


title: Egan_SB_Lane_13


title: Egan_SB_Lane_12


title: Egan_SB_Lane_7


title: Egan_SB_Lane_1


title: Egan_SB_Lane_4


title: RNA-seq in HP1g -/-, PMA-treated MEF-derived cell line, replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
STAR version 2.5.0a  (parameters: --outFilterMultimapNmax 30 --outSAMmultNmax 1 --outMultimapperOrder Random) was used for alignment on the reference genome (Mus musculus mm9 from UCSC)
Genes were counted using featureCounts version 1.4.6-p3  from Subreads package (parameters: -t CDS -g ID -s 1).
Genome_build: Mus musculus mm9 from UCSC
Supplementary_files_format_and_content: Matrix of total counts

molecule: total RNA

source_name: knock-out for the expression of HP1g/CBX3 treated with PMA

growth_protocol: Cells were grown in DMEM supplemented with 10% (v/v) fetal calf serum and 100 U.ml-1 penicillin-streptomycin.

extract_protocol:
Total RNA was extracted by guanidinium thiocyanate-phenol-chloroform extraction (AGPC) followed by proteinase K and Dnase I treatment.
Total RNA library preparation was performed on DNase-treated RNA samples by Novogene Co., Ltd, as a lncRNA sequencing service, including lncRNA directional library preparation with rRNA depletion (Ribo-Zero Magnetic Kit), quantitation and pooling. Sequencing (100M raw reads/sample) was performed on the Illumina Hiseq2500 platform to generate paired-end 150 bp reads bearing strand specificity.

treatment_protocol: PMA-treated samples were obtained by addition of 100 nM of Phorbol 12-Myristate 13-Acetate (PMA) in DMSO for 30 min on nearly confluent cells.

tag: cell type

value: MEF-derived cell lines

value: HP1g/CBX3 knockout


title: RNA-seq in HP1g -/-, PMA-treated MEF-derived cell line, replicate 2


title: RNA-seq in HP1g -/-, PMA-treated MEF-derived cell line, replicate 1


title: Egan_SB_Lane_3


title: Egan_SB_Lane_2


title: Egan_SB_Lane_5


title: RNA-seq in HP1g -/- MEF-derived cell line, replicate 3

source_name: knock-out for the expression of HP1g/CBX3


title: RNA-seq in HP1g expressing, PMA-treated MEF-derived cell line, replicate 3

source_name: recomplemented for the expression of HP1g treated with PMA


title: RNA-seq in HP1g -/- MEF-derived cell line, replicate 2


title: RNA-seq in HP1g -/- MEF-derived cell line, replicate 1


title: RNA-seq in HP1g expressing, PMA-treated MEF-derived cell line, replicate 1

value: recomplemented for the expression of HP1g


title: RNA-seq in HP1g expressing MEF-derived cell line, replicate 1

source_name: recomplemented for the expression of HP1g


title: RNA-seq in HP1g expressing MEF-derived cell line, replicate 3


title: RNAchIP-seq HP1g-IP, PMA-treated HP1g expressing cell line, replicate 3

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
STAR version 2.5.0a  (parameters: --outFilterMultimapNmax 30 --outSAMmultNmax 1 --outMultimapperOrder Random) was used for alignment on the reference genome (Mus musculus mm9 from UCSC)
Genes were counted using featureCounts version 1.4.6-p3  from Subreads package (parameters: -t CDS -g ID -s 1).
MACS2 version 2.1.0  was used to call HP1-binding peaks on RNA-ChIP data (parameters: --nomodel --extsize=150 -q 0.1). Bamcoverage from Deeptools was used to produce normalized BigWig files to 1X.
Genome_build: Mus musculus mm9 from UCSC
Supplementary_files_format_and_content: Bigwig files from deeptools

source_name: recomplemented for the expression of HP1g_PMA-treated

extract_protocol:
A chromatin-enriched fraction (input) was obtained by a combination of Dnase-treatment and sonication of nuclei submitted to a low formaldehyde crosslinking procedure. RNAchIP samples (HP1g-IP) were obtained out of the solubilized chromatin fraction by immunoprecipitation of HP1g. Subsequent RNA extraction was performed by guanidinium thiocyanate-phenol-chloroform extraction (AGPC) followed by proteinase K and Dnase I treatment.
RNA quality and yield were assessed by the RNA integrity number (RIN) algorithm, using the 2100 Bioanalyzer. Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit-Pico Input Mammalian kit following the manufacturer’s instructions (Clontech, 635005). The quality of all libraries was verified with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen). Clusters were generated for the resulting libraries, with the Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed using the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were then processed with the Illumina Pipeline software, Casava version 1.9

tag: cell line

tag: rip


title: Egan_SB_Lane_9


title: GS_L1C_H05


title: RNAchIP-seq HP1g-IP, PMA-treated HP1g expressing cell line, replicate 2


title: RNA-seq in HP1g expressing MEF-derived cell line, replicate 2


title: RNAchIP-seq HP1g-IP, PMA-treated HP1g expressing cell line, replicate 1


title: RNAchIP-seq HP1g-IP, HP1g expressing cell line, replicate 3


title: RNAchIP-seq HP1g-IP, HP1g expressing cell line, replicate 2


title: RNAchIP-seq HP1g-IP, HP1g expressing cell line, replicate 1


title: RNAchIP-seq input, PMA-treated HP1g expressing cell line, replicate 2

value: input


title: RNAchIP-seq input, PMA-treated HP1g expressing cell line, replicate 3


title: RNAchIP-seq input, HP1g expressing cell line, replicate 2


title: RNAchIP-seq input, HP1g expressing cell line, replicate 3


title: RNAchIP-seq input, HP1g expressing cell line, replicate 1


title: eds1-2_0h_r3 (RNA-Seq)

city: Cologne

first: Thomas

last: Griebel

address: Carl-von-Linne-Weg 10

department: Department of Plant Microbe Interactions

country: Germany

institute: Max-Planck Institute for Plant Breeding Research

description:
1785.AP
1785_AP_S50_L002

data_processing:
RNA-seq reads were mapped to the annotated genome of Arabidopsis thaliana (TAIR10) using TOPHAT2 (a = 10, g = 10) and transformed into a read count per gene per sample using the htseq-count script (s = reverse, t = exon) in the package HTSeq
Genes with less than 100 reads in all samples together were discarded; subsequently, the count data of the remaining genes were TMM normalized and log2 transformed using functions ‘calcNormFactors’ and ‘voom’
To be able to analyze differential gene expression at different time-points after infection between the different genotypes a linear model with the explanatory variable ‘genotype_timepoint’ (i.e., encoding information on both genotype and timepoint after infection) was fitted for each gene using the function lmFit (R package limma). Subsequently, moderated t tests were performed over the contrasts of interest.
In all cases, the resulting P values were adjusted for false discoveries due to multiple hypothesis testing via the Benjamini-Hochberg procedure. Sets of significantly differentially expressed genes between the tested conditions were extracted based on adjusted P values (p adj < 0.05) and log2 fold changes (|log2FCI| ≥ 1).
Genome_build: TAIR10
Supplementary_files_format_and_content: Log2 fold changes and FDR of each gene transcript in each genotype (tpr1, t3, eds1-2 ) and time point compared to Col-0 of the corresponding time point

organism: Arabidopsis thaliana

source_name: eds1-2_0h_5-wk old leaves

growth_protocol: Plants were grown on soil with a daily 10 h light period (150-200 μE/m2s) at 22 °C and 60 % relative humidity. Plant leaf material was harvested after 5 weeks of growth.

extract_protocol:
Total RNA purification with an RNeasy Plant Mini Kit (Qiagen)
mRNA sequencing libraries were constructed with barcodes using the TrueSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: untreated

value: 5-week old leaves


title: eds1-2_24h_r3 (RNA-Seq)

description:
1785.AR
1785_AR_S52_L002

source_name: eds1-2_24h_5-wk old leaves


title: t3_24h_r3 (RNA-Seq)

description:
1785.AO
1785_AO_S49_L002

source_name: tpr1 tpl tpr4 -KO_24h_5-wk old leaves

value: tpr1 tpl tpr4 -KO


title: eds1-2_8h_r3 (RNA-Seq)

description:
1785.AQ
1785_AQ_S51_L002

source_name: eds1-2_8h_5-wk old leaves


title: tpr1_24h_r3 (RNA-Seq)

description:
1785.AL
1785_AL_S46_L002

source_name: tpr1-KO_24h_5-wk old leaves


title: RNA-seq in HP1g expressing, PMA-treated MEF-derived cell line, replicate 2


title: t3_0h_r3 (RNA-Seq)

description:
1785.AM
1785_AM_S47_L002

source_name: tpr1 tpl tpr4 -KO_0h_5-wk old leaves


title: t3_8h_r3 (RNA-Seq)

description:
1785.AN
1785_AN_S48_L002

source_name: tpr1 tpl tpr4 -KO_8h_5-wk old leaves


title: tpr1_8h_r3 (RNA-Seq)

description:
1785.AK
1785_AK_S45_L002

source_name: tpr1-KO_8h_5-wk old leaves


title: Col0_24h_r3 (RNA-Seq)

description:
1785.AI
1785_AI_S69_L003

source_name: Col-0_24h_5-wk old leaves


title: Col0_0h_r3 (RNA-Seq)

description:
1785.AG
1785_AG_S67_L003

source_name: Col-0_0h_5-wk old leaves


title: Col0_8h_r3 (RNA-Seq)

description:
1785.AH
1785_AH_S68_L003

source_name: Col-0_8h_5-wk old leaves


title: tpr1_0h_r3 (RNA-Seq)

description:
1785.AJ
1785_AJ_S70_L003

source_name: tpr1-KO_0h_5-wk old leaves


title: RNAchIP-seq input, PMA-treated HP1g expressing cell line, replicate 1


title: eds1-2_8h_r2 (RNA-Seq)

description:
1785.AE
1785_AE_S65_L003


title: eds1-2_0h_r2 (RNA-Seq)

description:
1785.AD
1785_AD_S64_L003


title: A549 dnCRTC, biological rep2

type: RNA

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

country: USA

institute: University of Florida

hyb_protocol: Following fragmentation, sscDNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized using RMA normalization approach with Affymetrix Expression Console.

label: biotin

organism: Homo sapiens

source_name: A549 dnCRTC

label_protocol: Biotinylated sscDNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA.

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% inactivated fetal bovine serum and penicillin/streptomycin (100U/ml) at 37°C under 5% CO2.

extract_protocol: RNA was isolated with the Trizol Reagent (Invitrogen) and purified by the Qiagen Column with in column DNase digestion.

treatment_protocol: GFP control and dnCRTC

value: human lung carcinoma epithelial cells

tag: genotype/variation

value: pMSCV retroviruses expressing dnCRTC [CRTC1(1-55aa)-nls-GFP]


title: A549 GFP, biological rep2

source_name: A549 GFP

value: pMSCV retroviruses expressing GFP control


title: tpr1_8h_r2 (RNA-Seq)

description:
1785.Y
1785_Y_S59_L003


title: tpr1_0h_r2 (RNA-Seq)

description:
1785.X
1785_X_S58_L003


title: A549 GFP, biological rep1


title: Col0_8h_r2 (RNA-Seq)

description:
1785.V
1785_V_S77_L004
1785_V_S22_L001


title: t3_8h_r2 (RNA-Seq)

description:
1785.AB
1785_AB_S62_L003


title: tpr1_24h_r2 (RNA-Seq)

description:
1785.Z
1785_Z_S60_L003


title: t3_0h_r2 (RNA-Seq)

description:
1785.AA
1785_AA_S61_L003


title: t3_24h_r2 (RNA-Seq)

description:
1785.AC
1785_AC_S63_L003


title: Col0_0h_r2 (RNA-Seq)

description:
1785.U
1785_U_S76_L004


title: A549 dnCRTC, biological rep1


title: eds1-2_0h_r1 (RNA-Seq)

description:
1785.R
1785_R_S73_L004


title: Col0_24h_r2 (RNA-Seq)

description:
1785.W
1785_W_S78_L004


title: eds1-2_24h_r1 (RNA-Seq)

description:
1785.T
1785_T_S75_L004


title: t3_8h_r1 (RNA-Seq)

description:
1785.P
1785_P_S30_L001
1785_P_S23_L002


title: t3_24h_r1 (RNA-Seq)

description:
1785.Q
1785_Q_S72_L004


title: t3_0h_r1 (RNA-Seq)

description:
1785.O
1785_O_S29_L001
1785_O_S21_L001


title: tpr1_8h_r1 (RNA-Seq)

description:
1785.M
1785_M_S27_L001


title: eds1-2_24h_r2 (RNA-Seq)

description:
1785.AF
1785_AF_S66_L003


title: Col0_8h_r1 (RNA-Seq)

description:
1785.J
1785_J_S24_L001


title: Col0_0h_r1 (RNA-Seq)

description:
1785.I
1785_I_S71_L004


title: Col0_24h_r1 (RNA-Seq)

description:
1785.K
1785_K_S25_L001
1785_K_S18_L001


title: tpr1_0h_r1 (RNA-Seq)

description:
1785.L
1785_L_S26_L001
1785_L_S19_L001


title: TPR1-GFP eds1-2_r3 (RNA-Seq)

data_processing:
RNA-seq reads were mapped to the annotated genome of Arabidopsis thaliana (TAIR10) using TOPHAT2 (a = 10, g = 10) and transformed into a read count per gene per sample using the htseq-count script (s = reverse, t = exon) in the package HTSeq
Genes with less than 100 reads in all samples together were discarded; subsequently, the count data of the remaining genes were TMM normalized and log2 transformed using functions ‘calcNormFactors’ and ‘voom’
P values were adjusted for false discoveries due to multiple hypothesis testing via the Benjamini-Hochberg procedure.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fold changes, log2 fold changes, and FDR of each gene transcript in TPR1-OX compared to Col-0, TPR1-OX sid2-1, and TPR1-OX eds1-2

source_name: 5-week old leaves

value: pTPR1:TPR1-GFP eds1-2

value: leaves


title: TPR1-GFP eds1-2_r2 (RNA-Seq)


title: TPR1-GFP eds1-2_r1 (RNA-Seq)


title: TPR1-GFP sid2-1_r3 (RNA-Seq)

value: pTPR1:TPR1-GFP sid2-1


title: eds1-2_8h_r1 (RNA-Seq)

description:
1785.S
1785_S_S74_L004


title: TPR1-GFP sid2-1_r2 (RNA-Seq)


title: TPR1-GFP_r3 (RNA-Seq)

value: pTPR1:TPR1-GFP (Col-0)


title: TPR1-GFP_r1 (RNA-Seq)


title: TPR1-GFP sid2-1_r1 (RNA-Seq)


title: Col0_r2 (RNA-Seq)


title: Col0_r3 (RNA-Seq)


title: PXB-cells GRP78 -

city: Maebashi

first: hagiwra

last: kei

state: Gunma

address: 3-39-22 Showa-machi

department: General Surgical Science

country: Japan

institute: Gunma University Graduate School of Medicine

data_processing:
Sequenced reads were mapped to hg19 using BWA. Unmapped reads are then mapped to hg19 whole genome using HiSAT2 with the parameters set as default, to map the reads that covers at least a part of exon2 as well as exon1.
TSS clustering and tags per million reads (TPM) were calculated using CAGEr (Nucleic Acids Res. 2015 Apr 30;43(8)).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample

source_name: PXB-cells

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer's instructions
First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags.

tag: tag

value: 7 days after purchase


title: VDR KO plus 3

city: Iwaki

first: Yoshiaki

last: Kanemoto

state: Fukushima

address: kaminodai 57, jyobankamiyunagaya-town

institute: Jyoban Hospital

data_processing:
library strategy: NET-CAGE
Basecalls performed using BWA software (v0.5.9)
CAGE library preparation, sequencing, mapping, and gene expression and motif discovery analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). In brief, RNA quality was assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0, and A260/280 and 260/230 ratios are over 1.7. First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags and the sequenced CAGE tags were mapped to the mouse mm9 genomes using BWA software (v0.5.9) after discarding ribosomal or non A/C/G/T basecontaining RNAs.
For tag clustering, CAGEtag 5' coordinates were input for Reclu clustering,with maxmum irreproducible discovery rate (IDR) 0.1 and minimum count per million (CPM) value 0.1 (Ohmiya et al, BMC Genomics 2014, 15:269).
Genome_build: mouse mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM and peak values for each sample.

source_name: HaCaT_VDR KO _VitaminD plus

growth_protocol: HaCaT WT and VDR KO cells were routinely culutured in DMEM supplemented with 10% fetal bovine serume at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol according to the manufacturer's instructions.
The RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: Three replicates cultured on 6 well-plate were treated with 1,25(OH)2D3 for 8hrs.

value: HaCaT

value: Keratinocyte

value: VDR KO

value: VitaminD plus


title: WT plus 1

source_name: HaCaT_wild type_VitaminD plus

value: wild type


title: VDR KO plus 2


title: WT minus 2

source_name: HaCaT_wild type_VitaminD muinus

value: VitaminD muinus


title: VDR KO minus 3

source_name: HaCaT_VDR KO _VitaminD muinus


title: VDR KO minus 2


title: WT plus 2


title: PXB-cells GRP78 +


title: WT plus 3


title: WT minus 3


title: VDR KO plus 1


title: TPR1-GFP_r2 (RNA-Seq)


title: WT minus 1


title: MB135iDUX4-Ribo_14h_rep3

city: Aurora

first: Amy

middle: E.

last: Campbell

state: CO

institute: University of Colorado Anschutz Medical Campus

description: ribosome-protected RNA

data_processing:
Library strategy: Ribo-seq
Fastq files were stripped of the adapter sequences using cutadapt.
UMI sequences were removed, and reads were collapsed to fasta format.
Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs, and miRNA (retrieved using the UCSC table browser) using bowtie2.
Remaining reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 25 .gtf file.
A maximum of two mismatches and mapping to a minimum of 50 positions was allowed; de-novo splice junction discovery was disabled for all datasets; only the best alignment per each read was retained.
Quality control and read counting was performed with RiboseQC.
Differential analysis of the RNA-seq and Ribo-seq data was performed using DEseq2 using an interaction model between the tested condition and RNA-seq - Ribo-seq counts; only reads mapping uniquely to coding sequence regions were used.
In addition, ORFquant was used to derive de-novo isoform-specific translation events, by pooling the RiboseQC output from all Ribo-seq samples, using uniquely mapping reads.
DEXSeq was used to perform differential exon usage along the DUX4 time course data, using Ribo-seq counts on exonic bins and junctions belonging to different ORFquant-derived translated regions.
Genome_build: hg38
Supplementary_files_format_and_content: bam
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: comma-separated values file output of the DEseq2 pipeline

source_name: MB135iDUX4 myoblasts

growth_protocol: MB135iDUX4 myoblasts were maintained in Ham’s F-10 Nutrient Mix supplemented with 20% Fetal Bovine Serum, 10 ng/mL recombinant human basic fibroblast growth factor, 1 uM dexamethasone, and 2 ug/mL puromycin dihydrochloride.

extract_protocol:
Ribosome-protected RNA was extracted as in PMID:32601440.
Libraries were prepared using the NEXTflex Small RNA-Seq Kit v3.

treatment_protocol: Induction of the DUX4 transgene was achieved by culturing cells in 1 ug/mL doxycycline hyclate for 4, 8, or 14 h.

value: skeletal muscle myoblast

value: treated with doxycycline for 14 h


title: MB135iDUX4-Ribo_08h_rep2

description: ribosome-protected RNA

value: treated with doxycycline for 8 h


title: MB135iDUX4-Ribo_08h_rep3

description: ribosome-protected RNA


title: MB135iDUX4-Ribo_04h_rep3

description: ribosome-protected RNA

value: treated with doxycycline for 4 h


title: MB135iDUX4-Ribo_14h_rep1

description: ribosome-protected RNA


title: MB135iDUX4-Ribo_14h_rep2

description: ribosome-protected RNA


title: MB135iDUX4-Ribo_04h_rep2

description: ribosome-protected RNA


title: MB135iDUX4-Ribo_08h_rep1

description: ribosome-protected RNA


title: MB135iDUX4-Ribo_00h_rep1

description: ribosome-protected RNA

value: untreated


title: MB135iDUX4-Ribo_00h_rep2

description: ribosome-protected RNA


title: MB135iDUX4-RNA_14h_rep3

data_processing:
Fastq files were stripped of the adapter sequences using cutadapt.
UMI sequences were removed, and reads were collapsed to fasta format.
Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs, and miRNA (retrieved using the UCSC table browser) using bowtie2.
Remaining reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 25 .gtf file.
A maximum of two mismatches and mapping to a minimum of 50 positions was allowed; de-novo splice junction discovery was disabled for all datasets; only the best alignment per each read was retained.
Differential gene expression analysis was conducted using DEseq2.
featureCounts from the subread R package was used to assign aligned reads (in BAM format) to genomic features supplied with the GENCODE 25. gtf file.
The featureCounts output was then supplied to DEseq2 and differential expression analysis was conducted with the 0 h time point serving as the reference sample.
Genes with very low read count were filtered out by requiring at least a total of 10 reads across the 12 samples; log2 fold change shrinkage was done using the apeglm function.
Genome_build: hg38
Supplementary_files_format_and_content: bam
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: comma-separated values file output of the DEseq2 pipeline

extract_protocol:
Total RNA was extracted from whole cells using TRIzol Reagent.
Isolated RNA was subjected to ribosomal RNA depletion using the Ribo-Zero rRNA Removal Kit and libraries prepared using the NEXTflex Rapid Directional qRNA-Seq Kit.


title: MB135iDUX4-Ribo_00h_rep3

description: ribosome-protected RNA


title: Col0_r1 (RNA-Seq)


title: MB135iDUX4-RNA_14h_rep1


title: MB135iDUX4-RNA_14h_rep2


title: MB135iDUX4-RNA_08h_rep2


title: MB135iDUX4-RNA_08h_rep3


title: VDR KO minus 1


title: MB135iDUX4-RNA_04h_rep3


title: MB135iDUX4-RNA_04h_rep2


title: MB135iDUX4-RNA_0h_rep1


title: MB135iDUX4-RNA_04h_rep1


title: MB135iDUX4-RNA_0h_rep2


title: MB135iDUX4-RNA_0h_rep3


title: MB135iDUX4-Ribo_04h_rep1

description: ribosome-protected RNA


title: MM14

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

country: Spain

institute: Universidad de Navarra

data_processing:
Demultiplexing, alignment and gene counts were performed with Cell Ranger Single-Cell Software Suite (v3.01, 10X Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix including gene-count values for each sample

source_name: Multiple myeloma

extract_protocol:
For scRNAseq, clonal PCs were sorted and viable cells were loaded in the 10x-Genomics Chromium instrument (10X Genomics, USA).
scRNAseq libraries were prepared following 10X-Genomics v2 protocol recommendations (10X Genomics, USA).

value: Plasma cells + B cells + T/NK cells


title: MM6


title: MM10


title: MM5

value: Plasma cells


title: MM13


title: MM12


title: MM15


title: MM3


title: MM2


title: MM11


title: MM1


title: MM7


title: MM9


title: MM4


title: MM8


title: MB135iDUX4-RNA_08h_rep1


title: AL5

source_name: AL amyloidosis


title: AL2


title: AL3


title: AL1


title: MB PCs3

source_name: Healthy bone marrow


title: AL4


title: PB PCs3

source_name: Peripheral blood


title: MB PCs1


title: PB PCs2


title: PB PCs1


title: SLO BM PCs3

source_name: Tonsils


title: SLO BM PCs1


title: RNAseq111_MM_CPP

data_processing:
BCL files were converted into FASTQ file format with bcl2fastq (v2.19) (Illumina, USA) and resulting reads were trimmed with cutadapt (v1.18).
Clean reads were aligned to the human genome reference (hg19) with STAR (Dobin et al., 2013) (v2.5.3)
Read counts per gene were calculated with quant3p (github.com/ctlab/quant3p)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix including gene-count values for each sample

extract_protocol:
Samples in RLT were defrosted and gDNA plus RNA were isolated with AllPrep DNA/RNA Micro Kit (Qiagen, USA) following manufacturer’s instructions. Samples in DMSO were defrosted, washed with PBS and suspended in lysis binding buffer (Ambion). Poly-A RNA was selected with Dynabeads Oligo (dT) (Ambion), and un-binded DNA was selected with SPRIselect beads, washed with EtOH and suspended in buffer EB.
We used a 3’ end RNAseq method optimized for generating libraries from low-input starting material (MARSeq), adapted for bulk RNAseq (Jaitin et al., 2014; Lavin et al., 2017) with minor modifications.

tag: diagnosis

value: Multiple myeloma


title: SLO BM PCs2


title: RNAseq109_MM_CPP


title: RNAseq107_MM_CPP


title: RNAseq108_MM_CPP


title: RNAseq110_MM_CPP


title: RNAseq102_MM_CPP


title: RNAseq106_MM_CPP


title: RNAseq103_MM_CPP


title: RNAseq99_MM_CPP


title: RNAseq101_MM_CPP


title: AL6


title: RNAseq100_MM_CPP


title: RNAseq98_MM_CPP


title: MB PCs2


title: RNAseq96_MM_CPP


title: RNAseq94_MM_CPP


title: RNAseq95_MM_CPP


title: RNAseq93_MM_CPP


title: RNAseq90_MM_CPP


title: RNAseq89_MM_CPP


title: RNAseq86_MM_CPP


title: RNAseq104_MM_CPP


title: RNAseq105_MM_CPP


title: RNAseq87_MM_CPP


title: RNAseq88_MM_CPP


title: RNAseq85_MM_CPP


title: RNAseq83_MM_CPP


title: RNAseq84_MM_CPP


title: RNAseq81_MM_CPP


title: RNAseq80_MM_CPP


title: RNAseq77_MGUS_CPP

source_name: MGUS

value: MGUS


title: RNAseq82_MM_CPP


title: RNAseq79_MGUS_CPP


title: RNAseq78_MGUS_CPP


title: RNAseq74_MGUS_CPP


title: RNAseq75_MGUS_CPP


title: RNAseq97_MM_CPP


title: RNAseq72_HA_Plasmablasts_IgM

source_name: Healthy adult

value: Healthy adult


title: RNAseq92_MM_CPP


title: RNAseq71_HA_Plasmablasts_IgM


title: RNAseq91_MM_CPP


title: RNAseq67_HA_Plasmablasts_IgA


title: RNAseq69_HA_Plasmablasts_IgG


title: RNAseq68_HA_Plasmablasts_IgG


title: RNAseq70_HA_Plasmablasts_IgG


title: RNAseq66_HA_Plasmablasts_IgA


title: RNAseq65_HA_Plasmablasts_IgA


title: RNAseq76_MGUS_CPP


title: RNAseq54_HA_CD39posCD19posCD81posCD56neg_PCs


title: RNAseq59_HA_Circulating_PCs_IgApos


title: RNAseq61_HA_Circulating_PCs_IgGpos


title: RNAseq60_HA_Circulating_PCs_IgGpos


title: RNAseq57_HA_CD39posCD19posCD81posCD56neg_PCs


title: RNAseq58_HA_Circulating_PCs_IgApos


title: RNAseq73_HA_Plasmablasts_IgM


title: RNAseq62_HA_Circulating_PCs_IgMpos


title: RNAseq55_HA_CD39posCD19posCD81posCD56neg_PCs


title: RNAseq52_HA_CD39negCD19posCD81posCD56neg_PCs


title: RNAseq50_HA_CD39negCD19posCD81posCD56neg_PCs


title: RNAseq49_HA_CD39negCD19posCD81posCD56neg_PCs


title: RNAseq63_HA_Circulating_PCs_IgMpos


title: RNAseq56_HA_CD39posCD19posCD81posCD56neg_PCs


title: RNAseq47_HA_CD39negCD19posCD81posCD56neg_PCs


title: RNAseq53_HA_CD39posCD19posCD81posCD56neg_PCs


title: RNAseq46_HA_CD39negCD19posCD81posCD56neg_PCs


title: tpr1_24h_r1 (RNA-Seq)

description:
1785.N
1785_N_S28_L001
1785_N_S20_L001

source_name: tpr1-KO_24h_5-wk old leaves

value: 5-week old leaves


title: RNAseq45_HA_CD39negCD19posCD81posCD56neg_PCs


title: RNAseq44_HA_CD39negCD19negCD81posCD56neg_PCs


title: RNAseq43_HA_CD39negCD19negCD81posCD56neg_PCs


title: RNAseq48_HA_CD39negCD19posCD81posCD56neg_PCs


title: RNAseq42_HA_CD39negCD19negCD81posCD56neg_PCs


title: RNAseq39_HA_CD39negCD19negCD81negCD56pos_PCs


title: RNAseq40_HA_CD39negCD19negCD81posCD56neg_PCs


title: RNAseq37_HA_CD39negCD19negCD81negCD56pos_PCs


title: RNAseq51_HA_CD39negCD19posCD81posCD56neg_PCs


title: RNAseq35_HA_CD39negCD19negCD81negCD56neg_PCs


title: RNAseq33_HA_CD39negCD19negCD81negCD56neg_PCs


title: RNAseq36_HA_CD39negCD19negCD81negCD56pos_PCs


title: RNAseq34_HA_CD39negCD19negCD81negCD56neg_PCs


title: RNAseq32_AL_CPP

value: AL amyloidosis


title: RNAseq28_AL_CPP


title: RNAseq30_AL_CPP


title: RNAseq29_AL_CPP


title: RNAseq64_HA_Circulating_PCs_IgMpos


title: RNAseq25_AL_CPP


title: RNAseq23_AL_CPP


title: RNAseq21_AL_CPP


title: RNAseq20_AL_CPP


title: RNAseq24_AL_CPP


title: RNAseq31_AL_CPP


title: RNAseq27_AL_CPP


title: RNAseq22_AL_CPP


title: RNAseq19_AL_CPP


title: RNAseq26_AL_CPP


title: RNAseq41_HA_CD39negCD19negCD81posCD56neg_PCs


title: RNAseq18_AL_CPP


title: RNAseq17_AL_CPP


title: RNAseq13_AL_CPP


title: RNAseq16_AL_CPP


title: RNAseq15_AL_CPP


title: RNAseq38_HA_CD39negCD19negCD81negCD56pos_PCs


title: RNAseq14_AL_CPP


title: RNAseq12_AL_CPP


title: RNAseq11_AL_CPP


title: RNAseq10_AL_CPP


title: RNAseq6_AL_CPP


title: RNAseq5_AL_CPP


title: RNAseq7_AL_CPP


title: RNAseq3_AL_CPP


title: RNAseq8_AL_CPP


title: RNAseq9_AL_CPP


title: Naive Exo_2

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description: naïve culture

data_processing:
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Log normal shrinkage was used to remove batch effect between runs
Counts with a maximum of less than 2 were filtered out for a normal distribution
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files, includes RPKM values for each sample

source_name: MSC conditioned media

growth_protocol: MSC were co-cultured with/without breast cancer cells (BCCs) for 24 hrs. in DMEM supplemented with  10% FCS and glutamine

extract_protocol:
Exosomes were isolated by ultracentrifugation. Total RNA  was extracted from purifed exosomes according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.

treatment_protocol: Primed MSC were co-cultured with BCCs for 24 hrs. in a transwell co culture system  with 0.4 μm membrane (BD Falcon, ThermoFisher). Cells were plated at 1:1 ratio of 5e4. After 24 hrs insert containing BCCs were removed and media was replaced with DMEM supplemented with 2% exosome depleted FCS for 48 hrs.

value: MSC

tag: cellular component

value: exosome

tag: tissue source

value: bone marrow

tag: passage

tag: replicate

tag: co-culture


title: Primed Exo_1

description: primed culture

value: with breast cancer cells


title: RNAseq2_AL_CPP


title: Primed Exo_3

description: primed culture


title: RNAseq1_AL_CPP


title: Naive Exo_1

description: naïve culture


title: Naive Exo_3

description: naïve culture


title: RNAseq4_AL_CPP


title: Primed Exo_2

description: primed culture


title: Subject_HCAF088_Day28

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: Samples were hybridized on  HG-133 plus 2.0 PM  chips

scan_protocol: Plates were scanned on GeneTitan multichannel instrument (Affymetrix)

data_processing: Probe level processing was done by RMA with log2 transform and probe summary by median polish

label: Biotin

source_name: Subject HCAF088, Day28 post vaccination

label_protocol: Fragemented cRNA was lebeled with biotin

extract_protocol: RNA was isolated from whole blood Paxgene tubes using RNAeasy kit (Quagen)

tag: subject

tag: day post vacciantion

tag: vaccine


title: Subject_HCAF098_Day3

source_name: Subject HCAF098, Day3 post vaccination


title: Subject_HCAF098_Day22

source_name: Subject HCAF098, Day22 post vaccination


title: Subject_HCAF088_Day0

source_name: Subject HCAF088, Day0 post vaccination


title: Subject_HCAF098_Day21

source_name: Subject HCAF098, Day21 post vaccination


title: Subject_HCAF098_Day0

source_name: Subject HCAF098, Day0 post vaccination


title: Subject_HCAF098_Day28

source_name: Subject HCAF098, Day28 post vaccination


title: Subject_HCAF087_Day21

source_name: Subject HCAF087, Day21 post vaccination


title: Subject_HCAF088_Day3

source_name: Subject HCAF088, Day3 post vaccination


title: Subject_HCAF088_Day24

source_name: Subject HCAF088, Day24 post vaccination


title: Subject_HCAF098_Day24

source_name: Subject HCAF098, Day24 post vaccination


title: Subject_HCAF087_Day7

source_name: Subject HCAF087, Day7 post vaccination


title: Subject_HCAF098_Day1

source_name: Subject HCAF098, Day1 post vaccination


title: Subject_HCAF087_Day24

source_name: Subject HCAF087, Day24 post vaccination


title: Subject_HCAF087_Day28

source_name: Subject HCAF087, Day28 post vaccination


title: Subject_HCAF098_Day7

source_name: Subject HCAF098, Day7 post vaccination


title: Subject_HCAF087_Day22

source_name: Subject HCAF087, Day22 post vaccination


title: Subject_HCAF088_Day7

source_name: Subject HCAF088, Day7 post vaccination


title: Subject_HCAF085_Day1

source_name: Subject HCAF085, Day1 post vaccination


title: Subject_HCAF087_Day0

source_name: Subject HCAF087, Day0 post vaccination


title: Subject_HCAF088_Day1

source_name: Subject HCAF088, Day1 post vaccination


title: Subject_HCAF087_Day1

source_name: Subject HCAF087, Day1 post vaccination


title: Subject_HCAF088_Day21

source_name: Subject HCAF088, Day21 post vaccination


title: Subject_HCAF085_Day0

source_name: Subject HCAF085, Day0 post vaccination


title: Subject_HCAF081_Day3

source_name: Subject HCAF081, Day3 post vaccination


title: Subject_HCAF085_Day7

source_name: Subject HCAF085, Day7 post vaccination


title: Subject_HCAF085_Day3

source_name: Subject HCAF085, Day3 post vaccination


title: Subject_HCAF081_Day7

source_name: Subject HCAF081, Day7 post vaccination


title: Subject_HCAF088_Day22

source_name: Subject HCAF088, Day22 post vaccination


title: Subject_HCAF087_Day3

source_name: Subject HCAF087, Day3 post vaccination


title: Subject_HCAF081_Day28

source_name: Subject HCAF081, Day28 post vaccination


title: Subject_HCAF081_Day24

source_name: Subject HCAF081, Day24 post vaccination


title: Subject_HCAF081_Day22

source_name: Subject HCAF081, Day22 post vaccination


title: Subject_HCAF081_Day0

source_name: Subject HCAF081, Day0 post vaccination


title: Subject_HCAF079_Day22

source_name: Subject HCAF079, Day22 post vaccination


title: Subject_HCAF079_Day3

source_name: Subject HCAF079, Day3 post vaccination


title: Subject_HCAF079_Day1

source_name: Subject HCAF079, Day1 post vaccination


title: Subject_HCAF079_Day24

source_name: Subject HCAF079, Day24 post vaccination


title: Subject_HCAF079_Day7

source_name: Subject HCAF079, Day7 post vaccination


title: Subject_HCAF076_Day28

source_name: Subject HCAF076, Day28 post vaccination


title: Subject_HCAF079_Day21

source_name: Subject HCAF079, Day21 post vaccination


title: Subject_HCAF081_Day21

source_name: Subject HCAF081, Day21 post vaccination


title: Subject_HCAF077_Day1

source_name: Subject HCAF077, Day1 post vaccination


title: Subject_HCAF077_Day22

source_name: Subject HCAF077, Day22 post vaccination


title: Subject_HCAF076_Day21

source_name: Subject HCAF076, Day21 post vaccination


title: Subject_HCAF077_Day28

source_name: Subject HCAF077, Day28 post vaccination


title: Subject_HCAF077_Day7

source_name: Subject HCAF077, Day7 post vaccination


title: Subject_HCAF076_Day0

source_name: Subject HCAF076, Day0 post vaccination


title: Subject_HCAF076_Day22

source_name: Subject HCAF076, Day22 post vaccination


title: Subject_HCAF081_Day1

source_name: Subject HCAF081, Day1 post vaccination


title: Subject_HCAF077_Day0

source_name: Subject HCAF077, Day0 post vaccination


title: Subject_HCAF079_Day28

source_name: Subject HCAF079, Day28 post vaccination


title: Subject_HCAF076_Day7

source_name: Subject HCAF076, Day7 post vaccination


title: Subject_HCAF079_Day0

source_name: Subject HCAF079, Day0 post vaccination


title: Subject_HCAF077_Day24

source_name: Subject HCAF077, Day24 post vaccination


title: Subject_HCAF076_Day1

source_name: Subject HCAF076, Day1 post vaccination


title: Subject_HCAF076_Day3

source_name: Subject HCAF076, Day3 post vaccination


title: Subject_HCAF076_Day24

source_name: Subject HCAF076, Day24 post vaccination


title: Subject_HCAF077_Day21

source_name: Subject HCAF077, Day21 post vaccination


title: Subject_HCAF077_Day3

source_name: Subject HCAF077, Day3 post vaccination


title: Subject_HCAF075_Day7

source_name: Subject HCAF075, Day7 post vaccination


title: Subject_HCAF073_Day24

source_name: Subject HCAF073, Day24 post vaccination


title: Subject_HCAF075_Day21

source_name: Subject HCAF075, Day21 post vaccination


title: Subject_HCAF075_Day28

source_name: Subject HCAF075, Day28 post vaccination


title: Subject_HCAF073_Day22

source_name: Subject HCAF073, Day22 post vaccination


title: Subject_HCAF075_Day24

source_name: Subject HCAF075, Day24 post vaccination


title: Subject_HCAF075_Day1

source_name: Subject HCAF075, Day1 post vaccination


title: Subject_HCAF073_Day21

source_name: Subject HCAF073, Day21 post vaccination


title: Subject_HCAF075_Day0

source_name: Subject HCAF075, Day0 post vaccination


title: Subject_HCAF070_Day7

source_name: Subject HCAF070, Day7 post vaccination


title: Subject_HCAF073_Day1

source_name: Subject HCAF073, Day1 post vaccination


title: Subject_HCAF073_Day0

source_name: Subject HCAF073, Day0 post vaccination


title: Subject_HCAF071_Day21

source_name: Subject HCAF071, Day21 post vaccination


title: Subject_HCAF071_Day3

source_name: Subject HCAF071, Day3 post vaccination


title: Subject_HCAF073_Day3

source_name: Subject HCAF073, Day3 post vaccination


title: Subject_HCAF071_Day28

source_name: Subject HCAF071, Day28 post vaccination


title: Subject_HCAF071_Day24

source_name: Subject HCAF071, Day24 post vaccination


title: Subject_HCAF073_Day7

source_name: Subject HCAF073, Day7 post vaccination


title: Subject_HCAF070_Day3

source_name: Subject HCAF070, Day3 post vaccination


title: Subject_HCAF073_Day28

source_name: Subject HCAF073, Day28 post vaccination


title: Subject_HCAF071_Day22

source_name: Subject HCAF071, Day22 post vaccination


title: Subject_HCAF070_Day24

source_name: Subject HCAF070, Day24 post vaccination


title: Subject_HCAF075_Day22

source_name: Subject HCAF075, Day22 post vaccination


title: Subject_HCAF071_Day0

source_name: Subject HCAF071, Day0 post vaccination


title: Subject_HCAF070_Day28

source_name: Subject HCAF070, Day28 post vaccination


title: Subject_HCAF070_Day1

source_name: Subject HCAF070, Day1 post vaccination


title: Subject_HCAF071_Day1

source_name: Subject HCAF071, Day1 post vaccination


title: Subject_HCAF070_Day22

source_name: Subject HCAF070, Day22 post vaccination


title: Subject_HCAF070_Day21

source_name: Subject HCAF070, Day21 post vaccination


title: Subject_HCAF071_Day7

source_name: Subject HCAF071, Day7 post vaccination


title: Subject_HCAF069_Day3

source_name: Subject HCAF069, Day3 post vaccination


title: Subject_HCAF069_Day21

source_name: Subject HCAF069, Day21 post vaccination


title: Subject_HCAF069_Day1

source_name: Subject HCAF069, Day1 post vaccination


title: Subject_HCAF069_Day22

source_name: Subject HCAF069, Day22 post vaccination


title: Subject_HCAF069_Day24

source_name: Subject HCAF069, Day24 post vaccination


title: Subject_HCAF069_Day0

source_name: Subject HCAF069, Day0 post vaccination


title: Subject_HCAF067_Day3

source_name: Subject HCAF067, Day3 post vaccination


title: Subject_HCAF067_Day7

source_name: Subject HCAF067, Day7 post vaccination


title: Subject_HCAF064_Day3

source_name: Subject HCAF064, Day3 post vaccination


title: Subject_HCAF067_Day22

source_name: Subject HCAF067, Day22 post vaccination


title: Subject_HCAF069_Day7

source_name: Subject HCAF069, Day7 post vaccination


title: Subject_HCAF070_Day0

source_name: Subject HCAF070, Day0 post vaccination


title: Subject_HCAF066_Day3

source_name: Subject HCAF066, Day3 post vaccination


title: Subject_HCAF066_Day24

source_name: Subject HCAF066, Day24 post vaccination


title: Subject_HCAF066_Day21

source_name: Subject HCAF066, Day21 post vaccination


title: Subject_HCAF066_Day7

source_name: Subject HCAF066, Day7 post vaccination


title: Subject_HCAF067_Day1

source_name: Subject HCAF067, Day1 post vaccination


title: Subject_HCAF067_Day0

source_name: Subject HCAF067, Day0 post vaccination


title: Subject_HCAF064_Day0

source_name: Subject HCAF064, Day0 post vaccination


title: Subject_HCAF066_Day22

source_name: Subject HCAF066, Day22 post vaccination


title: Subject_HCAF066_Day28

source_name: Subject HCAF066, Day28 post vaccination


title: Subject_HCAF064_Day21

source_name: Subject HCAF064, Day21 post vaccination


title: Subject_HCAF067_Day21

source_name: Subject HCAF067, Day21 post vaccination


title: Subject_HCAF067_Day24

source_name: Subject HCAF067, Day24 post vaccination


title: Subject_HCAF064_Day7

source_name: Subject HCAF064, Day7 post vaccination


title: Subject_HCAF066_Day0

source_name: Subject HCAF066, Day0 post vaccination


title: Subject_HCAF064_Day22

source_name: Subject HCAF064, Day22 post vaccination


title: Subject_HCAF064_Day1

source_name: Subject HCAF064, Day1 post vaccination


title: Subject_HCAF064_Day28

source_name: Subject HCAF064, Day28 post vaccination


title: Subject_HCAF063_Day7

source_name: Subject HCAF063, Day7 post vaccination


title: Subject_HCAF063_Day22

source_name: Subject HCAF063, Day22 post vaccination


title: Subject_HCAF063_Day0

source_name: Subject HCAF063, Day0 post vaccination


title: Subject_HCAF061_Day7

source_name: Subject HCAF061, Day7 post vaccination


title: Subject_HCAF062_Day0

source_name: Subject HCAF062, Day0 post vaccination


title: Subject_HCAF062_Day24

source_name: Subject HCAF062, Day24 post vaccination


title: Subject_HCAF061_Day3

source_name: Subject HCAF061, Day3 post vaccination


title: Subject_HCAF063_Day28

source_name: Subject HCAF063, Day28 post vaccination


title: Subject_HCAF063_Day21

source_name: Subject HCAF063, Day21 post vaccination


title: Subject_HCAF066_Day1

source_name: Subject HCAF066, Day1 post vaccination


title: Subject_HCAF062_Day3

source_name: Subject HCAF062, Day3 post vaccination


title: Subject_HCAF063_Day1

source_name: Subject HCAF063, Day1 post vaccination


title: Subject_HCAF062_Day1

source_name: Subject HCAF062, Day1 post vaccination


title: Subject_HCAF063_Day3

source_name: Subject HCAF063, Day3 post vaccination


title: Subject_HCAF062_Day21

source_name: Subject HCAF062, Day21 post vaccination


title: Subject_HCAF062_Day7

source_name: Subject HCAF062, Day7 post vaccination


title: Subject_HCAF061_Day28

source_name: Subject HCAF061, Day28 post vaccination


title: Subject_HCAF061_Day24

source_name: Subject HCAF061, Day24 post vaccination


title: Subject_HCAF061_Day22

source_name: Subject HCAF061, Day22 post vaccination


title: Subject_HCAF061_Day21

source_name: Subject HCAF061, Day21 post vaccination


title: Subject_HCAF061_Day1

source_name: Subject HCAF061, Day1 post vaccination


title: Subject_HCAF060_Day7

source_name: Subject HCAF060, Day7 post vaccination


title: Subject_HCAF061_Day0

source_name: Subject HCAF061, Day0 post vaccination


title: Subject_HCAF060_Day22

source_name: Subject HCAF060, Day22 post vaccination


title: Subject_HCAF060_Day3

source_name: Subject HCAF060, Day3 post vaccination


title: Subject_HCAF060_Day21

source_name: Subject HCAF060, Day21 post vaccination


title: Subject_HCAF060_Day24

source_name: Subject HCAF060, Day24 post vaccination


title: Subject_HCAF060_Day1

source_name: Subject HCAF060, Day1 post vaccination


title: Subject_HCAF060_Day28

source_name: Subject HCAF060, Day28 post vaccination


title: Subject_HCAF062_Day22

source_name: Subject HCAF062, Day22 post vaccination


title: Subject_HCAF059_Day24

source_name: Subject HCAF059, Day24 post vaccination


title: Subject_HCAF059_Day28

source_name: Subject HCAF059, Day28 post vaccination


title: Subject_HCAF059_Day22

source_name: Subject HCAF059, Day22 post vaccination


title: Subject_HCAF058_Day3

source_name: Subject HCAF058, Day3 post vaccination


title: Subject_HCAF059_Day21

source_name: Subject HCAF059, Day21 post vaccination


title: Subject_HCAF058_Day24

source_name: Subject HCAF058, Day24 post vaccination


title: Subject_HCAF058_Day7

source_name: Subject HCAF058, Day7 post vaccination


title: Subject_HCAF060_Day0

source_name: Subject HCAF060, Day0 post vaccination


title: Subject_HCAF058_Day21

source_name: Subject HCAF058, Day21 post vaccination


title: Subject_HCAF058_Day22

source_name: Subject HCAF058, Day22 post vaccination


title: Subject_HCAF059_Day3

source_name: Subject HCAF059, Day3 post vaccination


title: Subject_HCAF058_Day0

source_name: Subject HCAF058, Day0 post vaccination


title: Subject_HCAF059_Day0

source_name: Subject HCAF059, Day0 post vaccination


title: Subject_HCAF059_Day1

source_name: Subject HCAF059, Day1 post vaccination


title: Subject_HCAF058_Day1

source_name: Subject HCAF058, Day1 post vaccination


title: Subject_HCAF059_Day7

source_name: Subject HCAF059, Day7 post vaccination


title: Subject_HCAF057_Day3

source_name: Subject HCAF057, Day3 post vaccination


title: Subject_HCAF057_Day1

source_name: Subject HCAF057, Day1 post vaccination


title: Subject_HCAF058_Day28

source_name: Subject HCAF058, Day28 post vaccination


title: Subject_HCAF057_Day28

source_name: Subject HCAF057, Day28 post vaccination


title: Subject_HCAF053_Day7

source_name: Subject HCAF053, Day7 post vaccination


title: Subject_HCAF053_Day28

source_name: Subject HCAF053, Day28 post vaccination


title: Subject_HCAF057_Day24

source_name: Subject HCAF057, Day24 post vaccination


title: Subject_HCAF057_Day21

source_name: Subject HCAF057, Day21 post vaccination


title: Subject_HCAF057_Day22

source_name: Subject HCAF057, Day22 post vaccination


title: Subject_HCAF053_Day3

source_name: Subject HCAF053, Day3 post vaccination


title: Subject_HCAF057_Day0

source_name: Subject HCAF057, Day0 post vaccination


title: Subject_HCAF053_Day24

source_name: Subject HCAF053, Day24 post vaccination


title: Subject_HCAF053_Day1

source_name: Subject HCAF053, Day1 post vaccination


title: Subject_HCAF053_Day22

source_name: Subject HCAF053, Day22 post vaccination


title: Subject_HCAF050_Day7

source_name: Subject HCAF050, Day7 post vaccination


title: Subject_HCAF050_Day22

source_name: Subject HCAF050, Day22 post vaccination


title: Subject_HCAF050_Day21

source_name: Subject HCAF050, Day21 post vaccination


title: Subject_HCAF049_Day24

source_name: Subject HCAF049, Day24 post vaccination


title: Subject_HCAF049_Day21

source_name: Subject HCAF049, Day21 post vaccination


title: Subject_HCAF050_Day28

source_name: Subject HCAF050, Day28 post vaccination


title: Subject_HCAF047_Day28

source_name: Subject HCAF047, Day28 post vaccination


title: Subject_HCAF047_Day7

source_name: Subject HCAF047, Day7 post vaccination


title: Subject_HCAF053_Day0

source_name: Subject HCAF053, Day0 post vaccination


title: Subject_HCAF049_Day1

source_name: Subject HCAF049, Day1 post vaccination


title: Subject_HCAF050_Day24

source_name: Subject HCAF050, Day24 post vaccination


title: Subject_HCAF050_Day1

source_name: Subject HCAF050, Day1 post vaccination


title: Subject_HCAF047_Day24

source_name: Subject HCAF047, Day24 post vaccination


title: Subject_HCAF049_Day0

source_name: Subject HCAF049, Day0 post vaccination


title: Subject_HCAF050_Day3

source_name: Subject HCAF050, Day3 post vaccination


title: Subject_HCAF046_Day7

source_name: Subject HCAF046, Day7 post vaccination


title: Subject_HCAF049_Day22

source_name: Subject HCAF049, Day22 post vaccination


title: Subject_HCAF049_Day7

source_name: Subject HCAF049, Day7 post vaccination


title: Subject_HCAF053_Day21

source_name: Subject HCAF053, Day21 post vaccination


title: Subject_HCAF047_Day22

source_name: Subject HCAF047, Day22 post vaccination


title: Subject_HCAF047_Day21

source_name: Subject HCAF047, Day21 post vaccination


title: Subject_HCAF049_Day28

source_name: Subject HCAF049, Day28 post vaccination


title: Subject_HCAF047_Day3

source_name: Subject HCAF047, Day3 post vaccination


title: Subject_HCAF050_Day0

source_name: Subject HCAF050, Day0 post vaccination


title: Subject_HCAF049_Day3

source_name: Subject HCAF049, Day3 post vaccination


title: Subject_HCAF046_Day24

source_name: Subject HCAF046, Day24 post vaccination


title: Subject_HCAF046_Day28

source_name: Subject HCAF046, Day28 post vaccination


title: Subject_HCAF047_Day1

source_name: Subject HCAF047, Day1 post vaccination


title: Subject_HCAF047_Day0

source_name: Subject HCAF047, Day0 post vaccination


title: Subject_HCAF046_Day21

source_name: Subject HCAF046, Day21 post vaccination


title: Subject_HCAF045_Day3

source_name: Subject HCAF045, Day3 post vaccination


title: Subject_HCAF046_Day1

source_name: Subject HCAF046, Day1 post vaccination


title: Subject_HCAF043_Day1

source_name: Subject HCAF043, Day1 post vaccination


title: Subject_HCAF043_Day24

source_name: Subject HCAF043, Day24 post vaccination


title: Subject_HCAF043_Day28

source_name: Subject HCAF043, Day28 post vaccination


title: Subject_HCAF043_Day3

source_name: Subject HCAF043, Day3 post vaccination


title: Subject_HCAF043_Day22

source_name: Subject HCAF043, Day22 post vaccination


title: Subject_HCAF043_Day7

source_name: Subject HCAF043, Day7 post vaccination


title: Subject_HCAF045_Day0

source_name: Subject HCAF045, Day0 post vaccination


title: Subject_HCAF045_Day21

source_name: Subject HCAF045, Day21 post vaccination


title: Subject_HCAF045_Day24

source_name: Subject HCAF045, Day24 post vaccination


title: Subject_HCAF045_Day7

source_name: Subject HCAF045, Day7 post vaccination


title: Subject_HCAF045_Day28

source_name: Subject HCAF045, Day28 post vaccination


title: Subject_HCAF040_Day28

source_name: Subject HCAF040, Day28 post vaccination


title: Subject_HCAF043_Day21

source_name: Subject HCAF043, Day21 post vaccination


title: Subject_HCAF045_Day1

source_name: Subject HCAF045, Day1 post vaccination


title: Subject_HCAF046_Day22

source_name: Subject HCAF046, Day22 post vaccination


title: Subject_HCAF046_Day0

source_name: Subject HCAF046, Day0 post vaccination


title: Subject_HCAF045_Day22

source_name: Subject HCAF045, Day22 post vaccination


title: Subject_HCAF040_Day24

source_name: Subject HCAF040, Day24 post vaccination


title: Subject_HCAF043_Day0

source_name: Subject HCAF043, Day0 post vaccination


title: Subject_HCAF040_Day7

source_name: Subject HCAF040, Day7 post vaccination


title: Subject_HCAF046_Day3

source_name: Subject HCAF046, Day3 post vaccination


title: Subject_HCAF039_Day22

source_name: Subject HCAF039, Day22 post vaccination


title: Subject_HCAF057_Day7

source_name: Subject HCAF057, Day7 post vaccination


title: Subject_HCAF036_Day28

source_name: Subject HCAF036, Day28 post vaccination


title: Subject_HCAF039_Day1

source_name: Subject HCAF039, Day1 post vaccination


title: Subject_HCAF034_Day7

source_name: Subject HCAF034, Day7 post vaccination


title: Subject_HCAF040_Day1

source_name: Subject HCAF040, Day1 post vaccination


title: Subject_HCAF036_Day0

source_name: Subject HCAF036, Day0 post vaccination


title: Subject_HCAF036_Day24

source_name: Subject HCAF036, Day24 post vaccination


title: Subject_HCAF036_Day1

source_name: Subject HCAF036, Day1 post vaccination


title: Subject_HCAF039_Day28

source_name: Subject HCAF039, Day28 post vaccination


title: Subject_HCAF036_Day22

source_name: Subject HCAF036, Day22 post vaccination


title: Subject_HCAF036_Day7

source_name: Subject HCAF036, Day7 post vaccination


title: Subject_HCAF034_Day28

source_name: Subject HCAF034, Day28 post vaccination


title: Subject_HCAF040_Day3

source_name: Subject HCAF040, Day3 post vaccination


title: Subject_HCAF039_Day3

source_name: Subject HCAF039, Day3 post vaccination


title: Subject_HCAF039_Day7

source_name: Subject HCAF039, Day7 post vaccination


title: Subject_HCAF039_Day0

source_name: Subject HCAF039, Day0 post vaccination


title: Subject_HCAF040_Day22

source_name: Subject HCAF040, Day22 post vaccination


title: Subject_HCAF036_Day3

source_name: Subject HCAF036, Day3 post vaccination


title: Subject_HCAF034_Day3

source_name: Subject HCAF034, Day3 post vaccination


title: Subject_HCAF039_Day21

source_name: Subject HCAF039, Day21 post vaccination


title: Subject_HCAF034_Day21

source_name: Subject HCAF034, Day21 post vaccination


title: Subject_HCAF034_Day0

source_name: Subject HCAF034, Day0 post vaccination


title: Subject_HCAF034_Day1

source_name: Subject HCAF034, Day1 post vaccination


title: Subject_HCAF036_Day21

source_name: Subject HCAF036, Day21 post vaccination


title: Subject_HCAF039_Day24

source_name: Subject HCAF039, Day24 post vaccination


title: Subject_HCAF034_Day22

source_name: Subject HCAF034, Day22 post vaccination


title: Subject_HCAF040_Day0

source_name: Subject HCAF040, Day0 post vaccination


title: Subject_HCAF040_Day21

source_name: Subject HCAF040, Day21 post vaccination


title: Subject_HCAF034_Day24

source_name: Subject HCAF034, Day24 post vaccination


title: Subject_HCAF029_Day7

source_name: Subject HCAF029, Day7 post vaccination


title: Subject_HCAF029_Day3

source_name: Subject HCAF029, Day3 post vaccination


title: Subject_HCAF029_Day28

source_name: Subject HCAF029, Day28 post vaccination


title: Subject_HCAF029_Day24

source_name: Subject HCAF029, Day24 post vaccination


title: Subject_HCAF030_Day7

source_name: Subject HCAF030, Day7 post vaccination


title: Subject_HCAF030_Day0

source_name: Subject HCAF030, Day0 post vaccination


title: Subject_HCAF028_Day1

source_name: Subject HCAF028, Day1 post vaccination


title: Subject_HCAF030_Day3

source_name: Subject HCAF030, Day3 post vaccination


title: Subject_HCAF029_Day22

source_name: Subject HCAF029, Day22 post vaccination


title: Subject_HCAF028_Day22

source_name: Subject HCAF028, Day22 post vaccination


title: Subject_HCAF028_Day21

source_name: Subject HCAF028, Day21 post vaccination


title: Subject_HCAF028_Day3

source_name: Subject HCAF028, Day3 post vaccination


title: Subject_HCAF030_Day1

source_name: Subject HCAF030, Day1 post vaccination


title: Subject_HCAF028_Day24

source_name: Subject HCAF028, Day24 post vaccination


title: Subject_HCAF026_Day7

source_name: Subject HCAF026, Day7 post vaccination


title: Subject_HCAF028_Day0

source_name: Subject HCAF028, Day0 post vaccination


title: Subject_HCAF028_Day28

source_name: Subject HCAF028, Day28 post vaccination


title: Subject_HCAF028_Day7

source_name: Subject HCAF028, Day7 post vaccination


title: Subject_HCAF029_Day21

source_name: Subject HCAF029, Day21 post vaccination


title: Subject_HCAF026_Day0

source_name: Subject HCAF026, Day0 post vaccination


title: Subject_HCAF026_Day21

source_name: Subject HCAF026, Day21 post vaccination


title: Subject_HCAF026_Day3

source_name: Subject HCAF026, Day3 post vaccination


title: Subject_HCAF024_Day7

source_name: Subject HCAF024, Day7 post vaccination


title: Subject_HCAF026_Day28

source_name: Subject HCAF026, Day28 post vaccination


title: Subject_HCAF026_Day22

source_name: Subject HCAF026, Day22 post vaccination


title: Subject_HCAF029_Day0

source_name: Subject HCAF029, Day0 post vaccination


title: Subject_HCAF024_Day3

source_name: Subject HCAF024, Day3 post vaccination


title: Subject_HCAF024_Day24

source_name: Subject HCAF024, Day24 post vaccination


title: Subject_HCAF029_Day1

source_name: Subject HCAF029, Day1 post vaccination


title: Subject_HCAF026_Day1

source_name: Subject HCAF026, Day1 post vaccination


title: Subject_HCAF024_Day0

source_name: Subject HCAF024, Day0 post vaccination


title: Subject_HCAF026_Day24

source_name: Subject HCAF026, Day24 post vaccination


title: Subject_HCAF024_Day22

source_name: Subject HCAF024, Day22 post vaccination


title: Subject_HCAF024_Day1

source_name: Subject HCAF024, Day1 post vaccination


title: Subject_HCAF019_Day3

source_name: Subject HCAF019, Day3 post vaccination


title: Subject_HCAF021_Day3

source_name: Subject HCAF021, Day3 post vaccination


title: Subject_HCAF024_Day21

source_name: Subject HCAF024, Day21 post vaccination


title: Subject_HCAF021_Day1

source_name: Subject HCAF021, Day1 post vaccination


title: Subject_HCAF021_Day24

source_name: Subject HCAF021, Day24 post vaccination


title: Subject_HCAF021_Day21

source_name: Subject HCAF021, Day21 post vaccination


title: Subject_HCAF019_Day22

source_name: Subject HCAF019, Day22 post vaccination


title: 2Jiyoye_F3sh

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

description: processed data file: Jiyoyescr-VS-JiyoyeF3sh.DEseq2_Method.GeneDiffExp.txt

data_processing:
SOAPnuke software was used for data filtering (version：v1.5.2, parameters: -l 15 -q 0.2 -n 0.05)
Bowtie2 was used to map clean reads to reference (Version: v2.2.5, Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200)
RSEM was used to calculate gene expression level (Version: v1.2.12, Parameters: default)
DEseq2 was used to detect DEGs (Parameters: Fold Change >= 2.00 and Adjusted P value <= 0.05)
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: Jiyoye_FOXO3 shRNA

growth_protocol: BL cells were grown in RPMI1640 medium with addition of 15 % FBS, glutamine and antibiotics at 37 ºC, 5% CO2.

extract_protocol:
Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.
RNA libraries were prepared for sequencing using standard BGI protocols (oligo dT mRNA enrichment)

treatment_protocol: BL cells were transduced with a lentiviral vector expressing scrambled shRNA of shRNA tageting human FOXO3. The infected cells were sorted on day 4 after transduction. The experiment was done in triplicates. Total RNA was isolated with RNeasy mini kit (QIAGEN).

value: Jiyoye

value: BL cell line

tag: genotype

value: FOXO3 shRNA


title: 3Jiyoye_F3sh


title: 1Jiyoye_F3sh


title: Subject_HCAF024_Day28

source_name: Subject HCAF024, Day28 post vaccination


title: Subject_HCAF019_Day24

source_name: Subject HCAF019, Day24 post vaccination


title: Subject_HCAF019_Day7

source_name: Subject HCAF019, Day7 post vaccination


title: Subject_HCAF021_Day0

source_name: Subject HCAF021, Day0 post vaccination


title: Subject_HCAF021_Day22

source_name: Subject HCAF021, Day22 post vaccination


title: Subject_HCAF018_Day7

source_name: Subject HCAF018, Day7 post vaccination


title: Subject_HCAF018_Day24

source_name: Subject HCAF018, Day24 post vaccination


title: Subject_HCAF018_Day3

source_name: Subject HCAF018, Day3 post vaccination


title: Subject_HCAF019_Day28

source_name: Subject HCAF019, Day28 post vaccination


title: Subject_HCAF019_Day21

source_name: Subject HCAF019, Day21 post vaccination


title: Subject_HCAF018_Day22

source_name: Subject HCAF018, Day22 post vaccination


title: Subject_HCAF021_Day28

source_name: Subject HCAF021, Day28 post vaccination


title: Subject_HCAF021_Day7

source_name: Subject HCAF021, Day7 post vaccination


title: Subject_HCAF019_Day0

source_name: Subject HCAF019, Day0 post vaccination


title: 3Jiyoye_scr

source_name: Jiyoye_scrambled control

value: scrambled control


title: Subject_HCAF018_Day21

source_name: Subject HCAF018, Day21 post vaccination


title: 2Jiyoye_scr


title: 1Jiyoye_scr


title: 3Nam_F3sh

description: processed data file: Namalwascr-VS-NamalwaF3sh.DEseq2_Method.GeneDiffExp.txt

source_name: Namalwa_FOXO3 shRNA

value: Namalwa


title: Subject_HCAF018_Day28

source_name: Subject HCAF018, Day28 post vaccination


title: 1Nam_F3sh


title: 3Nam_scr

source_name: Namalwa_scrambled control


title: 2Nam_scr


title: 3BL-41_F3sh

description: processed data file: BL-41scr-VS-BL-41F3sh.DEseq2_Method.GeneDiffExp.txt

source_name: BL-41_FOXO3 shRNA


title: 2BL-41_F3sh


title: 1Nam_scr


title: Subject_HCAF017_Day7

source_name: Subject HCAF017, Day7 post vaccination


title: Subject_HCAF017_Day24

source_name: Subject HCAF017, Day24 post vaccination


title: Subject_HCAF018_Day0

source_name: Subject HCAF018, Day0 post vaccination


title: Subject_HCAF018_Day1

source_name: Subject HCAF018, Day1 post vaccination


title: 1BL-41_F3sh


title: 3BL-41_scr

source_name: BL-41_scrambled control


title: 2BL-41_scr


title: Subject_HCAF017_Day3

source_name: Subject HCAF017, Day3 post vaccination


title: Subject_HCAF015_Day3

source_name: Subject HCAF015, Day3 post vaccination


title: Subject_HCAF017_Day21

source_name: Subject HCAF017, Day21 post vaccination


title: Subject_HCAF015_Day7

source_name: Subject HCAF015, Day7 post vaccination


title: Subject_HCAF017_Day22

source_name: Subject HCAF017, Day22 post vaccination


title: Subject_HCAF017_Day1

source_name: Subject HCAF017, Day1 post vaccination


title: 1BL-41_scr


title: Subject_HCAF017_Day28

source_name: Subject HCAF017, Day28 post vaccination


title: Notch2-shRNA2 rep2

city: Hefei

first: Fazhi

last: Yu

address: huangshan road 443

institute: USTC

data_processing:
Sequence reads were aligned to the human reference genome with GRCh38.p11(hg38) or hg19.
Genome_build: GRCh38.p11(hg38) for Notch2-KD, and hg19 for Ribosome profiling.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
For ribosome profiling, HeLa cells were synchronized by double thymidine (2 mM, Sigma). Cells were lysed in lysis buffer (20 mM Tris pH 7.5, 150 mM KCl, 5 mM MgCl2, 1 mM dithiothreitol, 8% glycerol) supplemented with 0.5% Triton X-100, 30 U/ml Turbo DNase (Ambion, Life Technologies, CA, United States) and 100 μg/ml cycloheximide (Sigma Aldrich, MO, United States); ribosomeprotected fragments were then isolated and sequenced as previously described (Nat Protoc. 2012 Jul 26;7(8):1534-50.). Total RNA was isolated from cells using Trizol Reagent (Ambion). Polyadenylated RNA was purified from total RNA using magnetic oligo(dT) beads. The resulting mRNA was modestly fragmented by partial hydrolysis in bicarbonate buffer so that the average size of fragments was ∼80 bp. The fragmented mRNA was separated by denaturing PAGE and fragments 50–80 nt were selected. The sequencing libraries were prepared and sequenced as previously described (Nat Protoc. 2012 Jul 26;7(8):1534-50.).  For transcriptomes of OVCAR8 cells, mRNA was extracted from OVCAR8 cells using Trizol Reagent according to the manufacturer’s protocol. RNA samples were quantified using Nanodrop (Life Technologies, Carlsbad, CA, USA) and send to The Beijing Genomics Institute (BGI, Shenzhen, China) for RNA integrity checking, library preparation and sequencing. RNA quality was confirmed using an Agilent 2100 Bioanalyzer by BGI again.
For ribosome profiling mRNA, RNA libraries were prepared for sequencing using standard Illumina protocols.  For Notch2 knockdown mRNA, Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Ovarian cancer

value: Notch2 knockdown


title: Subject_HCAF015_Day28

source_name: Subject HCAF015, Day28 post vaccination


title: Subject_HCAF015_Day24

source_name: Subject HCAF015, Day24 post vaccination


title: Notch2-shRNA2 rep1


title: Notch2-shRNA1 rep2


title: Notch2-shRNA1 rep1


title: NTC rep1

source_name: NTC

value: control


title: Subject_HCAF015_Day22

source_name: Subject HCAF015, Day22 post vaccination


title: NTC rep2


title: Subject_HCAF019_Day1

source_name: Subject HCAF019, Day1 post vaccination


title: Subject_HCAF015_Day1

source_name: Subject HCAF015, Day1 post vaccination


title: Subject_HCAF015_Day21

source_name: Subject HCAF015, Day21 post vaccination


title: Subject_HCAF015_Day0

source_name: Subject HCAF015, Day0 post vaccination


title: PEG-IM-MP treated group_1

city: Nanjing

first: Chao

last: Zhang

address: tongjiaxiang 24

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.7 software was used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 ) were removed by software SeqPrep.
Sequenced reads were mapped to whole genome using Bowtie2 software to get mapped data (reads) for subsequent transcription assembly, expression count, etc.
Based on the selected reference genome sequence, the mapped reads were spliced using Stringtie software
The gene / transcript was compared with six databases (NR, Swiss prot, Pfam, eggnog, go and KEGG), and the annotation information of gene / transcript was obtained
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes Transcripts Per Million reads (TPM) values for each Sample

source_name: BMDC

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: BALB/c

value: bone marrow-derived dendritic cells

tag: treatment

value: PEG-IM-MP


title: SPL-WT9

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
Bulk RNAseq samples were processed and aligned to the mm10 genome using Illumina BaseSpace RNAseq protocol v1.1.0 with default parameters.
10X Genomics 3’ single-cell data were processed with Cell Ranger v3.0.2 using default settings
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: CSV files contain non-normalized gene level read counts for each bulk RNAseq sample.  H5 files contain non-normalized gene X cell UMI counts from 10X single-cell RNAseq data.

source_name: Splenic CD4 cells sorted by flow cytometry

extract_protocol:
Bulk RNAseq samples were extracted using TRIzol and mRNA was enriched using NEBNext polyA mRNA  magnetic isolate module. Single cell RNAseq libraries were constructed using the 10X Genomics Single Cell 3’ v2 kit.
Bulk RNAseq samples were prepared for sequencing using the NEBNext Ultra RNA library prep kit for Illumina. Single cell RNAseq libraries were constructed using the 10X Genomics Single Cell 3’ v2 kit.

value: St3gal1 flox/flox

tag: cell type

value: Splenic CD4 cells


title: PEG-IM-MP treated group_3


title: WT_10X_RNA

source_name: Bone marrow cells positively selected for B220+ CD11c+ cells with negative selection of Ter119, CD11b, CD8 and Gr1 by flow cytometry

value: Bone marrow cells


title: PEG-IM-MP treated group_2


title: 2Nam_F3sh

source_name: Namalwa_FOXO3 shRNA

tag: cell line


title: PEG-MP treated group_3

value: PEG-MP


title: Subject_HCAF013_Day7

source_name: Subject HCAF013, Day7 post vaccination


title: Subject_HCAF013_Day3

source_name: Subject HCAF013, Day3 post vaccination


title: PEG-MP treated group_1


title: Control treated group_3

value: Control


title: Control treated group_2


title: Subject_HCAF017_Day0

source_name: Subject HCAF017, Day0 post vaccination


title: Control treated group_1


title: Subject_HCAF012_Day24

source_name: Subject HCAF012, Day24 post vaccination


title: Subject_HCAF012_Day7

source_name: Subject HCAF012, Day7 post vaccination


title: TA_WT_1

city: Oxford

middle: C

last: Roberts

address: Paediatrics, University of Oxford, Le Gros Clark Building, South Parks Road

country: United Kingdom

institute: University of Oxford

data_processing:
Base-calling was performed at sequencing core facility (WTCHG, Oxford, UK)
Reads were trimmed using Trim_galore and aligned to the mouse genome (GRCm38) using HISAT2
Reads were counted in known transcript features using htseq-count
Differential expression analysis was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix of all un-normalized raw counts data in text file

source_name: Untreated C57BL/6 mouse TA

growth_protocol: Mice were harvested at 11 weeks of age

extract_protocol:
Maxwell RNA extraction robot (Promega)
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Mice were injected IV at 5 weeks of age

tag: tissue

value: Tibialis anterior

value: C57BL/6 (wild-type)

value: Untreated

tag: age

value: 11 weeks


title: TA_WT_3


title: Subject_HCAF013_Day21

source_name: Subject HCAF013, Day21 post vaccination


title: PEG-MP treated group_2


title: Subject_HCAF013_Day24

source_name: Subject HCAF013, Day24 post vaccination


title: TA_WT_2


title: Subject_HCAF012_Day1

source_name: Subject HCAF012, Day1 post vaccination


title: Subject_HCAF012_Day3

source_name: Subject HCAF012, Day3 post vaccination


title: Subject_HCAF013_Day28

source_name: Subject HCAF013, Day28 post vaccination


title: Subject_HCAF013_Day1

source_name: Subject HCAF013, Day1 post vaccination


title: TA_B_3

source_name: AAV-GFP-treated A100Q mouse TA

value: AR100Q (SBMA)


title: Subject_HCAF012_Day21

source_name: Subject HCAF012, Day21 post vaccination


title: Subject_HCAF013_Day0

source_name: Subject HCAF013, Day0 post vaccination


title: TA_B_2


title: Subject_HCAF012_Day28

source_name: Subject HCAF012, Day28 post vaccination


title: TA_B_1


title: Subject_HCAF009_Day7

source_name: Subject HCAF009, Day7 post vaccination


title: TA_A_3

source_name: AAV-AR45-treated A100Q mouse TA


title: Subject_HCAF009_Day28

source_name: Subject HCAF009, Day28 post vaccination


title: Subject_HCAF009_Day3

source_name: Subject HCAF009, Day3 post vaccination


title: TA_A_2


title: Subject_HCAF012_Day22

source_name: Subject HCAF012, Day22 post vaccination


title: Subject_HCAF009_Day21

source_name: Subject HCAF009, Day21 post vaccination


title: Subject_HCAF012_Day0

source_name: Subject HCAF012, Day0 post vaccination


title: Subject_HCAF009_Day22

source_name: Subject HCAF009, Day22 post vaccination


title: TA_A_1


title: Subject_HCAF009_Day1

source_name: Subject HCAF009, Day1 post vaccination


title: Subject_HCAF009_Day24

source_name: Subject HCAF009, Day24 post vaccination


title: si_luc-4 days – 1

city: Moscow

first: Evgeniya

last: Shcherbinina

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
For mapping samples, genome annotations were obtained from Ensembl, release 93.
Reads were mapped using STAR v2.5.3a with default settings except for the following one: –quantMode GeneCounts.
The resulting gene counts were further processed with R package DESeq2, where it was further normalized using RLE method.
To take into account unwanted variation in the data, we obtained by sva package additional variables and introduced them into design matrix to capture unwanted variations.
DESeq2 package were used for performing differential expression analysis based on Wald test. We defined genes as differentially expressed if they passed the thresholds: FDR < 0.05.
Genome_build: Ensembl, release 93.
Supplementary_files_format_and_content: FC and p-value for knockdown samples versus control

source_name: Hepatoma cells

growth_protocol: Cultured in DMEM supplemented with Glutamax, 10% fetal bovine serum and 1% pen/strep

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Neb indexes prior to 12 cycles of PCR.
Library was prepared with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB 7760, New England Biolabs, Ipswich, MA, USA), according to the manufacturer’s protocol.

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and treated with 10 nM siRNA#5 and siRNA#7 for 4 days.   1 mg/kg siRNA#5 and siRNA#7 were formulated in lipid nanoparticles and injected in murine tail vein for 6 and 13 days.

value: treated with control (luciferase) siRNA, 4 days after transfection


title: si_luc -4 days – 2


title: si_luc -4 days – 3


title: Liver_NASH-HCC_Tumor_49

city: Barcelona

first: Marta

last: Piqué

state: Barcelona

address: Rosselló, 153

institute: IDIBAPS

hyb_protocol: Total mRNA was prepared for hybridization using the GeneChip 3’ IVT Pico Kit assay (Thermo Fisher) following the manufacturer’s protocols. Samples were hybridized to the Human Genome U219 Array (Affymetrix) also following the manufacturer protocols.

scan_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

data_processing: Gene expression profiles that passed the quality control were submitted to the GenePattern ExpressionFileCreator Module20 to generate the final dataset. In this last step, the background was corrected with the Robust Multi-array Average (RMA) algorithm and data were normalized using quantiles.

label_protocol: Double-stranded cDNAs were synthesized from total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.

extract_protocol: 50ng of total mRNA was isolated from FFPE samples using the miRNeasy FFPE kit (Qiagen). The Qiacube system (Qiagen) was used to automatize the extraction process.  DNA FFPE kits (Qiagen).

value: NASH-HCC tumor


title: Subject_HCAF004_Day7

source_name: Subject HCAF004, Day7 post vaccination


title: Liver_NASH-HCC_Tumor_50


title: Subject_HCAF004_Day3

source_name: Subject HCAF004, Day3 post vaccination


title: Liver_NASH-HCC_Tumor_52


title: Subject_HCAF004_Day24

source_name: Subject HCAF004, Day24 post vaccination


title: si_7-4 days – 2

value: treated with siRNA 7 for DDX3 knockdown, 4 days after transfection


title: si_7-4 days – 3


title: Subject_HCAF004_Day1

source_name: Subject HCAF004, Day1 post vaccination


title: Liver_NASH-HCC_Tumor_46


title: Liver_NASH-HCC_Tumor_47


title: Subject_HCAF004_Day0

source_name: Subject HCAF004, Day0 post vaccination


title: Subject_HCAF004_Day21

source_name: Subject HCAF004, Day21 post vaccination


title: Liver_NASH-HCC_Tumor_51


title: Liver_NASH-HCC_Tumor_48


title: Subject_HCAF004_Day28

source_name: Subject HCAF004, Day28 post vaccination


title: si_7-4 days – 1


title: Liver_NASH-HCC_Tumor_53


title: Liver_NASH-HCC_Tumor_43


title: Liver_NASH-HCC_Tumor_44


title: Subject_HCAF003_Day7

source_name: Subject HCAF003, Day7 post vaccination


title: Liver_NASH-HCC_Tumor_41


title: Subject_HCAF003_Day3

source_name: Subject HCAF003, Day3 post vaccination


title: Liver_NASH-HCC_Tumor_40


title: Liver_NASH-HCC_Tumor_45


title: Liver_NASH-HCC_Tumor_42


title: Subject_HCAF003_Day28

source_name: Subject HCAF003, Day28 post vaccination


title: si_5-4 days – 2

value: treated with siRNA 5 for DDX3 knockdown, 4 days after transfection


title: si_5-4 days – 3


title: Liver_NASH-HCC_Tumor_39


title: Subject_HCAF003_Day24

source_name: Subject HCAF003, Day24 post vaccination


title: si_5-4 days – 1


title: si_7-13 days – 3

source_name: Liver

value: liver

value: Balb/c

value: treated with LNP-siRNA 7 for DDX3 knockdown, 13 days after injection


title: si_7-13 days – 2


title: si_7-13 days – 1


title: si_5-13 days – 3

value: treated with LNP-siRNA 5 for DDX3 knockdown, 13 days after injection


title: si_5-13 days – 2


title: Liver_NASH-HCC_Tumor_34


title: Liver_NASH-HCC_Tumor_33


title: Liver_NASH-HCC_Tumor_35


title: si_5-13 days – 1


title: Liver_NASH-HCC_Tumor_37


title: Liver_NASH-HCC_Tumor_36


title: Liver_NASH-HCC_Tumor_32


title: Subject_HCAF003_Day22

source_name: Subject HCAF003, Day22 post vaccination


title: Liver_NASH-HCC_Tumor_29


title: Liver_NASH-HCC_Tumor_38


title: Subject_HCAF003_Day0

source_name: Subject HCAF003, Day0 post vaccination


title: Subject_HCAF003_Day1

source_name: Subject HCAF003, Day1 post vaccination


title: Liver_NASH-HCC_Tumor_23


title: Liver_NASH-HCC_Tumor_26


title: Liver_NASH-HCC_Tumor_31


title: Liver_NASH-HCC_Tumor_30


title: Subject_HCAF002_Day7

source_name: Subject HCAF002, Day7 post vaccination


title: Liver_NASH-HCC_Tumor_28


title: Subject_HCAF002_Day3

source_name: Subject HCAF002, Day3 post vaccination


title: Subject_HCAF003_Day21

source_name: Subject HCAF003, Day21 post vaccination


title: Subject_HCAF002_Day28

source_name: Subject HCAF002, Day28 post vaccination


title: Liver_NASH-HCC_Tumor_25


title: Liver_NASH-HCC_Tumor_24


title: Subject_HCAF002_Day24

source_name: Subject HCAF002, Day24 post vaccination


title: si_luc-13 days – 3

value: treated with control (luciferase) LNP-siRNA, 13 days after injection


title: si_luc-13 days – 2


title: si_luc-13 days – 1


title: Liver_NASH-HCC_Tumor_22


title: Liver_NASH-HCC_Tumor_27


title: si_7-6 days – 3

value: treated with LNP-siRNA 7 for DDX3 knockdown, 6 days after injection


title: si_7-6 days – 2


title: Subject_HCAF002_Day22

source_name: Subject HCAF002, Day22 post vaccination


title: si_7-6 days – 1


title: si_5-6 days – 3

value: treated with LNP-siRNA 5 for DDX3 knockdown, 6 days after injection


title: Liver_NASH-HCC_Tumor_21


title: Control smooth muscle cells

city: Kahoku-gun

first: Yasuo

last: Yoshitomi

state: Ishikawa

address: 1-1 Daigaku, Uchinada-machi

department: Biochemistry

institute: Kanazawa Medical University

description: Gene expression data from non-treated human aortic smooth muscle cells

hyb_protocol: Fragmented and labeled cDNAs were then hybridized onto Affymetrix GeneChip Human Gene 1.0 ST arrays in a GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: Arrays were then washed and stained using a GeneChip Fluidics Station 450 and detected using a 3000 7G GeneChip Scanner (Affymetrix).

data_processing: All arrays passed quality control criteria of Expression Console (Affymetrix). Raw data CEL files were then normalized using the RMA algorithm, and data were exported using Expression Console or Gene Spring (Agilent Technologies, Santa Clara, CA, USA). DNA microarray analysis of untreated SMCs, H2O2-treated SMCs, and H2O2- and CTP-treated SMCs was performed identical to HAECs cultured in HuMedia-SG2 medium containing 2.5% (v/v) FBS

source_name: SMC

label_protocol: Subsequently, 300 ng of total RNA was labeled using a GeneChip WT Sense Target Labeling Kit (Affymetrix, Santa Clara, CA, USA) according to manufacturer’s instructions.

growth_protocol: HAECs were cultured at 37°C at 5% CO2 and maintained in HuMedia-EG2 medium containing 2% (v/v) FBS, 10 ng/mL hEGF, 1.34 µg/mL hydrocortisone hemisuccinate, and 10 µg/mL heparin (growth medium) according to the manufacturer’s instructions (Kurabo Corp.). SMCs were cultured at 37°C at 5% CO2 and maintained in HuMedia-SG2 medium containing 5% (v/v) FBS, 5 ng/mL hEGF, 5 ng/mL hFGF-B, and 5 µg/mL insulin according to the manufacturer’s instructions (Kurabo Corp.).

extract_protocol: After CTP treatment, total RNA was extracted from untreated HAECs, H2O2-treated HAECs, and H2O2- and CTP-treated HAECs using a RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA quality was determined by the ratio of 28S to 18S ribosomal RNA band intensities on electrophoretic gels under denaturing conditions.

treatment_protocol: HAECs were seeded at 5,000 cells/cm2 and cultured in growth medium. At 60% cell density, cells were preincubated in HuMedia-EG2 medium containing 1% (v/v) FBS, 5 ng/mL hFGF-B, and 10 µg/mL heparin (assay medium) at 37°C for 2 h. After a 2-h preincubation, H2O2 (200 µM) was added, and cells were then incubated at 37°C for 10 min. Next, CTP (CTP-50) was added to the culture at 100 µg/mL and incubated at 37°C for 24 h.

value: aortic smooth muscle cells (SMCs)

value: control