title: Bulk 2 Minute Spin then RNAProtect

city: New York

first: Sydney

middle: B

last: Blattman

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

description:
cDNA
exponential GFP and exponential RFP E. coli mixed
SB361_SB362_SB363_bulk_FC

data_processing:
Barcode demultiplexing with cutadapt 1.18
UMIs extracted with UMI-tools version 0.5.5
Reads aligned with bwa version 0.7.17
Features called with featureCounts version 1.6.3
Final matrix generated by collapsing reads by UMI with a custom script in python 2.7.15
Genome_build: Genbank U00096; Genbank CP000255.1
Supplementary_files_format_and_content: tab-delimited txt

organism: Escherichia coli

source_name: Liquid Culture

growth_protocol: Cells were diluted 1:100 or 1:50 into fresh media from an overnight culture and grown 2 hours (exponential) or 5 hours (stationary)

extract_protocol:
PETRI-seq libraries were subjected to in situ RT and ligations followed by cell lysis with detergent and proteinase K; Bulk libraries were prepared from fixed cells after lysis with detergent and proteinase K
Double-stranded cDNA was made by second strand synthesis. Libraries were tagmented and amplified using the Nextera XT kit

tag: library prep

value: Bulk

tag: growth stage

value: Exponential

tag: fixed

value: No


title: Bulk Immediate RNAProtect

status: Public on May 25 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA


title: siTPR_tot_rep4

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Quantification using RSEM
Alignment to the hg19 human genome using STAR
Preparation of bigWig files using wigToBigWIg
Genome_build: hg19
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage, summary files for half-lives estimated for SLAM-seq and UMI count for MPRA data

molecule: polyA RNA

organism: Homo sapiens

source_name: WCE, siTPR cells, rep4

growth_protocol: MCF7 cells (ATCC) were grown in DMEM (Gibco) containing 10% fetal bovine serum and Penicillin-Streptomycin mixture (1%) at 37°C in a humidified incubator with 5% CO2. For export factor knockdown, cells were transfected with 10nM siRNA pool targeting indicated genes or with a control pool (Dharmacon) using Lipofectamin 3000 reagent (L3000001, Thermo Fisher). For double knockdowns, 5nM of each pool were used for a total mix of 10nM. Cells were collected for cytosolic and nuclear fractionation 72h post-transfection for all export factor depletion assays, except for siNXF1 and siALY+UAP56, where we collected the cells 48h post-transfection.

extract_protocol:
Cells were washed in cold PBS and detached from plates by 10mM EDTA, a fraction was transferred to a new tube and RNA was extracted with TRIREAGENT (MRC) to obtain WCE. Remaining cells were washed in cold PBS, resuspended in 180µl RLN buffer (50mM Tris•Cl pH8, 140mM NaCl, 1.5mM MgCl2, 10mM EDTA, 1mM DTT, 0.5% NP-40, 10U/ml RNAse inhibitor), and incubated on ice for 5 min. The extract was centrifuged for 5min at 300g in a cold centrifuge, the supernatant was transferred to a new tube and centrifuged again for 1min at 500g in a cold centrifuge. The supernatant (cytoplasmic fraction) was transferred to a new tube and RNA was extracted using TRIREAGENT. The nuclear pellet was washed once in 180µl RLN buffer, resuspended in 1ml of buffer S1 (250mM Sucrose, 10mM MgCl2, 10U/ml RNAse inhibitor), layered over 3ml of buffer S3 (880mM Sucrose, 0.5mM MgCl2, 10U/ml RNAse inhibitor), and centrifuged for 10min at 2800g in a cold centrifuge. The supernatant was removed and RNA was extracted from the nuclear pellet using TRIREAGENT.
Lexogen SENSE mRNA-seq kit

tag: tissue

value: MCF-7 cell line


title: EBOV_S_14

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Sequenced reads were trimmed for low-quality sequence, then mapped to hg19 whole genome using Star 2.5.3 with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Aligned reads were quantified to annotation model hg19 - GENCODE Genes - release 19, with Partek E/M and counts normalized by the counts per million (CPM + 0.0001) method with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized_counts CPM+0.0001 59 samples.txt

source_name: Blood

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the Illumina TruSeq® Stranded mRNA kit. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at VRI genomic Platform

value: Blood

tag: status

value: Ebola virus disease survivors


title: EBOV_S_19


title: Bulk Stationary Wild-Type E. coli

description:
cDNA
prepared from the same cells as SB442
SB432_SB433_FC

value: Stationary

value: Yes


title: sample_rep2_SensMix

city: Fribourg

first: G. Larisa

last: Maier

address: Ch. du Musée 10

department: Department of Biology

country: Switzerland

institute: University of Fribourg

data_processing:
After pre-processing, read alignment was performed using the Drosophila melanogaster reference genome Ensembl version 86 using STAR version 2.7.0.e.
BAM file were processed for read-count matrices generation.
Downstream analysis was performed in Seurat 3.1.2 package in R.
Supplementary_files_format_and_content: txt files containing read counts for each experiment.

organism: Drosophila melanogaster

source_name: larval peripheral chemosensory organs

extract_protocol:
3rd instar fruit fly larvae were dissected in PBS. The tissue was treated enzymatically with elastase for separation of sense organs. Fluorescently labelled sense organs were manually isolated and further processed with a mix of collagenase and elastase for dissociation of individual neurons. Single cells were suspended in PBS-BSA-Optiprep buffer for processing  with DisCo.
Co-encapsulation of single cells with barcoded beads was followed by bead capture and transfer to a bead collection chip. Reverse transcription was performed on-chip. Beads containing cDNA were eluted followed by cDNA amplification for 21 cycles with Kapa HiFi Hot ready mix. Purified cDNA was qualitatively assessed with Fragment Analyzer.
Sequencing of libraries was performed on NextSeq 500 Illumina sequencing system following original Dropseq protocol recommendations (20bp – read 1, 50bp – read 2).

value: larval peripheral chemosensory organs

tag: age

value: 3rd instar


title: P211_A2_5xFAD_C57BL/6J_hippocampus_rep1

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Individual Fastq files were aligned to the mouse Genome (Gencode M11 / GRCm38) using the STAR aligner version 2.5.2b with parameters STAR --runThreadN <cpu> --genomeDir <index> --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn <fastq> --readFilesCommand zcat --outFileNamePrefix <sampleID> --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
Gene counts were obtained from BAM files using featureCounts v1.5.1 with parameters -a <Gencode_vM11.gtf> -G <GRCm38.primary_assembly.genome.fa> -o counts.txt -F GTF -R -g gene_id -t exon -T 12 --largestOverlap <bamfiles>
single cell RNAseq analysis and clustering was performed using RaceId/StemId2 (Grün, D., L. Kester, and A. van Oudenaarden. 2014. “Validation of noise models for single-cell transcriptomics.” Nat. Methods 11 (6): 637–40.). Cells with less than 500 detected genes, less than 5000 aligned reads or more than 700 000 aligned reads were discarded. Only genes with a count of 5 in at least a single cell were used for analysis.
Genome_build: Gencode M11 / GRCm38
Supplementary_files_format_and_content: comma separated (csv) file with gene counts per sample

organism: Mus musculus

source_name: microglia

extract_protocol:
After transcardial perfusion with PBS, brains were roughly minced and homogenized with a potter in HBSS containing 15 mM HEPES buffer and 0.54 % Glucose. Whole-brain homogenate was separated by 70/37/30 % layered Percoll gradient centrifugation at 800 g for 30 min at 4 °C (no brake). The CNS macrophages containing interphase was then collected and washed once with PBS containing 2% FCS and 10mM EDTA before staining. Cells were stained with primary antibodies directed against CD11b (M1/70, BioLegend), CD45 (30-F11, BD Biosciences), Ly6C (AL-21, BD Biosciences) and Ly6G (1A8, BD Biosciences) for 20 min, and CD206 (C068C2, BioLegend) for 45 min at 4 °C. After washing, cells were analyd using a MoFlo Astrios (Beckman Coulter). microglia were FACS-sorted from six different CNS regions of healthy and diseased brains (see gating strategy shown in supplementary Fig.2) into a 384-well plate containing a lysis buffer.
Single cell RNAseq libraries were generated following the published SmartSeq2 protocol (Picelli et al. Nature Metods 2013)

tag: strain

value: hippocampus

tag: genotype


title: P211_A20_5xFAD_C57BL/6J_cerebellum_rep3

value: cerebellum


title: P211_A21_5xFAD_C57BL/6J_cerebellum_rep3


title: siTPR_tot_rep1

source_name: WCE, siTPR cells, rep1


title: Bulk Immediately Flash Frozen


title: sample_rep3_SensSingle


title: siTPR_nuc_rep4

source_name: Nuclear fraction, siTPR cells, rep4


title: P211_A24_5xFAD_C57BL/6J_cerebellum_rep3


title: sample_rep1_Sens40M


title: siTPR_nuc_rep3

source_name: Nuclear fraction, siTPR cells, rep3


title: Bulk Exponential Wild-Type E. coli


title: EBOV_S_12


title: P211_A22_5xFAD_C57BL/6J_cerebellum_rep3


title: EBOV_S_11


title: P211_A18_5xFAD_C57BL/6J_cerebellum_rep2


title: siTPR_tot_rep3

source_name: WCE, siTPR cells, rep3


title: P211_A19_5xFAD_C57BL/6J_cerebellum_rep2


title: PETRI-seq Experiment 1.12det

description:
Barcoded cDNA
exponential wild-type E. coli in rows A-D and wild-type stationary E. coli in columns rows F-H of RT plate (row E used for testing condition not shown in publication)

value: PETRI-seq

value: Exponential/Stationary


title: PETRI-seq Experiment 1.12

description:
Barcoded cDNA
Exponential GFP E. coli mixed with Stationary RFP E. coli; 1x ligation oligos used for Round 3 columns 1-6, 4x ligation oligos used for Round 3 columns 7-12


title: EBOV_S_10


title: siTPR_nuc_rep1

source_name: Nuclear fraction, siTPR cells, rep1


title: siTPR_cyt_rep3

source_name: Cytoplasmic fraction, siTPR cells, rep3


title: P211_A17_5xFAD_C57BL/6J_cerebellum_rep2


title: EBOV_S_9


title: EBOV_S_13


title: Fixed Bulk Exponential GFP E. coli

description:
all_bulk_FC
SB372

value: Expon


title: P211_A15_5xFAD_C57BL/6J_cerebellum_rep1


title: EBOV_S_8


title: P211_A16_5xFAD_C57BL/6J_cerebellum_rep2


title: siNXF1_tot_rep4

source_name: WCE, siNXF1 cells, rep4


title: EBOV_S_7


title: P211_A14_5xFAD_C57BL/6J_cerebellum_rep1


title: Fixed Bulk Stationary RFP E. coli

description:
all_bulk_FC
SB369


title: EBOV_S_6


title: siTPR_cyt_rep1

source_name: Cytoplasmic fraction, siTPR cells, rep1


title: Fixed Bulk Exponential RFP E. coli and Exponential GFP E. coli

description:
Prepared from the same E. coli cells as SB345 and SB346
Processed counts available in supplementary file: all_bulk_FC
SB365


title: siNXF1_tot_rep3

source_name: WCE, siNXF1 cells, rep3


title: siNXF1_tot_rep1

source_name: WCE, siNXF1 cells, rep1


title: siU2AF_cyt_rep4

source_name: Cytoplasmic fraction, siU2AF2 cells, rep4


title: P211_A13_5xFAD_C57BL/6J_cerebellum_rep1


title: EBOV_S_4


title: siNXF1_nuc_rep4

source_name: Nuclear fraction, siNXF1 cells, rep3


title: EBOV_S_5


title: siTPR_cyt_rep4

source_name: Cytoplasmic fraction, siTPR cells, rep4


title: P211_A12_5xFAD_C57BL/6J_cerebellum_rep1


title: PETRI-seq Experiment 1.10

description: Barcoded cDNA

source_name: Liquid Culture


title: PETRI-seq Experiment 1.06

description: Barcoded cDNA


title: P211_A11_5xFAD_C57BL/6J_hippocampus_rep3


title: EBOV_S_3

source_name: Blood


title: P211_A10_5xFAD_C57BL/6J_hippocampus_rep3


title: EBOV_S_2


title: siNXF1_nuc_rep3

source_name: Nuclear fraction, siNXF1 cells, rep2


title: Standard Bulk Exponential GFP E. coli

description:
Standard Bulk E. coli RNA from exponential GFP cells
SB371
processed counts in all_bulk_FC


title: Gcn2 KO +AA - Ribosome profiling

city: Princeton

first: Michel

last: Nofal

state: NJ

address: Washington Road

department: LSI

institute: Princeton University

data_processing:
Reads were truncated using cutadapt, then mapped with STAR RNA-seq alignment software. Read counts were generated using FeatureCounts from the Subread software package.
Genome_build: GRCm38 from Illumina's iGenomes
Supplementary_files_format_and_content: Read counts for each transcript in each condition

source_name: Gcn2 KO +AA

extract_protocol: Cells were extracted using the lysis buffer containing 100 ug/mL cycloheximide, standard salt concentrations, and 1% Triton X-100 (see McGlincy and Ingolia, 2017 for full recipe). The lysate was triturated 3X with a 26G syringe, then clarified. Footprints were generated with ribonuclease I, then purified, linker was ligated, the result reverse transcribed, and the cDNA library amplified by PCR. RNAseq libraries were generated with standard Illumina protocols.

tag: strain background

tag: genotype/variation

value: Gcn2 KO

tag: cell line

value: KRPC-A cells (from gen. eng. murine tumors)

tag: cell type

value: PDAC-like pancreatic tumor cells

tag: treatment

value: switched to amino acid-replete for 1hr

tag: molecule subtype

value: ribosome footprints


title: Gcn2 KO -Leu - Ribosome profiling

source_name: Gcn2 KO -Leu

value: switched to leucine-free medium for 1hr


title: HD_33

value: Blood

value: Healthy


title: siNXF1_nuc_rep1

source_name: Nuclear fraction, siNXF1 cells, rep1

value: MCF-7 cell line


title: P211_A1_5xFAD_C57BL/6J_hippocampus_rep1

source_name: microglia


title: Gcn2 WT +AA - Ribosome profiling

source_name: Gcn2 WT +AA

value: Gcn2 WT


title: siNXF1_cyt_rep3

source_name: Cytoplasmic fraction, siNXF1 cells, rep2


title: HD_32


title: siNXF1_cyt_rep4

source_name: Cytoplasmic fraction, siNXF1 cells, rep3


title: Gcn2 KO -Leu - RNAseq

value: untreated


title: HD_31


title: EBOV_S_1

value: Ebola virus disease survivors


title: siNT_tot_rep4

source_name: WCE, siNT control for siNXF1, siTPR, siU2AF2 cells, rep3


title: siNXF1_cyt_rep1

source_name: Cytoplasmic fraction, siNXF1 cells, rep1


title: HD_30


title: Gcn2 WT -Leu - RNAseq

source_name: Gcn2 WT -Leu


title: siNT_tot_rep3

source_name: WCE, siNT control for siNXF1, siTPR, siU2AF2 cells, rep2


title: HD_29


title: Gcn2 KO +AA - RNAseq


title: Gcn2 WT -Leu - Ribosome profiling


title: HD_28


title: siNT_nuc_rep4

source_name: Nuclear fraction, siNT control for siNXF1, siTPR, siU2AF2 cells, rep3


title: Gcn2 WT +AA - RNAseq


title: siNT_tot_rep1

source_name: WCE, siNT control for siNXF1, siTPR, siU2AF2 cells, rep1


title: HD_23


title: HD_22


title: HD_26


title: HD_25


title: siNT_cyt_rep1

source_name: Cytoplasmic fraction, siNT control for siNXF1, siTPR, siU2AF2 cells, rep1


title: siNT_cyt_rep4

source_name: Cytoplasmic fraction, siNT control for siNXF1, siTPR, siU2AF2 cells, rep3


title: siNT2_tot_rep3

source_name: WCE, siNT control for siALY+UAP56 cells, rep3


title: HD_21

source_name: Blood


title: siNT_nuc_rep3

source_name: Nuclear fraction, siNT control for siNXF1, siTPR, siU2AF2 cells, rep2


title: siNT_nuc_rep1

source_name: Nuclear fraction, siNT control for siNXF1, siTPR, siU2AF2 cells, rep1


title: HD_27


title: siNT_cyt_rep3

source_name: Cytoplasmic fraction, siNT control for siNXF1, siTPR, siU2AF2 cells, rep2


title: siNT2_tot_rep1

source_name: WCE, siNT control for siALY+UAP56 cells, rep1


title: HD_20


title: HD_18


title: siNT2_nuc_rep3

source_name: Nuclear fraction, siNT control for siALY+UAP56 cells, rep3


title: siNT2_nuc_rep2

source_name: Nuclear fraction, siNT control for siALY+UAP56 cells, rep2


title: 293HEK: Capsid Set B

city: Louisville

first: Kevin

middle: J

last: Sokoloski

state: KY

address: 505 S. Hancock St.

department: Microbiology and Immunology

institute: University of Louisville

description: Library generated from total RNA immunoprecipitated with anti-Capsid polyclonal sera, and fragmented with RNAse A

data_processing:
Libraries were demultiplex on the MiSeq interface to generate the raw sequence files.
All analyses of data sets were performed using the Galaxy web services found at Usegalaxy.org, where applicable the programs utilized are indicated by "_" and the version is noted by the (_) following immediately after. Deviations from the default settings are noted.
All libraries were trimmed using "Trimmomatic" (0.36.5) to remove adaptor sequences and set a minimum length of >10nt.
Library quality was assessed using "FastQC"
The cDNA libraries were aligned to the VEE TC-83.dsGFP genome via "Bowtie2" (2.3.4.2) with the following parameters- Search Plus sense only, Require 22bp word with 1 allowable mismatch druing mutliseed, Gap open penalty= default, Gap Extension. Penalty= default,
Bowtie2 output files were converted from SAM format to BAM format using "SAM-to-BAM" (2.1.1) using the VEEV TC-83.dsGFP genome.
Depth of coverage was determined using SAMTools to generate a pileup file for each library via "Generate Pileup" (1.2.2).
Base representation, identity, and coverage was determined via the filtering of the pileup data using "Filter Pileup" (1.0.2) to report coverage at each nucleotide.
Tabular data from the filtered pileup files was imported into Excel and analyzed via subtractive analysis to determine regions of significant enrichment for each cDNA library.
Genome_build: VEEV TC-83.dsGFP Genomic Sequence
Supplementary_files_format_and_content: Single Processed Data File, in .xlsx format. This file contains summary information for the analysis, the depth of coverage at a nucleotide level of resolution for each cDNA library (on different tabs), and the subtractive analysis used to identify the sites of interaction is included on a separate tab.

source_name: 293HEK cells

growth_protocol: 293HEK cells were maintained in MEM supplemented with 10% FBS at 37 degrees Celsius in the presence of 5% CO2.

extract_protocol:
Lysates were generated via the addition of RIPA buffer (50mM Tris [pH 7.6] / 150mM NaCl / 1.0% NP-40 / 0.5% Sodium Deoxycholate / 0.1% SDS). The lysates were clarified via centrifugation and immunoprecipitated with either nonspecific control sera, or a cross-reactive anti-VEEVCapsid polyclonal sera and Protein A agarose beads. Purified RNA:Protein complexes were treated with RNAse A for 15 minutes at room temperature, washed several times to remove contaminating sequences and then released from the resin via proteinase K digestion at 37 degrees Celsius for 30 minutes.
The libraries were generated using the NEBNext Small RNA Library Prep Set for Illumina, with the following Index / Sample pairs- (Nonspecific, Illumina 7 GATCTG) (Capsid Set A, Illumina 8 TCAAGT) (Capsid Set B, Illumina 12 TACAAG)

treatment_protocol: Per library, a total of 2E7 293HEK tissue culture cells were infected with VEEV TC-83.dsGFP at an MOI of 5 PFU/cell. Infection was allowed to proceed for 18 hours prior to UV crosslinking via 5700x100 ujoules per cm2.

value: 293HEK cells

value: VEEV TC-83.dsGFP

tag: antibody

value: Anti-Capsid

tag: rna treatment

value: RNAse A


title: siNT2_tot_rep2

source_name: WCE, siNT control for siALY+UAP56 cells, rep2


title: HD_19


title: 293HEK: Capsid Set A


title: HD_24


title: HD_17


title: siNT2_nuc_rep1

source_name: Nuclear fraction, siNT control for siALY+UAP56 cells, rep1


title: 293HEK: Nonspecific Control

description: Library generated from total RNA immunoprecipitated with nonspecific polyclonal sera, and fragmented with RNAse A

value: Preimmune IgG


title: HD_16


title: siNT2_cyt_rep2

source_name: Cytoplasmic fraction, siNT control for siALY+UAP56 cells, rep2


title: HD_15


title: siNT2_cyt_rep3

source_name: Cytoplasmic fraction, siNT control for siALY+UAP56 cells, rep3


title: siALY_UAP56_tot_rep3

source_name: WCE, siALY+UAP56 cells, rep3


title: HD_12


title: HD_14


title: Untreated Control 2 (PI3K panel)

type: RNA

city: Mineola

first: Douglas

last: Marks

address: 120 Mineola Boulevard

institute: NYU Langone Health

description:
PI3K Pathway Panel
20180323_207794830719_POST-C2_08.RCC

hyb_protocol: RNA samples that passed quality and concentration standards were hybridized in a multiplexed to target specific probes and for 20 hours at 65C using 100-400 ng of RNA

scan_protocol: Following hybridization, the target-probe complexes were purified and immobilized on the nCounter prep station, Digital counts for each gene-specific target RNA were then acquired on the nCounter detection analyzer and normalized to account for differences in tissue mRNA quntiy, as well as slight differences in assay efficiency.

data_processing: For nanoString analysis, data quality assessment, differential expression and statistical comparison was performed by the systems biology data-driven network-based Bayesian inference of drivers (NetBID, https://github.com/jyyulab/NetBID).16 Gene Set Enrichment Analysis (GSEA) was performed using MSigDB (v6.1) and “fgsea” package in R, with default parameters.  Multiple comparison analysis was performed using Benjamini-Hochberg method.

label: Nanostring bar coding

source_name: breast cancer

label_protocol: Specimens were labeled with decode assignment which was linked to clinical details and treatment received (MK-2206 vs. control)

extract_protocol: mRNA was manually extracted from macrodissected tumor rich areas of surgical specimens of patients treated with MK-2206 (e.g. MK-2206 Patient 1) as well as prospectively enrolled untreated control patients (e.g. Untreated Control 1) and stored at -80C.

value: primary breast cancer

tag: histology

value: ILC

tag: Sex

value: Female

tag: grade

value: Untreated


title: Untreated Control 5 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-C5_11.RCC

value: IDC


title: siNT2_cyt_rep1

source_name: Cytoplasmic fraction, siNT control for siALY+UAP56 cells, rep1


title: Untreated Control 3 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-C3_09.RCC


title: Untreated Control 4 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-C4_10.RCC


title: HD_11


title: siALY_UAP56_tot_rep2

source_name: WCE, siALY+UAP56 cells, rep2


title: siALY_UAP56_nuc_rep3

source_name: Nuclear fraction, siALY+UAP56 cells, rep3


title: HD_10

source_name: Blood


title: Untreated Control 1 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-C1_07.RCC


title: MK-2206 Patient 5 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-AKT5_05.RCC


title: siALY_UAP56_nuc_rep2

source_name: Nuclear fraction, siALY+UAP56 cells, rep2


title: HD_9


title: MK-2206 Patient 4 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-AKT4_04.RCC


title: MK-2206 Patient 3 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-ALT3_03.RCC


title: HD_8


title: siALY_UAP56_cyt_rep3

source_name: Cytoplasmic fraction, siALY+UAP56 cells, rep3


title: HD_13


title: siALY_UAP56_cyt_rep2

source_name: Cytoplasmic fraction, siALY+UAP56 cells, rep2


title: MK-2206 Patient 2 (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-AKT2_02.RCC


title: ChIP_seq_IP_UAP56_2

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

library_source: genomic

data_processing:
DRIPc-seq, DRIP-seq, ChIP-seq and RNA-seq: All fastq files were trimmed with FASTQ Toolkit before mapping
DRIPc-seq, DRIP-seq and ChIP-seq reads were aligned to the hg 38 Canonical genome using Bowtie2/BWA.
DRIPc-seq and ChIP-seq peaks were called using MACS2 callpeak.
RNA-seq reads were aligned to the hg 38  genome using HISAT2, counted using FeatureCounts and normalized by RPKM.
Bigwig files were generated using bedtools bamcoverage
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: Erythromyeloblastoid leukemia cell line

extract_protocol:
Genomic DNA was extracted from K562 cells, sonicated and immunoprecipitated with UAP56 specific antibody.
ThruPLEX DNA-Seq 6S (12rxn)

value: UAP56 (Proteintech 14798-1-AP)


title: HD_7

value: Blood


title: HD_6

value: Healthy


title: MK-2206 Patient 1  (PI3K panel)

description:
PI3K Pathway Panel
20180323_207794830719_POST-AKT1_01.RCC


title: HD_5


title: Day14 Ventral cDNA

city: Copenhagen

first: Gaurav

middle: Singh

last: Rathore

address: Department of Neuroscience Faculty of Health and Medical Sciences Blegdamsvej 3B, Building 7, 4th floor

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

data_processing:
Read alignment: The Cellranger 2.0 pipeline (10x Genomics, USA) was used to align reads, quantify unique molecular identifiers (UMI) and generate feature-barcode expression matrices. Index read number is 8 base pairs. Read 1 (26 base pairs) consists of the 10x barcode and UMIs and Read 2 comprises of 56 base pairs. The reads were mapped to hg19 transcriptome a reference package provided by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Genome_build: hg19
Supplementary_files_format_and_content: Format: barcodes.tsv for detected cellular barcodes obtained through cell ranger pipeline. genes.tsv contains the list of detected genes mapped on reference transcriptome. matrix.mtx files are sparse matrices which contains numbers of UMIs associated with genes and barcodes (https://kb.10xgenomics.com/hc/en-us/articles/115000794686-How-is-the-MEX-format-used-for-the-gene-barcode-matrices).

source_name: MiSTR tissue

growth_protocol: Human embryonic stem cells (H9 cells) differentiated using neural patterning media: 1:1 mix of DMEM/F12 and NeuroMedium, plus N2 supplement (1:200) and Neuro-Brew 21 without vitamin A (1:100); supplemented from day 1 to 9 with: 10uM SB431542 and 100ng/ml of rh-Noggin and a 0-2uM gradient of CHIR99021. Ventralized samples were further supplemented from day 1 to 9 with SHH-C24II (200ng/ml) and Purmorphamine (0.5uM).

extract_protocol:
MiSTR tissue was divided into two halves along the gradient, one side used to collect the five A-E samples for mRNA analysis. The other side was dissociated into a single-cell suspension using Accutase (Thermofisher), for day 0, day 1 and day 2 samples, or with Neural dissociation kit (P) on a GentleMACS dissociator (both from Miltenyi Biotec) for day 14 samples. The cells were then frozen in CS10 CryoStor (Stemcell Technologies) and stored at -150oC until needed. In the meantime, each sample underwent mRNA analysis for quality control selection for scRNA-seq. Cryopreserved cells, quality control cleared, were thawed, counted and mixed in equal numbers into a final single-cell suspension of 350 to 500 cells/ml solution in 0.01% BSA in PBS. For 0 to 48h tissues, cells from 3 biological MiSTR tissue replicates were pooled prior to sequencing. For day 14 tissues, the sequenced samples contained a mix of cells from regions A to E (n=1-3 biological replicates per region). A total of 9000-17000 cells were loaded per lane onto the 10X Chromium (10X Genomics) . For day14 ventral Cells from region A-E were hashed with hashtagging antibodies and then loaded on 10X chromium to generate hashing and cDNA libraries simultaneously.
Chromium Single Cell 3' Reagent Kits (v2 Chemistry).

tag: cell type of origin

value: H9 human embryonic stem cells

tag: day of differentiation

value: day 14

tag: location

value: Ventral


title: ChIP_seq_IP_UAP56_1


title: WTAP6_total

data_processing:
SLAM-seq - RNA-seq reads were mapped to the human genome (hg19 assembly) with STAR, and then filtered for 4-Thiouridine-labeled reads using a custom-written Java code, requiring at least 2 T->C mutations in each read pair. Labeled reads were then quantified using RSEM, Bowtie2 and GENCODE v26 annotation, and Cyto/Nuc ratios were normalized as in (Carlevaro-Fita and Johnson 2019). For each sample and fraction, we used genes whose expression levels were between the 50th and 90th percentiles of all annotated genes to estimate the normalization coefficients using a linear regression analysis. These coefficients were used to normalize the Cyto and Nuc data and obtain absolute localization values.
CytoLib - The sequenced reads were used to count individual library tiles using a custom Java script as in (Lubelsky and Ulitsky 2018). We considered only R1 reads that contained the TAGGAGGCCTCATCTGACTG adaptor sequence, and extracted the unique molecular identifier (UMI) sequence preceding the adaptor. Each read was then matched to the sequences in the library, without allowing indels. The matching allowed mismatches only at positions with Illumina sequencing quality of at least 35 and we allowed up to two mismatches in the first 15 nt (‘seed’), and no more than four overall mismatches. If a read matched more than one library sequence, the sequence with the fewest mismatches was selected, and if the read matched more than one library sequence with the same number of mismatches, it was discarded. The output from this step was a table of counts of reads mapping to each library sequence. Only fragments with at least 20 reads on average in the WCE samples were used in subsequent analysis. We then used these to compute nuclear/cytoplasmic and WCE/input ratios after adding a pseudocount of 0.5 to each UPM.
annotation - GENCODE v26
Genome_build: hg19
Supplementary_files_format_and_content: SLAM-seq - nascent_RNA_expression_and_localization.csv contains mean TPM values from RSEM quantification, as well as mean normalized Cyto/Nuc log2 ratios ("localization" columns)
Supplementary_files_format_and_content: CytoLib - finalTab_siRBM15_and_siWTAP_CytoLib.xlsx contains normalized counts for 2 biological replicates, and mean values of WCE/input and of Cyto/Nuc ratios of all library variants

source_name: MCF7 cell line

growth_protocol: MCF7 cells (ATCC) were grown in DMEM (Gibco) containing 10% fetal bovine serum and Penicillin-Streptomycin mixture (1%) at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
One microgram of RNA was used for cDNA production using the qScript Flex cDNA synthesis kit (95049, Quanta) and a gene specific primer containing part of the Illumina RD2 region. The entire cDNA reaction was diluted into 100 μl second strand reaction with a primer containing a unique molecular identifier (UMI) and part of the Illumina RD1 region. The second strand reaction was carried for a single cycle using Phusion Hot Start Flex DNA Polymerase (NEB, M0535), purified using AMpure beads and eluted in 20μl ddH2O. 20µl of the second strand reaction was used for amplification with barcoded primers, and the amplified libraries were purified by two-sided AMpure purification.
Cells were fractionated for WCE, nuclear and cyoplasmic fractions. RNA was extracted with TRIREAGENT (MRC)

treatment_protocol: For export factor knockdown, cells were transfected with 10nM siRNA pool targeting indicated genes or with a control pool (Dharmacon) using Lipofectamin 3000 reagent (L3000001, Thermo Fisher).

tag: library type

value: cytoLib fragments

value: MCF-7 cells were transfected first with siRNAs targeting NXF1 or non-targeting controls for 48h, and then with the CytoLib plasmids for 24h.

value: MCF7 cell line

tag: fraction

value: total RNA


title: SAMPLE 15_BAY1436032+Azacitidine simultaneous replicate 3

type: genomic

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

institute: Universitätsklinikum Halle

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Raw data were processed and quality checked using Illumina’s GenomeStudioV2011.1 methylation module (v.1.8).

label: cy3, cy5

source_name: BAY1436032+Azacitidine simultaneous

label_protocol: standard Illumina protocol

growth_protocol: Human AML cells isolated from  the spleen and bone marrow of IDH1 R132C (PDX1) mice were cultured in IMDM medium (Stemcell Technology Inc. Vancouver, Canada) supplemented with 10% FBS (Sigma-Aldrich, Munich, Germany), 2 mM L-Glutamine (Life Technologies, Karlsruhe, Germany), 1% Penicillin/Streptomycin (Gibco, ThermoFischer Scientific, Braunschweig, Germany) , 20 ng/ml human GMCSF, 20 ng/ml human GCSF, 20 ng/ml human IL6, 50 ng/μl, human SCF and 20 ng/μl human IL-3 (all from PeproTech, Hamburg, Germany) and were incubated at 37 °C with 5% CO2 in humidified atmosphere

extract_protocol: bisulfite-treated using the EZ-96 DNA Methylation-Lightning MagPrep Kit

treatment_protocol: Treatment was carried out with DMSO (vehicle), 500nm of azacitidine for day 1 to day 4, 50nm of BAY1436032 for day 1 to day 5, sequential combination (azacitidine for day 1 to day 4 and BAY1436032 for day 5 to day 9) and simultaneous combination (azacitidine for day 1 to day 4 and BAY1436032 for day 1 to day 5).  RNA was isolated on day 6 for cells treated with vehicle, azacitidine, BAY1436032 and simultaneous combination and on day 10 for sequential combination

value: Human CD45+ cells from bone marrow of PDX mouse

value: BAY1436032+Azacitidine simultaneous


title: ChIP_seq_INPUT_UAP56_2


title: SAMPLE 11_BAY1436032+Azacitidine sequential replicate 2

source_name: BAY1436032+Azacitidine sequential

value: BAY1436032+Azacitidine sequential


title: SAMPLE 8_Azacitidine replicate 2

source_name: Azacitidine

value: Azacitidine


title: SAMPLE 6_BAY1436032 replicate 3


title: SAMPLE 4_BAY1436032 replicate 1


title: SAMPLE 10_BAY1436032+Azacitidine sequential replicate 1


title: upf1∆prp18∆ replicate 2

city: Los Angeles

last: Roy

state: CA

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

data_processing:
rename read IDs to contain chronological numbers: zcat < $SUBSAMPLED_DIR$prefix"_R1.fastq.gz" | awk '{print (NR%4 == 1) ? "@" ++i "_R1": $0}' | gzip -c > $NUMBERED_READS_DIR$prefix"_R1.fastq.gz"
reads were trimmed at the 5´ and 3´ ends for low quality base calls, at 3´ends for TruSeq adapters, and finally trimmed for poly(A) tails by removing T homopolymers at 5´ end of read 1 and A homopolymers at 3´ end of read 2, respectively using cutadapt version 1.18: cutadapt --overlap 2 -j 0 -q 20,20 -g "T{100}" -a AGATCGGAAGAGC -A AGATCGGAAGAGC -A "A{100}"  -n 2 --trim-n  --minimum-length 50 --max-n 4 -o $out_R1  -p $out_R2 $in_R1 $in_R2
Trimmed reads were then mapped to the R64-2-1 version of the S. cerevisiae genome downloaded from the Saccharomyces Genome Database (SGD) with STAR version 2.7.0d using parameters --alignEndsType EndToEnd --outSAMattributes NH HI NM MD AS nM jM jI XS
STAR CIGAR fields reformatted with: java -jar /Applications/jvarkit/dist/samfixcigar.jar -r $GENOME_FASTA_FILE $out"Aligned.out.sam" -o $out"_reformatted_cigar.sam"
Trimmed reads were also mapped to the R64-2-1 version of the S. cerevisiae genome downloaded from the Saccharomyces Genome Database (SGD) with BBMap version 38.32 (Bushnell, 2014) using parameters intronlen=20 nhtag=t mdtag=t nhtag=t xmtag=t  amtag=t  nmtag=t
STAR and BBMap alignments were integrated to select the best alignments as determined by lowest edit distance of paired-end alignment to the reference, disallowing soft-clipping and allowing gaps >20 bp without a penalty, using software developed for this study (COMPASS, available at https://github.com/k-roy/COMPASS).
Genome_build: Saccharomyces cerevisiae R64-2-1
Supplementary_files_format_and_content: custom splice junction format, where each row represents a distinct splice junction, and each column an attribute of that junction

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: upf1∆::HIS3 and upf1∆::HIS3 prp18∆::kanMX6 colonies were inoculated for overnight growth in YPD, seeded in 50 mL fresh YPD the following day at OD 0.05 and grown to mid-log phase OD600 of 0.6.

extract_protocol:
Samples were harvested by spinning down at 3k rpm for 5 minutes, flash-frozen in liquid nitrogen, and purified by standard phenol-chloroform extraction.
Fragmented libraries were prepared by the Illumina TruSeq stranded mRNA library prep kit (catalogue #20020594).
Illumina TruSeq stranded mRNA

treatment_protocol: Yeast cells grown in YPD rich medium and harvested at mid-log phase.

tag: genetic background

tag: genotype

value: upf1-delta::HIS3MX6 prp18-delta::kanMX6


title: SAMPLE 5_BAY1436032 replicate 2


title: upf1∆prp18∆ replicate 1


title: SAMPLE 9_Azacitidine replicate 3


title: HD_4

tag: tissue

tag: status


title: SAMPLE 7_Azacitidine replicate 1

tag: cell type


title: SAMPLE 2_Vehicle replicate 2

source_name: Vehicle

tag: treatment

value: Vehicle


title: SAMPLE 12_BAY1436032+Azacitidine sequential replicate 3


title: upf1∆prp18∆ replicate 3


title: upf1∆ replicate 3


title: WTAP6_cyto

description: finalTab_siRBM15_and_siWTAP_CytoLib.xlsx

tag: cell line

value: cytoplamic RNA


title: WTAP6_nuc

value: nuclear RNA


title: WTAP5_total


title: HD_2

value: Blood


title: RNA_seq_siC_2

extract_protocol:
Total RNA was extracted from K562 cells using RNeasy Mini kit (Qiagen) and further processed with the TruSeq Stranded Total RNA Illumina Kit
Illumina TruSeq protocol

tag: antibody

tag: genotype/variation

value: siC control


title: SAMPLE 13_BAY1436032+Azacitidine simultaneous replicate 1


title: HD_1

value: Healthy


title: DRIP_seq_siC_untreated

data_processing:
Library strategy: DRIP-seq
DRIPc-seq, DRIP-seq, ChIP-seq and RNA-seq: All fastq files were trimmed with FASTQ Toolkit before mapping
DRIPc-seq, DRIP-seq and ChIP-seq reads were aligned to the hg 38 Canonical genome using Bowtie2/BWA.
DRIPc-seq and ChIP-seq peaks were called using MACS2 callpeak.
RNA-seq reads were aligned to the hg 38  genome using HISAT2, counted using FeatureCounts and normalized by RPKM.
Bigwig files were generated using bedtools bamcoverage
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

extract_protocol:
Genomic DNA from K562 cells enzimatically fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Samples were treated or not with RNaseH in vitro. Monoclonal S9.6 antibody was used to immunoprecipitate RNA-DNA hybrids.
ThruPLEX DNA-Seq 6S (12rxn)

value: Monoclonal S9.6


title: WTAP5_nuc


title: RNA_seq_siC_1


title: ChIP_seq_INPUT_UAP56_1


title: WTAP5_cyto


title: si-Lnc-Dpf3/Med

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

country: China

institute: Zhejiang University

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

source_name: dendritic cells

growth_protocol: Dendritic cells are cultured in RPMI1640 medium plus GM-CSF and IL4 for 5 days and further stimulated with LPS (100 ng/ml) for 24 h to generate mature BMDCs (mDCs).

extract_protocol:
Total RNA was extracted from treated mDCs using TRIzol reagent (Invitrogen) according to manufacturer’s protocol.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.

treatment_protocol: mDCs were transfected with si-Lnc-Dpf3 or si-NC and stimulated with or without CCR7 ligand CCL19 and CCL21 (CCR7L) for 12 h or left unstimulated (Med), and then subjected to RNA seq

tag: strain

tag: cells

value: LPS-stimulated mature DCs


title: upf1∆ replicate 1


title: SAMPLE 1_Vehicle replicate 1


title: si-NC/CCR7L


title: RBM6_cyto

value: cytoLib fragments


title: si-NC/Med


title: DRIPc_seq_siUAP56_2

extract_protocol:
Genomic DNA from K562 cells enzimatically fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.  Monoclonal S9.6 antibody was used to immunoprecipitate RNA-DNA hybrids.
Standard illumina protocol


title: Lipoma_21

city: Leipzig

first: Mehmet

middle: Volkan

last: Cakir

state: Saxony

address: Johannisallee 30

department: Medical Science

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
RNA-seq raw reads were demultiplexed and trimmed of adaptors.
Mapping of the reads to the reference genome is carried out by STAR (version 2.6.1d). To detect gene fusions and increase the sensitivity for novel splice junctions the following options in addition to default parameters were used: --chimSegmentMin 10 --chimOutType WithinBAM SoftClip --chimJunctionOverhangMin 10 --chimScoreMin 1 --chimScoreDropMax 30 –chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentReadGapMax 3
The transcription level of each gene was determined using htseq-count that results in count files.
Genome_build: GRCh38
Supplementary_files_format_and_content: The only processed data type we present for each sample is tab separated text file the first column of which is ensembl gene id whereas the second column is the count.

source_name: Lipoma

extract_protocol:
For library preparation and sequencing, total RNA was extracted from n=15 lipomas and the matched normal SAT using RNeasy® Lipid Tissue Kit (Qiagen). The quality and quantity of the purified RNA was determined by measuring the absorbance at 260/280 nm and 260/230 nm using a NanoDrop spectrophotometer and by gel electrophoresis to visualize the 28S and 18S rRNA bands as indicators of total RNA integrity
Indexed cDNA libraries were constructed with an average insert size of 300 bp using the TruSeq RNA sample preparation kits v2 (Illumina, San Diego, CA). Libraries were sequenced on an Illumina HiSeq platform as 101 bp paired-end reads to an average of 46.9 million reads per library.

value: Lipoma

tag: subtype


title: Lipoma_11


title: SAMPLE 3_Vehicle replicate 3


title: DRIPc_seq_siC_2


title: Lipoma_15


title: RBM6_total

value: MCF-7 cells were transfected first with siRNAs targeting NXF1 or non-targeting controls for 48h, and then with the CytoLib plasmids for 24h.

value: MCF7 cell line


title: upf1∆ replicate 2


title: si-Lnc-Dpf3/CCR7L


title: Lipoma_14


title: Lipoma_16


title: RBM6_nuc


title: larvae, POP70_4

city: Utrecht

first: Jorke

last: Kamstra

state: Non United States Or Canada

address: PO Box 80177

department: Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

data_processing:
Adaptor trimming using trim_galore (v0.4.5, Babraham Institute, UK) under standard parameters
Alignment was performed with STAR aligner (v2.5.4b) to align and map sequences to the zebrafish genome (GRCz11, https://www.ensembl.org) with a recent release of the zebrafish transcriptome GTF (v92, www.ensembl.org)
Generated BAM files were loaded to SeqMonk sequence analysis tool (v1.41, Babraham institute, UK) and mRNAs were quantified using the built-in mRNA seq pipeline. Library quality was evaluated with the RNA-seq QC plot and cumulative distribution plots using SeqMonk. Filter was applied to analyze mRNAs that had at least a log2 = 0 expression in either of the samples, to assure that for statistical analysis only mRNAs with enough reads were included. Deseq2 filter using R (v3.5.0) within SeqMonk was used on raw read counts to calculate differential expression. After Deseq2 analysis, data were normalized by reads per million (RPM)
Genome_build: GRCz11
Supplementary_files_format_and_content: Excel file containing log2 normalized data

organism: Danio rerio

source_name: Whole zebrafish larvae

extract_protocol:
RNA from samples for RNA-seq analysis were purified using NucleoSpin® RNA extraction kit (Macherey-Nagel, Germany). RA1 lysismix (Macherey-Nagel, Germany) was added to each sample (10 larvae per sample) and samples were passed through a 21-gauge needle (HSW HENKE-JECT®, Germany) until complete homogenization. Total RNA was extracted from samples following manufacturer’s instructions. Each sample was eluted in 50 μL RNase-free water and stored at -80 °C until further analysis
A total of 2 μg was used for library preparation. A quality check (QC) of total RNA was performed with a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), Agilent 2100 (Agilent Technologies, CA, USA) and agarose gel electrophoresis prior to library construction. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, mRNA was purified from total RNA using poly-T oligo attached magnetic beads. Fragments were randomly created in fragmentation buffer. First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina, CA, USA) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. PCR products were purified (AMPure XP system, Beckman, US) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Libraries were analyzed with a Hiseq 4000 (Illumina, Ca, USA), using 150bp paired-end reads, with a depth of 20 million reads per sample.

value: AB wild type

tag: developmental stage

value: 96 hpf

value: whole larvae


title: larvae, POP70_3


title: SAMPLE 14_BAY1436032+Azacitidine simultaneous replicate 2

value: Human CD45+ cells from bone marrow of PDX mouse

value: BAY1436032+Azacitidine simultaneous


title: Lipoma_9


title: Day 14 Dorsal patterned Cells round 3

data_processing:
Read alignment: The Cellranger 2.0 pipeline (10x Genomics, USA) was used to align reads, quantify unique molecular identifiers (UMI) and generate feature-barcode expression matrices. Index read number is 8 base pairs. Read 1 (26 base pairs) consists of the 10x barcode and UMIs and Read 2 comprises of 56 base pairs . The reads were mapped to hg19 transcriptome a reference package provided by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Genome_build: hg19
Supplementary_files_format_and_content: Format: barcodes.tsv for detected cellular barcodes obtained through cell ranger pipeline. genes.tsv contains the list of detected genes mapped on reference transcriptome. matrix.mtx  files are sparse matrices which contains numbers of UMIs associated with genes  and barcodes (https://kb.10xgenomics.com/hc/en-us/articles/115000794686-How-is-the-MEX-format-used-for-the-gene-barcode-matrices).

extract_protocol:
MiSTR tissue was divided into two halves along the gradient, one side used to collect the five A-E samples for mRNA analysis. The other side was dissociated into a single-cell suspension using Accutase (Thermofisher), for day 0, day 1 and day 2 samples, or with Neural dissociation kit (P) on a GentleMACS dissociator (both from Miltenyi Biotec) for day 14 samples. The cells were then frozen in CS10 CryoStor (Stemcell Technologies) and stored at -150oC until needed. In the meantime, each sample underwent mRNA analysis for quality control selection for scRNA-seq. Cryopreserved cells, quality control cleared, were thawed, counted and mixed in equal numbers into a final single-cell suspension of 350 to 500 cells/ml solution in 0.01% BSA in PBS. For 0 to 48h tissues, cells from 3 biological MiSTR tissue replicates were pooled prior to sequencing. For day 14 tissues, the sequenced samples contained a mix of cells from regions A to E (n=1-3 biological replicates per region). A total of 9000-17000 cells were loaded per lane onto the 10X Chromium (10X Genomics) .
Chromium Single Cell 3' Reagent Kits (v2 Chemistry)

tag: cell type of origin

value: H9 human embryonic stem cells

tag: day of differentiation

value: day 14

value: Dorsal


title: Day 14 Dorsal patterned Cells round 2

tag: location


title: larvae, POP70_1


title: larvae, POP70_2


title: Lipoma_20


title: Lipoma_8


title: Day 14 Dorsal patterned Cells round 1


title: larvae, POP10_4


title: Day 2 Ventral patterned Cells

value: day 2

value: Ventral


title: RBM5_nuc

tag: library type

tag: fraction

value: nuclear RNA


title: NT6_total

value: total RNA


title: NT6_nuc


title: Lipoma_6


title: Lipoma_10


title: Day 2 Dorsal Patterned cells


title: RBM5_total


title: Lipoma_7


title: larvae, POP10_1


title: Lipoma_5


title: larvae, POP10_2


title: Day 1 Dorsal Patterned cells

value: day 1


title: Lipoma_4


title: NT5_total

value: cytoLib fragments


title: NT6_cyto

value: cytoplamic RNA


title: Day 1 Ventral Patterned cells


title: Day 0 Embryonic Stem cells (H9)

value: day 0


title: NT5_nuc

value: MCF-7 cells were transfected first with siRNAs targeting NXF1 or non-targeting controls for 48h, and then with the CytoLib plasmids for 24h.

value: MCF7 cell line


title: NT5_cyto


title: Lipoma_3

value: Lipoma


title: larvae, PFOS70_3

value: AB wild type

value: 96 hpf

value: whole larvae


title: larvae, POP10_3


title: siNXF1_tot_rep4

description: nascent_RNA_expression_and_localization.csv

extract_protocol:
SENSE mRNA-Seq Library prep kit (Lexogen)
Cells were fractionated for WCE, nuclear and cyoplasmic fractions. RNA was extracted with TRIREAGENT (MRC)

value: SLAM-seq

value: Cells were treated with siRNA for 16h, followed by 4-Thiouridine labeling for 4h.

value: 4sU-labeled, iodoacetamide treated, poly(A) enriched total RNA


title: Exp6_2h

city: Solna

first: Gabriele

last: Girelli

state: Stockholm

address: Tomtebodavägen 23A

department: MBB

country: Sweden

institute: Karolinska Institutet / Science for Life Laboratory

data_processing:
BED file generated by gpseq-seq-gg (v2.0.2/3) pipeline. Briefly performs: pattern filtering with scan_for_matches, mapping with bwa-mem (v0.7.17), mapping filtering, detection of orphan reads, quality filtering, UMI de-duplication.
BED files are corrected for chromosome translocations using bed-fix-chrom-rearrangement (v0.0.1, d.o.i.: 10.5281/zenodo.3365906).
GPSeq score is estimated from the translocation-corrected BED files using the gpseqc (v2.3.6) pipeline.
chromflock (v0.1) was used to build 3D genome structures.
Genome_build: Grch37/hg19
Supplementary_files_format_and_content: fastq.gz; gzipped fastq format.
Supplementary_files_format_and_content: bed; UCSC BED format with chromosome, chromStart, chromEND, name, and de-duplicated UMI count per cutsite. Generated by the gpseq-seq-gg pipeline.
Supplementary_files_format_and_content: transCorrected.bed; UCSC BED format corrected for chromosome translocations.
Supplementary_files_format_and_content: zipped gpseqc output; see supplementary files format below.
Supplementary_files_format_and_content: settings.txt; settings for gpseqc pipeline
Supplementary_files_format_and_content: log.txt; log of gpseqc pipeline run
Supplementary_files_format_and_content: combined.tsv; gpseqc pipeline intermediate table
Supplementary_files_format_and_content: estimated.tsv; raw GPSeq score estimated by gpseqc pipeline
Supplementary_files_format_and_content: rescaled.tsv; rescaled GPSeq score estimated by gpseqc pipeline
Supplementary_files_format_and_content: zipped chromflock output; see chromflock.README.md
Supplementary_files_format_and_content: csv (chromflock bead labels)
Supplementary_files_format_and_content: markdown

extract_protocol:
Phenol-chlorophorm DNA extraction
DNA shearing, In Vitro Transcription, RNA clean-up, RA3(Illumina)-adapter ligation, Reverse Transcription, PCR, DNA clean-up

treatment_protocol: In situ HindIII/MboI digestion, dephosphorylation, linker ligation

tag: Sex

value: female

value: blood

tag: digestion time

value: 2 h

tag: growth protocol

value: RPMI-1640 + 2 mM L-glutamine + 15% FBS


title: Lipoma_1

tag: tissue


title: larvae, PFOS70_2

tag: treatment


title: Exp6_30min

value: 30 min


title: siNXF1_nuc_rep4

tag: cell line

value: 4sU-labeled, iodoacetamide treated, poly(A) enriched nuclear RNA


title: larvae, PFOS70_1


title: Lip_Control_20

source_name: subcutaneous adipose tissue (SAT)

value: subcutaneous adipose tissue (SAT)


title: RBM5_cyto

value: cytoLib fragments

value: cytoplamic RNA


title: siNXF1_tot_rep3

value: MCF7 cell line


title: Exp6_15min

value: 15 min


title: Lip_Control_21


title: siNXF1_nuc_rep3


title: larvae, PFOS10_3

value: AB wild type


title: siNXF1_cyt_rep4

value: 4sU-labeled, iodoacetamide treated, poly(A) enriched cytoplamic RNA


title: larvae, PFOS70_4

value: 96 hpf

value: whole larvae


title: Exp5_2h


title: Lip_Control_15


title: larvae, PFOS10_4


title: Lip_Control_16


title: Exp5_30min


title: siNXF1_cyt_rep3

value: SLAM-seq

value: Cells were treated with siRNA for 16h, followed by 4-Thiouridine labeling for 4h.


title: Lip_Control_14


title: Lip_Control_11


title: Exp5_15min

value: female


title: larvae, PFOS10_1


title: siNT_tot_rep4

value: 4sU-labeled, iodoacetamide treated, poly(A) enriched total RNA


title: Exp5_10min

value: blood

value: 10 min


title: Exp6_10min

value: RPMI-1640 + 2 mM L-glutamine + 15% FBS


title: siNT_tot_rep3


title: siNT_nuc_rep4

value: 4sU-labeled, iodoacetamide treated, poly(A) enriched nuclear RNA


title: Lip_Control_10

value: subcutaneous adipose tissue (SAT)


title: Exp1_6h

data_processing:
BED file generated by gpseq-seq-gg (v2.0.2/3) pipeline. Briefly performs: pattern filtering with scan_for_matches, mapping with bwa-mem (v0.7.17), mapping filtering, detection of orphan reads, quality filtering, UMI de-duplication.
BED files are corrected for chromosome translocations using bed-fix-chrom-rearrangement (v0.0.1, d.o.i.: 10.5281/zenodo.3365906).
GPSeq score is estimated from the translocation-corrected BED files using the gpseqc (v2.3.6) pipeline.
chromflock (v0.1) was used to build 3D genome structures.
Genome_build: Grch37/hg19
Supplementary_files_format_and_content:
bed; UCSC BED format with chromosome, chromStart, chromEND, name, and de-duplicated UMI count per cutsite. Generated by the gpseq-seq-gg pipeline.
transCorrected.bed; UCSC BED format corrected for chromosome translocations.
zipped gpseqc output; see supplementary files format below.
settings.txt; settings for gpseqc pipeline
log.txt; log of gpseqc pipeline run
combined.tsv; gpseqc pipeline intermediate table
estimated.tsv; raw GPSeq score estimated by gpseqc pipeline
rescaled.tsv; rescaled GPSeq score estimated by gpseqc pipeline
zipped chromflock output; see chromflock.README.md
csv (chromflock bead labels)
markdown

growth_protocol: IMDM + 10% FBS

value: male

value: bone marrow

tag: disease

value: Chronic Myeloid Leukemia

value: 6 h

value: IMDM + 10% FBS


title: larvae, Control2

value: AB wild type

value: Control


title: Exp1_45min

value: 45 min


title: Lip_Control_8


title: larvae, PFOS10_2

value: 96 hpf

value: whole larvae


title: Lip_Control_9


title: HD_3

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Sequenced reads were trimmed for low-quality sequence, then mapped to hg19 whole genome using Star 2.5.3 with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Aligned reads were quantified to annotation model hg19 - GENCODE Genes - release 19, with Partek E/M and counts normalized by the counts per million (CPM + 0.0001) method with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized_counts CPM+0.0001 59 samples.txt

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the Illumina TruSeq® Stranded mRNA kit. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at VRI genomic Platform

value: Blood

tag: status

value: Healthy


title: siNT_nuc_rep3

value: SLAM-seq

value: Cells were treated with siRNA for 16h, followed by 4-Thiouridine labeling for 4h.

value: MCF7 cell line


title: Lip_Control_7


title: siNT_cyt_rep3

value: 4sU-labeled, iodoacetamide treated, poly(A) enriched cytoplamic RNA


title: Exp4_10min

description:
Exp4.chrWide.zip
Exp4.1Mb.zip
Exp4.100kb.zip
Exp4.1Mb.fish.zip
Exp4.100kb.fish.zip

data_processing:
Library strategy: Genomic loci Positioning by Sequencing (GPSeq)
BED file generated by gpseq-seq-gg (v2.0.2/3) pipeline. Briefly performs: pattern filtering with scan_for_matches, mapping with bwa-mem (v0.7.17), mapping filtering, detection of orphan reads, quality filtering, UMI de-duplication.
BED files are corrected for chromosome translocations using bed-fix-chrom-rearrangement (v0.0.1, d.o.i.: 10.5281/zenodo.3365906).
GPSeq score is estimated from the translocation-corrected BED files using the gpseqc (v2.3.6) pipeline.
chromflock (v0.1) was used to build 3D genome structures.
Genome_build: Grch37/hg19
Supplementary_files_format_and_content:
bed; UCSC BED format with chromosome, chromStart, chromEND, name, and de-duplicated UMI count per cutsite. Generated by the gpseq-seq-gg pipeline.
transCorrected.bed; UCSC BED format corrected for chromosome translocations.
zipped gpseqc output; see supplementary files format below.
settings.txt; settings for gpseqc pipeline
log.txt; log of gpseqc pipeline run
combined.tsv; gpseqc pipeline intermediate table
estimated.tsv; raw GPSeq score estimated by gpseqc pipeline
rescaled.tsv; rescaled GPSeq score estimated by gpseqc pipeline
zipped chromflock output; see chromflock.README.md
csv (chromflock bead labels)
markdown

source_name: bone marrow

value: 10 min


title: Exp4_30min

value: male

value: 30 min


title: siNT_cyt_rep4


title: larvae, Control1

tag: strain


title: larvae, Control3


title: Lip_Control_6

value: subcutaneous adipose tissue (SAT)


title: larvae, Control4


title: Exp4_5min

value: bone marrow

value: Chronic Myeloid Leukemia

value: 5 min


title: ATCC 31280 18 h

city: Shanghai

first: yuanting

last: wu

address: 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the  Actinosynnema pretiosum ATCC 31280 genome assembly using bowtie2（version: 2-2.0.5）.
Gene abundance measurements were generationed and normalized  using BEDTools（version:2.16.1） ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Genome_build: Actinosynnema pretiosum ATCC 31280 (CP029607, not released yet)
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values for each Sample

organism: Actinosynnema pretiosum

source_name: bacteria

growth_protocol: For fermentation, the first seed medium (3.0% tryptone soya broth powder, 0.5% yeast extract, and 5.0% sucrose (w/v), pH 7.5) was inoculated with agar-grown mycelia and cultivated at 30 °C, 220 rpm for 24 h. Subsequently, the second seed medium (3.0% tryptone soya broth powder, 0.5% yeast extract and 2.5% sucrose, 1.0% soluble starch (w/v), 0.05% isobutanol, and 0.05% isopropanol (v/v), pH 7.5) was inoculated with 1 mL of the first seed culture, incubated for another 24 h at 30 °C. Fermentation medium (yeast extract 0.8%, malt extract 1.0%, sucrose 1.5%, soluble starch 2.5% (w/v), isobutanol 0.5% and isopropanol 1.2% (v/v), pH 7.5) was inoculated with the second seed culture at 10% (v/v) and incubated at 25 °C and 220 rpm for 7 days

extract_protocol:
One mililiter culture was collected at 15 h, 18 h and 24 h during fermentation process. The total RNA was extracted with Redzol reagent according to the procedures recommended by the manufacturer (SBS Genetech, China). Total DNA was removed by DNase I (Thermo Fisher, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: genotype

value: wildtype


title: BAY1436032+Azacitidine simultaneous replicate 3 [RNA-seq]

data_processing:
Sequences are aligned to human genome hg19 with alignment program STAR_2.5.2b using Gencode v.25
Mapping to the transcriptome and gene expression analysis done with Cufflinks v2.2.1 using Gencode v.25
Gene expression quantified by FPKM (Fragments Per Kilobase per Million)
Genome_build: hg19
Supplementary_files_format_and_content: For each Gene: Ensembl_ID, Gene_symbol, Locus (chr:start-end), FPKM

extract_protocol:
AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany)
Sequenced as paired-end reads each 50bp (PE100)

tag: cell type

value: Human CD45+ cells from bone marrow of PDX mouse

value: BAY1436032+Azacitidine simultaneous


title: BAY1436032+Azacitidine simultaneous replicate 2 [RNA-seq]


title: Lip_Control_4

tag: subtype


title: BAY1436032+Azacitidine simultaneous replicate 1 [RNA-seq]


title: Exp3_30min

description:
Exp3.chrWide.zip
Exp3.1Mb.zip
Exp3.100kb.zip
Exp3.1Mb.fish.zip
Exp3.100kb.fish.zip

value: IMDM + 10% FBS


title: Lip_Control_3


title: Exp4_1min

value: 1 min


title: PETRI-seq Experiment 2.01

city: New York

last: Blattman

address: 1150 St. Nicholas Ave

description:
Barcoded cDNA
exponential wild-type E. coli in columns 1-6 and wild-type stationary E. coli in columns 7-12 of RT plate (barcodes 7-12, 19-24, 31-36, etc.)

data_processing:
Barcode demultiplexing with cutadapt 1.18
UMIs extracted with UMI-tools version 0.5.5
Reads aligned with bwa version 0.7.17
Features called with featureCounts version 1.6.3
Final matrix generated by collapsing reads by UMI with a custom script in python 2.7.15
Genome_build: Genbank U00096; Genbank CP000255.1
Supplementary_files_format_and_content: tab-delimited txt

organism:
Escherichia coli
Staphylococcus aureus

source_name: Liquid Culture

extract_protocol:
PETRI-seq libraries were subjected to in situ RT and ligations followed by cell lysis with detergent and proteinase K; Bulk libraries were prepared from fixed cells after lysis with detergent and proteinase K
Double-stranded cDNA was made by second strand synthesis. Libraries were tagmented and amplified using the Nextera XT kit

tag: library prep

value: PETRI-seq

tag: growth stage

value: Exponential/Stationary

tag: fixed

value: Yes


title: Exp3_10min


title: ATCC 31280 24 h


title: PETRI-seq Experiment 2.01no_det

value: Exponential


title: Lip_Control_1


title: PETRI-seq Experiment 1.06SaEc-replicate

description: Barcoded cDNA


title: BAY1436032+Azacitidine sequential replicate 2 [RNA-seq]

value: BAY1436032+Azacitidine sequential


title: BAY1436032+Azacitidine sequential replicate 3 [RNA-seq]


title: Exp2_2h

description:
Exp2.chrWide.zip
Exp2.1Mb.zip
Exp2.100kb.zip
Exp2.1Mb.fish.zip
Exp2.100kb.fish.zip

value: 2 h


title: Fixed Bulk S. aureus

description:
Prepared from the same S. aureus cells as SB345 and SB346
Processed counts available in supplementary file: all_bulk_FC_staph
SB366

organism: Staphylococcus aureus

value: Bulk


title: Lip_Control_5


title: Exp3_5min

value: male


title: Exp3_1min


title: BAY1436032+Azacitidine sequential replicate 1 [RNA-seq]


title: ATCC 31280 15 h


title: Exp2_1h

value: 1 h


title: 8h uncaged rep1

city: Dortmund

first: Daniel

last: Summerer

state: NRW

address: Otto-Hahn-Str. 4a

department: Chemistry and Chemical Biology

institute: TU Dortmund University

data_processing:
BGI Genomics' DNBSEQ-G50 was used for basecalling.
Sequenced reads were trimmed for adaptor sequences; contamination and low-quality reads from raw reads were removed by BGI Genomics. Cleaned reads were mapped to the GENCODE reference annotation of the human transcriptome (v32) expanded to include transcripts from the transfected plasmids using GRCh38 primary assembly (v32) as decoy. Mapping was perfromed with Salmon v1.1.0 adopting a k-mer length of 27 and the --validateMappings option.
Transcript abundance was quantified with Salmon v1.1.0 considering a fragment length of 205±45 bp while correcting for hexamer priming bias.
Count data was anlayzed with DESEq2 in R v3.6.1 after projecting transcript counts onto genes using tximeta.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delmited text files including count estimates for each sample

source_name: HEK293T cells

growth_protocol: HEK293T cells routinely passaged every 3–4 days in DMEM with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin, 0.1 mg/mL streptomycin. Cells were co-transfected with pShP2419 and pStH1169

extract_protocol:
500,000 transfected cells were sorted by flow cytometry and total RNA was extracted using TRIzol; samples were enriched for mRNA during cDNA synthesis by BGI Genomics.
RNA libraries were prepared for sequencing using the standard DNBseq workflow of BGI Genomics.

treatment_protocol: Transfected cells were grown in the presence of 0.1 mM 4,5-dimethoxy-2-nitrobenzyl-L-serine for 48h, washed in DPBS, placed on a 365 nm UV transilluminator for 3 min if applicable, and incubated further 4h or 8h in growth medium.

tag: transfected with

value: Co-transfected with pShP2419 and pStH1169

value: light, 3min

tag: time


title: 4h uncaged rep2


title: Azacitidine replicate 2 [RNA-seq]

value: Azacitidine


title: 8h uncaged rep2


title: Azacitidine replicate 1 [RNA-seq]


title: Exp2_30min

tag: Sex

value: bone marrow

value: Chronic Myeloid Leukemia

tag: digestion time

value: 30 min


title: PETRI-seq Experiment 1.06SaEc

first: Sydney

institute: Columbia University

description: Barcoded cDNA


title: BAY1436032 replicate 3 [RNA-seq]

value: Human CD45+ cells from bone marrow of PDX mouse


title: 0h caged rep2

value: no light


title: Exp2_15min

tag: tissue

value: 15 min

tag: growth protocol

value: IMDM + 10% FBS


title: 4h uncaged rep1

tag: cell line

tag: treatment


title: Untreated Control 5 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-C5_11.RCC

data_processing: For nanoString analysis, data quality assessment, differential expression and statistical comparison was performed by the systems biology data-driven network-based Bayesian inference of drivers (NetBID, https://github.com/jyyulab/NetBID).16 Gene Set Enrichment Analysis (GSEA) was performed using MSigDB (v6.1) and “fgsea” package in R, with default parameters.  Multiple comparison analysis was performed using Benjamini-Hochberg method.

source_name: breast cancer

extract_protocol: mRNA was manually extracted from macrodissected tumor rich areas of surgical specimens of patients treated with MK-2206 (e.g. MK-2206 Patient 1) as well as prospectively enrolled untreated control patients (e.g. Untreated Control 1) and stored at -80C.

value: primary breast cancer

tag: histology

value: IDC

value: Female

tag: grade

value: Untreated


title: Untreated Control 3 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-C3_09.RCC

value: ILC

tag: age


title: Untreated Control 4 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-C4_10.RCC


title: Azacitidine replicate 3 [RNA-seq]


title: Exp2_10min

value: male

tag: disease

value: 10 min


title: 0h caged rep1

value: Co-transfected with pShP2419 and pStH1169


title: Exp1_1h

description:
Exp1.chrWide.zip
Exp1.1Mb.zip
Exp1.100kb.zip
Exp1.1Mb.fish.zip
Exp1.100kb.fish.zip
chromflock.10000G_intra.zip.gz
chromflock.10000G.zip.gz
chromflock.README.md.gz
chromflock.metadata.csv.gz

value: 1 h


title: Exp1_2h

value: 2 h


title: Untreated Control 2 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-C2_08.RCC


title: Vehicle replicate 3 [RNA-seq]

tag: cell type

value: Vehicle


title: MK-2206 Patient 5 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-AKT5_05.RCC


title: MK-2206 Patient 4 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-AKT4_04.RCC


title: SHR-MA

city: London

first: Wenduo

last: Gu

address: James Black Centre, 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.0.2.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting,  UMI counting, and to generate  feature-barcode matices.
Supplementary_files_format_and_content: datamatrix folder from output of cell ranger command

organism: Rattus norvegicus

source_name: Mesenteric artery

extract_protocol:
The whole mesenteric artery or aorta were cut into fine pieces and digested with 2 mg/ml collagenase I  and 2 mg/ml dispase II in Hank’s balanced salt solution containing calcium and magnesium for a total 40 min. The remaining aortic media and endothelium were cut open longitudinally and digested with 1 mg/ml papain , 0.5 mg/ml 1,4-Dithioerythritol, 0.156 mg/ml Taurine; 0.25 mg/ml bovine serum albumin in PBS. Single nucleated live cells were sorted into PBS with 0.04% BSA using a flow cytometer and were then analyzed on a 10x Chromium instrument using Chromium Single Cell 3' Reagent Kit v2 chemistry (10X Genomics), following a standard protocol.
Library was generated and sequenced on a NovaSeq platform (Illumina) with paired-end 150 bp (PE 150) sequencing strategy.
Single-cell RNA-seq

tag: strain

value: SHR

value: Mesenteric artery

tag: disease state

value: Spontaneously hypertensive rats

value: 16-18 week old


title: SHR-AA

source_name: Aortic artery

value: Aortic artery


title: Vehicle replicate 2 [RNA-seq]

value: Human CD45+ cells from bone marrow of PDX mouse


title: WKY-AA

value: WKY

value: Wistar Kyoto


title: Exp1_15min

value: bone marrow

value: Chronic Myeloid Leukemia

value: 15 min

value: IMDM + 10% FBS


title: Vehicle replicate 1 [RNA-seq]


title: BAY1436032 replicate 2 [RNA-seq]


title: WKY-MA


title: MK-2206 Patient 2 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-AKT2_02.RCC

value: primary breast cancer

value: IDC

value: Female


title: NOGEOID_5: secondary_AML

status: Public on May 24 2020

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

data_processing:
Perfomed adapter clipping with Cutadapt v1.7.1, as well as removing the first 6 bases from the forward reads and 9 bases from the reverse reads
Quality trimming performed with Trimmomatic v0.32 using the "MAXINFO" option (“target read length”: 40, “strictness”: 0.5); orphaned reads were discarded
STAR v2.5.1b used for sequence alignment with the GRCh37 genome build
STAR v2.5.1b used for second pass alignment with the GRCh37 genome build along with splice junction information from all samples (junctions in the mitochondrial sequences were removed) with the default parameters recommended for gene-fusion detection
Picard v1.136.0 used for merging properly paired and discordant paired reads
Salmon v0.9.1 used to create isoform and gene counts (GRCh37)
Raw gene counts: Raw gene counts for all Ensembl genes (GRCh37). Table created with salmon after adapater clipping with Cutadapt and quality trimming with Trimmomatic. Rows correspond to Ensembl gene identifiers and columns to samples.
Raw isoform counts: Raw isoform counts for all Ensembl isoforms (GRCh37). Table created with salmon after adapater clipping with Cutadapt and quality trimming with Trimmomatic. Rows correspond to Ensembl transcript identifiers and columns to samples.
Known splice junction counts: Uniquely aligned reads supporting each known splice junction extracted from the SJ.out.tab-file after two-pass alignment with STAR. Row names correspond to splice junction identifiers (in the form „chromosome:start-end“). An expression filter has been applied and only splice junctions with at least 3 supporting reads in at least 3 samples and at least 10 supporting reads in at least 1 sample are shown. Samples containing SF mutations not in SRSF2, U2AF1 or SF3B1 are not provided in this table as filtering was performed after their exclusion (n=6).
Novel splice junction counts: Uniquely aligned reads supporting each novel splice junction extracted from the SJ.out.tab-file after two-pass alignment with STAR. Row names correspond to splice junction identifiers (in the form chromosome:start-end). An expression filter has been applied and only splice junctions with at least 10 supporting reads in at least 3 samples and at least 30 supporting reads in at least 1 sample are shown. Samples containing SF mutations not in SRSF2, U2AF1 or SF3B1 are not provided in this table as filtering was performed after their exclusion (n=6).
Exon counts: Raw counts for each non-overlapping exonic segment (GRCh37), produced with DEXSeq after adapter clipping, quality trimming and alignment with STAR. First column corresponds to the exon identifier (in the form „gene:exon number“). Chromosome and strand information, as well as exon start and ending positions are provided.
Intron counts: Raw counts for each non-overlapping intronic segment (GRCh37). The table was produced after creating a gtf-file containing introns and counting with DEXSeq. First column corresponds to the intron identifier (in the form „gene:intron number“). Chromosome and strand information, as well as intron start and ending positions are provided.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab delimited text files including gene counts, isoform counts, uniquely aligned reads supporting known and novel splice junctions and counts for each non-overlapping exonic and intronic segment

source_name: bone marrow or peripheral blood mononuclear cells

extract_protocol:
Mononuclear cells from peripheral blood (PB) or bone marrow (BM) were enriched by Ficoll gradient centrifugation.
RNAseq libraries were prepared using the Sense mRNA Seq Library Prep Kit V2 following the manufractur´s instruction. Between 500-1000 ng total RNA (RNA integrity number [RIN] >7) were used as input material. All sequencing was paired end and performed using polyadenylated-selected and stranded RNA sequencing.

treatment_protocol: Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML)

tag: gender

value: female

tag: study

tag: diagnosis

tag: cytogenetics

tag: mrc

tag: fab

tag: ecog

value: dead

tag: relapse

value: YES

tag: wbc

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa

value: NO


title: BAY1436032 replicate 1 [RNA-seq]

tag: treatment


title: NOGEOID_4: primary_AML

value: death_from_indeterminate cause


title: NOGEOID_9: secondary_AML

value: CRi


title: Untreated Control 1 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-C1_07.RCC

tag: tissue

tag: histology

tag: age

tag: Sex

tag: grade

value: Untreated


title: NOGEOID_8: primary_AML

tag: gender

tag: study

tag: diagnosis

value: Adverse


title: NOGEOID_7: primary_AML

tag: cytogenetics

tag: mrc

value: favorable

tag: fab


title: NOGEOID_6: primary_AML

tag: ecog

tag: relapse

tag: wbc


title: Exp1_10min

tag: cell line

value: male

tag: disease

tag: digestion time

value: 10 min

tag: growth protocol


title: NOGEOID_3: primary_AML

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa


title: NOGEOID_2: primary_AML

tag: gender

value: alive

value: CR


title: NOGEOID_1: secondary_AML

tag: study

value: CN-AML

value: Intermediate


title: GEO-95: primary_AML

tag: diagnosis


title: GEO-96: primary_AML

tag: cytogenetics

value: del(7q)/monosomy 7


title: GEO-94: primary_AML

tag: mrc


title: GEO-97: primary_AML

tag: fab


title: DRIP_seq_siC_RNaseH_treated

source_name: Erythromyeloblastoid leukemia cell line

tag: antibody

value: Monoclonal S9.6

tag: genotype/variation

value: siC control


title: GEO-92: primary_AML

tag: ecog

value: dead

tag: relapse

tag: wbc


title: MK-2206 Patient 3 (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-AKT3_03.RCC

tag: tissue

value: primary breast cancer

tag: histology

value: IDC

tag: age

tag: Sex

value: Female

tag: grade

tag: treatment


title: GEO-93: primary_AML

tag: gender

value: female

value: NO

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa


title: GEO-87: primary_AML

tag: study

tag: diagnosis

tag: cytogenetics

value: Various

tag: mrc

value: Adverse

tag: fab

value: YES


title: GEO-90: primary_AML

value: male

tag: ecog

tag: relapse

tag: wbc


title: GEO-89: primary_AML

value: favorable

value: alive


title: GEO-91: primary_AML

value: CN-AML

value: CR


title: GEO-86: treatment-associated_AML

value: death_from_indeterminate cause


title: MK-2206 Patient 1  (IO360 panel)

description:
IO360 Panel
20180202_207795020719_POST-AKT1_01.RCC

tag: tissue

tag: histology

tag: age


title: GEO-85: primary_AML

value: Intermediate

value: CRi


title: GEO-79: primary_AML


title: GEO-81: secondary_AML

value: dead


title: GEO-82: primary_AML


title: GEO-78: primary_AML


title: GEO-73: primary_AML


title: GEO-74: primary_AML


title: GEO-72: primary_AML


title: GEO-84: primary_AML


title: GEO-83: primary_AML


title: GEO-77: primary_AML


title: GEO-80: primary_AML


title: GEO-76: secondary_AML


title: Exp1_30min

tag: cell line

tag: Sex

value: bone marrow

tag: disease

value: Chronic Myeloid Leukemia

tag: digestion time

value: 30 min

tag: growth protocol

value: IMDM + 10% FBS


title: GEO-71: primary_AML

tag: gender

value: NO

tag: ldh

tag: haemoglobin

tag: platelets

tag: cebpa


title: GEO-65: primary_AML

value: female

tag: study

tag: diagnosis

tag: cytogenetics

value: Various

tag: mrc

tag: fab


title: GEO-98: primary_AML

value: Complex Cytogenetics

value: Adverse

tag: ecog

tag: relapse

value: YES

tag: wbc


title: GEO-67: primary_AML

value: del(7q)/monosomy 7


title: GEO-66: primary_AML

value: CN-AML

value: favorable

value: alive


title: GEO-64: primary_AML

value: Intermediate

value: CR


title: GEO-63: primary_AML

value: dead


title: GEO-70: primary_AML


title: GEO-60: primary_AML


title: GEO-59: primary_AML

value: male


title: GEO-58: primary_AML


title: GEO-57: primary_AML


title: GEO-56: primary_AML


title: GEO-52: primary_AML


title: GEO-55: primary_AML


title: GEO-53: primary_AML


title: GEO-50: primary_AML


title: GEO-51: primary_AML


title: GEO-54: primary_AML


title: GEO-69: primary_AML

value: death_from_indeterminate cause


title: GEO-46: primary_AML


title: GEO-44: primary_AML

value: del(5q)/monosomie 5


title: GEO-48: primary_AML


title: GEO-45: primary_AML


title: GEO-47: primary_AML


title: GEO-62: primary_AML


title: GEO-38: primary_AML


title: GEO-36: primary_AML


title: GEO-35: primary_AML


title: GEO-61: primary_AML


title: GEO-42: primary_AML


title: GEO-41: primary_AML


title: GEO-31: primary_AML


title: GEO-29: primary_AML


title: GEO-28: primary_AML


title: GEO-32: primary_AML


title: GEO-30: primary_AML


title: GEO-33: primary_AML


title: GEO-27: primary_AML


title: GEO-39: primary_AML


title: GEO-257: primary_AML

value: CRi


title: GEO-255: treatment-associated_AML

value: NO


title: GEO-26: primary_AML


title: GEO-258: primary_AML

value: female


title: GEO-254: primary_AML


title: GEO-43: primary_AML

value: Various


title: GEO-256: secondary_AML


title: GEO-40: primary_AML

value: Complex Cytogenetics


title: GEO-252: primary_AML


title: GEO-253: primary_AML


title: GEO-251: treatment-associated_AML

value: Adverse


title: GEO-37: primary_AML

value: YES


title: GEO-25: secondary_AML


title: GEO-250: secondary_AML


title: GEO-246: primary_AML


title: GEO-244: primary_AML


title: GEO-247: primary_AML


title: GEO-245: primary_AML


title: GEO-248: primary_AML


title: GEO-243: primary_AML


title: GEO-242: primary_AML

value: del(7q)/monosomy 7


title: GEO-237: primary_AML


title: GEO-236: treatment-associated_AML

value: CN-AML


title: GEO-238: primary_AML


title: GEO-241: primary_AML


title: GEO-24: primary_AML


title: GEO-23: secondary_AML


title: GEO-231: treatment-associated_AML


title: GEO-234: secondary_AML


title: GEO-235: primary_AML


title: GEO-226: secondary_AML

value: favorable


title: GEO-230: primary_AML

value: alive


title: GEO-233: primary_AML


title: GEO-249: primary_AML

value: Intermediate


title: GEO-224: primary_AML

value: CR


title: GEO-229: secondary_AML

value: dead


title: GEO-232: primary_AML


title: GEO-222: primary_AML


title: GEO-223: primary_AML

value: male


title: GEO-228: primary_AML


title: GEO-227: primary_AML


title: GEO-218: primary_AML


title: GEO-22: primary_AML


title: GEO-221: primary_AML

value: death_from_indeterminate cause


title: GEO-240: treatment-associated_AML


title: GEO-220: primary_AML


title: GEO-219: primary_AML


title: GEO-217: primary_AML


title: GEO-239: primary_AML


title: GEO-216: primary_AML


title: GEO-213: primary_AML


title: GEO-215: primary_AML


title: GEO-211: primary_AML


title: GEO-214: primary_AML


title: GEO-212: primary_AML


title: GEO-225: primary_AML


title: GEO-21: primary_AML


title: GEO-206: treatment-associated_AML


title: GEO-207: primary_AML


title: GEO-210: primary_AML


title: GEO-208: secondary_AML


title: GEO-205: primary_AML


title: GEO-203: primary_AML


title: GEO-20: secondary_AML


title: GEO-198: secondary_AML


title: GEO-201: primary_AML


title: GEO-200: primary_AML


title: GEO-197: secondary_AML


title: GEO-195: primary_AML


title: GEO-196: secondary_AML


title: GEO-191: primary_AML


title: GEO-189: primary_AML


title: GEO-19: secondary_AML


title: GEO-190: primary_AML


title: GEO-192: treatment-associated_AML


title: GEO-187: primary_AML


title: GEO-202: secondary_AML


title: GEO-186: primary_AML


title: GEO-193: primary_AML


title: GEO-183: primary_AML


title: GEO-194: primary_AML


title: GEO-181: primary_AML


title: GEO-204: primary_AML


title: GEO-185: primary_AML


title: GEO-182: primary_AML


title: GEO-184: secondary_AML


title: GEO-178: primary_AML


title: GEO-179: primary_AML


title: GEO-199: primary_AML


title: GEO-18: primary_AML


title: GEO-177: primary_AML


title: GEO-175: primary_AML


title: GEO-174: primary_AML


title: GEO-180: treatment-associated_AML


title: GEO-176: primary_AML


title: GEO-173: primary_AML


title: GEO-171: primary_AML


title: GEO-172: primary_AML


title: GEO-17: secondary_AML


title: GEO-169: primary_AML

value: del(5q)/monosomie 5


title: GEO-170: primary_AML


title: GEO-168: primary_AML


title: GEO-166: secondary_AML


title: GEO-188: primary_AML


title: GEO-165: primary_AML


title: GEO-163: primary_AML


title: GEO-162: secondary_AML

value: CRi


title: GEO-161: primary_AML

value: NO


title: GEO-159: primary_AML

value: female


title: GEO-160: primary_AML


title: XBP1_LKO_RNA-Seq_CT46_Rep1

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: Total RNA-seq

data_processing:
Fastq files containing raw RNA-seq reads were aligned to the mouse genome (mm10/NCBI38) using HISAT2. RNA-seq quantification was performed with htseq-count (default parameters). Protein-coding genes were quantified by iGenome annotation. Quantification values were normalized with DESeq2, followed by filtering out of zero expression genes in each replicate or time point.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: Liver

extract_protocol: These RNA samples (200ng of total RNA for each sample) were converted into strand-specific total mRNA-seq libraries with the Universal Plus mRNA-seq kit (NuGen) per the manufacturer’s protocol. The size selected libraries were analyzed for quality control with High Sensitivity DNA chip on a Bioanalyzer 2100 (Agilent), and the pooled libraries were sequenced with the NovaSeq 6000 (Illumina) using a 100-bp paired-end for an average of 40 million paired-end reads per sample at the University of Houston Sequencing Core.

treatment_protocol: RNA samples were isolated from two biological replicates of mouse liver tissues from circadian time 0 (CT0) every 2 hours for 48 hours with the miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions.

tag: strain

value: C57BJ/L6 background

tag: genotype

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)

value: Male

tag: age

value: 12-16 weeks

tag: tissue

value: Liver

tag: time point


title: GEO-16: primary_AML

tag: gender

value: Various

value: Adverse

value: YES

tag: ldh


title: XBP1_LKO_RNA-Seq_CT44_Rep2

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT44_Rep1

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT46_Rep2

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT42_Rep2

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT42_Rep1

description: Total RNA-seq


title: GEO-157: primary_AML

value: CN-AML

value: Intermediate

tag: haemoglobin

tag: platelets


title: XBP1_LKO_RNA-Seq_CT40_Rep2

description: Total RNA-seq


title: GEO-164: primary_AML

tag: study

value: alive

tag: cebpa


title: GEO-156: primary_AML

tag: diagnosis

tag: cytogenetics

value: favorable

value: dead

value: CR


title: GEO-167: primary_AML

value: male

tag: mrc

tag: fab

value: CRi


title: XBP1_LKO_RNA-Seq_CT38_Rep2

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT38_Rep1

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT40_Rep1

description: Total RNA-seq


title: GEO-155: primary_AML

value: female

tag: ecog

tag: relapse

value: NO


title: XBP1_LKO_RNA-Seq_CT36_Rep2

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)


title: GEO-158: treatment-associated_AML

tag: wbc


title: GEO-154: secondary_AML


title: XBP1_LKO_RNA-Seq_CT36_Rep1

description: Total RNA-seq

tag: genotype

value: Male

tag: age

value: 12-16 weeks


title: GEO-153: primary_AML

value: Various


title: A549 E6E7 Cy5 rep 1

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

hyb_protocol: The labeled cDNA was purified by Minelute columns (QIAGEN). Absorbance readings at 260, 550 and 650 nm were measured to estimate labeling efficiency using a Nanodrop1000 spectrophotometer (Thermo Scientific). 39 uL the labeled cDNA were combined with 45 ul of formamide solution 2X (0.2% SDS, 0.2 ug/mL fish sperm DNA, 10X SSC buffer) and denatured at 95° C for 3 min. The total 90 uL of this mixture were deposited on the microarray, covered with a LifterSlip and incubated in a ArrayIt hybridization cassette for 22 h at 42° C.

scan_protocol: The slides were showing four times with showing solutions for two min and then analyzing into the scan (Perkin Elmer Scan Array Lite).

data_processing: The output Image was analyzed with GenePix pro 6.0 and the normalization of dates was make in the TMEV software. Lowess normalized log2 ratio representing test/reference (Cy5/Cy3) in sample 1 and 3, and dye swap replicates test/reference (Cy3/Cy5) in sample 2 and 4. columns B and D, and dye swap replicates test/reference (Cy3/Cy5) in columns C and E.

source_name: Alveolar lung cell

label_protocol: RNA quality was verified by 0.9% agarose gel electrophoresis. 15 μg of RNA  were labeled by reverse transcription in a 35 uL reaction containing 3 ug of random primers, 3 ug oligo-dT, 10 nmoles of dATP, dGTP and dTCP, 4 nmoles of dTTP, 2.5 nmol of either Cy3 or Cy5-dUTP, 40 U of RNAsin and 800 U of M-MLV Reverse Transcriptase (Promega). After incubation at 37ºC for 2 h, 300 additional U of enzyme and further incubated for 2 h.

growth_protocol: Cells were grown in RPMI-1640 basal medium supplemented with 10% FBS and antibiotics (gentamicin, penicillin and streptomicin) at 37ºC with 5% CO2 atmosphere. For subculture, cells were trypsinized 3-5 min and treated with fresh medium containing FBS. Stably transfected A-549 cells were selected and grown in a culture medium containing 0.1 μg/mL G418.

extract_protocol: Total RNA was obtained using 1 mL of Trizol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured to 80% confluence and serum depleted for 24 h. Then, cells were exposed to CSC (Kentucky University) dissolved in RPMI-1640 medium at 10 μg/mL.

tag: cell type

value: A549 ATCC

tag: transfection

value: empty pLXSN vector

value: E6E7 HPV-16 genes using pLXSN vector


title: A549 E6E7 Cy5 rep 2


title: GEO-152: primary_AML

tag: gender

value: CN-AML

value: Intermediate

tag: ldh

value: YES


title: A549 E6E7 Cy3 rep 1


title: XBP1_LKO_RNA-Seq_CT34_Rep2

description: Total RNA-seq

tag: tissue

value: Liver

tag: time point


title: XBP1_LKO_RNA-Seq_CT34_Rep1

description: Total RNA-seq


title: GEO-150: primary_AML

tag: study

value: Adverse

value: dead

tag: haemoglobin

tag: platelets

tag: cebpa


title: XBP1_LKO_RNA-Seq_CT30_Rep2

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT32_Rep2

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT32_Rep1

description: Total RNA-seq


title: GEO-149: primary_AML

tag: diagnosis

tag: cytogenetics

tag: mrc

value: favorable

tag: fab

value: CR


title: GEO-15: secondary_AML

value: female

tag: ecog

tag: relapse

tag: wbc

value: NO


title: A549 E6E7 Cy3 rep 2

tag: cell type


title: GEO-148: primary_AML

value: male

value: alive


title: GEO-143: primary_AML


title: XBP1_LKO_RNA-Seq_CT30_Rep1

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

tag: genotype

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)

value: Male

tag: age

value: 12-16 weeks


title: GEO-144: primary_AML

tag: gender

value: del(7q)/monosomy 7

tag: ldh


title: XBP1_LKO_RNA-Seq_CT28_Rep2

description: Total RNA-seq

tag: tissue

tag: time point


title: XBP1_LKO_RNA-Seq_CT24_Rep1

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT24_Rep2

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT26_Rep1

description: Total RNA-seq


title: XBP1_LKO_RNA-Seq_CT26_Rep2

description: Total RNA-seq


title: GEO-142: primary_AML

tag: study

value: CN-AML

tag: haemoglobin

tag: platelets


title: GEO-141: primary_AML

tag: diagnosis

tag: cytogenetics

value: Intermediate

tag: cebpa


title: XBP1_LKO_RNA-Seq_CT22_Rep2

description: Total RNA-seq


title: GEO-140: primary_AML

tag: mrc

tag: fab

tag: ecog

value: YES


title: XBP1_LKO_RNA-Seq_CT22_Rep1

description: Total RNA-seq

value: Liver


title: GEO-14: primary_AML

value: Various

value: Adverse

tag: relapse

tag: wbc


title: XBP1_LKO_RNA-Seq_CT20_Rep2

description: Total RNA-seq

tag: strain

tag: genotype


title: GEO-151: primary_AML

tag: gender

value: Complex Cytogenetics


title: XBP1_LKO_RNA-Seq_CT28_Rep1

description: Total RNA-seq

tag: age


title: GEO-139: primary_AML

value: favorable

value: CR

tag: ldh


title: XBP1_LKO_RNA-Seq_CT20_Rep1

description: Total RNA-seq

tag: tissue

tag: time point


title: GEO-147: primary_AML

tag: study

value: dead

tag: haemoglobin

value: NO


title: XBP1_LKO_RNA-Seq_CT18_Rep2

description: Total RNA-seq


title: GEO-145: primary_AML

value: male

tag: diagnosis

value: alive

tag: platelets


title: GEO-138: treatment-associated_AML

value: female

tag: cytogenetics

tag: cebpa


title: GEO-137: primary_AML

tag: mrc

tag: fab

value: CRi


title: GEO-136: primary_AML

tag: ecog

tag: relapse


title: GEO-134: primary_AML

tag: wbc


title: XBP1_LKO_RNA-Seq_CT18_Rep1

description: Total RNA-seq

tag: strain

value: C57BJ/L6 background

tag: genotype

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)

value: Male

value: 12-16 weeks


title: XBP1_LKO_RNA-Seq_CT16_Rep2

description: Total RNA-seq

tag: gender

tag: age


title: GEO-133: primary_AML

value: del(7q)/monosomy 7

value: YES

tag: ldh


title: XBP1_LKO_RNA-Seq_CT14_Rep1

description: Total RNA-seq

tag: tissue

value: Liver

tag: time point


title: XBP1_LKO_RNA-Seq_CT16_Rep1

description: Total RNA-seq


title: GEO-132: primary_AML

tag: study

value: CN-AML

value: Intermediate

tag: haemoglobin


title: GEO-131: primary_AML

tag: diagnosis

value: Complex Cytogenetics

value: Adverse

tag: platelets


title: XBP1_LKO_RNA-Seq_CT12_Rep1

description: Total RNA-seq


title: GEO-130: primary_AML

tag: cytogenetics

tag: cebpa


title: XBP1_LKO_RNA-Seq_CT14_Rep2

description: Total RNA-seq


title: GEO-13: primary_AML

tag: mrc

tag: fab

value: dead


title: GEO-129: primary_AML

tag: ecog

tag: relapse

value: NO


title: XBP1_LKO_RNA-Seq_CT10_Rep1

description: Total RNA-seq

tag: strain


title: GEO-128: secondary_AML

value: favorable

value: CR

tag: wbc


title: XBP1_LKO_RNA-Seq_CT08_Rep2

description: Total RNA-seq

tag: genotype

tag: gender


title: GEO-127: primary_AML

value: male

value: alive

tag: ldh


title: Endothelial cells ApoE4/4 - rep6 [S30_44_F]

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

institute: Nestle Institute Of Health Sciences

data_processing:
Demultiplexing using BcltoFastQ (Illumina)
Alignment to the human genome (hs_GRCh38.p2) using STAR
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: csv file including raw counts for each sample (column) and each gene (row). The raw counts within genes were quantified by HTSeq using as annotation file GRCh38.80.gtf

source_name: Endothelial cells ApoE4/4

extract_protocol: For each well of frozen cells, RNA was extracted with the Agencourt RNAdvance Tissue kit (Beckman Coulter), quantified, and its quality verified on a Fragment Analyzer (Advanced Analytical).

treatment_protocol: Endothelial cells were cultured in 6 well plates for 3 days, washed once with ice-cold PBS and frozen at -80C until RNA extraction.

tag: genotype/variation

tag: cell type

value: iPSC-derived endothelial cells


title: XBP1_LKO_RNA-Seq_CT06_Rep2

description: Total RNA-seq

value: C57BJ/L6 background

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)

tag: age

tag: tissue

tag: time point


title: GEO-126: primary_AML

tag: study

tag: diagnosis

value: CRi

tag: haemoglobin

tag: platelets


title: GEO-125: primary_AML

tag: cytogenetics

tag: mrc

tag: fab

tag: cebpa


title: XBP1_LKO_RNA-Seq_CT06_Rep1

description: Total RNA-seq

tag: strain

value: Male

value: 12-16 weeks


title: XBP1_LKO_RNA-Seq_CT04_Rep2

description: Total RNA-seq

tag: genotype

value: Liver


title: Endothelial cells ApoE4/4 - rep5 [S29_44_E]


title: Endothelial cells ApoE4/4 - rep2 [S26_44_B]


title: Endothelial cells ApoE4/4 - rep1 [S25_44_A]


title: GEO-124: secondary_AML

tag: gender

value: CN-AML

tag: ecog

tag: relapse

value: YES

tag: wbc


title: XBP1_LKO_RNA-Seq_CT04_Rep1

description: Total RNA-seq

tag: age


title: XBP1_LKO_RNA-Seq_CT02_Rep2

description: Total RNA-seq

tag: tissue


title: GEO-123: primary_AML

value: Complex Cytogenetics

tag: ldh


title: XBP1_LKO_RNA-Seq_CT10_Rep2

description: Total RNA-seq

tag: time point


title: XBP1_LKO_RNA-Seq_CT12_Rep2

description: Total RNA-seq


title: Endothelial cells ApoE3/3 - rep4 [S34_33_D]

source_name: Endothelial cells ApoE3/3

tag: genotype/variation

tag: cell type


title: Endothelial cells ApoE3/3 - rep5 [S35_33_E]


title: XBP1_LKO_RNA-Seq_CT08_Rep1

description: Total RNA-seq


title: GEO-121: primary_AML

value: female

tag: study

tag: diagnosis

value: Intermediate

value: Adverse

tag: haemoglobin

tag: platelets


title: XBP1_LKO_RNA-Seq_CT02_Rep1

description: Total RNA-seq


title: Endothelial cells ApoE3/3 - rep3 [S33_33_C]


title: Endothelial cells ApoE3/3 - rep2 [S32_33_B]


title: GEO-120: primary_AML

tag: cytogenetics

tag: mrc

value: favorable

tag: fab

value: dead

value: NO

tag: cebpa


title: XBP1_LKO_RNA-Seq_CT00_Rep2

description: Total RNA-seq

tag: strain

tag: genotype

tag: gender


title: Endothelial cells ApoE3/3 - rep1 [S31_33_A]


title: Endothelial cells ApoE4/4 - rep4 [S28_44_D]


title: Endothelial cells ApoE4/4 - rep3 [S27_44_C]


title: Endothelial cells ApoE3/3 - rep6 [S36_33_F]


title: GEO-119: primary_AML

value: male

tag: ecog

value: alive

tag: relapse

tag: wbc


title: GEO-118: primary_AML

value: CR

tag: ldh


title: XBP1_LKO_RNA-Seq_CT00_Rep1

description: Total RNA-seq

value: C57BJ/L6 background

value: AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout)

tag: age

tag: tissue

tag: time point


title: WT_RNA-Seq_CT46_Rep2

description: Total RNA-seq

value: Xbp1 flx/flx (WT, wild-type)

value: Male


title: WT_RNA-Seq_CT46_Rep1

description: Total RNA-seq

value: 12-16 weeks

value: Liver


title: GEO-122: primary_AML

tag: study

tag: diagnosis

value: CN-AML

value: YES

value: CRi


title: FXS 69.5 neuron-1

city: Singapore

first: Kagistia

middle: Hana

last: Utami

address: 8A Biomedical Grove

country: Singapore

institute: Translational Laboratory in Genetic Medicine

description:
FXS Disease sample biological rep 1
FXS vs Control hiPSC normalized counts, Log2FC FXS vs Control hiPSC

data_processing:
RNA seq quantification directly from the reads with Salmon v0.9.1 19 using hg38 human reference genome.
Data was imported into R using tximport and analyzed for differentially expressed genes with DESeq2
Significant hits were identified using FDR <0.05 cut-off and divided into upregulated (Log2FC >0) and downregulated (Log2FC<0)
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: hiPSC-derived neurons

growth_protocol: neurons were differentiated from human NPCs-derived hiPSC, with a midbrain-patterning differentiation protocol

extract_protocol:
cells were harvested at the last day of differentiation (37 days in culture), total RNA was extracted by RNAeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell

value: 37 days neurons

tag: Sex

value: FXS disease


title: FXS 100.2 neuron-3

description:
FXS Disease sample biological rep 3
FXS vs Control hiPSC normalized counts, Log2FC FXS vs Control hiPSC


title: FXS 69.5 neuron-2

description:
FXS Disease sample biological rep 2
FXS vs Control hiPSC normalized counts, Log2FC FXS vs Control hiPSC


title: FXS 69.5 neuron-3


title: FXS 100.2 neuron-1