title: LbK538R-POLQ2 GUIDE seq identified Off-targets U2OS

city: Wuhan

first: chen

last: peng

address: College of Life Sciences, Wuhan University

department: College of Life Sciences

institute: Wuhan University

description: LbK538R POLQ2 U2OS

library_source: genomic

data_processing:
Library strategy: GUIDE-seq
The clean data was generated by trimming low quality bases at both ends of read and remove short fragments, this work was completed by sequencing company
For guide-seq, the sequencing data was processed by corresponding software named guideseq,the human genome version used in the analysis is hg19;
Genome_build: hg19
Supplementary_files_format_and_content: DNA sequences for each sample

source_name: U2OS cells

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)

value: osteosarcoma

tag: read length


title: G1

status: Public on Oct 09 2021

type: genomic

city: Parkville

first: Shivanthan

last: Shanthikumar

state: VIC

address: 50 Flemington Road

country: Australia

institute: Royal Children's Hospital

description:
pooled sample
granulocytes purified from bronchoalveolar lavage
SAMPLE 5

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip  using standard Illumina protocol

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

data_processing: Bead studio software

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA from granulocytes

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from samples using the Qiagen QIAamp DNA Micro Kit according to standard instructions

tag: tissue

value: bronchoalveolar lavage

tag: cell type

value: granulocytes

tag: disease state

value: cystic fibrosis

tag: Sex

value: not applicable


title: Covid 50029 acute phase PBMC

type: SRA

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

description:
single cell RNA
cell_metadata_table.tsv.gz
105_n_149_a_50029_a_108_c_PBMC_5_filtered_feature_bc_matrix.h5
105_n_149_a_50029_a_108_c_PBMC_5_filtered_contig_annotations.csv
105_n_149_a_50029_a_108_c_PBMC_5_donor_ids.tsv
105_n_149_a_50029_a_108_c_PBMC_5_clonotypes.csv

library_source: transcriptomic

data_processing:
The Cell Ranger Software Suite (Version 5.0.0) was used to process raw sequencing data, using the cellranger multi workflow and the GRCh38 references for gene expression and VDJ data and totalSeq antibody barcode sequences for feature barcoding data. Multiplexed samples from multiple donors were demultiplexed by detecting SNPs using CellSNP-lite (Huang and Huang, 2021).
For each sample, the number of RNA counts per cell was mean-normalized, and cells with a mean-normalized RNA count lower than 0.45 and higher than 5 were excluded from the analysis, as well as cells with a percentage of mitochondrial reads higher than 10%.
Genome_build: GRCh38
Supplementary_files_format_and_content:
CSV, clonotypes cell ranger output
CSV, TCR contig annotation cell ranger output
H5 file, count matrices as cell ranger output
TSV, count matrix with cells as columns, and genes as rows.
TSV, donor ID SNP demultiplexing output
TSV, metadata annotation of all cells (incl. clusters,VDJ)

molecule: total RNA

source_name: PBMC

extract_protocol:
Human peripheral blood mononuclear cells (PBMCs) were isolated from heparinized whole blood by density gradient centrifugation over Pancoll (density: 1,077g /ml, PAN-Biotech). Subsequently the cells were counted, frozen and stored in liquid nitrogen.
On the day of the experiment the frozen PBMCs were thawed in pre-warmed thawing medium. About 2-3 x10^5 PBMCs were resuspended in staining buffer (DPBS, Gibco; 0,5% BSA, Miltenyi; 2 mM EDTA, Gibco) and hashtagged with 0,5 µg Total-Seq-C Hashtag antibodies for 30 min at 4°C. After the incubation PBMCs were washed three times. Subsequently PBMC were counted and up to four different samples were pooled equally. T-cell libraries were generated by staining with antibodies recognizing CD3, CD4, CD8 and CD38 for later flow cytometry sorting and simultaneously hashtagged as described above. Subsequently, CD3+CD4+CD38+ cells and CD3+CD8+CD38+ cells were sorted using the FACS Aria (BD Bioscience). Afterwards CD4+CD38+ and CD8+ CD38+ cells from each donor were pooled equally and then CD38+ T cells from up to four samples were also pooled in equal proportions.
The cell suspension was loaded with 40.000 - 50.000 cells per lane, in the Chromium Controller. scRNA libraries were generated using 10X 5' sequencing library kit v1.1. For additional VDJ and hashtag libraries the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10x Genomics) and the Chromium Single Cell 5’ Feature Barcode Library Kit (10x Genomics) were used respectively
Cells from up to 4 samples were pooled, and TotalSeq C Hashtag antibodies were used to identify samples

tag: disease  state

value: CV

tag: patient id

tag: disease phase

value: acute

tag: disease severity

value: mild

value: PBMC

tag: library


title: Embryo 18hpf_20160610_bath study 18hpf 25-05 strip1_ 2_02.RCC

type: RNA

city: Moscow

first: Leonid

last: Uroshlev

address: Gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics RAS

description: This sample has associated processed data in the sample table.

hyb_protocol: Hybridize with both Reporter and Capture probes. NanoString manufacturer's protocol

scan_protocol: nCounter analysis system

data_processing: We removed cells with poor total counts of test probes other than those of housekeeping genes (rpl13 and kanamycin), assuming that most of them related to cell types expressing other cell markers than those represented in our panel. In addition, we removed data for probes (genes) that displayed expression in only a small number of cells. We used the NanoStringNorm R package, and removed a number of cells with poor norm factors and noisy background.  Normalization was performed using the sum of probes (kanamycin spike-in and rpl13 internal controls) as the reference housekeeping class with ‘mean and 2sd’ selected for the background.  We filtered the expression matrix nullifying elements with values less than 30 and imputed for dropouts using drImpute. In total about 20% of zero counts have been imputed into meaningful quantitative values.

label: NanoString manufacturer's protocol

molecule: polyA RNA

organism: Danio rerio

source_name: Neural Crest

label_protocol: NanoString manufacturer's protocol

growth_protocol: Embryos were obtained from natural crosses and staged according to Kimmel et al. System water is made up from Reverse Osmosis water, with synthetic sea salt added at an amount such that the conductivity of the water is kept at approximately 800uS. Average water quality data are as follows: pH: 7.30, general Hardness: 160mg/l CaCO3, Ammonia: 0 mg/l NH3, Nitrite: 0 mg/l NO2, Nitrate: < 10 mg/l NO3- and Conductivity: around 800μS/cm. Light cycle is 14 hours light/10 hours dark (Lights on at 08:00, off at 22:00 daily). All fish were in general good health and no specific diseases were observed throughout the colony. The fish were fed Paramecium from 5-15dpf, followed by Ziegler Larval AP100 powder from day 16 – 22dpf. From 23dpf onwards they are fed Sparos Zebrafeed and Brine Shrimp. Fish euthanized by schedule 1 killing were given an overdose of an anaesthetic (5 drops of 0.48% MS-222 added to a petridish of water)

extract_protocol: To extract RNA from Trizol stocks we used Direct-zol™ RNA MicroPrep (Cat.# R2062, ZymoResearch, USA) according the manufacturer’s protocol. The total RNA was extracted in 10 ml, measured using Nanodrop-2000, and tested with Experion™ RNA HighSens Analysis Kits (Cat.# 700-7105, Bio-Rad ) using the Experion™ Automated Electrophoresis System (Bio-Rad). 5 ml of total RNA from either melanocytes or iridophore (50-60 ng/ml) was used directly for NanoString expression analysis

tag: age (hpf)

tag: genotype

value: wild type

value: whole embryos


title: M4

description:
pooled sample
alveolar macrophages purified from bronchoalveolar lavage
SAMPLE 10

source_name: Genomic DNA from alveolar macrophages

value: alveolar macrophages


title: Covid 50029 convalescent PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
70_c_325_a_50029_c_218_a_59_a_PBMC_5_filtered_feature_bc_matrix.h5
70_c_325_a_50029_c_218_a_59_a_PBMC_5_filtered_contig_annotations.csv
70_c_325_a_50029_c_218_a_59_a_PBMC_5_donor_ids.tsv
70_c_325_a_50029_c_218_a_59_a_PBMC_5_clonotypes.csv

value: convalescent


title: female_WT_2

city: Boston

first: Dilansu

last: Guneykaya

state: MA

address: 220 Longwood Avenue

department: Neurobiology

country: USA

institute: Harvard Medical School

data_processing:
Illumina software used for basecalling.
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1(Trapnell et al., 2012)
Raw counts were normalized using TMM normalization and then log2-transformed.
Genome_build: mmusculus_gene_ensembl
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: whole brain microglia

extract_protocol:
RNA was isolated 1,000 isolated Ly6C-CD11b+Fcrls+ microglia were lysed in 5ul TCL buffer +1%beta-mercaptoethanol. Smart-Seq2 libraries were prepared and sequenced by the Broad Genomic Platform.
RNA libraries were prepared for sequencing using smartseq-2 protocol 5 from Broad genomic facility

value: WT

tag: strain

value: female

tag: group

value: female ctrl

value: whole brain

value: microglia


title: Embryo 18hpf_20160610_bath study 18hpf 25-05 strip1_ 1_01.RCC


title: Embryo 21hpf_20160315_bath study 4 21hpf_10_10.RCC


title: As-POLQ2 GUIDE seq identified Off-targets U2OS

country: China

description: As POLQ2 U2OS

value: osteosarcoma


title: As-Site1 GUIDE seq identified Off-targets U2OS

description: As site1 U2OS


title: Covid 37 convalescent PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
37_c_21_a_12_a_136_c_PBMC_5_filtered_feature_bc_matrix.h5
37_c_21_a_12_a_136_c_PBMC_5_filtered_contig_annotations.csv
37_c_21_a_12_a_136_c_PBMC_5_donor_ids.tsv
37_c_21_a_12_a_136_c_PBMC_5_clonotypes.csv


title: Covid 37 convalescent Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
37_c_21_a_12_a_136_c_Tcells_5_filtered_feature_bc_matrix.h5
37_c_21_a_12_a_136_c_Tcells_5_filtered_contig_annotations.csv
37_c_21_a_12_a_136_c_Tcells_5_donor_ids.tsv
37_c_21_a_12_a_136_c_Tcells_5_clonotypes.csv

source_name: CD38+ T cells

value: CD38+ T cells


title: Embryo 24hpf_20160301_bath study 3_74_11.RCC


title: Covid 39 acute phase PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
22_39_PBMC_5_filtered_feature_bc_matrix.h5
22_39_PBMC_5_filtered_contig_annotations.csv
22_39_PBMC_5_donor_ids.tsv
22_39_PBMC_5_clonotypes.csv

value: severe


title: Embryo 24hpf_20160301_bath study 3_71_08.RCC


title: AsK548R-Site1 GUIDE seq identified Off-targets U2OS

description: AsK548R site1 U2OS


title: Embryo 21hpf_20160315_bath study 4 21hpf_7_07.RCC


title: Covid 39 acute phase Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
22_39_Tcells_5_filtered_feature_bc_matrix.h5
22_39_Tcells_5_filtered_contig_annotations.csv
22_39_Tcells_5_donor_ids.tsv
22_39_Tcells_5_clonotypes.csv


title: Embryo 21hpf_20160315_bath study 4 21hpf_9_09.RCC


title: Covid 37 acute phase Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
37_a_21_c_12_c_136_a_Tcells_5_filtered_feature_bc_matrix.h5
37_a_21_c_12_c_136_a_Tcells_5_filtered_contig_annotations.csv
37_a_21_c_12_c_136_a_Tcells_5_donor_ids.tsv
37_a_21_c_12_c_136_a_Tcells_5_clonotypes.csv


title: Embryo 24hpf_20160301_bath study 3_69_06.RCC


title: Covid 70 acute phase Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
79_n_139_a_70_a_Tcells_5_filtered_feature_bc_matrix.h5
79_n_139_a_70_a_Tcells_5_filtered_contig_annotations.csv
79_n_139_a_70_a_Tcells_5_donor_ids.tsv
79_n_139_a_70_a_Tcells_5_clonotypes.csv


title: Covid 29 convalescent PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
29_88_PBMC_5_filtered_feature_bc_matrix.h5
29_88_PBMC_5_filtered_contig_annotations.csv
29_88_PBMC_5_donor_ids.tsv
29_88_PBMC_5_clonotypes.csv


title: Embryo 21hpf_20160315_bath study 4 21hpf_6_06.RCC


title: Lb-Site1 GUIDE seq identified Off-targets U2OS

description: Lb site1 U2OS


title: Covid 39 convalescent PBMC


title: Embryo 24hpf_20160301_bath study 2_30_12.RCC


title: Lb-POLQ2 GUIDE seq identified Off-targets

description: Lb POLQ2

source_name: HEK 293 cells

value: embryonic kidney


title: Covid 88 convalescent PBMC

value: CV


title: Covid 41 acute phase Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
41_68_Tcells_5_filtered_feature_bc_matrix.h5
41_68_Tcells_5_filtered_contig_annotations.csv
41_68_Tcells_5_donor_ids.tsv
41_68_Tcells_5_clonotypes.csv

value: acute


title: Covid 50029 acute phase Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
105_n_149_a_50029_a_108_c_Tcells_5_filtered_feature_bc_matrix.h5
105_n_149_a_50029_a_108_c_Tcells_5_filtered_contig_annotations.csv
105_n_149_a_50029_a_108_c_Tcells_5_donor_ids.tsv
105_n_149_a_50029_a_108_c_Tcells_5_clonotypes.csv

value: mild


title: Covid 499 convalescent PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
79_n_139_a_70_a_499_c_PBMC_5_filtered_feature_bc_matrix.h5
79_n_139_a_70_a_499_c_PBMC_5_filtered_contig_annotations.csv
79_n_139_a_70_a_499_c_PBMC_5_donor_ids.tsv
79_n_139_a_70_a_499_c_PBMC_5_clonotypes.csv

value: PBMC


title: Lb-POLQ2 GUIDE seq identified Off-targets U2OS

description: Lb POLQ2 U2OS

value: wild type


title: Flu-like-illness 138 PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
143_a_140_a_138_a_144_a_PBMC_5_filtered_feature_bc_matrix.h5
143_a_140_a_138_a_144_a_PBMC_5_filtered_contig_annotations.csv
143_a_140_a_138_a_144_a_PBMC_5_donor_ids.tsv
143_a_140_a_138_a_144_a_PBMC_5_clonotypes.csv

value: FLI


title: Embryo 21hpf_20160315_bath study 4 21hpf_3_03.RCC

value: whole embryos


title: Embryo 21hpf_20160315_bath study 4 21hpf_11_11.RCC


title: Covid 57 acute phase Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
57_Tcells_5_filtered_feature_bc_matrix.h5
57_Tcells_5_filtered_contig_annotations.csv
57_Tcells_5_clonotypes.csv


title: Lb-POLQ1 GUIDE seq identified Off-targets

description: Lb POLQ1


title: Flu-like-illness 138 Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
143_a_140_a_138_a_144_a_Tcells_5_filtered_feature_bc_matrix.h5
143_a_140_a_138_a_144_a_Tcells_5_filtered_contig_annotations.csv
143_a_140_a_138_a_144_a_Tcells_5_donor_ids.tsv
143_a_140_a_138_a_144_a_Tcells_5_clonotypes.csv
143_a_140_a_138_a_144_a_Tcells_5_GEM2_filtered_feature_bc_matrix.h5
143_a_140_a_138_a_144_a_Tcells_5_GEM2_filtered_contig_annotations.csv
143_a_140_a_138_a_144_a_Tcells_5_GEM2_donor_ids.tsv
143_a_140_a_138_a_144_a_Tcells_5_GEM2_clonotypes.csv


title: Covid 59 acute phase PBMC


title: Covid 50029 convalescent Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
70_c_325_a_50029_c_218_a_59_a_Tcells_5_filtered_feature_bc_matrix.h5
70_c_325_a_50029_c_218_a_59_a_Tcells_5_filtered_contig_annotations.csv
70_c_325_a_50029_c_218_a_59_a_Tcells_5_donor_ids.tsv
70_c_325_a_50029_c_218_a_59_a_Tcells_5_clonotypes.csv

value: convalescent


title: LbK538R-Site1 GUIDE seq identified Off-targets

description: LbK538R site1


title: Covid 58 acute phase Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
58_Tcells_5_filtered_feature_bc_matrix.h5
58_Tcells_5_filtered_contig_annotations.csv
58_Tcells_5_clonotypes.csv


title: Covid 59 acute phase Tcells


title: Flu-like-illness 139 Tcells


title: Flu-like-illness 139 PBMC


title: LbK53R-Site1 GUIDE seq identified Off-targets U2OS

description: LbK538R site1 U2OS


title: Covid 68 acute phase Tcells


title: Flu-like-illness 140 PBMC


title: LbK538R-PRKCH GUIDE seq identified Off-targets

description: LbK538R PRKCH


title: Embryo 24hpf_20160301_bath study 2_25_07.RCC

description: This sample has associated processed data in the sample table.


title: LbK538R-POLQ2 GUIDE seq identified Off-targets

description: LbK538R POLQ2


title: Embryo 24hpf_20160301_bath study 2_24_06.RCC


title: Covid 70 acute phase PBMC


title: Flu-like-illness 143 PBMC


title: Flu-like-illness 143 Tcells


title: AsK548R-POLQ2 GUIDE seq identified Off-targets U2OS

description: AsK548R POLQ2 U2OS


title: Covid 70 convalescent PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
70_c_325_a_50029_c_218_a_59_a_PBMC_5_filtered_feature_bc_matrix.h5
70_c_325_a_50029_c_218_a_59_a_PBMC_5_filtered_contig_annotations.csv
70_c_325_a_50029_c_218_a_59_a_PBMC_5_donor_ids.tsv
70_c_325_a_50029_c_218_a_59_a_PBMC_5_clonotypes.csv


title: Lb-Site1 GUIDE seq identified Off-targets

description: Lb site1


title: Covid 88 acute phase PBMC


title: Flu-like-illness 145 PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
145_a_442_n_358_n_385_n_PBMC_5_filtered_feature_bc_matrix.h5
145_a_442_n_358_n_385_n_PBMC_5_filtered_contig_annotations.csv
145_a_442_n_358_n_385_n_PBMC_5_donor_ids.tsv
145_a_442_n_358_n_385_n_PBMC_5_clonotypes.csv


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 13-24_   _03.RCC

value: decapitated embryos


title: Lb-PRKCH GUIDE seq identified Off-targets

description: Lb PRKCH


title: Lb-B2M GUIDE seq identified Off-targets

description: Lb B2M


title: Covid 70 convalescent Tcells


title: Embryo 24hpf_20160301_bath study 3_65_02.RCC


title: Embryo 24hpf_20160301_bath study 2_28_10.RCC


title: Flu-like-illness 144 Tcells


title: Flu-like-illness 149 Tcells


title: Flu-like-illness 149 PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
105_n_149_a_50029_a_108_c_PBMC_5_filtered_feature_bc_matrix.h5
105_n_149_a_50029_a_108_c_PBMC_5_filtered_contig_annotations.csv
105_n_149_a_50029_a_108_c_PBMC_5_donor_ids.tsv
105_n_149_a_50029_a_108_c_PBMC_5_clonotypes.csv


title: Covid 88 convalescent Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
29_88_Tcells_5_filtered_feature_bc_matrix.h5
29_88_Tcells_5_filtered_contig_annotations.csv
29_88_Tcells_5_donor_ids.tsv
29_88_Tcells_5_clonotypes.csv


title: Embryo 24hpf_20160301_bath study 2_29_11.RCC


title: Covid 88 acute phase Tcells


title: Lb2-Site1 GUIDE seq identified Off-targets

description: Lb2 site1


title: LbK538R-POLQ1 GUIDE seq identified Off-targets

description: LbK538R POLQ1


title: Lb2K518R-Site1 GUIDE seq identified Off-targets

description: Lb2K518R site1


title: Hepatitis B 5 Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
01_a_02_a_05_a_06_a_Tcells_5_filtered_feature_bc_matrix.h5
01_a_02_a_05_a_06_a_Tcells_5_filtered_contig_annotations.csv
01_a_02_a_05_a_06_a_Tcells_5_donor_ids.tsv
01_a_02_a_05_a_06_a_Tcells_5_clonotypes.csv

value: HBV


title: Hepatitis B 5 PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
01_a_02_a_05_a_06_a_PBMC_5_filtered_feature_bc_matrix.h5
01_a_02_a_05_a_06_a_PBMC_5_filtered_contig_annotations.csv
01_a_02_a_05_a_06_a_PBMC_5_donor_ids.tsv
01_a_02_a_05_a_06_a_PBMC_5_clonotypes.csv


title: Flu-like-illness 145 Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
145_a_442_n_358_n_385_n_Tcells_5_filtered_feature_bc_matrix.h5
145_a_442_n_358_n_385_n_Tcells_5_filtered_contig_annotations.csv
145_a_442_n_358_n_385_n_Tcells_5_donor_ids.tsv
145_a_442_n_358_n_385_n_Tcells_5_clonotypes.csv


title: Lb2-POLQ1 GUIDE seq identified Off-targets

description: Lb2 POLQ1


title: Embryo 24hpf_20160301_bath study 2_26_08.RCC


title: Flu-like-illness 148 Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
91_n_148_a_108_a_325_c_Tcells_5_filtered_feature_bc_matrix.h5
91_n_148_a_108_a_325_c_Tcells_5_filtered_contig_annotations.csv
91_n_148_a_108_a_325_c_Tcells_5_donor_ids.tsv
91_n_148_a_108_a_325_c_Tcells_5_clonotypes.csv


title: Hepatitis B 1 PBMC


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _12.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 13-24_   _05.RCC


title: Lb2-PRKCH GUIDE seq identified Off-targets

description: Lb2 PRKCH


title: Healthy control 105 PBMC

value: HC


title: Flu-like-illness 140 Tcells


title: Lb2-POLQ2 GUIDE seq identified Off-targets

description: Lb2 POLQ2


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _06.RCC


title: LbK538R-B2M GUIDE seq identified Off-targets

description: LbK538R B2M


title: Hepatitis B 2 PBMC


title: Flu-like-illness 148 PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
91_n_148_a_108_a_325_c_PBMC_5_filtered_feature_bc_matrix.h5
91_n_148_a_108_a_325_c_PBMC_5_filtered_contig_annotations.csv
91_n_148_a_108_a_325_c_PBMC_5_donor_ids.tsv
91_n_148_a_108_a_325_c_PBMC_5_clonotypes.csv


title: Hepatitis B 1 Tcells


title: Healthy control 105 Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
105_n_149_a_50029_a_108_c_Tcells_5_filtered_feature_bc_matrix.h5
105_n_149_a_50029_a_108_c_Tcells_5_filtered_contig_annotations.csv
105_n_149_a_50029_a_108_c_Tcells_5_donor_ids.tsv
105_n_149_a_50029_a_108_c_Tcells_5_clonotypes.csv


title: Healthy control 358 PBMC


title: Flu-like-illness 144 PBMC


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _11.RCC


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _05.RCC


title: Healthy control 385 PBMC


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _03.RCC


title: Healthy control 79 PBMC

description:
single cell RNA
cell_metadata_table.tsv.gz
79_n_139_a_70_a_499_c_PBMC_5_filtered_feature_bc_matrix.h5
79_n_139_a_70_a_499_c_PBMC_5_filtered_contig_annotations.csv
79_n_139_a_70_a_499_c_PBMC_5_donor_ids.tsv
79_n_139_a_70_a_499_c_PBMC_5_clonotypes.csv


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _10.RCC


title: Hepatitis B 6 PBMC


title: Healthy control 79 Tcells

description:
single cell RNA
cell_metadata_table.tsv.gz
79_n_139_a_70_a_Tcells_5_filtered_feature_bc_matrix.h5
79_n_139_a_70_a_Tcells_5_filtered_contig_annotations.csv
79_n_139_a_70_a_Tcells_5_donor_ids.tsv
79_n_139_a_70_a_Tcells_5_clonotypes.csv


title: Healthy control 91 PBMC


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _09.RCC


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _01.RCC


title: As-Site1 GUIDE seq identified Off-targets

description: As site1


title: Hepatitis B 6 Tcells


title: IPF_Base_6

city: Perth

first: Zhenjun

last: Deng

state: Western Australia

address: 35 Stirling Highway

institute: The University of Western Australia

data_processing:
Real Time Analysis (RTA) v3.4.4 software used for base-calling. Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data
Merge the two files for each sample prior to secondary analyses
Fastp used for trimming.
STAR used for aligment and SAMtools used to generate bam files for further analyses
DESeq2 used for differential gene expresson analyses
Genome_build: hg19
Supplementary_files_format_and_content: CSV files with raw abundance counts

source_name: basal region of lung

growth_protocol: Lung fibroblasts were grown with DMEM media containing high glucose supplemented with 2 mM L-glutamine, 1% penicillin/streptomycin and 10% FBS.

extract_protocol:
Fibroblasts were harvest by trypsinization using 0.05% trypsin-EDTA and washed in PBS before total RNA was extracted. RNA extraction of collected cells was performed using the RNeasy Mini kit according to the manufacturers’ protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: fibroblast

tag: diagnosis

value: idiopathic pulmonary fibrosis (IPF)


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _07.RCC


title: Hepatitis B 2 Tcells

value: CD38+ T cells


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _08.RCC


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _10.RCC


title: Lb2K518R-POLQ1 GUIDE seq identified Off-targets

description: Lb2K518R POLQ1


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _08.RCC


title: As-POLQ2 GUIDE seq identified Off-targets

description: As POLQ2


title: Lb2K518R-POLQ2 GUIDE seq identified Off-targets

description: Lb2K518R POLQ2


title: IPF_Base_1


title: CTR_Base_6

value: control donor


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _05.RCC


title: Healthy control 358 Tcells


title: CTR_Base_3


title: CTR_Base_4


title: Healthy control 442 Tcells


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 53-64_   _04.RCC


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _04.RCC


title: Healthy control 385 Tcells


title: Lb2K518R-PRKCH GUIDE seq identified Off-targets

description: Lb2K518R PRKCH

value: embryonic kidney


title: Lb2-B2M GUIDE seq identified Off-targets

description: Lb2 B2M


title: Healthy control 442 PBMC


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _06.RCC


title: CTR_Base_1


title: AsK548R-PRKCH GUIDE seq identified Off-targets

description: AsK548R PRKCH


title: AsK548R-POLQ1 GUIDE seq identified Off-targets

description: AsK548R POLQ1


title: IPF_Base_5


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _07.RCC


title: IPF_Apex_4

source_name: apical region of lung


title: Healthy control 91 Tcells


title: AsK548R-Site1 GUIDE seq identified Off-targets

description: AsK548R site1


title: IPF_Apex_3


title: IPF_Base_4


title: As-PRKCH GUIDE seq identified Off-targets

description: As PRKCH


title: As-POLQ1 GUIDE seq identified Off-targets

description: As POLQ1


title: H3K27ac_IR_BaF3

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: Rm 368 - 3649 Promenade Sir William Osler

department: Physiology

country: Canada

institute: McGill University

data_processing:
Reads quality filtered according to the Illumina pipeline
Experimental and input control sequence reads were mapped to the mouse mm9 reference genome assembly with Bowtie 1.0.0 using the following settings: --best --trim5 2 mm9.
Chromatin binding sites of MYSM1 were identified using peak detection algorithm MACS (version 1.4.1, default parameters), with comparisons for read enrichment against control input DNA from the same cells (Input ChIP-Seq are submitted in GSE150667 and described in PMID: 32641579).
The resulting binding sites were filtered to remove regions with < 5 fold enrichment compared to the input DNA and < 5 normalized tag counts within 200bp to the peak summit.
Genome_build: mm9
Supplementary_files_format_and_content: .bed file

source_name: Ba/F3 cell line stably expressing triple-FLAG-tagged murine MYSM1 (cell lines described in PMID: 26768662)

growth_protocol: The Ba/F3 cell line stably expressing triple-Flag-tagged MYSM1 was maintained at 0.5-2 x 10^6 cells/mL in RPMI-1640 (Wisent) with 10% Fetal Calf Serum (FCS, Wisent), 2mM L-Glutamine, 100μg/mL streptomycin, 100U/mL penicillin (Wisent), 5% WEHI conditioned media as the source of IL-3, and under 2μg/mL puromycin selection (Wisent). The HPC7 cell line stably expressing triple-Flag-tagged MYSM1 was cultured at 0.5-2 x 10^6 cells/mL in IMDM (Life Technologies), with 10% FCS (Gibco, Life Technologies), 100μg/mL streptomycin, 100U/mL penicillin (Wisent), 7.48x10^-5M MTG (M6145, Sigma-Aldrich), 100 ng/mL murine SCF (Shenandoah Biotechnology, Cedarlane), and under 2μg/mL puromycin selection (Wisent).

extract_protocol:
Cells were fixed with 1% formaldehyde in the culture media for 10 minutes at room temperature, followed by addition of 0.125M of glycine to stop fixation. Nuclei were extracted with 5 minutes lysis in 0.25% Triton buffer (10mM Tris-HCl pH8, 10mM EDTA, 0.5mM EGTA), followed by 30 minutes in 200mM NaCl buffer (10mM Tris-HCl pH8, 1mM EDTA, 0.5mM EGTA). Nuclei were resuspended in sonication buffer (10mM Tris pH8, 140mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.5% SDS, 0.5% Triton X-100, 0.05% NaDOC) and sonicated for fourteen cycles of 30 seconds with a digital sonifier (Branson Ultrasonics) at 80%, with 30 seconds rest in cooled circulating water. Beads were prepared overnight with 40μL of Dynabeads Protein G (Invitrogen, Life Technologies) conjugated to 5μg of antibody against p53 (1C12, Cell Signaling Technology) or H3K27ac (ab4729, Abcam). Immunoprecipitation was performed by overnight incubation of antibody-bead matrices with sheared chromatin from the equivalent of 5x106 cells. Immune complexes were washed sequentially for 2 min at room temperature with 1 ml of the following buffers: wash B (1% Triton X-100, 0.1% SDS, 150-mM NaCl, 2-mM EDTA, and 20-mM Tris-HCl, pH 8), wash C (1% Triton X-100, 0.1% SDS, 500-mM NaCl, 2-mM EDTA, and 20-mM Tris-HCl, pH 8), wash D (1% NP-40, 250-mM LiCl, 1-mM EDTA, and 10-mM Tris-HCl, pH 8), and TEN buffer (50-mM NaCl, 10-mM Tris-HCl, pH 8, and 1-mM EDTA). The samples were de-crosslinked by overnight incubation at 65̊C in 1% SDS buffer (50mM Tris-HCl pH8, 10mM EDTA). Following RNaseA and Proteinase K enzymatic treatments, ChIP DNA was purified using Qiaquick PCR Cleanup kit (Qiagen).
ChIP-Seq libraries were prepared using the Illumina TruSeq kit and sequenced on an Illumina HiSeq 2500 sequencer in paired-end 50bp configuration, with input DNA from the same cells sequenced as negative control (Input ChIP-Seq are submitted in GSE150667 and described in PMID: 32641579).

value: Ba/F3 cells

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: RNA-seq (rRNA-depleted) from udd/+ ovaries, replicate 2

first: Valentin

last: Poltorachenko

state: Moscow

address: Akademika Kurchatova square, 2

institute: Institute of Molecular Genetics of National Research Centre «Kurchatov Institute»

data_processing:
ChIP-seq: Two biological replicates of udd/+ reads, one biological replicate of udd 1 / udd null reads and one biological replicate of input from udd/+ were adapter clipped; mapped to the reference sequences (rDNA, R1, R2) and also mapped to the dmel-r5.57 ( from https://flybase.org/ ) by bowtie2 (Langmead 2012); counted by samtools ( http://www.htslib.org/ ) and bedtools ( https://bedtools.readthedocs.io/en/latest/ ) softwares on the 100-bp genomic bins. The results counts were converted to RPM and normalized on input by R.
RNA-seq: Two biological replicates of udd/+ reads and two of udd 0683-G4 / udd null reads were adapter clipped; mapped to reference sequences (rDNA, R1, R2) and also mapped to the dmel-r5.57 ( from https://flybase.org/ ) by bowtie2 (Langmead 2012), also mapped sequences were filtered from mature rRNA sequence by samtools software  ( http://www.htslib.org/ ); Then counted by samtools and bedtools ( https://bedtools.readthedocs.io/en/latest/ ) softwares on the 100-bp genomic bins. The results counts were converted to RPM.
Genome_build: dmel-r5.57 ( from https://flybase.org/ )
Supplementary_files_format_and_content: csv files for RNA-seq and ChIP-seq profiles represent read counts per 100-nt bins generated using bedtools software ( https://bedtools.readthedocs.io/en/latest/ )

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
RNA-seq: Total RNA samples were isolated from ovaries using Trizol reagent (Invitrogen) according to the standard protocol and treated with DNase using the DNA-free DNA Removal Kit (Invitrogen). rRNA was removed by hybridization of 200 ng of total RNA with biotinylated oligonucleotides complementary to different regions of rRNA followed by binding to Dynabead MyOn Streptavidin C1 (Invitrogen). After precipitation, supernatants containing rRNA-depleted RNA were precipitated with isopropanol and used for libraries preparation.
ChIP-seq: ChIP using guinea pig anti-Udd (a gift from Michael Buszczak) was performed according to the published procedure (Chanas et al., 2004). Chromatin was fragmented by sonication on Vibra-Cell (Sonics) with amplitude 15% during 35 pulses of 10s with 10s pause intervals.
RNA Library Prep Set V3.1 for RNA-seq
Accel-NGS 1S Plus DNA Library Kit for ChIP-seq
ChIP-seq; RNA-seq

value: ovaries

value: udd/+ (mix of udd0683-G4/+ and udd null/+)

tag: biological replicate


title: p53_UT_HPC7

source_name: HPC7 cell line stably expressing triple-FLAG-tagged murine MYSM1 (cell lines described in PMID: 26768662)

value: HPC7 cells

value: anti-p53 (1C12, Cell Signaling Technology)


title: IPF_Base_2


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _03.RCC

value: wild type


title: Lb2K518R-B2M GUIDE seq identified Off-targets

description: Lb2K518R B2M

tag: read length


title: CTR_Base_5

tag: tissue


title: p53_IR_BaF3

tag: cell type


title: IPF_Base_3


title: Flat-1

city: Philadelphia

first: Mariana

last: Franco Fragoso

state: PA

address: 333 Cottman Avenue

department: Cancer Prevention and Control

institute: Fox Chase Cancer Center

description: Epithelial cells from FFPE were microdissected from flat lesions

hyb_protocol: Samples were diluted 1:10, and 5ul each miRNA-tag sample (equivalent to 10ng total RNA) were added to hybridizations with 10 ul or reporter code set, 10 ul hybridization buffer and 5 ul of capture probe set.

scan_protocol: Scans were completed with GEN2 Digital Analyzer.

data_processing: NanoString raw counts were normalized using nSolver (v2.0)

label: miR-taq, Reporter Code Set and Capture Probe Set

source_name: colon

label_protocol: ~100ng (or 3ul) of each RNA sample was added to the miRNA-tag ligation reaction for annealing, followed by ligation and purification.

growth_protocol: Female Swiss Webster mice (7 weeks of age) were maintained in the animal facility and received food and water ad libitum. Animals were treated with AOM (7.4 mg/kg, i.p.) and 4% DSS for 3 cycles (one cycle = 7 days of DSS plus 21 days of water). At the time of the sacrifice, colons were cut into sections and fixed in formalin. Fixed sections were cut at 10 um for sample collection by Laser Capture Microdissection (LEICA LMD 6500 system).

extract_protocol: RNA was extracted from pure populations of colonic epithelial cells using the RecoverAll™ Isolation kit (Life Technologies). All RNAs were subjected to DNAse treatment. Quality was assessed on RNA 6000 Pico LabChip and evaluated on Agilent Bioanalyzer 2100 using Eukaryote Total RNA Pico Assay.

treatment_protocol: Only untreated animals were used in this array

value: Female

value: Swiss Webster

tag: lesion

value: Flat dysplasia


title: AsK548R-POLQ2 GUIDE seq identified Off-targets

description: AsK548R POLQ2


title: IPF_Apex_6


title: p53_UT_BaF3


title: CTR_Base_2


title: IPF_Apex_1


title: IPF_Apex_2


title: RNA-seq (rRNA-depleted) from udd/+ ovaries, replicate 1


title: AsK548R-B2M GUIDE seq identified Off-targets

description: AsK548R B2M


title: CTR_Apex_6


title: CTR_Apex_2


title: HSPC_p53KO_IR_rep3

description: Sex: male and female and sex-matched across experimental groups

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
Low-quality bases were trimmed from read extremities using Trimmomatic v.0.33.
Trimmed reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithms.
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.4.2).
Pairwise comparisons were performed between samples across different mouse genotypes and genes with changes in expression ≥ |2| folds and Benjamini-Hochberg adjusted p values ≤ 0.05 were considered significant.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values after quantile normalization
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)

source_name: FACS-sorted Lin-cKit+Sca1+CD150+ HSPCs

growth_protocol: The mice were maintained under specific pathogen-free conditions.

extract_protocol:
Briefly, bone marrow was flushed in PBS supplemented with 0.1% BSA and 2mM EDTA, filtered through 40μm cell-strainers, and subjected to red blood cell lysis in ACK buffer (0.15M NH4Cl, 10mM KHCO3, 0.1mM EDTA). The samples were stained with biotin anti-mouse Lineage Panel (BioLegend), PE-Cy7 cKit (clone 2B8, BioLegend), APC-Cy7 Sca-1 (D7, BioLegend), FITC CD48 (HM48-1, eBioscience), APC CD150 (TC15-12F12.2, BioLegend), PE Flt3 (A2F10, eBioscience), Brilliant Violet 421 CD34 (RAM34, BD Biosciences), and streptavidin-PECy5 (BioLegend). Cell sorting was performed on FACSAria, with FACS Diva software (BD Biosciences). The Hematopoietic stem and progenitor cells (HSPC) were sorted using FACS, gating on Lin-cKit+Sca1+CD150+.
RNA was isolated using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech). The libraries were sequenced on Illumina HiSeq 2000 and 2500 sequencers in paired-end 50bp configuration (two sequencing runs).

tag: age

value: 8-14 weeks of age and age-matched between groups

value: Bone marrow

value: FACS-sorted Lin-cKit+Sca1+CD150+ HSPCs

value: Trp53 homozygous knockout

tag: treatment

value: Cells collected 3 hours after 3Gy whole-body irradiation


title: As-B2M GUIDE seq identified Off-targets

description: As B2M


title: Flat-2

tag: Sex


title: HSPC_p53KO_IR_rep2


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _02.RCC

value: decapitated embryos


title: IPF_Apex_5

value: lung

value: fibroblast

value: idiopathic pulmonary fibrosis (IPF)


title: RNA-seq (rRNA-depleted) from udd0683-G4/udd null ovaries, replicate 1

value: ovaries

value: udd0683-G4/udd null


title: Polypoid-4

description: Epithelial cells from FFPE were microdissected from polypoid lesions

value: Polypoid dysplasia


title: Embryo 36hpf_20160826_bath study 36hpf 13-04 samples 25-36_ _01.RCC


title: Flat-3


title: WT pool 1

city: Paris

first: Onnik

last: Agbulut

address: 7 quai st-bernard

country: France

institute: Sorbonne Université

description: Comparison of the gene expression profile between Desmin WT expressing line versus Non-modified C2C12 cells.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).
grl*txt files contain the Resolver Software allows the export of a gene list with all normalized Cy5/Cy3-log10 ratios, Cy5/Cy3-fold changes, sequence description, p-values, etc., referred to as gene ratio list (of all genes).
ps*txt files contain putative candidate genes with a fold change >2 and p-value <0.01 are summarized in the pre-selected candidate gene list.

source_name: C2C12 expressing WT human desmin

label_protocol: For the linear T7-based amplification step, 1 μg of each total RNA sample was used as starting material. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies). Control samples are labeled with Cy3 and experimental samples are labeled with Cy5.

growth_protocol: C2C12 were cultured in DMEM supplemented with 10% FCS and 1% penicilin-streptomicin. At 80 % confluency cells were passaged once and cultured for 2 days. They were recovered using a cell scrapper and frozen in liquid nitrogen.

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin® RNA II, Macherey-Nagel). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies). The RNA extracted from 2 independant cultures were pooled to obtain each analyzed sample (for the control and the different experimental conditions tested).

tag: cell line

tag: genome modification

value: pcDNA3 modified with the mouse promoter of desmin, c-myc tag, human desmin gene, polyA and puroR/AmpiR genes

tag: number of independent culture pooled

source_name: Pool control


title: CTR_Apex_4

value: control donor


title: Polypoid-3

value: Female


title: CTR_Apex_5


title: HSPC_p53KO_UT_rep2

value: untreated


title: CTR_Apex_3


title: HSPC_p53KO_IR_rep1


title: CTR_Apex_1


title: RNA-seq (rRNA-depleted) from udd 0683-G4/udd null ovaries, replicate 2


title: HSPC_p53KO_UT_rep1


title: I451M pool 29

description: Comparison of the gene expression profile between Desmin mutant (I451M) expressing line versus Non-modified C2C12 cells. Biological replicate 2.

source_name: C2C12 expressing I451M mutant human desmin

value: pcDNA3 modified with the mouse promoter of desmin, c-myc tag, human desmin gene (with mutation I451M), polyA and puroR/AmpiR genes


title: Polypoid-1

value: Swiss Webster


title: Inflamed-4

description: Epithelial cells from FFPE were microdissected from inflamed areas

value: Non-dysplastic inflamed


title: Inflamed-1


title: HeLa-S3 VIVO rep2

city: Shanghai

first: Jiayong

last: Yin

state: Shanghai

address: Fenglin street

department: Institutes of Biomedical Sciences

institute: Fudan University

data_processing:
Library strategy: snOG-seq
Paired-end sequence reads were aligned to hg19 genome using BWA Version 0.7.17 with default paramatres.
The Picard Version 2.25.0  was used to remove read duplicates.
Then deduped reads in BAM-format were further filtered with Python scripts. Briefly, one alignd read will be discarded if it meets any of the following exclusion criteria: 1) is unmapped; 2) is READ2 in a read pair; 3) is not proper pair; 4) mapq<60; 5) is secondary 6) the base type 1-nt upstream of the read start is not guanine ...
Bigwig files were generated using deeptools bamCoverage Version 3.5.0 with the parametres: --normalizeUsing RPKM, --Offset 5
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: Cervical carcinoma

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin at 37 °C in a 5% CO2 humidified chamber

extract_protocol:
Hela cells from one R150 dish was collected by trypsinization and lysed by 4ml DNAzol with the addition of DTT to a final concentration of 10 mM. Genomic DNA were precipitated following the manufacturer’s instruction. DNA pellets were resolved in 300 μl of Alkaline Resolving Buffer (8 mM NaOH and 100 μM TEMPO). Typically, more than 200 μg of genomic DNA were obtained from one dish, which were used for ELISA or/and snOG-seq immediately. Notably, all buffers and reagents used in DNA extraction, ELISA and chemical labeling steps were prepared with supelco-grade deionized water in order to prevent further DNA oxidation during these steps, while DTT and TEMPO were added for the same purpose.
Selective chemical labeling: Extracted DNA (8-10 μg) were incubated with 20 mM of NH2-(PEG)11-biotin and 5 mM of K2IrBr6 in the presence of sodium phosphate (100 mM, pH 8.0) for 5 min on ice. The reaction was terminated by passing through a Microspin G50 column (GE) which was pre-washed with ice-cold deionized water, then labeled DNA were ethanol precipitated and dissolved in 1xTE buffer. Because artificial DNA oxidation after labeling reaction couldn’t interfere with following steps, biotinylated genomic DNA could be stored at -20°C until next step; Fragmentation, End-repair and first adaptor ligation: These steps were performed as previously described. Briefly, biotinylated DNA were sheared by a Qsonica Q800 Sonicator to generate fragments averaging 600 bp in length. Purified DNA fragments (up to 5 µg) were used for End-repair and dA-tailing by NEBNext DNA Library Prep Kit following the manufacture’s instruction. Subsequently, Ad1 (100 pmol/µg of input DNA) was ligated to both ends by NEBNext T4 Quick Ligase at 4°C overnight. The ligation products were purified by 0.7 × NEBselect beads and eluted in 15 µl 0.1x TE; Affinity purification and primer extension  Each samples was incubated with 5 µl of Dynabeads MyOne Streptavidin C1 beads in 1x binding buffer in the presence of 10 µg of salmon sperm DNA at 4°C for 1 h. Then the beads were sequentially washed twice with 1x B&W buffer, twice with OG-wash buffer IV (100 mM pH 8.0 Tris-Cl, 1 mM EDTA, 0.5 M LiCl, 1% CA630, 1% sodium deoxycholate), twice with wash buffer V (1 mM pH 8.0 Tris-Cl, 0.1 mM EDTA, 100 mM NaCl, 2% SDS) , one time with 1X TE and finally one time with 0.1X TE, followed by resuspending in 6 µl 0.1x TE. For primer extension reaction, 30 pmol of Extension Primer was attached to biotinylated DNA which were still bound on beads and extended by KAPA HiFi DNA polymerase (98°C 20 s, 62°C 15 s, 72°C 15 s). Excess primers were degraded by incubating with 1.5 µL of ExoI at 37°C for 10 min. The reaction was ended by adding equal volume of 1% SDS. Next, the beads were sequentially washed twice with 1x B&W buffer, twice with OG-wash buffer IV and twice with wash buffer V. Extension products were released from templates by incubation with fresh NaOH elution buffer (0.1 M NaOH plus 0.1% CA630) at room temperature for 2 min to release the complementary strands. The collected DNA were neutralized with 0.5M HAc and purified by ethanol precipitation; Second adaptor ligation, PCR amplification and high-throughput sequencing: The precipitated DNA were dissolved and subjected to ligation with 40 pmol of Ad2 by Instant Stick Ends Ligase Master Mix (NEB) at 4°C overnight. The ligation products were purified by 0.8 × NEB select beads. Two percent of ligated DNA were used for library quality check while the rest were amplified with NEBNext index primer set for Illumina by NEBNext UltraII Q5 DNA polymerase following the manufacturer’s instruction to generate sequencing libraries. Qualified libraries were pooled and sequenced on Illumina Hiseq X platform by WuXiNextCODE Company.

treatment_protocol: For VIVO samples, KBrO3 and GSH were added to the medium to a final concentration of 20 mM and 2.5 mM, respectively. After incubation at 37°C for 30 min , medium was removed and cells were washed four times with 1xPBS with Ca and Mg. Then cells were further cultured in fresh medium for 30 min before harvesting.  For VITRO samples, genomic DNA from untreated cells were incubated with 1 mM of KBrO3 and 2 mM of GSH in sodium phosphate buffer (10 mM, pH 7.8) at 37°C for 1 hour 20 min.

tag: condition

value: vivo

value: Cervical carcinoma cells


title: D1.8C

city: Hà Nội

first: Ly

middle: Hàn

last: Lưu

state: Cau giay District

address: Trần Đăng Ninh, Cầu Giấy

country: Viet Nam

institute: Institute of Genome Research

data_processing:
Illumina RTA3 software used for base calling
The raw reads dataset was first processed to remove the adaptor sequences, contaminant DNA or low quality reads by Trimmomatic 0.38.
Trimmed reads were de novo assembly by using the Trinity software (version trinityrnaseq r20140717), and then used
the CD-HIT-EST program was used to filter and cluster into the non-redundant unigenes
These contigs were processed to read align and abundance estimate using Bowtie 1.1.2 and RSEM, respectively
To calculate unigene expression, we used Fragments per Kilobase of exon per Million -fragments mapped (FPKM) method
Genome_build: de novo assembly
Supplementary_files_format_and_content: Tab-delimited text files include read count and FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts and annotation for every gene and every sample

organism: Panax vietnamensis

source_name: Roots

extract_protocol:
The leaves and roots were collected separately, cut into small pieces, immediately frozen in liquid nitrogen. The total RNA was isolated from leaves and roots by the RNeasy Plant Mini Kit (Qiagen, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Roots

value: 1 year old


title: R406W pool 24

description: Comparison of the gene expression profile between Desmin mutant (R406W) expressing line versus Non-modified C2C12 cells.

source_name: C2C12 expressing R406W mutant human desmin

value: pcDNA3 modified with the mouse promoter of desmin, c-myc tag, human desmin gene (with mutation R406W), polyA and puroR/AmpiR genes


title: HSPC_WT_IR_rep3

value: 8-14 weeks of age and age-matched between groups

value: Bone marrow

value: FACS-sorted Lin-cKit+Sca1+CD150+ HSPCs

tag: genotype

value: wildtype

value: Cells collected 3 hours after 3Gy whole-body irradiation


title: Polypoid-2

tag: strain

value: Polypoid dysplasia


title: HeLa-S3 WT rep3

value: wild type


title: HSPC_p53KO_UT_rep3

value: Trp53 homozygous knockout


title: HSPC_WT_IR_rep2


title: D1.8L

source_name: Leaves

value: Leaves


title: HSPC_WT_IR_rep1


title: Inflamed-3

value: Female


title: LNCaP_Ev_hypoxia

city: Portland

first: David

last: Qian

address: 3303 SW Bond Ave, CH14R

institute: Oregon Health & Science University

description: Gene expression due to androgen

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: LNCaP

label_protocol: standard Affymetrix protocol

growth_protocol: RPMI media with 5% charcoal-stripped FBS with 1nM androgen R1881

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: with or without hypoxia (1% O2) for 24 hours.

value: prostate cancer cell line


title: D1.6L


title: HSPC_WT_UT_rep3

value: untreated


title: HeLa-S3 WT rep1


title: HeLa-S3 VIVO rep1

value: vivo


title: Udd ChIP-seq from udd/+ ovaries, replicate 2

value: ovaries

value: udd/+ (mix of udd1/+ and udd null/+)


title: HeLa-S3 INPUT rep3

value: input

value: Cervical carcinoma cells


title: Inflamed-2

value: Swiss Webster

value: Non-dysplastic inflamed


title: CC014

status: Public on Oct 08 2021

city: Cleveland

first: Bo

last: Hu

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing:
demuplexing using cellranger
alignment using cellranger
filtering using cellranger
Genome_build: CRCh38
Supplementary_files_format_and_content: tsv and mtx: barcodes, features and counts

source_name: cultured human pulmonary arterial endothelial cells

growth_protocol: We published all details in Scientifc Reports | (2021) 11:14714

extract_protocol:
cells were harvested from culture plates by gentle treatment with trypsine
Followed the 10X genomics pipeline

tag: disease state

value: pulmonary arterial hypertension


title: I451M pool 27

description: Comparison of the gene expression profile between Desmin mutant (I451M) expressing line versus Non-modified C2C12 cells. Biological replicate 1.

value: pcDNA3 modified with the mouse promoter of desmin, c-myc tag, human desmin gene (with mutation I451M), polyA and puroR/AmpiR genes


title: HeLa-S3 VITRO rep2

value: vitro


title: CC027

value: cultured human pulmonary arterial endothelial cells


title: A677

value: healthy


title: HeLa-S3 VITRO rep1


title: D1.2L

value: 1 year old


title: HEK293T_AnkG_RIP_Rep2

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

institute: Univeritätsklinikum Erlangen

data_processing:
Alignment of reads using
Samtools version 1.12 to generate bam files
Expression analysis using Cufflinks version 2.2.1
Differential expression analysis using Cuffdiff (Cufflinks version 2.2.1)
Genome_build: hg38 / GRC38, UCSC
Supplementary_files_format_and_content: Output generated by cuffdiff showing the rpkm value per gene per different condition and the fold change and pvalue for differential expression analysis

source_name: HEK293T cell line

growth_protocol: HEK293T cells (human embryonic kidney cells), were cultured at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (Invitrogen) containing 10% heat-inactivated fetal bovine serum (Biochrom).

extract_protocol:
RIP-Seq assay was performed utilizing EZ-Magna Nuclear RIP (Cross-Linked) Nuclear RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to manufacturer’s protocol.
libraries were generated by GATC / Eurofins as strand specific c-DNA libraries

treatment_protocol: For RNA-sequencing HEK293T cells were transfected with GFP or GFP-NLS-AnkG, GFP-sorted in cooperation with the FACS-CORE unit Erlangen. RNA was isolated with TriFast reagent (VWR). For RIP-Seq HEK293T cells were transfected with plasmids for GFP-NLS-AnkG. After 24 h RNA-IP was performed using an anti-GFP antibody and a RIP-assay (EZ-Magna Nuclear RIP (Cross-Linked) Nuclear RNA-Binding Protein Immunoprecipitation Kit (Millipore)).

tag: transfected with

value: GFP-NLS-AnkG


title: HeLa-S3 WT rep2

value: wild type


title: HEK293T_AnkG_RIP_Rep3


title: LNCaP_ID1

description: Gene expression due to androgen

value: prostate cancer cell line


title: ribo_stm1_3_b7_s1

first: Sergey

middle: E.

last: Dmitriev

address: Leninskie Gory, 1

institute: Lomonosov Moscow State University

data_processing:
Library strategy: Ribo-seq
Reads were trimmed using cutadapt v. 2.10. 3’ adapter sequences for Ribo-Seq data: CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and RNA-Seq data: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
Ribo-Seq reads were deduplicated with seqkit rmdup v. 0.10.1 by unique barcodes indexes.
After barcode trimming, reads were aligned against eukaryotic rRNA sequences taken from silva-euk [10.1093/nar/gks1219] and rfam [10.1093/nar/gkaa1047] databases using bowtie2 v. 1.2.3 [10.1038/nmeth.1923]. Only unmapped reads were saved for further analysis.
Read counting and mapping against the Saccharomyces_cerevisiae.R64-1-1.95 (Ensembl) genome assembly were obtained with STAR v. 2.7.9a
Genome_build: Ensembl Saccharomyces_cerevisiae.R64-1-1.95 (genome-build-accession GCA_000146045.2)
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: The cells were grown in YPD (2% glucose, 2% peptone, 1% yeast extract) or SD (0,67% YNB w/o amino acids, 2% glucose) at 30C and 220 rpm to exponential growth stage.

extract_protocol:
Cells were resuspended in polysome lysis bufer (20 mM Tris pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 100  g/ml cycloheximide, 1% Triton), flash frozen in liquid nitrogen and homogenyzed by grinding. Part of the cell lysates was used for mRNA isolation, another part was treated with ribonuclease I for polysome disassembly and applied to sucrose gradient fractionation with subsequent isolation of ribosome-bound RNA fragments from monosome fraction. mRNA was isolated using Oligo(dT) beads  and ribosome-bound RNA was isolated using acidic-phenol extraction.
cDNA libraries for Ribo-Seq and RNA-Seq were constructed in parallel using standard ribosomal profiling library construction protocol (described in Ingolia NT et al., 2009, Science).

treatment_protocol: Cycloheximide was added to yeast media to final concentration 100µg/ml and growth was continued for 3 minutes then cells were harvested by filtration.

tag: batch

tag: molecule subtype

value: Ribosome-bound RNA


title: ribo_eif2a_3_b5_s1


title: LNCaP_ID1_hypoxia

description: Gene expression due to androgen in hypoxia


title: ribo_eif2a_2_b4_s1


title: D1.5L

value: Leaves


title: D1.2C

value: Roots


title: ribo_eif2a_1_b3_s1


title: LNCaP_Ev

description: Gene expression due to androgen


title: Udd ChIP-seq from udd1/udd null ovaries.

value: ovaries

value: udd1/udd null

tag: biological replicate


title: HeLa-S3 INPUT rep2

value: input

value: Cervical carcinoma cells


title: AH006


title: Input sample of Udd ChIP-seq from udd/+ ovaries

tag: tissue

value: udd/+ (mix of udd0683-G4/+ and udd null/+)


title: ribo_tma46_1_b1_s1


title: Udd ChIP-seq from udd/+ ovaries, replicate 1

value: udd/+ (mix of udd1/+ and udd null/+)


title: HSPC_WT_UT_rep2

value: 8-14 weeks of age and age-matched between groups

value: Bone marrow

tag: cell type

value: FACS-sorted Lin-cKit+Sca1+CD150+ HSPCs

value: wildtype

value: untreated


title: HeLa-S3 INPUT rep1


title: HEK293T_AnkG_RIP_Rep1

value: GFP-NLS-AnkG


title: U87_W_C: IWCA coculture U87

city: Bronx

first: Sean

last: McCutcheon

state: NY

address: 1410 Pelham Pwky S, Kennedy Center Rm. 840

department: Neuroscience

institute: Albert Einstein College of Medicine

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi).
Supplementary_files_format_and_content: Excel files

source_name: IWCA coculture U87

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1% antibacterial-antimycotic

extract_protocol:
miRNA was isolated using the small RNA extraction kit:  ThermoFisher Scientific  #AM1560
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing 50bp on an Illumina Hiseq 2500 at the LC Sciences (Hangzhou, China)

treatment_protocol: Cells were cocultured for 24 hours.

value: Human

value: immortalized human GBM

tag: cx43 expression

value: Cx43 WT


title: AH021

value: cultured human pulmonary arterial endothelial cells

value: healthy


title: CC015

value: pulmonary arterial hypertension


title: ribo_stm1_1_b6_s1

value: Ribosome-bound RNA


title: U87: Human GBM cell line

source_name: Human GBM cell line


title: HSPC_WT_UT_rep1

tag: age


title: U87_K_C: IKOCA coculutre U87

source_name: IKOCA coculutre U87


title: ribo_wt_2_b2_s1

value: wt


title: rna_stm1_2_b7_s1

data_processing:
Reads were trimmed using cutadapt v. 2.10. 3’ adapter sequences for Ribo-Seq data: CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and RNA-Seq data: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
Ribo-Seq reads were deduplicated with seqkit rmdup v. 0.10.1 by unique barcodes indexes.
After barcode trimming, reads were aligned against eukaryotic rRNA sequences taken from silva-euk [10.1093/nar/gks1219] and rfam [10.1093/nar/gkaa1047] databases using bowtie2 v. 1.2.3 [10.1038/nmeth.1923]. Only unmapped reads were saved for further analysis.
Read counting and mapping against the Saccharomyces_cerevisiae.R64-1-1.95 (Ensembl) genome assembly were obtained with STAR v. 2.7.9a
Genome_build: Ensembl Saccharomyces_cerevisiae.R64-1-1.95 (genome-build-accession GCA_000146045.2)
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.

value: Total RNA


title: ribo_stm1_4_b7_s1


title: rna_stm1_3_b7_s1


title: ribo_tma46_2_b2_s1


title: ribo_eif2a_4_b6_s1


title: rna_stm1_4_b7_s1


title: rna_tma46_2_b2_s1


title: rna_eif2a_3_b5_s1


title: ribo_stm1_2_b7_s1


title: ribo_wt_1_b1_s1


title: rna_tma46_1_b1_s1


title: rna_wt_2_b2_s1


title: ribo_tma46_4_b5_s1


title: ribo_wt_4_b4_s1


title: ribo_tma46_3_b3_s1


title: ShControl#2

city: Jinan

first: Yang

last: Han

state: Shandong

address: No.324, Jingwu Road

institute: Shandong Provincial Hospital

data_processing:
Basecalls performed using Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files.xlsx (FPKMs)

growth_protocol: Cells are cultured using IMDM basic medium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis. Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEC-1 cells were infected with lentivirus vectors that encoded either shNUSAP1 or an empty vector (control) according to the manufacturers’ instruction

value: CLL cell line

value: Control


title: ShControl#1


title: rna_eif2a_4_b6_s1


title: MGC803_NC_miR-138

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

source_name: gastric cancer cell

growth_protocol: The gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and miR-138-mimics. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The GC cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and the miR-138 mimics (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

value: gastric cancer cell line

tag: transfection

value: negative control siRNA


title: ShNUSAP1#1


title: GIST-T1/816 P176 24h COMBO replicate 3

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
RNAseq reads were aligned to the GRCh38 genome assembly with Gencode v.25 gene annotation, using STAR (v2.5.2a) with ENCODE suggested defaults parameters
Gene counts were assesed with RSEM (v1.2.28) with suggested default options
Genome_build: Ensembl 88 GRCh38
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: cell line

growth_protocol: Iscove's Modified Dulbecos Medium (IMDM) supplemented with 1% L-Glutamine and 15% fetal bovine serum (FBS)

extract_protocol:
RNA extraction was performed using the RNeasy KIT from QIAGEN according to the manufacturer protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated 4 and 24 hours. Drugs were dissolved in DMSO. All treatment were performed in serum-free media

tag: disease

value: gastrointestinal stromal tumor

tag: treatment

value: COMBO

tag: timepoint

tag: replicate


title: rna_eif2a_2_b4_s1


title: ribo_wt_3_b3_s1


title: GIST-T1/816 P176 24h GDC0980 500 replicate 3

tag: cell line


title: GIST-T1/816 P176 24h GSK100 replicate 3


title: rna_eif2a_1_b3_s1

tag: genotype


title: GIST-T1/816 P176 4h COMBO replicate 2


title: rna_tma46_3_b3_s1


title: GIST-T1/816 P176 24h COMBO replicate 2


title: rna_tma46_4_b5_s1


title: GIST-T1/816 P176 4h GSK100 replicate 2


title: GIST-T1/816 P176 24h DMSO replicate 2

value: DMSO


title: GIST-T1/816 P176 4h DMSO replicate 2


title: rna_wt_1_b1_s1


title: rna_wt_3_b3_s1


title: rna_wt_4_b4_s1


title: ShNUSAP1#2


title: GIST-T1/816 P176 4h GSK100 replicate 1


title: GIST-T1/816 P176 4h DMSO replicate 1


title: MGC803_NC_miR-138_mimics

value: miR-138-5p mimics


title: ShControl#3


title: GIST-T1/816 P176 4h GDC0980 500 replicate 3


title: GIST-T1/816 P176 24h COMBO replicate 1


title: ShNUSAP1#3


title: GIST-T1/816 P176 24h GDC0980 500 replicate 1


title: rna_stm1_1_b6_s1


title: GIST-T1/816 P176 BaseLine replicate 1

value: BaseLine


title: GIST-T1/816 P176 BaseLine replicate 3


title: GIST-T1/816 P176 BaseLine replicate 2


title: GIST-T1/816 P176 24h GSK100 replicate 1


title: GIST-T1 p88 24h IM500 replicate 3


title: GIST-T1 p88 24h IM500 replicate 2


title: GIST-T1/816 P176 24h DMSO replicate 1


title: GIST-T1 p88 24h IM500 replicate 1


title: GIST-T1/816 P176 24h GDC0980 500 replicate 2


title: GIST-T1/670 P88 24h COMBO replicate 3


title: GIST-T1/816 P176 24h GSK100 replicate 2


title: GIST-T1/670 P88 4h COMBO replicate 3


title: GIST-T1/670 P88 24h DMSO replicate 3


title: GIST-T1/816 P176 24h DMSO replicate 3


title: GIST-T1/670 P88 4h GDC0980 500 replicate 3


title: GIST-T1/670 P88 4h GSK100 replicate 3


title: GIST-T1/670 p88 BaseLine replicate 3


title: GIST-T1/670 P88 24h COMBO replicate 2


title: GIST-T1/670 P88 4h GSK100 replicate 2


title: GIST-T1 p88 4h IM500 replicate 1


title: GIST-T1/816 P176 4h COMBO replicate 3


title: GIST-T1/670 P88 24h GDC0980 500 replicate 3


title: GIST-T1/816 P176 4h GDC0980 500 replicate 2


title: GIST-T1/670 P88 24h COMBO replicate 1


title: GIST-T1/670 P88 24h GSK100 replicate 1


title: GIST-T1/670 P88 24h GDC0980 500 replicate 1


title: GIST-T1/670 P88 4h COMBO replicate 1


title: GIST-T1/816 P176 4h COMBO replicate 1


title: GIST-T1/670 P88 4h GSK100 replicate 1


title: GIST-T1/816 P176 4h GSK100 replicate 3


title: GIST-T1 p88 4h IM500 replicate 2


title: GIST-T1/816 P176 4h GDC0980 500 replicate 1


title: GIST-T1/670 P88 4h GDC0980 500 replicate 1


title: GIST-T1/670 P88 4h DMSO replicate 3


title: GIST882 p240 24h COMBO replicate 2


title: GIST882 p240 24h GDC0980 500 replicate 2


title: GIST-T1/816 P176 4h DMSO replicate 3


title: GIST882 p240 24h DMSO replicate 2


title: GIST882 p240 4h GDC0980 500 replicate 2


title: GIST882 p240 4h COMBO replicate 2


title: GIST-T1/670 P88 24h DMSO replicate 2


title: GIST-T1/670 P88 24h GDC0980 500 replicate 2


title: GIST-T1 p88 4h IM500 replicate 3


title: GIST-T1/670 P88 4h GDC0980 500 replicate 2


title: GIST-T1/670 P88 24h GSK100 replicate 2


title: GIST-T1/670 P88 4h COMBO replicate 2


title: GIST-T1/670 P88 4h DMSO replicate 1


title: GIST-T1/670 P88 24h GSK100 replicate 3


title: GIST-T1/670 P88 24h DMSO replicate 1


title: GIST882 p248 4h GDC0980 500 replicate 1


title: GIST882 p240 4h GSK100 replicate 2


title: GIST882 p248 4h COMBO replicate 1


title: GIST882 p248 4h GSK100 replicate 1


title: GIST-T1/670 P88 4h DMSO replicate 2


title: GIST882 p240 24h COMBO replicate 3


title: GIST-T1/670 p88 BaseLine replicate 1


title: GIST-T1/670 p88 BaseLine replicate 2


title: GIST882 p240 4h COMBO replicate 3


title: GIST882 p240 BaseLine replicate 3


title: GIST882 p240 24h GDC0980 500 replicate 3


title: GIST-T1 p90 24h GDC0980 500 replicate 3


title: GIST-T1 p90 24h GSK100 replicate 3


title: GIST882 p240 24h GSK100 replicate 3


title: GIST882 p240 4h GDC0980 500 replicate 3


title: GIST882 p240 BaseLine replicate 2


title: GIST882 p240 4h DMSO replicate 2


title: GIST-T1 p90 4h GDC0980 500 replicate 3


title: GIST-T1 p90 4h GSK100 replicate 3


title: GIST-T1 p90 4h DMSO replicate 3


title: GIST882 p240 4h GSK100 replicate 3


title: GIST-T1 p96 BaseLine replicate 3


title: GIST882 p248 24h COMBO replicate 1


title: GIST882 p248 4h DMSO replicate 1


title: GIST-T1 p96 24h GSK100 replicate 2


title: GIST-T1 p96 4h GDC0980 500 replicate 2


title: GIST882 p240 BaseLine replicate 1


title: GIST-T1 p90 24h COMBO replicate 1


title: GIST-T1 p90 24h DMSO replicate 1


title: GIST-T1 p90 4h GDC0980 500 replicate 1


title: GIST-T1 p90 24h COMBO replicate 3


title: GIST-T1 p96 24h DMSO replicate 2


title: GIST-T1 p90 4h COMBO replicate 3


title: GIST882 p248 24h DMSO replicate 1


title: GIST-T1 p96 24h COMBO replicate 2


title: GIST882 p240 24h GSK100 replicate 2


title: GIST882 p248 24h GDC0980 500 replicate 1


title: GIST-T1 p90 4h COMBO replicate 1


title: GIST882 p248 24h GSK100 replicate 1


title: GIST-T1 p90 24h DMSO replicate 3


title: H25DEN20T1

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

data_processing:
Alignment: The fastq files were aligned on the UCSC rn6 genome using STAR (2.7.1a) [PMID:23104886] to produce bam files.
Counts: Bam files were counted using HTSeq framework (0.11.2) [PMID:25260700] with options: -t exon -f bam -r pos –stranded=reverse -m intersection-strict –nonunique none
Normalization and differential analysis: Normalization and differential analysis were performed using the R software [R Core Team. R: A language and environment for statistical computing. Vienna, Austria : R Foundation for Statistical Computing, 2017], DESeq2 (1.22.2) [PMID:20979621, PMID:25516281] and SARTools [PMID:27280887] packages.
Genome_build: rn6

organism: Rattus norvegicus

source_name: liver

growth_protocol: Adult Fischer 344 male rats

extract_protocol:
Total RNA was extracted from rat liver tissue samples preserved with an RNA stabilization solution (Thermo scientific, USA). RNA purification was performed with RNeasy Mini Kit® (Qiagen, USA) according to the instructions provided by the manufacturer and quality assessment for the RNA Integrity Number (RIN) was performed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit (Illumina, San Diego, USA), starting with 1 μg of total RNA. mRNAs were purified, fragmented and converted to cDNA with reverse transcriptase. The resulting cDNAs were converted to double stranded cDNAs and subjected to end-repair, A-tailing, and adapter ligation.
The constructed libraries were amplified using 15 cycles of PCR. Libraries were quantified by qPCR with the LightCycler 480 real-time PCR instrument (Roche, Basel, Switzerland). Normalized and pooled libraries were sequenced on a NovaSeq 6000 platform with S1 flow cell (200 cycles) (Illumina, San Diego, CA, USA) in 75 bp paired-end.

treatment_protocol: 7-week-old Fischer 344 male rats  were treated weekly with intra-peritoneal injections of 50 mg/kg DEN. We analysed 3 different time points of DEN treatment: i) after 8 weeks of DEN injections (DEN08), ii) after 14 weeks of DEN injections (DEN14) and iii) after 14 weeks of DEN injection followed by 6 weeks of no DEN injection (DEN20). Animals of the same age, treated with no DEN were used as controls for 8 weeks (NOD08), 14 weeks (NOD14) and 20 weeks time points (NOD20). Non-tumoral (NT) tissues and Tumoral (T) tissues were analysed separately.

tag: rat

value: DEN


title: H26DEN20NT

value: NT


title: GIST-T1 p96 4h DMSO replicate 2


title: H28DEN20T2


title: GIST-T1 p72 BaseLine replicate 1


title: GIST-T1 p96 4h COMBO replicate 2


title: GIST-T1 p96 24h GDC0980 500 replicate 2


title: GIST882 p240 24h DMSO replicate 3


title: H23DEN14T1


title: GIST-T1 p90 24h GSK100 replicate 1


title: H21DEN14T2


title: GIST-T1 p90 4h DMSO replicate 1


title: H21DEN14NT


title: H17DEN08NT


title: GIST-T1 p96 4h GSK100 replicate 2


title: H22DEN14T1


title: H14NOD20NT

value: NOD


title: H12NOD14NT


title: H28DEN20T1


title: H11NOD14NT


title: GIST-T1 p72 BaseLine replicate 2


title: H21DEN14T1


title: H23DEN14NT


title: H22DEN14NT


title: H25DEN20T2


title: H22DEN14T2


title: H25DEN20NT


title: H08NOD08NT


title: H28DEN20NT


title: H05NOD08NT


title: GIST-T1 p90 4h GSK100 replicate 1


title: H26DEN20T2


title: H18DEN08NT


title: F09DEN08NT


title: F06DEN14T1


title: H23DEN14T2


title: F10DEN08NT


title: GIST-T1 p90 24h GDC0980 500 replicate 1


title: H10NOD14NT


title: H26DEN20T1


title: H16NOD20NT


title: H09NOD14NT


title: H07NOD08NT


title: H06NOD08NT


title: H15NOD20NT


title: F03DEN20T1


title: F06DEN14T2


title: F03DEN20NT


title: H13NOD20NT


title: F03DEN20T2


title: F06DEN14NT


title: Whole blood, SLE Patient 136 Dose 4 on Week 12 ; IFN-K

city: Brussels

first: Frédéric

middle: A

last: HOUSSIAU

address: Avenue Hippocrate 10

department: Institut de recherche expérimentale et clinique (IREC)

country: Belgium

institute: Université catholique de Louvain

description:
SP220496A08
A2786_2737

hyb_protocol: Following fragmentation and biotin labeling, 4.4 µg of cDNA were hybridized for 16 hours at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed and RMA normalized using the Affymetrix Expression Console software v.1.4.1.

label: biotin

source_name: SLE Patient 136 Dose 4 on Week 12

label_protocol: 100 ng total RNA was labeled using the NuGen WB Solution kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from PAXgene blood RNA tubes using the QIASymphony SP extraction robot from QIAGEN. The QIASymphony PAXgene blood RNA Extraction kit and PAXgene_RNA protocol were used.

treatment_protocol: Patients with SLE (185) with moderate to severe disease activity and positive interferon (IFN) gene signature were randomised to receive IFN-K or PBO intramuscular injections (on W0, W1, W4 and W12 and W24). At randomisation (D0) and W12, W24 and W36, the IFN gene signature, including the 21 IFN-regulated genes, was evaluated by Affymetrix.

tag: diagnosis

value: SLE

value: IFN-K

tag: time point

value: Dose 4 on Week 12

value: Blood

tag: patient

value: Patient 136


title: Whole blood, SLE Patient 115 Dose 4 on Week 12; IFN-K

description:
AP506297A07
A2786_2845

source_name: SLE Patient 115 Dose 4 on Week 12

value: Patient 115


title: Whole blood, SLE Patient 115 Follow-up on Week 36; IFN-K

description:
AP293361B07
A2786_2842

source_name: SLE Patient 115 Follow-up on Week 36

value: Follow-up on Week 36


title: Whole blood, SLE patient 40 Follow-up on Week 36, placebo

description:
AP519060B08
A2786_2739

source_name: SLE Patient 40 Follow-up on Week 36

value: PBO

value: Patient 40


title: Whole blood, SLE Patient 115 Dose 5 on Week 24; IFN-K

description:
AP106569B07
A2786_2844

source_name: SLE Patient 115 Dose 5 on Week 24

value: Dose 5 on Week 24


title: Whole blood, SLE Patient 115 Dose 1 on Week 0; IFN-K

description:
AP506293A29
A2786_2843

source_name: SLE Patient 115 Dose 1 on Week 0

value: Dose 1 on Week 0


title: Whole blood, SLE patient 50 Dose 1 on Week 0, placebo

description:
SP221057A07
A2786_2738

source_name: SLE Patient 50 Dose 1 on Week 0

value: Patient 50


title: GIST882 p240 4h DMSO replicate 3

value: gastrointestinal stromal tumor

value: DMSO


title: Whole blood, SLE Patient 1 Follow-up on Week 36, placebo

description:
LP103646A07
A2786_2729

source_name: SLE Patient 1 Follow-up on Week 36

value: Patient 1


title: Whole blood, SLE patient 50 Dose 5 on Week 24, placebo

description:
SP468820A08
A2786_2734

source_name: SLE Patient 50 Dose 5 on Week 24


title: Whole blood, SLE Patient 1 Dose 4 on Week 12, placebo

description:
LP068411A07
A2786_2730

source_name: SLE Patient 1 Dose 4 on Week 12


title: Whole blood, SLE Patient 136 Dose 5 on Week 24 ; IFN-K

description:
SP468819A08
A2786_2735

source_name: SLE Patient 136 Dose 5 on Week 24


title: Whole blood, SLE patient 50 Dose 4 on Week 12, placebo

description:
SP220491A08
A2786_2732

source_name: SLE Patient 50 Dose 4 on Week 12


title: Whole blood, SLE Patient 176 Follow-up on Week 36 ; IFN-K

description:
EP420630B30
A2786_2722

source_name: SLE Patient 176 Follow-up on Week 36

value: Patient 176


title: Whole blood, SLE Patient 136 Follow-up on Week 36 ; IFN-K

description:
SP477814A08
A2786_2736

source_name: SLE Patient 136 Follow-up on Week 36


title: Whole blood, SLE patient 50 Follow-up on Week 36, placebo

description:
SP477815A08
A2786_2731

source_name: SLE Patient 50 Follow-up on Week 36


title: Whole blood, SLE Patient 136 Dose 1 on Week 0; IFN-K

description:
SP221064A07
A2786_2733

source_name: SLE Patient 136 Dose 1 on Week 0


title: Whole blood, SLE patient 87 Dose 4 on Week 12, placebo

description:
EP938060A29
A2786_2720

source_name: SLE Patient 87 Dose 4 on Week 12

value: Patient 87


title: Whole blood, SLE Patient 1 Dose 5 on Week 24, placebo

description:
LP103641A07
A2786_2728

source_name: SLE Patient 1 Dose 5 on Week 24

value: SLE


title: Whole blood, SLE patient 84 Dose 5 on Week 24, placebo

description:
EP668291A33
A2786_2719

source_name: SLE Patient 84 Dose 5 on Week 24

value: Patient 84


title: Whole blood, SLE Patient 177 Dose 5 on Week 24 ; IFN-K

description:
EP002669B29
A2786_2716

source_name: SLE Patient 177 Dose 5 on Week 24

value: IFN-K

value: Patient 177


title: Whole blood, SLE Patient 175 Dose 5 on Week 24; IFN-K

description:
EP905792A28
A2786_2718

source_name: SLE Patient 175 Dose 5 on Week 24

value: Blood

value: Patient 175


title: Whole blood, SLE Patient 1 Dose 1 on Week 0, placebo

description:
LP068403A07
A2786_2727

source_name: SLE Patient 1 Dose 1 on Week 0


title: Whole blood, SLE patient 84 Dose 4 on Week 12, placebo

description:
EP905793A07
A2786_2711

source_name: SLE Patient 84 Dose 4 on Week 12

value: Dose 4 on Week 12


title: Whole blood, SLE Patient 174 Dose 4 on Week 12; IFN-K

description:
EP905796A28
A2786_2721

source_name: SLE Patient 174 Dose 4 on Week 12

value: Patient 174


title: Whole blood, SLE Patient 173 Follow-up on Week 36 ; IFN-K

description:
EP273625B08
A2786_2708

source_name: SLE Patient 173 Follow-up on Week 36

value: Follow-up on Week 36

value: Patient 173


title: Whole blood, SLE Patient 176 Dose 4 on Week 12 ; IFN-K

description:
EP592202A08
A2786_2705

source_name: SLE Patient 176 Dose 4 on Week 12


title: Whole blood, SLE Patient 175 Dose 4 on Week 12; IFN-K

description:
EP905794A07
A2786_2710

source_name: SLE Patient 175 Dose 4 on Week 12


title: Whole blood, SLE Patient 176 Dose 5 on Week 24 ; IFN-K

description:
EP002674B29
A2786_2715

source_name: SLE Patient 176 Dose 5 on Week 24

value: Dose 5 on Week 24


title: Whole blood, SLE patient 87 Dose 5 on Week 24, placebo

description:
EP938062A29
A2786_2717

source_name: SLE Patient 87 Dose 5 on Week 24

value: PBO


title: Whole blood, SLE Patient 175 Follow-up on Week 36 ; IFN-K

description:
EP265267B30
A2786_2714

source_name: SLE Patient 175 Follow-up on Week 36


title: Whole blood, SLE patient 86 Dose 5 on Week 24, placebo

description:
EP002671B08
A2786_2706

source_name: SLE Patient 86 Dose 5 on Week 24

value: Patient 86


title: Whole blood, SLE Patient 173 Dose 4 on Week 12; IFN-K

description:
EP905797A07
A2786_2707

source_name: SLE Patient 173 Dose 4 on Week 12


title: Whole blood, SLE patient 86 Follow-up on Week 36, placebo

description:
EP420631B08
A2786_2713

source_name: SLE Patient 86 Follow-up on Week 36


title: Whole blood, SLE patient 87 Follow-up on Week 36, placebo

description:
EP574305A08
A2786_2712

source_name: SLE Patient 87 Follow-up on Week 36


title: Whole blood, SLE patient 65 Dose 5 on Week 24, placebo

description:
EP875870A08
A2786_2704

source_name: SLE Patient 65 Dose 5 on Week 24

value: Patient 65


title: Whole blood, SLE Patient 177 Follow-up on Week 36 ; IFN-K

description:
EP420629B30
A2786_2723

source_name: SLE Patient 177 Follow-up on Week 36


title: Whole blood, SLE patient 87 Dose 1 on Week 0, placebo

description:
EP564559A07
A2786_2695

source_name: SLE Patient 87 Dose 1 on Week 0

value: Dose 1 on Week 0


title: Whole blood, SLE Patient 174 Dose 1 on Week 0; IFN-K

description:
EP594043A07
A2786_2700

source_name: SLE Patient 174 Dose 1 on Week 0


title: Whole blood, SLE patient 65 Follow-up on Week 36, placebo

description:
EP875878A08
A2786_2703

source_name: SLE Patient 65 Follow-up on Week 36


title: Whole blood, SLE Patient 175 Dose 1 on Week 0; IFN-K

description:
EP594044A07
A2786_2701

source_name: SLE Patient 175 Dose 1 on Week 0


title: Whole blood, SLE patient 86 Dose 4 on Week 12, placebo

description:
EP592199A08
A2786_2697

source_name: SLE Patient 86 Dose 4 on Week 12


title: Whole blood, SLE Patient 173 Dose 5 on Week 24; IFN-K

description:
EP905795A07
A2786_2709

source_name: SLE Patient 173 Dose 5 on Week 24


title: Whole blood, SLE patient 85 Dose 4 on Week 12, placebo

description:
EP959052A08
A2786_2698

source_name: SLE Patient 85 Dose 4 on Week 12

value: Patient 85


title: Whole blood, SLE patient 65 Dose 1 on Week 0, placebo

description:
EP416170A07
A2786_2694

source_name: SLE Patient 65 Dose 1 on Week 0


title: Whole blood, SLE patient 85 Dose 5 on Week 24, placebo

description:
EP959054A08
A2786_2702

source_name: SLE Patient 85 Dose 5 on Week 24


title: Whole blood, SLE Patient 177 Dose 4 on Week 12 ; IFN-K

description:
EP668284A08
A2786_2692

source_name: SLE Patient 177 Dose 4 on Week 12


title: Whole blood, SLE patient 86 Dose 1 on Week 0, placebo

description:
EP592190A07
A2786_2696

source_name: SLE Patient 86 Dose 1 on Week 0


title: Whole blood, SLE Patient 174 Follow-up on Week 36 ; IFN-K

description:
EP265266B08
A2786_2699

source_name: SLE Patient 174 Follow-up on Week 36


title: Whole blood, SLE Patient 177 Dose 1 on Week 0; IFN-K

description:
EP585816A07
A2786_2693

source_name: SLE Patient 177 Dose 1 on Week 0


title: Whole blood, SLE Patient 173 Dose 1 on Week 0; IFN-K

description:
EP585773A07
A2786_2691

source_name: SLE Patient 173 Dose 1 on Week 0


title: Whole blood, SLE patient 65 Dose 4 on Week 12, placebo

description:
EP875871A08
A2786_2687

source_name: SLE Patient 65 Dose 4 on Week 12


title: Whole blood, SLE Patient 91 Dose 5 on Week 24 ; IFN-K

description:
AP125322B08
A2786_2679

source_name: SLE Patient 91 Dose 5 on Week 24

value: Patient 91


title: Whole blood, SLE patient 85 Dose 1 on Week 0, placebo

description:
EP571903A07
A2786_2684

source_name: SLE Patient 85 Dose 1 on Week 0

value: SLE


title: Whole blood, SLE Patient 174 Dose 5 on Week 24 ; IFN-K

description:
EP668293A08
A2786_2688

source_name: SLE Patient 174 Dose 5 on Week 24


title: Whole blood, SLE patient 84 Dose 1 on Week 0, placebo

description:
EP668289A08
A2786_2685

source_name: SLE Patient 84 Dose 1 on Week 0

value: Patient 84


title: Whole blood, SLE Patient 91 Follow-up on Week 36 ; IFN-K

description:
AP683890B08
A2786_2677

source_name: SLE Patient 91 Follow-up on Week 36

value: IFN-K


title: Whole blood, SLE patient 33 Dose 5 on Week 24, placebo

description:
AP433770A35
A2786_2740

source_name: SLE Patient 33 Dose 5 on Week 24

value: Patient 33


title: Whole blood, SLE patient 40 Dose 1 on Week 0, placebo

description:
AP488860A07
A2786_2672

source_name: SLE Patient 40 Dose 1 on Week 0

value: Blood

value: Patient 40


title: Whole blood, SLE Patient 116 Dose 4 on Week 12; IFN-K

description:
AP927646A07
A2786_2671

source_name: SLE Patient 116 Dose 4 on Week 12

value: Dose 4 on Week 12

value: Patient 116


title: Whole blood, SLE Patient 116 Follow-up on Week 36; IFN-K

description:
AP260126B29
A2786_2741

source_name: SLE Patient 116 Follow-up on Week 36

value: Follow-up on Week 36


title: Whole blood, SLE patient 84 Follow-up on Week 36, placebo

description:
EP468296B08
A2786_2689

source_name: SLE Patient 84 Follow-up on Week 36


title: Whole blood, SLE Patient 91 Dose 4 on Week 12; IFN-K

description:
AP012719B08
A2786_2673

source_name: SLE Patient 91 Dose 4 on Week 12


title: Whole blood, SLE patient 33 Dose 4 on Week 12, placebo

description:
AP109047B08
A2786_2681

source_name: SLE Patient 33 Dose 4 on Week 12


title: Whole blood, SLE Patient 91 Dose 1 on Week 0; IFN-K

description:
AP898880A07
A2786_2670

source_name: SLE Patient 91 Dose 1 on Week 0


title: Whole blood, SLE patient 33 Dose 1 on Week 0, placebo

description:
AP433748A07
A2786_2669

source_name: SLE Patient 33 Dose 1 on Week 0


title: Whole blood, SLE patient 33 Follow-up on Week 36, placebo

description:
AP543118B08
A2786_2674

source_name: SLE Patient 33 Follow-up on Week 36


title: Whole blood, SLE patient 85 Follow-up on Week 36, placebo

description:
EP441829B08
A2786_2690

source_name: SLE Patient 85 Follow-up on Week 36


title: Whole blood, SLE Patient 176 Dose 1 on Week 0; IFN-K

description:
EP592189A07
A2786_2686

source_name: SLE Patient 176 Dose 1 on Week 0

value: Patient 176


title: Whole blood, SLE patient 24 Dose 4 on Week 12, placebo

description:
AP954548A28
A2786_2666

source_name: SLE Patient 24 Dose 4 on Week 12

value: Patient 24


title: Whole blood, SLE patient 24 Early termination, placebo

description:
AP295941B30
A2786_2667

source_name: SLE Patient 24 Early termination

value: PBO

value: Patient 24 Early termination


title: Whole blood, SLE Patient 116 Dose 1 on Week 0; IFN-K

description:
AP649063A08
A2786_2668

source_name: SLE Patient 116 Dose 1 on Week 0


title: Whole blood, SLE Patient 116 Dose 5 on Week 24; IFN-K

description:
AP927647A07
A2786_2678

source_name: SLE Patient 116 Dose 5 on Week 24

value: Dose 5 on Week 24


title: Whole blood, SLE patient 10 Follow-up on Week 36, placebo

description:
AP489601B08
A2786_2661

source_name: SLE Patient 10 Follow-up on Week 36

value: Patient 10


title: Whole blood, SLE patient 10 Dose 5 on Week 24, placebo

description:
AP061085B33
A2786_2660

source_name: SLE Patient 10 Dose 5 on Week 24


title: Whole blood, SLE Patient 120 Dose 4 on Week 12; IFN-K

description:
AP433772A28
A2786_2663

source_name: SLE Patient 120 Dose 4 on Week 12

value: Patient 120


title: Whole blood, SLE Patient 120 Early termination; IFN-K

description:
AP109056B33
A2786_2664

source_name: SLE Patient 120 Early termination

value: Patient 120 Early termination


title: Whole blood, SLE patient 40 Dose 4 on Week 12, placebo

description:
AP119274A07
A2786_2683

source_name: SLE Patient 40 Dose 4 on Week 12

value: SLE


title: Whole blood, SLE patient 24 Dose 1 on Week 0, placebo

description:
AP704146A07
A2786_2665

source_name: SLE Patient 24 Dose 1 on Week 0

value: Dose 1 on Week 0


title: Whole blood, SLE patient 28 Follow-up on Week 36, placebo

description:
AP293362B29
A2786_2650

source_name: SLE Patient 28 Follow-up on Week 36

value: Patient 28


title: Whole blood, SLE Patient 130 Dose 4 on Week 12 ; IFN-K

description:
SP221181A29
A2786_2644

source_name: SLE Patient 130 Dose 4 on Week 12

value: IFN-K

value: Patient 130


title: Whole blood, SLE Patient 172 Follow-up on Week 36 ; IFN-K

description:
EP125657B30
A2786_2642

source_name: SLE Patient 172 Follow-up on Week 36

value: Blood

value: Patient 172


title: Whole blood, SLE Patient 130 Dose 1 on Week 0; IFN-K

description:
SP221168A29
A2786_2643

source_name: SLE Patient 130 Dose 1 on Week 0


title: Whole blood, SLE Patient 130 Dose 5 on Week 24 ; IFN-K

description:
SP054756A39
A2786_2645

source_name: SLE Patient 130 Dose 5 on Week 24


title: Whole blood, SLE Patient 120 Dose 1 on Week 0; IFN-K

description:
AP433743A29
A2786_2662

source_name: SLE Patient 120 Dose 1 on Week 0


title: Whole blood, SLE Patient 98 Dose 5 on Week 24 ; IFN-K

description:
AP296987B29
A2786_2637

source_name: SLE Patient 98 Dose 5 on Week 24

value: Patient 98


title: Whole blood, SLE Patient 172 Dose 4 on Week 12 ; IFN-K

description:
EP576876A29
A2786_2640

source_name: SLE Patient 172 Dose 4 on Week 12

value: Dose 4 on Week 12


title: Whole blood, SLE Patient 130 Follow-up on Week 36 ; IFN-K

description:
SP477811A08
A2786_2646

source_name: SLE Patient 130 Follow-up on Week 36

value: Follow-up on Week 36


title: Whole blood, SLE patient 28 Dose 1 on Week 0, placebo

description:
AP651622A29
A2786_2647

source_name: SLE Patient 28 Dose 1 on Week 0


title: Whole blood, SLE patient 10 Dose 1 on Week 0, placebo

description:
AP511434A29
A2786_2651

source_name: SLE Patient 10 Dose 1 on Week 0


title: Whole blood, SLE Patient 98 Dose 4 on Week 12 ; IFN-K

description:
AP042707B29
A2786_2636

source_name: SLE Patient 98 Dose 4 on Week 12


title: Whole blood, SLE Patient 172 Dose 1 on Week 0; IFN-K

description:
EP576873A29
A2786_2639

source_name: SLE Patient 172 Dose 1 on Week 0


title: Whole blood, SLE Patient 104 Dose 1 on Week 0; IFN-K

description:
EP446307A29
A2786_2625

source_name: SLE Patient 104 Dose 1 on Week 0

value: Patient 104


title: Whole blood, SLE Patient 101 Dose 1 on Week 0; IFN-K

description:
EP523935A29
A2786_2627_rh

source_name: SLE Patient 101 Dose 1 on Week 0

value: Patient 101


title: Whole blood, SLE patient 32 Dose 4 on Week 12, placebo

description:
AP433774A28
A2786_2622

source_name: SLE Patient 32 Dose 4 on Week 12

value: PBO

value: Patient 32


title: Whole blood, SLE Patient 101 Dose 4 on Week 12; IFN-K

description:
EP743975A28
A2786_2634

source_name: SLE Patient 101 Dose 4 on Week 12


title: Whole blood, SLE patient 32 Dose 5 on Week 24, placebo

description:
AP109048B29
A2786_2623

source_name: SLE Patient 32 Dose 5 on Week 24

value: Dose 5 on Week 24


title: Whole blood, SLE patient 28 Dose 5 on Week 24, placebo

description:
AP106568B28
A2786_2649

source_name: SLE Patient 28 Dose 5 on Week 24


title: Whole blood, SLE Patient 98 Follow-up on Week 36 ; IFN-K

description:
AP296994B30
A2786_2638

source_name: SLE Patient 98 Follow-up on Week 36


title: Whole blood, SLE Patient 172 Dose 5 on Week 24 ; IFN-K

description:
EP664466A29
A2786_2641

source_name: SLE Patient 172 Dose 5 on Week 24


title: Whole blood, SLE Patient 104 Dose 4 on Week 12; IFN-K

description:
EP446312A28
A2786_2626

source_name: SLE Patient 104 Dose 4 on Week 12


title: Whole blood, SLE patient 32 Dose 1 on Week 0, placebo

description:
AP433747A29
A2786_2621

source_name: SLE Patient 32 Dose 1 on Week 0


title: Whole blood, SLE Patient 98 Dose 1 on Week 0; IFN-K

description:
AP637890A07
A2786_2676

source_name: SLE Patient 98 Dose 1 on Week 0


title: Whole blood, SLE patient 69 Early termination, placebo

description:
AP700714A28
A2786_2620

source_name: SLE Patient 69 Early termination

value: Patient 69 Early termination

value: Patient 69


title: Whole blood, SLE patient 69 Dose 1 on Week 0, placebo

description:
AP700702A30
A2786_2619

source_name: SLE Patient 69 Dose 1 on Week 0

value: SLE


title: Whole blood, SLE patient 10 Dose 4 on Week 12, placebo

description:
AP699467A29
A2786_2659

source_name: SLE Patient 10 Dose 4 on Week 12

value: Patient 10


title: Whole blood, SLE patient 83 Follow-up on Week 36, placebo

description:
EP125656B30
A2786_2618

source_name: SLE Patient 83 Follow-up on Week 36

value: Patient 83


title: Whole blood, SLE patient 32 Follow-up on Week 36, placebo

description:
AP543119B30
A2786_2624

source_name: SLE Patient 32 Follow-up on Week 36


title: Whole blood, SLE patient 28 Dose 4 on Week 12, placebo

description:
AP506296A28
A2786_2648

source_name: SLE Patient 28 Dose 4 on Week 12

value: Patient 28


title: Whole blood, SLE patient 83 Dose 5 on Week 24, placebo

description:
EP664468A29
A2786_2617

source_name: SLE Patient 83 Dose 5 on Week 24


title: Whole blood, SLE patient 83 Dose 1 on Week 0, placebo

description:
EP239509A29
A2786_2615

source_name: SLE Patient 83 Dose 1 on Week 0

value: Dose 1 on Week 0


title: Whole blood, SLE patient 41 Follow-up on Week 36, placebo

description:
AP202742B08
A2786_2614

source_name: SLE Patient 41 Follow-up on Week 36

value: Blood

value: Patient 41


title: Whole blood, SLE patient 83 Dose 4 on Week 12, placebo

description:
EP576877A29
A2786_2616

source_name: SLE Patient 83 Dose 4 on Week 12


title: Whole blood, SLE patient 41 Dose 4 on Week 12, placebo

description:
AP697220A28
A2786_2612

source_name: SLE Patient 41 Dose 4 on Week 12


title: Whole blood, SLE patient 34 Dose 1 on Week 0, placebo

description:
AP439435A29
A2786_2600

source_name: SLE Patient 34 Dose 1 on Week 0

value: Patient 34


title: Whole blood, SLE patient 41 Dose 5 on Week 24, placebo

description:
AP202738B29
A2786_2613

source_name: SLE Patient 41 Dose 5 on Week 24


title: Whole blood, SLE patient 41 Dose 1 on Week 0, placebo

description:
AP697212A07
A2786_2675

source_name: SLE Patient 41 Dose 1 on Week 0


title: Whole blood, SLE patient 34 Follow-up on Week 36, placebo

description:
AP019500B30
A2786_2603

source_name: SLE Patient 34 Follow-up on Week 36


title: Whole blood, SLE patient 34 Dose 4 on Week 12, placebo

description:
AP762642A28
A2786_2601

source_name: SLE Patient 34 Dose 4 on Week 12

value: Dose 4 on Week 12


title: Whole blood, SLE Patient 97 Dose 1 on Week 0; IFN-K

description:
AP276004A29
A2786_2597

source_name: SLE Patient 97 Dose 1 on Week 0

value: IFN-K

value: Patient 97


title: Whole blood, SLE patient 64 Follow-up on Week 36, placebo

description:
EP875879A08
A2786_2596

source_name: SLE Patient 64 Follow-up on Week 36

value: Follow-up on Week 36

value: Patient 64


title: Whole blood, SLE patient 64 Dose 1 on Week 0, placebo

description:
EP416167A29
A2786_2586

source_name: SLE Patient 64 Dose 1 on Week 0

value: PBO


title: Whole blood, SLE patient 64 Dose 4 on Week 12, placebo

description:
EP416181A29
A2786_2587

source_name: SLE Patient 64 Dose 4 on Week 12


title: Whole blood, SLE patient 34 Dose 5 on Week 24, placebo

description:
AP018097B29
A2786_2602

source_name: SLE Patient 34 Dose 5 on Week 24

value: Dose 5 on Week 24


title: Whole blood, SLE patient 26 Follow-up on Week 36, placebo

description:
AP134051B29
A2786_2585

source_name: SLE Patient 26 Follow-up on Week 36

value: Patient 26


title: Whole blood, SLE patient 26 Dose 5 on Week 24, placebo

description:
AP134043B28
A2786_2584

source_name: SLE Patient 26 Dose 5 on Week 24


title: Whole blood, SLE Patient 97 Dose 4 on Week 12 ; IFN-K

description:
AP659501A29
A2786_2598

source_name: SLE Patient 97 Dose 4 on Week 12


title: Whole blood, SLE patient 4 Follow-up on Week 36, placebo

description:
AP321308B08
A2786_2581

source_name: SLE Patient 4 Follow-up on Week 36

value: Patient 4


title: Whole blood, SLE Patient 97 Dose 5 on Week 24 ; IFN-K

description:
AP042706B29
A2786_2599

source_name: SLE Patient 97 Dose 5 on Week 24

value: SLE


title: Whole blood, SLE patient 26 Dose 1 on Week 0, placebo

description:
AP329190A29
A2786_2582

source_name: SLE Patient 26 Dose 1 on Week 0


title: Whole blood, SLE patient 64 Dose 5 on Week 24, placebo

description:
EP875869A29
A2786_2588

source_name: SLE Patient 64 Dose 5 on Week 24


title: Whole blood, SLE patient 26 Dose 4 on Week 12, placebo

description:
AP329228A33
A2786_2583

source_name: SLE Patient 26 Dose 4 on Week 12


title: Whole blood, SLE patient 4 Dose 5 on Week 24, placebo

description:
AP020571B07
A2786_2580

source_name: SLE Patient 4 Dose 5 on Week 24


title: Whole blood, SLE patient 9 Dose 4 on Week 12, placebo

description:
AP699470A08
A2786_2575

source_name: SLE Patient 9 Dose 4 on Week 12

value: Patient 9