title: dge1_O04 RNA-seq of ReNcell VM treated with 10 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 10 uM ruxolitinib
barcode: GGAGGG batch: dge1

value: 10 uM ruxolitinib

value: ReNcell VM

value: ruxolitinib


title: dge1_O11 RNA-seq of ReNcell VM treated with 0.3 uM kw2449

status: Public on Jan 14 2021

type: SRA

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

country: USA

institute: Harvard Medical School

description:
RNA-seq of ReNcell VM treated with 0.3 uM kw2449
barcode: GGGGAC batch: dge1

library_source: transcriptomic

data_processing:
Raw RNA reads were aligned against the reference genome and quantified using the bcbio-nextgen single cell/DGE RNA-seq analysis pipeline (https://bcbio-nextgen.readthedocs.io/). The pipeline consists of the following steps:
Well barcodes and unique molecular identifiers (UMIs) were extracted from the first read. All reads not within the edit distance of a single nucleotide from a predefined well barcode were discarded.
Each extant read was quasialigned to the human transcriptome (version GRCh38) using RapMap.
Reads per well were counted using the UMIs, discarding reads originating from the same original RNA molecule with duplicate UMI, weighting multi-mapped reads by the number of transcripts they aligned to and collapsing transcript counts to gene level by summing. across all transcripts of a gene.
Counts were normalized using the size factor method in DESeq2. Replicates with fewer than 30k total counts were excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: deduplicated_counts.csv.gz: CSV file of UMI-deduplicated counts of all 765 samples with Ensembl gene IDs.
Supplementary_files_format_and_content: normalized_counts.csv.gz: CSV file of UMI-deduplicated and normalized counts of all 765 samples with HUGO gene symbols.

molecule: polyA RNA

organism: Homo sapiens

source_name: in-vitro differentiated neural and glial cells

growth_protocol: A multiwell cell dispenser (catalog# 5840300, Thermo Scientific,Waltham, MA) with standard tubing (catalog# 24072670, Thermo Scientific,Waltham, MA) was used to plate 2500 neural stem cells (ReNcell VM, catalog# SCC008, Millipore, Billerica, MA) into each well of a 384-well cell culture plate (Perkin Elmer, Waltham, MA). Neural stem cells where differentiated into mature neural cells for one week.

extract_protocol:
For RNA extraction, the cell lysate plate was thawed and centrifuged for 1 min at 1000 rpm. Using a BRAVO (Agilent, Santa Clara, CA) liquid handler, the lysate was mixed thoroughly before transferring 10 ul to a 384 well PCR plate. 28 ul of home-made Serapure SPRI beads (GE Healthcare Life Sciences, Marlborough, MA) were added directly to the lysate, mixed and incubated for 5 min. The plate was transferred to a magnetic rack and incubated for 5 min prior to removing the liquid to aggregate the beads. The beads were washed with 80% ethanol twice, allowed to dry for 1 min, 20 ul of nuclease free water was added per well, the plate was removed from the magnetic rack and the beads were thoroughly resuspended. Following a 5 min incubation, the plate was returned to the magnetic rack and incubated an additional 5 min before transferring the supernatant to a fresh PCR plate.
5 ul of the RNA was transferred to a separate plate containing RT master mix and 3’ and 5’ adapters for reverse transcription and template switching, and incubated for 90 min at 42°C. The cDNA was pooled and purified with a QIAquick PCR purification kit according to the manufacturer’s directions with the final elution in 21 ul of nuclease free water. This was followed by exonuclease I treatment for 30 min at 37°C that was stopped with a 20 min incubation at 80°C. The cDNA was then amplified using the Advantage 2 PCR Enzyme System (Takara, Fremont, CA) for 6 cycles, and purified using AMPure XP magnetic beads (Beckman Coulter Genomics, Chaska, MN). Library preparation was performed using a Nextera XT DNA kit (Illumina, San Diego, CA) on 5 reactions per sample following the manufacturer’s instructions, amplified 12 cycles, and purified with AMPure XP magnetic beads (Beckman Coulter Genomics, Chaska, MN). The sample was then quantified by qPCR and sequenced on a single Illumina NextSeq run with 75bp paired end reads at the Harvard University Bauer Core Facility.

treatment_protocol: Differentiated cells were treated with compounds (Table 1) or DMSO using a D300 Digital Dispenser (Hewlett-Packard, Palo Alto, CA). D300 software was used to randomize dispensation of compounds. After 24 hours, the cells were washed once with PBS using an EL405x plate washer (BioTek, Winooski, VT) leaving 5-10 ul of PBS behind in each well. 10 ul of 1X TCL lysis buffer (catalog# 1070498, Qiagen, Hilden, Germany) with 1% (v/v) ß-mercaptoethanol was added per well, and the plates were stored at -80°C until the RNA extraction was performed.

tag: treatment


title: dge1_O01 RNA-seq of ReNcell VM treated with 3 uM torin1

description:
RNA-seq of ReNcell VM treated with 3 uM torin1
barcode: GCTCGC batch: dge1

value: in-vitro differentiated neural and glial cells

value: 3 uM torin1


title: dge1_O03 RNA-seq of ReNcell VM treated with 1 uM barasertib

description:
RNA-seq of ReNcell VM treated with 1 uM barasertib
barcode: GGAGCC batch: dge1

value: 1 uM barasertib

value: barasertib


title: dge1_O02 RNA-seq of ReNcell VM treated with 3 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 3 uM ldn-193189
barcode: GCTGCC batch: dge1


title: dge1_N24 RNA-seq of ReNcell VM treated with 3 uM torin1

description:
RNA-seq of ReNcell VM treated with 3 uM torin1
barcode: GCTCCG batch: dge1


title: dge1_N23 RNA-seq of ReNcell VM treated with 1 uM rotenone

description:
RNA-seq of ReNcell VM treated with 1 uM rotenone
barcode: GCGTGG batch: dge1

value: 1 uM rotenone

value: rotenone


title: dge1_N22 RNA-seq of ReNcell VM treated with 10 uM torin1

description:
RNA-seq of ReNcell VM treated with 10 uM torin1
barcode: GCGGGA batch: dge1

value: 10 uM torin1


title: dge1_P13 RNA-seq of ReNcell VM treated with 10 uM torin1

description:
RNA-seq of ReNcell VM treated with 10 uM torin1
barcode: GGTCCC batch: dge1


title: dge1_N13 RNA-seq of ReNcell VM treated with 1 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 1 uM pf04217903
barcode: GCCCCT batch: dge1


title: dge1_O06 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: GGCGAG batch: dge1

value: dmso


title: dge1_N20 RNA-seq of ReNcell VM treated with 0.3 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 0.3 uM r 59-022
barcode: GCGCGT batch: dge1


title: dge1_N16 RNA-seq of ReNcell VM treated with 3 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 3 uM r 59-022
barcode: GCCGGT batch: dge1


title: dge1_O05 RNA-seq of ReNcell VM treated with 1 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 1 uM fedratinib
barcode: GGCCAC batch: dge1

value: 1 uM fedratinib

value: fedratinib


title: dge1_N15 RNA-seq of ReNcell VM treated with 3 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 3 uM nvp-tae684
barcode: GCCGCA batch: dge1

value: 3 uM nvp-tae684


title: dge1_N19 RNA-seq of ReNcell VM treated with 0.3 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 0.3 uM gsk1059615
barcode: GCGCCA batch: dge1


title: dge1_N11 RNA-seq of ReNcell VM treated with 0.3 uM alisertib

description:
RNA-seq of ReNcell VM treated with 0.3 uM alisertib
barcode: GCAGGC batch: dge1

value: 0.3 uM alisertib

value: alisertib


title: dge1_N17 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: GCCTGC batch: dge1


title: dge1_N07 RNA-seq of ReNcell VM treated with 0.3 uM torin1

description:
RNA-seq of ReNcell VM treated with 0.3 uM torin1
barcode: GACGGG batch: dge1

value: 0.3 uM torin1


title: dge1_N09 RNA-seq of ReNcell VM treated with 1 uM barasertib

description:
RNA-seq of ReNcell VM treated with 1 uM barasertib
barcode: GAGGGC batch: dge1


title: dge1_N10 RNA-seq of ReNcell VM treated with 1 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 1 uM pazopanib
barcode: GCACCC batch: dge1

value: 1 uM pazopanib

value: pazopanib


title: dge1_N08 RNA-seq of ReNcell VM treated with 0.3 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 0.3 uM bortezomib
barcode: GAGCCC batch: dge1

value: 0.3 uM bortezomib

value: ReNcell VM

value: bortezomib


title: dge1_N03 RNA-seq of ReNcell VM treated with 1 uM mg-132

description:
RNA-seq of ReNcell VM treated with 1 uM mg-132
barcode: CTCCGC batch: dge1

value: in-vitro differentiated neural and glial cells


title: dge1_N06 RNA-seq of ReNcell VM treated with 10 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 10 uM nvp-tae684
barcode: GACCCG batch: dge1

value: 10 uM nvp-tae684


title: dge1_N04 RNA-seq of ReNcell VM treated with 3 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 3 uM pazopanib
barcode: CTCGGG batch: dge1

value: 3 uM pazopanib


title: dge1_N01 RNA-seq of ReNcell VM treated with 10 uM chitosan

description:
RNA-seq of ReNcell VM treated with 10 uM chitosan
barcode: CGTCGC batch: dge1

value: 10 uM chitosan

value: chitosan


title: dge1_N02 RNA-seq of ReNcell VM treated with 3 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 3 uM (+)-jq1
barcode: CGTGCC batch: dge1


title: dge1_M24 RNA-seq of ReNcell VM treated with 10 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 10 uM ruxolitinib
barcode: GCGTCC batch: dge1

value: 10 uM ruxolitinib

value: ruxolitinib


title: dge1_N12 RNA-seq of ReNcell VM treated with 3 uM alisertib

description:
RNA-seq of ReNcell VM treated with 3 uM alisertib
barcode: GCCACC batch: dge1

value: 3 uM alisertib


title: dge1_N21 RNA-seq of ReNcell VM treated with 1 uM barasertib

description:
RNA-seq of ReNcell VM treated with 1 uM barasertib
barcode: GCGGCT batch: dge1

value: 1 uM barasertib

value: barasertib


title: dge1_M20 RNA-seq of ReNcell VM treated with 10 uM mg-132

description:
RNA-seq of ReNcell VM treated with 10 uM mg-132
barcode: GCGCAC batch: dge1


title: dge1_N18 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: GCGACG batch: dge1

value: dmso


title: dge1_N14 RNA-seq of ReNcell VM treated with 0.3 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 0.3 uM pf04217903
barcode: GCCCGA batch: dge1


title: dge1_M23 RNA-seq of ReNcell VM treated with 10 uM metformin

description:
RNA-seq of ReNcell VM treated with 10 uM metformin
barcode: GCGGTC batch: dge1

value: 10 uM metformin

value: metformin


title: dge1_M21 RNA-seq of ReNcell VM treated with 0.3 uM kw2449

description:
RNA-seq of ReNcell VM treated with 0.3 uM kw2449
barcode: GCGCTG batch: dge1


title: dge1_M19 RNA-seq of ReNcell VM treated with 10 uM sb202190

description:
RNA-seq of ReNcell VM treated with 10 uM sb202190
barcode: GCGAGC batch: dge1


title: dge1_M18 RNA-seq of ReNcell VM treated with 3 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 3 uM pf04217903
barcode: GCCTCG batch: dge1


title: dge1_N05 RNA-seq of ReNcell VM treated with 1 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 1 uM plx-4720
barcode: CTGGGC batch: dge1


title: dge1_M17 RNA-seq of ReNcell VM treated with 1 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 1 uM plx-4720
barcode: GCCGTG batch: dge1


title: dge1_M16 RNA-seq of ReNcell VM treated with 3 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 3 uM zm-447439
barcode: GCCGAC batch: dge1


title: dge1_M15 RNA-seq of ReNcell VM treated with 3 uM kw2449

description:
RNA-seq of ReNcell VM treated with 3 uM kw2449
barcode: GCCCTC batch: dge1


title: dge1_M14 RNA-seq of ReNcell VM treated with 3 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 3 uM hg-9-91-01
barcode: GCCCAG batch: dge1


title: dge1_M12 RNA-seq of ReNcell VM treated with 3 uM r 59949

description:
RNA-seq of ReNcell VM treated with 3 uM r 59949
barcode: GCAGCG batch: dge1


title: dge1_M11 RNA-seq of ReNcell VM treated with 10 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 10 uM ruxolitinib
barcode: GCACGG batch: dge1


title: dge1_M13 RNA-seq of ReNcell VM treated with 0.3 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 0.3 uM gsk1070916
barcode: GCCAGG batch: dge1


title: dge1_M10 RNA-seq of ReNcell VM treated with 3 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 3 uM pazopanib
barcode: GAGGCG batch: dge1

value: pazopanib


title: dge1_M09 RNA-seq of ReNcell VM treated with 0.3 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM tofacitinib
barcode: GAGCGG batch: dge1

value: 0.3 uM tofacitinib

value: tofacitinib


title: dge1_M06 RNA-seq of ReNcell VM treated with 0.3 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 0.3 uM nvp-tae684
barcode: CTGGCG batch: dge1

value: 0.3 uM nvp-tae684

value: ReNcell VM


title: dge1_M08 RNA-seq of ReNcell VM treated with 0.3 uM alisertib

description:
RNA-seq of ReNcell VM treated with 0.3 uM alisertib
barcode: GACGCC batch: dge1

value: in-vitro differentiated neural and glial cells

value: 0.3 uM alisertib

value: alisertib


title: dge1_M07 RNA-seq of ReNcell VM treated with 10 uM kw2449

description:
RNA-seq of ReNcell VM treated with 10 uM kw2449
barcode: GACCGC batch: dge1


title: dge1_M05 RNA-seq of ReNcell VM treated with 1 uM metformin

description:
RNA-seq of ReNcell VM treated with 1 uM metformin
barcode: CTGCGG batch: dge1

value: 1 uM metformin


title: dge1_M02 RNA-seq of ReNcell VM treated with 10 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 10 uM r 59-022
barcode: CGTCCG batch: dge1


title: dge1_M03 RNA-seq of ReNcell VM treated with 0.3 uM barasertib

description:
RNA-seq of ReNcell VM treated with 0.3 uM barasertib
barcode: CGTGGG batch: dge1

value: 0.3 uM barasertib


title: dge1_M04 RNA-seq of ReNcell VM treated with 1 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 1 uM bortezomib
barcode: CTCCCG batch: dge1

value: 1 uM bortezomib

value: bortezomib


title: dge1_L23 RNA-seq of ReNcell VM treated with 0.3 uM a443654

description:
RNA-seq of ReNcell VM treated with 0.3 uM a443654
barcode: CGGGTC batch: dge1


title: dge1_M01 RNA-seq of ReNcell VM treated with 0.3 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 0.3 uM gsk1070916
barcode: CGGTGG batch: dge1


title: dge1_M22 RNA-seq of ReNcell VM treated with 3 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 3 uM nvp-tae684
barcode: GCGGAG batch: dge1

value: 3 uM nvp-tae684


title: dge1_L21 RNA-seq of ReNcell VM treated with 1 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 1 uM ruxolitinib
barcode: CGGCTG batch: dge1

value: 1 uM ruxolitinib

value: ruxolitinib


title: dge1_L20 RNA-seq of ReNcell VM treated with 0.3 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM cabozantinib
barcode: CGGCAC batch: dge1

value: 0.3 uM cabozantinib

value: cabozantinib


title: dge1_L19 RNA-seq of ReNcell VM treated with 10 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 10 uM plx-4720
barcode: CGGAGC batch: dge1


title: dge1_L18 RNA-seq of ReNcell VM treated with 10 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 10 uM pazopanib
barcode: CGCTCG batch: dge1

value: 10 uM pazopanib

value: pazopanib


title: dge1_L14 RNA-seq of ReNcell VM treated with 0.3 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 0.3 uM pazopanib
barcode: CGCCAG batch: dge1

value: 0.3 uM pazopanib


title: dge1_L15 RNA-seq of ReNcell VM treated with 0.3 uM barasertib

description:
RNA-seq of ReNcell VM treated with 0.3 uM barasertib
barcode: CGCCTC batch: dge1

value: barasertib


title: dge1_L16 RNA-seq of ReNcell VM treated with 0.3 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 0.3 uM gsk1070916
barcode: CGCGAC batch: dge1

value: ReNcell VM


title: dge1_L13 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: CGCAGG batch: dge1

value: in-vitro differentiated neural and glial cells

value: dmso


title: dge1_L24 RNA-seq of ReNcell VM treated with 1 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 1 uM nvp-tae684
barcode: CGGTCC batch: dge1

value: 1 uM nvp-tae684


title: dge1_L12 RNA-seq of ReNcell VM treated with 1 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 1 uM gsk1059615
barcode: CGAGCG batch: dge1


title: dge1_L05 RNA-seq of ReNcell VM treated with 10 uM chitosan

description:
RNA-seq of ReNcell VM treated with 10 uM chitosan
barcode: CCGCAG batch: dge1

value: 10 uM chitosan

value: chitosan


title: dge1_L07 RNA-seq of ReNcell VM treated with 3 uM bx-912

description:
RNA-seq of ReNcell VM treated with 3 uM bx-912
barcode: CCGGGT batch: dge1


title: dge1_L06 RNA-seq of ReNcell VM treated with 0.3 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM tofacitinib
barcode: CCGCGA batch: dge1

value: 0.3 uM tofacitinib

value: tofacitinib


title: dge1_L08 RNA-seq of ReNcell VM treated with 10 uM torin1

description:
RNA-seq of ReNcell VM treated with 10 uM torin1
barcode: CCGGTG batch: dge1

value: 10 uM torin1


title: dge1_L11 RNA-seq of ReNcell VM treated with 1 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 1 uM r 59-022
barcode: CGACGG batch: dge1


title: dge1_L02 RNA-seq of ReNcell VM treated with 1 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 1 uM zm-447439
barcode: CCCCCA batch: dge1


title: dge1_L10 RNA-seq of ReNcell VM treated with 3 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 3 uM gsk1059615
barcode: CCTGCG batch: dge1


title: dge1_L01 RNA-seq of ReNcell VM treated with 10 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 10 uM (+)-jq1
barcode: CCCCAC batch: dge1


title: dge1_L22 RNA-seq of ReNcell VM treated with 0.3 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 0.3 uM pf04217903
barcode: CGGGAG batch: dge1


title: dge1_L04 RNA-seq of ReNcell VM treated with 0.3 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 0.3 uM ldn-193189
barcode: CCCGGA batch: dge1


title: dge1_L03 RNA-seq of ReNcell VM treated with 1 uM alisertib

description:
RNA-seq of ReNcell VM treated with 1 uM alisertib
barcode: CCCGAG batch: dge1

value: 1 uM alisertib

value: alisertib


title: dge1_K24 RNA-seq of ReNcell VM treated with 0.3 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 0.3 uM ldn-193189
barcode: CGGGGA batch: dge1


title: dge1_K22 RNA-seq of ReNcell VM treated with 3 uM a443654

description:
RNA-seq of ReNcell VM treated with 3 uM a443654
barcode: CGGCGT batch: dge1


title: dge1_L17 RNA-seq of ReNcell VM treated with 3 uM brivanib

description:
RNA-seq of ReNcell VM treated with 3 uM brivanib
barcode: CGCGTG batch: dge1

value: 3 uM brivanib

value: brivanib


title: dge1_K21 RNA-seq of ReNcell VM treated with 3 uM r 59949

description:
RNA-seq of ReNcell VM treated with 3 uM r 59949
barcode: CGGCCA batch: dge1


title: dge1_K18 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: CGCGGT batch: dge1


title: dge1_K19 RNA-seq of ReNcell VM treated with 1 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 1 uM tofacitinib
barcode: CGCTGC batch: dge1

value: 1 uM tofacitinib


title: dge1_K20 RNA-seq of ReNcell VM treated with dsRNA

description:
RNA-seq of ReNcell VM treated with dsRNA
barcode: CGGACG batch: dge1

value: dsRNA

tag: stimulant


title: dge1_K17 RNA-seq of ReNcell VM treated with 10 uM alisertib

description:
RNA-seq of ReNcell VM treated with 10 uM alisertib
barcode: CGCGCA batch: dge1

value: 10 uM alisertib


title: dge1_K12 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: CGACCC batch: dge1


title: dge1_K10 RNA-seq of ReNcell VM treated with 3 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 3 uM zm-447439
barcode: CCGTGC batch: dge1


title: dge1_K14 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: CGCACC batch: dge1


title: dge1_K16 RNA-seq of ReNcell VM treated with 0.3 uM metformin

description:
RNA-seq of ReNcell VM treated with 0.3 uM metformin
barcode: CGCCGA batch: dge1

value: 0.3 uM metformin

value: metformin


title: dge1_K13 RNA-seq of ReNcell VM treated with 0.3 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 0.3 uM bortezomib
barcode: CGAGGC batch: dge1

value: in-vitro differentiated neural and glial cells

value: 0.3 uM bortezomib

value: ReNcell VM

value: bortezomib


title: dge1_K23 RNA-seq of ReNcell VM treated with 3 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 3 uM tofacitinib
barcode: CGGGCT batch: dge1

value: 3 uM tofacitinib


title: dge1_K09 RNA-seq of ReNcell VM treated with 1 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 1 uM gsk1070916
barcode: CCGTCG batch: dge1


title: dge1_K06 RNA-seq of ReNcell VM treated with 10 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 10 uM ldn-193189
barcode: CCGAGG batch: dge1


title: dge1_K03 RNA-seq of ReNcell VM treated with 0.3 uM metformin

description:
RNA-seq of ReNcell VM treated with 0.3 uM metformin
barcode: CCCCGT batch: dge1


title: dge1_J21 RNA-seq of ReNcell VM treated with 10 uM fccp

description:
RNA-seq of ReNcell VM treated with 10 uM fccp
barcode: CAGCGC batch: dge1

value: 10 uM fccp

value: fccp


title: dge1_J22 RNA-seq of ReNcell VM treated with 1 uM torin1

description:
RNA-seq of ReNcell VM treated with 1 uM torin1
barcode: CAGGCC batch: dge1

value: 1 uM torin1


title: dge1_K02 RNA-seq of ReNcell VM treated with 3 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 3 uM gsk1059615
barcode: CCCAGC batch: dge1


title: dge1_K04 RNA-seq of ReNcell VM treated with 0.3 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 0.3 uM zm-447439
barcode: CCCCTG batch: dge1


title: dge1_J23 RNA-seq of ReNcell VM treated with 10 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 10 uM hg-9-91-01
barcode: CCACGC batch: dge1


title: dge1_K15 RNA-seq of ReNcell VM treated with 1 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 1 uM nvp-tae684
barcode: CGCCCT batch: dge1

value: 1 uM nvp-tae684


title: dge1_J16 RNA-seq of ReNcell VM treated with 10 uM kw2449

description:
RNA-seq of ReNcell VM treated with 10 uM kw2449
barcode: AGCGCC batch: dge1


title: dge1_J24 RNA-seq of ReNcell VM treated with 10 uM alisertib

description:
RNA-seq of ReNcell VM treated with 10 uM alisertib
barcode: CCAGGG batch: dge1

value: alisertib


title: dge1_J18 RNA-seq of ReNcell VM treated with 10 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 10 uM fedratinib
barcode: AGGGCG batch: dge1

value: 10 uM fedratinib

value: fedratinib


title: dge1_K07 RNA-seq of ReNcell VM treated with 1 uM bx-912

description:
RNA-seq of ReNcell VM treated with 1 uM bx-912
barcode: CCGGAC batch: dge1


title: dge1_J19 RNA-seq of ReNcell VM treated with 10 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 10 uM zm-447439
barcode: CACCGG batch: dge1


title: dge1_J20 RNA-seq of ReNcell VM treated with 1 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 1 uM pazopanib
barcode: CACGCG batch: dge1

value: 1 uM pazopanib

value: pazopanib


title: dge1_J17 RNA-seq of ReNcell VM treated with 10 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 10 uM pazopanib
barcode: AGGCGG batch: dge1

value: 10 uM pazopanib


title: dge1_K11 RNA-seq of ReNcell VM treated with 3 uM bx-912

description:
RNA-seq of ReNcell VM treated with 3 uM bx-912
barcode: CCTGGC batch: dge1


title: dge1_J14 RNA-seq of ReNcell VM treated with 10 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 10 uM pha-665752
barcode: ACGGCC batch: dge1


title: dge1_J15 RNA-seq of ReNcell VM treated with 10 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 10 uM pha-665752
barcode: AGCCGC batch: dge1


title: dge1_J10 RNA-seq of ReNcell VM treated with 10 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 10 uM gsk1059615
barcode: GGACCA batch: dge1


title: dge1_J08 RNA-seq of ReNcell VM treated with 0.3 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 0.3 uM zm-447439
barcode: TTTGGC batch: dge1


title: dge1_J11 RNA-seq of ReNcell VM treated with 1 uM chitosan

description:
RNA-seq of ReNcell VM treated with 1 uM chitosan
barcode: ACCCGG batch: dge1

value: 1 uM chitosan

value: chitosan


title: dge1_J07 RNA-seq of ReNcell VM treated with 0.3 uM sb202190

description:
RNA-seq of ReNcell VM treated with 0.3 uM sb202190
barcode: TTGTCC batch: dge1

value: in-vitro differentiated neural and glial cells


title: dge1_J09 RNA-seq of ReNcell VM treated with 1 uM chitosan

description:
RNA-seq of ReNcell VM treated with 1 uM chitosan
barcode: CTCTCC batch: dge1


title: dge1_K01 RNA-seq of ReNcell VM treated with 0.3 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM cabozantinib
barcode: CCCACG batch: dge1

value: 0.3 uM cabozantinib

value: cabozantinib


title: dge1_J12 RNA-seq of ReNcell VM treated with 3 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 3 uM (+)-jq1
barcode: ACCGCG batch: dge1

value: ReNcell VM


title: dge1_K05 RNA-seq of ReNcell VM treated with 3 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 3 uM plx-4720
barcode: CCCTGG batch: dge1


title: dge1_J06 RNA-seq of ReNcell VM treated with 1 uM kw2449

description:
RNA-seq of ReNcell VM treated with 1 uM kw2449
barcode: TCGAAG batch: dge1


title: WT/a6Low/CD34-,replica3

first: Raul

last: Mostoslavsky

address: 185 Cambridge street, CPZN 4100

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Quality control: PICARD, Version: 1.100
Alignment: STAR, version 2.3.0
Allelic assignment: Reads were aligned separately to parental genomes. Unambiguous reads were then assigned to parent-specific alleles according to the method in Engström PG, et al. (2013) Nature Methods.
Read counts per gene: HTSeq, version 0.6.0 (unstranded) using Ensembl release 67 transcript annotations
Genome_build: mm9
Supplementary_files_format_and_content: text file contains HTSeq-calculated counts

molecule: total RNA

organism: Mus musculus

source_name: Mouse Skin tumor cells

extract_protocol:
FACS-isolated tumor cells were directly collected into RNA isolation buffer provided in the kit (Clontech, #740902.50). RNA isolation was conducted by the manufacturer's instruction.
Library construction was performed using SMART-Seq v4 Ultra Low Input RNA kit to produce cDNA (Clontech, #634888). Generation of final library was completed by using Low Input Library Prep Kit v2 (Clontech, #634899). The cDNA input amount was 10ng total. 7 cycles of PCR was performed for PCR amplification. Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit. Libraries were quantified using the Library Quantification kit (Kapa Biosystems, #KK4828) and the BioRad CFX96 instrument.

treatment_protocol: All the samples had been under DMBA/TPA treatment for more than 24 weeks to induce skin tumors.

tag: strain

tag: cell type

value: Skin tumor cells

tag: genotype

value: WT

tag: a6 status

tag: cd34+ status


title: dge1_J05 RNA-seq of ReNcell VM treated with 0.3 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM fedratinib
barcode: TCCAAC batch: dge1

value: 0.3 uM fedratinib


title: WT/a6High/CD34-,replica3


title: dge1_J13 RNA-seq of ReNcell VM treated with 3 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 3 uM pf04217903
barcode: ACGCGC batch: dge1


title: WT/a6High/CD34+,replica3


title: dge1_J03 RNA-seq of ReNcell VM treated with dsRNA + lipofectamine

description:
RNA-seq of ReNcell VM treated with dsRNA + lipofectamine
barcode: GTCAAG batch: dge1

value: dsRNA + lipofectamine


title: dge1_J04 RNA-seq of ReNcell VM treated with 3 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 3 uM hg-9-91-01
barcode: GTGACT batch: dge1


title: dge1_J02 RNA-seq of ReNcell VM treated with 1 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 1 uM plx-4720
barcode: GGCAAT batch: dge1


title: WT/a6High/CD34+,replica2


title: dge1_K08 RNA-seq of ReNcell VM treated with 1 uM torin1

description:
RNA-seq of ReNcell VM treated with 1 uM torin1
barcode: CCGGCA batch: dge1

value: 1 uM torin1


title: dge1_I23 RNA-seq of ReNcell VM treated with 10 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 10 uM fedratinib
barcode: CAGGGG batch: dge1


title: dge1_J01 RNA-seq of ReNcell VM treated with 1 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 1 uM pha-665752
barcode: GGACAT batch: dge1


title: KO/a6High/CD34-, replica2

value: SIRT6 KO (K14-cre; SIRT6 flox/flox)


title: KO/a6High/CD34+, replica2


title: WT/a6Low/CD34-,replica1


title: dge1_I18 RNA-seq of ReNcell VM treated with 10 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 10 uM nvp-tae684
barcode: AGGCCC batch: dge1

value: 10 uM nvp-tae684


title: WT/a6High/CD34+,replica1


title: WT/a6High/CD34-,replica2


title: dge1_I24 RNA-seq of ReNcell VM treated with 0.3 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 0.3 uM pazopanib
barcode: CCACCG batch: dge1

value: 0.3 uM pazopanib


title: KO/a6Low/CD34-,replica2


title: dge1_I22 RNA-seq of ReNcell VM treated with 0.3 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 0.3 uM ldn-193189
barcode: CAGCCG batch: dge1


title: dge1_I21 RNA-seq of ReNcell VM treated with 10 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 10 uM bortezomib
barcode: CACGGC batch: dge1

value: 10 uM bortezomib

value: bortezomib


title: WT/a6High/CD34-,replica1


title: dge1_I17 RNA-seq of ReNcell VM treated with 3 uM entinostat

description:
RNA-seq of ReNcell VM treated with 3 uM entinostat
barcode: AGCGGG batch: dge1

value: 3 uM entinostat

value: entinostat


title: KO/a6High/CD34+, replica1


title: KO/a6High/CD34-, replica1


title: dge1_I15 RNA-seq of ReNcell VM treated with 10 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 10 uM (+)-jq1
barcode: ACGGGG batch: dge1


title: KO/a6Low/CD34-,replica1


title: dge1_I16 RNA-seq of ReNcell VM treated with 10 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 10 uM nvp-tae684
barcode: AGCCCG batch: dge1


title: AH-S4_S4_L001_R1_001

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

library_source: genomic

data_processing:
The reads were mapped to the CRISPR GeCKO B sgRNA library and raw reads for each sgRNA were counted using the MAGeCK pipeline.
sgRNA enrichment was determined using the MAGeCK-MLE analysis pipeline.
Supplementary_files_format_and_content: Mapped reads counts

molecule: genomic DNA

source_name: A549 human lung epithelial cell line

growth_protocol: A549 cells maintained throughout in complete growth media.

extract_protocol:
Cells were sorted via flow cytometry, genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers. PCR amplified libraries were generated with independent barcodes to allow multiplexing.

treatment_protocol: Cells were transduced with the GeCKO B sgRNA library, incubated for 48 h, and collected.

tag: gecko b sgrna library transduction

value: GeCKO B sgRNA library transduced

tag: protocol(interferon treated, sorted, and cultured)

value: IFN treated and sorted (Sort Control 2)

tag: cultured post treatment

value: not cultured post IFN treatment


title: AH-S3_S3_L001_R1_001

value: IFN treated and sorted (Sort Control 1)


title: dge1_I13 RNA-seq of ReNcell VM treated with 3 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 3 uM ldn-193189
barcode: ACCGGC batch: dge1

value: in-vitro differentiated neural and glial cells

value: ReNcell VM


title: dge1_I12 RNA-seq of ReNcell VM treated with 1 uM fccp

description:
RNA-seq of ReNcell VM treated with 1 uM fccp
barcode: ACCCCC batch: dge1

value: 1 uM fccp

value: fccp


title: dge1_I19 RNA-seq of ReNcell VM treated with 3 uM a443654

description:
RNA-seq of ReNcell VM treated with 3 uM a443654
barcode: AGGGGC batch: dge1


title: WT/a6Low/CD34-,replica2

value: Skin tumor cells

value: WT


title: dge1_I14 RNA-seq of ReNcell VM treated with 3 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 3 uM ldn-193189
barcode: ACGCCG batch: dge1


title: NH03-Alfie3_S3_L001_R1_001

treatment_protocol: Cells were transduced with the GeCKO B sgRNA library, incubated for 72 h, then treated with interferon alpha for 6 h before washout and further culturing for 72 h.

value: IFN treated and sorted (Experimental Replicate 4)

value: cultured post IFN treatment


title: NH02-Alfie2_S2_L001_R1_001

value: IFN treated and sorted (Experimental Replicate 3)


title: dge1_I20 RNA-seq of ReNcell VM treated with 1 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 1 uM cabozantinib
barcode: CACCCC batch: dge1

value: 1 uM cabozantinib

value: cabozantinib


title: dge1_I08 RNA-seq of ReNcell VM treated with 0.3 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 0.3 uM pha-665752
barcode: TTCCTC batch: dge1


title: dge1_I09 RNA-seq of ReNcell VM treated with 0.3 uM barasertib

description:
RNA-seq of ReNcell VM treated with 0.3 uM barasertib
barcode: CCAACC batch: dge1

value: 0.3 uM barasertib

value: barasertib


title: dge1_I10 RNA-seq of ReNcell VM treated with 3 uM sb202190

description:
RNA-seq of ReNcell VM treated with 3 uM sb202190
barcode: CCTTCC batch: dge1


title: dge1_I11 RNA-seq of ReNcell VM treated with 1 uM kw2449

description:
RNA-seq of ReNcell VM treated with 1 uM kw2449
barcode: GTACCG batch: dge1


title: dge1_I07 RNA-seq of ReNcell VM treated with 0.3 uM torin1

description:
RNA-seq of ReNcell VM treated with 0.3 uM torin1
barcode: TCTGCA batch: dge1

value: 0.3 uM torin1


title: AH-S5_S5_L001_R1_001

value: GeCKO B sgRNA library transduced

value: IFN treated and sorted (Experimental Replicate 1)


title: WT + Mycobactin rep2

city: Winnipeg

first: Kangmin

last: Duan

state: MB

address: 66 Chancellors Cir

country: Canada

institute: University of Manitoba

data_processing:
After RNA-Sequencing, the obtained raw data were filtered according to the following standards: 1) removing reads with ≥ 10 % unidentified nucleotides (N); 2) removing reads with > 50 % bases having Phred quality scores of ≤ 20; 3) removing reads aligned to the barcode adapter using FASTP (https://github.com/OpenGene/fastp).
Quality trimmed reads were aligned using Bowtie2 (Langmead and Salzberg, 2012)  (version 2.2.8) to the P. aeruginosa PAO1 reference genome to identify known genes and calculated gene expression by RSEM (Li and Dewey, 2011).
The gene expression level was calculated and further normalized by using the fragments per kb of transcript per million (FPKM) mapped reads method to eliminate the influence of different gene lengths and amount of sequencing data on the calculation of gene expression.
The edgeR package (http://www.r-project.org/) was used to identify differentially expressed genes (DEGs) across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05.
Go terms and KEGG pathway were defined as being significantly enriched when the q value ≤ 0.05.
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: FPKM, counts

organism: Pseudomonas aeruginosa

source_name: WT + Mycobactin

growth_protocol: M9 medium

extract_protocol:
Strains were grown overnight at 37 °C followed by sub-culturing into fresh medium and grown to mid-exponential phase. Total RNA was extracted by TRIzol-based method (Life Technologies, CA, USA). In brief, the cultures were centrifuged at 12, 000 g for 5 minutes. The supernatant was discarded, cell pellets were resuspended in 1 ml of TRIzol and then incubated at room temperature for 5 minutes to permit complete dissociation of nucleoproteins complex. Followed by adding 0.2 ml chloroform into the tube and mix well, the samples were centrifuged (12, 000 g at 4 °C for 15 minutes) to form three layers. The upper aqueous phase was transferred to a fresh tube and added by 0.5 ml cold isopropanol to precipitate RNA. After centrifugation, the supernatant was removed, and the pellet was suspended in 1 ml 75% ethanol. Samples were centrifuged and the supernatant was discarded, air-dried RNA pellet was resolved in 50 µL RNase-free Water.
RNA integrity was measured using Bioanalyzer 2100 (Agilent, Santa Clara, CA) and rRNA was removed from 1 mg of total RNA with Ribo-Zero Magnetic Gold Kit (Epicentre Biotechnologies, Madison, WI, USA). To construct the RNA-Seq library, TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) was used. rRNA-depleted RNA was fragmented into small pieces using Elute Prime Fragment Mix. First-strand cDNA was synthesized with First Strand Master Mix and Super Script II reverse transcriptase (Invitrogen, Carlsbad, CA, USA). Following purification by Agencourt RNAClean XP beads (Beckman Coulter, CA, USA), the second-strand cDNA library was synthesized using Second Strand Master Mix and dATP, dGTP, dCTP, dUTP mix. Purified fragmented cDNA was end repaired (30 minutes at 37 °C) prior to ligating sequencing adapters. Amplified RNA-Seq libraries were purified by using AMPureXP Beads.

treatment_protocol: grow until mid-exponential phase in M9 with/without Mycobactin J

tag: genotype/variation

value: wild type

value: Mycobactin J


title: femI-KO +Mycobactin rep1

source_name: femI-KO +Mycobactin

value: femI deletion mutant


title: dge1_I06 RNA-seq of ReNcell VM treated with 0.3 uM brivanib

description:
RNA-seq of ReNcell VM treated with 0.3 uM brivanib
barcode: TAGTGG batch: dge1

value: in-vitro differentiated neural and glial cells

value: 0.3 uM brivanib

value: ReNcell VM

value: brivanib


title: femI-KO +Mycobactin rep2


title: dge1_I05 RNA-seq of ReNcell VM treated with 3 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 3 uM gsk1070916
barcode: GTTCGA batch: dge1


title: dge1_I03 RNA-seq of ReNcell VM treated with 0.3 uM brivanib

description:
RNA-seq of ReNcell VM treated with 0.3 uM brivanib
barcode: GGGATT batch: dge1


title: WT rep1

source_name: WT


title: dge1_I02 RNA-seq of ReNcell VM treated with 1 uM kw2449

description:
RNA-seq of ReNcell VM treated with 1 uM kw2449
barcode: GCTTAC batch: dge1


title: WT + Mycobactin rep1


title: AH-S1_S1_L001_R1_001

value: IFN treated and sorted (Experimental Replicate 2)


title: dge1_I01 RNA-seq of ReNcell VM treated with 10 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 10 uM cabozantinib
barcode: GCTAGA batch: dge1

value: 10 uM cabozantinib


title: dge1_H24 RNA-seq of ReNcell VM treated with 1 uM a443654

description:
RNA-seq of ReNcell VM treated with 1 uM a443654
barcode: GATCGT batch: dge1


title: dge1_H22 RNA-seq of ReNcell VM treated with 3 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 3 uM fedratinib
barcode: CGATTG batch: dge1

value: 3 uM fedratinib

value: fedratinib


title: dge1_H21 RNA-seq of ReNcell VM treated with 10 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 10 uM cabozantinib
barcode: CGACTT batch: dge1

value: cabozantinib


title: dge1_H19 RNA-seq of ReNcell VM treated with 10 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 10 uM gsk1059615
barcode: CATCAG batch: dge1


title: NH01-Alfie1_S1_L001_R1_001

value: Not IFN treated and not sorted (Transduction Control 2)

value: not cultured post IFN treatment


title: dge1_H18 RNA-seq of ReNcell VM treated with 0.3 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 0.3 uM bortezomib
barcode: CAAGCT batch: dge1

value: 0.3 uM bortezomib

value: bortezomib


title: dge1_H20 RNA-seq of ReNcell VM treated with 1 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 1 uM ldn-193189
barcode: CATGGT batch: dge1


title: dge1_I04 RNA-seq of ReNcell VM treated with 3 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 3 uM nvp-tae684
barcode: GTACAC batch: dge1

value: 3 uM nvp-tae684


title: PGAL-Mcm7-NLS_PGAL-Orc6-4A_PGAL-Cdc6_0h

city: Cambridge

first: Philip

last: Zegerman

address: 80, Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
Library strategy: Repli-Seq
Sequence reads were mapped using Bowtie2 (version 2.3.4).
Unique reads mapping to a single genomic location were summed in 1 kb bins, using Samtools (version 1.7.2) and Bedtools (version 2.26.0).
Genome_build: sacCer3
Supplementary_files_format_and_content: csv files containing number of unique reads in 1 kb bins normalised to G2 0h controls.

organism: Saccharomyces cerevisiae

source_name: Synchronised G2 phase yeast cells

growth_protocol: Mid log phase yeast culture grown in standard media (YPRaff ) and arrested in G2.

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation was carried out according to Illumina TruSeq Nano instructions.

treatment_protocol: Yeast cells arrested and maintained in G2 with 10ug/ml nocodazole, upon arrest of >90% of cells galactose added to induce overexpression of  Mcm7-NLS, Orc6-4A and Cdc6

value: MATa ade2-1 ura3::PGal-Cdc6-13myc::URA3 his3-11,15 trp1::orc6-4A-PGAL1-10-MCM7-2xNLS::TRP1 can1-100 YCLWdelta5::HphMX-EU2-ARS317-LEU::NFS1

tag: strain background


title: PGAL-Mcm7-NLS_PGAL-Orc6-4A_PGAL-Cdc6_4h

source_name: Re-replicating G2 phase yeast cells


title: sld3-A_dbf4-A_PGAL-Mcm7-NLS_PGAL-Orc6-4A_PGAL-Cdc6_4h

value: MATa ade2-1 ura3::PGal-Cdc6-13myc::URA3 his3-11,15 trp1::orc6-4A-PGAL1-10-MCM7-2xNLS::TRP1 can1-100 YCLWdelta5::HphMX-EU2-ARS317-LEU::NFS1 sld3-38A-10his13myc::KanmX dbf4-4A::HIS3


title: dge1_H15 RNA-seq of ReNcell VM treated with 10 uM metformin

description:
RNA-seq of ReNcell VM treated with 10 uM metformin
barcode: TTGGAT batch: dge1

value: 10 uM metformin

value: metformin


title: dge1_H16 RNA-seq of ReNcell VM treated with 10 uM r 59949

description:
RNA-seq of ReNcell VM treated with 10 uM r 59949
barcode: ACCGTA batch: dge1

value: in-vitro differentiated neural and glial cells


title: swi4-t_sld3-A_dbf4-A_40

data_processing:
Library strategy: Repli-Seq
Sequence reads were mapped using Bowtie2 (version 2.3.4).
Unique reads mapping to a single genomic location were summed in 1 kb bins, using Samtools (version 1.7.2) and Bedtools (version 2.26.0).
Genome_build: sacCer3
Supplementary_files_format_and_content: csv files containing number of unique reads in 1 kb bins normalised to G1 controls.

source_name: Replicating S phase yeast cells

growth_protocol: G1 arrested mid log phase yeast culture grown in standard media (YPRaff & YPGal) and released in to S-phase

treatment_protocol: 4-NQO was added to G1 arrested yeast cells and then cells released into S-phase in fresh medium without 4-NQO.

value: swi4-t sld3-A dbf4-A

value: MATa ade2-1 ura3-1 his3-11,15 trp1::PGAL-Swi4-t::TRP1 leu2-3,112 can1-100 rad5-535 sld3-38A-10his13myc::KanmX dbf4-4A::HIS3

tag: cell cycle phase

value: Replicating S


title: dge1_H17 RNA-seq of ReNcell VM treated with 0.3 uM entinostat

description:
RNA-seq of ReNcell VM treated with 0.3 uM entinostat
barcode: ATCGAG batch: dge1

value: 0.3 uM entinostat

value: ReNcell VM

value: entinostat


title: swi4-t_sld3-A_dbf4-A_30


title: dge1_H14 RNA-seq of ReNcell VM treated with 3 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 3 uM bortezomib
barcode: TTTTCT batch: dge1

value: 3 uM bortezomib


title: dge1_H13 RNA-seq of ReNcell VM treated with 1 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 1 uM ruxolitinib
barcode: TTTTAG batch: dge1

value: 1 uM ruxolitinib

value: ruxolitinib


title: swi4-t_sld3-A_dbf4-A_20


title: dge1_H12 RNA-seq of ReNcell VM treated with 3 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 3 uM ruxolitinib
barcode: TTTCAA batch: dge1

value: 3 uM ruxolitinib


title: swi4-t_40


title: swi4-t_sld3-A_dbf4-A_G1

source_name: Synchronised G1 phase yeast cells

value: Synchronised G1


title: MDA-MB-231/CN-3

type: RNA

city: Hengyang

first: Yingying

last: Shen

address: 69 Chuanshan Road

department: Institute of Clinical Medicine

country: China

institute: The First Affiliated Hospital of University of South China

description:
Sample name: 5
MDA-MB-231

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: MDA-MB-231 cells were cultured in DMEM medium and then treated with or without 3.75 μM DCC-2036 for 48 hours

tag: cell line

value: human triple negative breast cancer cell line MDA-MB-231

tag: agent

value: control


title: swi4-t_30


title: MDA-MB-231/CN-2

description:
Sample name: 3
MDA-MB-231


title: dge1_H11 RNA-seq of ReNcell VM treated with 1 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 1 uM zm-447439
barcode: TTTATG batch: dge1


title: MDA-MB-231/DCC-2036-1

description:
Sample name: 2
MDA-MB-231 treated with DCC-2036


title: MDA-MB-231/DCC-2036-2

description:
Sample name: 4
MDA-MB-231 treated with DCC-2036


title: dge1_H09 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: TTGTTA batch: dge1

value: dmso


title: swi4-t_20


title: swi4-t_G1


title: dge1_H08 RNA-seq of ReNcell VM treated with 0.3 uM brivanib

description:
RNA-seq of ReNcell VM treated with 0.3 uM brivanib
barcode: TTCTAA batch: dge1

value: 0.3 uM brivanib

value: brivanib


title: dge1_H06 RNA-seq of ReNcell VM treated with 3 uM metformin

description:
RNA-seq of ReNcell VM treated with 3 uM metformin
barcode: TTATGT batch: dge1

value: in-vitro differentiated neural and glial cells

value: 3 uM metformin

value: metformin


title: MDA-MB-231/CN-1

description:
Sample name: 1
MDA-MB-231


title: dge1_H05 RNA-seq of ReNcell VM treated with 3 uM a443654

description:
RNA-seq of ReNcell VM treated with 3 uM a443654
barcode: TTATCA batch: dge1


title: dge1_H03 RNA-seq of ReNcell VM treated with 10 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 10 uM fedratinib
barcode: TTACTA batch: dge1

value: 10 uM fedratinib

value: fedratinib


title: dge1_H04 RNA-seq of ReNcell VM treated with 3 uM alisertib

description:
RNA-seq of ReNcell VM treated with 3 uM alisertib
barcode: TTAGAA batch: dge1

value: 3 uM alisertib

value: ReNcell VM

value: alisertib


title: whole blood, DU14-02S0000008

first: Florica

last: Constantine

address: 304 Research Drive

institute: Duke University

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt

data_processing:
Generating genome indexes files using STAR v2.7.1a with parameters in the command line: runMode: genomeGenerate; runThreadN: 16;  genomeDir: path/index; genomeFastaFiles: path/Homo_sapiens.GRCh38.dna.primary_assembly.fa; sjdbGTFfile: path/Homo_sapiens.GRCh38.83.gtf
Mapping reads to the genome using STAR v2.7.1a with parameters in the command line: twopassMode: Basic; quantMode: GeneCounts; genomeDir: path/index; runThreadN: 16; readFilesIn: path/sampleid_R1.fastq.gz path/sampleid_R2.fastq.gz; outFileNamePrefix: path/sampleid; readFilesCommand: zcat.
Genes with counts per million greater than 1 in fewer than 20% of samples were dropped along with three samples that had a high proportion of lowly expressed reads.
Data was normalized using the TMM function from the Bioconductor package edgeR.
Data was log2 transformed
To get the gene length for calculating TPM, we first extracted transcript information from Homo_sapiens.GRCh38.83.gtf (same reference as STAR) by using the makeTxDbFromGFF function, then collect the exons per gene id using the exonsBy function and for each gene, reduce all the exons to a set of non-overlapping exons, calculate their lengths (widths) and sum them up. Use the median gene length if there are any duplicates.  Take the TMM normalized counts matrix from previous processing step, use the rpkm function from the to Bioconductor package edgeR v3.28.0 to calculate the RPKM and calculate TPM from RPKM based on the definition. Save the TPM counts matrix for CIBERSORTx analysis.
Genome_build: Homo_sapiens.GRCh38.83 (Homo_sapiens.GRCh38.83.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa); Reference Download: http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/Old/ENSEMBL/homo_sapiens/ENSEMBL.homo_sapiens.release-83/
Supplementary_files_format_and_content: counts_key.csv: csv file with demographic information for all samples
counts.csv: csv file with gene counts for all samples
key.csv: csv file with demographic information for all samples used in analyses
xpr_nlcpm.csv: csv file with the TMM normalized expression values on the log2 scale (analysis ready data)
xpr_tpm_geo.txt: tab-delimited text file with TPM calculated from TMM normalized data

source_name: whole blood

extract_protocol:
Total RNA was extracted from peripheral blood preserved in PAXgene Blood RNA tubes using QIAGEN PAXgene miRNA Extraction Kit according to manufacturer's instructions.
Libraries were prepared using NUGEN Universal Plus mRNA-seq with AnyDeplete Globin Kit according to manufacturer's instructions.

tag: age

tag: gender

tag: race

value: White

tag: cohort

value: CoV other

tag: hospitalized

tag: tissue

value: whole blood

tag: batch


title: whole blood, DU14-02S0000005


title: whole blood, DU09-03S0000632

value: Male

value: Influenza


title: whole blood, 105853

value: Female

value: Unknown/Not reported


title: whole blood, DU14-02S0000006


title: whole blood, 105848


title: dge1_H01 RNA-seq of ReNcell VM treated with 1 uM sb202190

description:
RNA-seq of ReNcell VM treated with 1 uM sb202190
barcode: TTAACT batch: dge1

tag: treatment


title: dge1_H10 RNA-seq of ReNcell VM treated with 1 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 1 uM pf04217903
barcode: TTTAAC batch: dge1


title: whole blood, 105847


title: dge1_G23 RNA-seq of ReNcell VM treated with 10 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 10 uM pazopanib
barcode: CTAGTG batch: dge1

value: 10 uM pazopanib

value: pazopanib


title: whole blood, DU14-02S0000009


title: whole blood, 434518


title: dge1_H07 RNA-seq of ReNcell VM treated with 3 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 3 uM pha-665752
barcode: TTCATA batch: dge1

value: in-vitro differentiated neural and glial cells


title: whole blood, 434517


title: whole blood, 434482

description:
excluded from analyses for poor data quality
counts_key.csv
counts.csv


title: dge1_G22 RNA-seq of ReNcell VM treated with 3 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 3 uM pha-665752
barcode: CCGATT batch: dge1


title: dge1_G21 RNA-seq of ReNcell VM treated with 10 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 10 uM pf04217903
barcode: CCACAT batch: dge1


title: whole blood, DU14-02S0000007


title: whole blood, 434537


title: dge1_G20 RNA-seq of ReNcell VM treated with 3 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 3 uM tofacitinib
barcode: CAGTCA batch: dge1

value: 3 uM tofacitinib

value: tofacitinib


title: dge1_G19 RNA-seq of ReNcell VM treated with 10 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 10 uM bortezomib
barcode: CACCAA batch: dge1

value: 10 uM bortezomib

value: bortezomib


title: MDA-MB-231/DCC-2036-3

description:
Sample name: 6
MDA-MB-231 treated with DCC-2036

value: human triple negative breast cancer cell line MDA-MB-231


title: dge1_H02 RNA-seq of ReNcell VM treated with 1 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 1 uM nvp-tae684
barcode: TTAAGA batch: dge1

value: 1 uM nvp-tae684

value: ReNcell VM


title: whole blood, 434596

value: White


title: whole blood, 434532

value: Asian

value: CoV other


title: dge1_G18 RNA-seq of ReNcell VM treated with 10 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 10 uM tofacitinib
barcode: AGGGAT batch: dge1

value: 10 uM tofacitinib


title: whole blood, 434557

value: whole blood


title: dge1_G17 RNA-seq of ReNcell VM treated with 0.3 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 0.3 uM gsk1059615
barcode: AGACCT batch: dge1


title: dge1_G16 RNA-seq of ReNcell VM treated with 10 uM a443654

description:
RNA-seq of ReNcell VM treated with 10 uM a443654
barcode: TCTTTC batch: dge1


title: dge1_G14 RNA-seq of ReNcell VM treated with 10 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 10 uM cabozantinib
barcode: TTTGTA batch: dge1

value: 10 uM cabozantinib

value: cabozantinib


title: dge1_G24 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: CTTCTG batch: dge1

value: dmso


title: whole blood, 434567

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt


title: dge1_G15 RNA-seq of ReNcell VM treated with lipofectamine

description:
RNA-seq of ReNcell VM treated with lipofectamine
barcode: TTTTGA batch: dge1

value: lipofectamine

tag: stimulant


title: whole blood, 434486


title: whole blood, DU14-02S0000002


title: dge1_G13 RNA-seq of ReNcell VM treated with 3 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 3 uM fedratinib
barcode: TTTCTT batch: dge1

value: in-vitro differentiated neural and glial cells

value: 3 uM fedratinib

value: fedratinib


title: whole blood, DU14-02S0000001


title: dge1_G11 RNA-seq of ReNcell VM treated with 1 uM metformin

description:
RNA-seq of ReNcell VM treated with 1 uM metformin
barcode: TTTACA batch: dge1

value: 1 uM metformin

value: metformin


title: dge1_G12 RNA-seq of ReNcell VM treated with 10 uM entinostat

description:
RNA-seq of ReNcell VM treated with 10 uM entinostat
barcode: TTTAGT batch: dge1

value: 10 uM entinostat

value: entinostat


title: dge1_G09 RNA-seq of ReNcell VM treated with 3 uM sb202190

description:
RNA-seq of ReNcell VM treated with 3 uM sb202190
barcode: TTGAAA batch: dge1

value: ReNcell VM


title: whole blood, DU14-02S0000004

value: White


title: whole blood, 434399


title: whole blood, 434393


title: dge1_G08 RNA-seq of ReNcell VM treated with 3 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 3 uM bortezomib
barcode: TTCAAT batch: dge1

value: 3 uM bortezomib

value: bortezomib


title: whole blood, 434333

value: Female

value: Asian

value: CoV other


title: dge1_G05 RNA-seq of ReNcell VM treated with 1 uM entinostat

description:
RNA-seq of ReNcell VM treated with 1 uM entinostat
barcode: TTAGTT batch: dge1

value: 1 uM entinostat


title: whole blood, 434316

value: Male

value: whole blood


title: dge1_G06 RNA-seq of ReNcell VM treated with 10 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 10 uM r 59-022
barcode: TTATAC batch: dge1

value: in-vitro differentiated neural and glial cells


title: whole blood, 234432

value: Black/African American


title: whole blood, 434570


title: whole blood, DU09-02S0000153

value: healthy


title: dge1_G03 RNA-seq of ReNcell VM treated with 3 uM r 59949

description:
RNA-seq of ReNcell VM treated with 3 uM r 59949
barcode: TTAATC batch: dge1


title: whole blood, 434294


title: WT rep2

tag: strain

value: wild type


title: dge1_G01 RNA-seq of ReNcell VM treated with 1 uM sb202190

description:
RNA-seq of ReNcell VM treated with 1 uM sb202190
barcode: TGTTTA batch: dge1


title: dge1_G02 RNA-seq of ReNcell VM treated with 10 uM bx-912

description:
RNA-seq of ReNcell VM treated with 10 uM bx-912
barcode: TTAAAG batch: dge1


title: whole blood, 234377


title: dge1_G07 RNA-seq of ReNcell VM treated with 0.3 uM sb202190

description:
RNA-seq of ReNcell VM treated with 0.3 uM sb202190
barcode: TTATTG batch: dge1


title: dge1_F24 RNA-seq of ReNcell VM treated with 1 uM mg-132

description:
RNA-seq of ReNcell VM treated with 1 uM mg-132
barcode: TGTTAT batch: dge1


title: dge1_G10 RNA-seq of ReNcell VM treated with 10 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 10 uM hg-9-91-01
barcode: TTGATT batch: dge1


title: dge1_G04 RNA-seq of ReNcell VM treated with 10 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 10 uM gsk1070916
barcode: TTACAT batch: dge1


title: whole blood, DU09-02S0000156


title: dge1_F23 RNA-seq of ReNcell VM treated with 0.3 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 0.3 uM pf04217903
barcode: TGTATT batch: dge1


title: whole blood, 234376

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt


title: whole blood, DU09-02S0000149


title: whole blood, DU14-02S0000003


title: whole blood, 434330


title: dge1_F21 RNA-seq of ReNcell VM treated with 0.3 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 0.3 uM r 59-022
barcode: TGAATA batch: dge1


title: dge1_F22 RNA-seq of ReNcell VM treated with 1 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 1 uM hg-9-91-01
barcode: TGATAA batch: dge1


title: whole blood, 434335


title: rd92brd9: BRD9 ChIP IBRD9 rep2

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

data_processing:
Data quality control and filtering was performed with Trim Galore.
Read-mapping against the human (hg19) genome was performed with bowtie2.
Alignment were filtered using SAMtools to keep only the reads with MAPQ < 10.
Filtered alignment (BAM) files were conveted to bigwig format using deeptools bamCoverage.
peaks were called using EPIC2.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig file are in an indexed binary format and contain genome-wide coverage information.
Supplementary_files_format_and_content: BED files are TAB delimited text files and contains peaks locations and other relevant information.

source_name: prostate cancer

growth_protocol: LNCaP prostate cancer cell lines were grown under normal conditions: RPMI with 10% FBS

extract_protocol:
Cells were fixed, washed, and lysed. The chromatin was sheared using a probe sonicator and protein/DNA complexes were isolated with antibody. Fragments were further sheared using a Covaris sonicator.
Libraries were constructed using Ovation® Ultralow V2 DNA-Seq Library Preparation Kit from Tecan, according the manufacturer's instructions

treatment_protocol: knockouts were generated using lentiviral mediated CRISPR-Cas9. DMSO and IBRD9 (10µM) were added 24h prior to harvest

value: prostate cancer cell line

tag: cell type

value: LNCaP

value: 10 uM IBRD9 for 24 h

tag: antibody

value: BRD9 (active motif AB_2614970)


title: whole blood, DU09-02S0000155

value: White


title: MSO1BRD9: BRD9 ChIP DMSO rep2

value: DMSO for 24h


title: whole blood, DU09-02S0000151


title: dge1_F20 RNA-seq of ReNcell VM treated with 10 uM fccp

description:
RNA-seq of ReNcell VM treated with 10 uM fccp
barcode: TCTATA batch: dge1

value: 10 uM fccp

value: ReNcell VM

value: fccp


title: MSO1BRD4: BRD4 ChIP DMSO rep2

value: BRD4 (Bethyl A301-985A)


title: whole blood, DU09-02S0000154_batch1, DU09-02S0000154_batch2

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt
batch1 raw files: SRR13081354
batch2 raw files: SRR13081355

value: Female

value: Asian


title: whole blood, DU09-02S0000150_batch1, DU09-02S0000150_batch2

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt
batch1 raw files: SRR13081356
batch2 raw files: SRR13081357

value: whole blood


title: dge1_F19 RNA-seq of ReNcell VM treated with 3 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 3 uM r 59-022
barcode: TCTAAT batch: dge1

value: in-vitro differentiated neural and glial cells


title: rd92i110: input from IBRD9 rep2

value: none (input)


title: whole blood, 434325

value: Male

value: CoV other


title: whole blood, 434777


title: whole blood, DU09-02S0000111

value: healthy


title: whole blood, 434323

value: Black/African American


title: whole blood, DU09-02S0000116


title: dge1_F17 RNA-seq of ReNcell VM treated with 1 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 1 uM (+)-jq1
barcode: TCAAAA batch: dge1


title: whole blood, DU09-02S0000157


title: dge1_F16 RNA-seq of ReNcell VM treated with 10 uM alisertib

description:
RNA-seq of ReNcell VM treated with 10 uM alisertib
barcode: TATTCA batch: dge1

value: 10 uM alisertib

value: alisertib


title: whole blood, DU09-02S0000120

value: Other/More than one race


title: dge1_F15 RNA-seq of ReNcell VM treated with 0.3 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 0.3 uM hg-9-91-01
barcode: TATTAC batch: dge1


title: whole blood, DU09-02S0000115

value: White


title: whole blood, DU09-02S0000158_batch1, DU09-02S0000158_batch2

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt
batch1 raw files: SRR13081343
batch2 raw files: SRR13081344


title: whole blood, DU09-02S0000114


title: ThpI shLEDGF/p75 #3

city: Columbus

first: Alessandro

last: Canella

state: OH

address: 700 Children’s Drive

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: RNA interference performed by shRNA

data_processing:
Adapters were filtered with ea-utils fastq-mcf v1.05
Splice-aware alignment was performed with HiSat2
BAM alignment files were handled with Samtools v1.5
Quantification of reads per gene was performed with HT-seq Count v2.7.14
Count-based differential expression analysis was done with DESeq2
Genome_build: Hg38

source_name: member of the LEDGF/p75 KD group

growth_protocol: cells have been grown in RPMI+10%FBS+ Zeocin as the selection agent

extract_protocol:
Aurum™ Total RNA Mini Kit
QuantSeq 3' mRNA-Seq Library Prep Kit

treatment_protocol: cells have not been subjected to any treatments

value: monocyte

tag: Stage

value: isolated from 1 years old male affected by acute monocytic leukemia (AML)

tag: Sex

value: male


title: dge1_F14 RNA-seq of ReNcell VM treated with 1 uM rotenone

description:
RNA-seq of ReNcell VM treated with 1 uM rotenone
barcode: TATCTA batch: dge1

value: 1 uM rotenone

value: ReNcell VM

value: rotenone


title: whole blood, 434794

value: whole blood


title: dge1_F18 RNA-seq of ReNcell VM treated with 1 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 1 uM gsk1070916
barcode: TCAATT batch: dge1

value: in-vitro differentiated neural and glial cells


title: dge1_F12 RNA-seq of ReNcell VM treated with 0.3 uM r 59949

description:
RNA-seq of ReNcell VM treated with 0.3 uM r 59949
barcode: TATACT batch: dge1


title: whole blood, DU09-02S0000146

value: Female


title: whole blood, DU09-02S0000113

value: Male


title: SO1IN110: input from DMSO rep2

value: prostate cancer cell line

value: LNCaP

value: DMSO for 24h

value: none (input)


title: whole blood, 434809

value: CoV other


title: dge1_F11 RNA-seq of ReNcell VM treated with dmso

description:
RNA-seq of ReNcell VM treated with dmso
barcode: TATAAG batch: dge1

value: dmso


title: whole blood, 434757

value: Asian


title: dge1_F13 RNA-seq of ReNcell VM treated with 0.3 uM r 59949

description:
RNA-seq of ReNcell VM treated with 0.3 uM r 59949
barcode: TATCAT batch: dge1


title: ThpI shCTRL #3

description: RNA interference performed by shRNA

source_name: member of the CTRL group

value: monocyte


title: ThpI shCTRL #4

description: RNA interference performed by shRNA

value: isolated from 1 years old male affected by acute monocytic leukemia (AML)


title: whole blood, 434735


title: ThpI shLEDGF/p75 #4

description: RNA interference performed by shRNA

value: male


title: dge1_H23 RNA-seq of ReNcell VM treated with 0.3 uM entinostat

description:
RNA-seq of ReNcell VM treated with 0.3 uM entinostat
barcode: GAAGAC batch: dge1

value: 0.3 uM entinostat

value: entinostat


title: whole blood, 434766

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt

value: White


title: sld3-A_dbf4-A_PGAL-Mcm7-NLS_PGAL-Orc6-4A_PGAL-Cdc6_0h

tag: genotype

value: MATa ade2-1 ura3::PGal-Cdc6-13myc::URA3 his3-11,15 trp1::orc6-4A-PGAL1-10-MCM7-2xNLS::TRP1 can1-100 YCLWdelta5::HphMX-EU2-ARS317-LEU::NFS1 sld3-38A-10his13myc::KanmX dbf4-4A::HIS3

tag: strain background


title: dge1_F10 RNA-seq of ReNcell VM treated with 1 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 1 uM ldn-193189
barcode: TAGATA batch: dge1

value: in-vitro differentiated neural and glial cells

value: ReNcell VM


title: ThpI shCTRL #2

description: RNA interference performed by shRNA

tag: cell line


title: ThpI shLEDGF/p75 #1

description: RNA interference performed by shRNA


title: whole blood, 234330

tag: age

value: Male

value: whole blood


title: ThpI shLEDGF/p75 #2

description: RNA interference performed by shRNA


title: ThpI shCTRL #1

description: RNA interference performed by shRNA


title: whole blood, DU09-02S0000106

tag: gender

value: healthy


title: dge1_F09 RNA-seq of ReNcell VM treated with 1 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 1 uM zm-447439
barcode: TAGAAT batch: dge1


title: whole blood, 434741

description:
excluded from analyses for poor data quality
counts_key.csv
counts.csv

value: Female

tag: race


title: dge1_F08 RNA-seq of ReNcell VM treated with 3 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 3 uM (+)-jq1
barcode: TACATT batch: dge1


title: whole blood, DU09-02S0000144

tag: cohort


title: whole blood, 434740

tag: hospitalized


title: Cell surface protein MSIT235

city: London

first: Janice

middle: A

last: Layhadi

address: South Kensington Campus

department: National Heart and Lung Institute

institute: Imperial College London

description: Protein

data_processing:
Pre-alignment quality control and trimming of bases,Cell Ranger Single Cell Software Suite (v3.0.2)
Barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
Single cell 3' gene counting, Cell Ranger Single Cell software Suite (v3.0.2)
Alignment, Cell Ranger Single Cell Software Suite (v.3.0.2)
Normalization of single cell counts, Partek Flow®
Genome_build: hg38
Supplementary_files_format_and_content: Normalized count matrix are generated as txt file and are provided for each samples and for combined samples.

source_name: Peripheral blood mononuclear cells

extract_protocol:
Human innate lymphoid cells (ILCs) were sorted from peripheral blood mononuclear cells using BD FACSAria instrument. Once sorted, ILCs were processed for single cell analysis using 10x Genomics kit (3' v3 chemistry). For gene expression libraries (GEX), 50 ng of amplified cDNA was used for library preparation, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per manufacturer's instructions. Libraries were sequenced on a HiSeq 4000 flow cells, targetting 25,000 read pairs/cell. For cell surface protein (CSP) libraries, 2 uL of amplified cDNA was used for library prepartion, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per manufacturer's instructions. Enriched libraries were sequenced on a HiSeq 4000 flow cell, targetting 5,000 read pairs/cell.
RNA and protein libraries were generated using 10x genomics protocol (3' v3 chemistry).

value: Innate lymphoid cells

value: Grass pollen allergics

tag: sample type

value: cell surface protein


title: whole blood, 434756

value: Native Hawaiian/Pacific Islander

value: CoV other

tag: tissue

tag: batch


title: whole blood, 434859

value: Asian


title: dge1_F07 RNA-seq of ReNcell VM treated with 1 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 1 uM hg-9-91-01
barcode: TACAAA batch: dge1

tag: treatment


title: whole blood, 434768


title: Cell surface protein MSIT232

description: Protein


title: whole blood, DU09-02S0000105


title: Cell surface protein MSIT114

description: Protein

value: Healthy


title: dge1_F06 RNA-seq of ReNcell VM treated with 3 uM kw2449

description:
RNA-seq of ReNcell VM treated with 3 uM kw2449
barcode: TAATCT batch: dge1


title: dge1_F05 RNA-seq of ReNcell VM treated with 0.3 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM cabozantinib
barcode: TAATAG batch: dge1

value: 0.3 uM cabozantinib

value: cabozantinib


title: whole blood, 234326


title: whole blood, DU09-02S0000103

value: White


title: whole blood, DU09-02S0000101


title: RNA MSIT235


title: RNA MSIT232


title: dge1_F04 RNA-seq of ReNcell VM treated with 1 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 1 uM gsk1059615
barcode: TAACTT batch: dge1


title: whole blood, 434602


title: whole blood, 434597


title: dge1_F03 RNA-seq of ReNcell VM treated with 0.3 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 0.3 uM pha-665752
barcode: TAACAA batch: dge1


title: RNA MSIT114


title: whole blood, 105927

value: Influenza


title: whole blood, DU09-02S0000145


title: whole blood, 105834


title: whole blood, 105842

value: American Indian/Alaska Native


title: dge1_F02 RNA-seq of ReNcell VM treated with 10 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 10 uM zm-447439
barcode: TAAACA batch: dge1

value: in-vitro differentiated neural and glial cells

value: ReNcell VM


title: dge1_F01 RNA-seq of ReNcell VM treated with 3 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 3 uM ruxolitinib
barcode: TAAAAC batch: dge1

value: 3 uM ruxolitinib

value: ruxolitinib


title: GP-SLIT 1 (24m)

data_processing:
Pre-alignment quality control and trimming of bases, Partek Flow®
RNA sequences Alignment using STAR v.2.6.1d, Partek Flow®; Protein sequence alignment using Bowtie v.1.0.0, Partek Flow®
Deduplication of UMI to remove contaminants, Partek Flow®
Quantification of barcodes, Partek Flow®
Normalization of single cell counts, Partek Flow®
Genome_build: hg38
Supplementary_files_format_and_content: Normalized count matrix are generated as txt file and are provided for each samples and for combined samples.

molecule: protein

extract_protocol:
Human innate lymphoid cells (ILCs) were sorted from peripheral blood mononuclear cells using BD FACSAria instrument. Once sorted, ILCs were in vitro stimulated with 50ng/mL of retinoic acid (RA), in the presence of recombinant human IL-2 (R&D), human IL-7 (Peprotech) and IL-33 (R&D) for 7 days at 37C, 5% CO2. Stimulants were replenished every 3 days. Following 7 days in vitro stimulation, ILCs were tested for viability using trypan blue exclusion and processed for single cell analysis using 10x Genomics kit (3' v3 chemistry). For gene expression libraries (GEX), 50 ng of amplified cDNA was used for library preparation, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per manufacturer's instructions. Libraries were sequenced on a HiSeq 4000 flow cells, targetting 25,000 read pairs/cell. For cell surface protein (CSP) libraries, 2 uL of amplified cDNA was used for library prepartion, consisting of fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per manufacturer's instructions. Enriched libraries were sequenced on a HiSeq 4000 flow cell, targetting 5,000 read pairs/cell.
RNA and protein libraries were generated using 10x genomics protocol (3' v3 chemistry).

value: Grass pollen sublingual immunotherapy

tag: time point

value: 24 months


title: GP-SLIT 2 (24m)

tag: cell type

value: Innate lymphoid cells


title: whole blood, 234435

value: Female

value: whole blood


title: whole blood, 234301

value: CoV other


title: dge1_E24 RNA-seq of ReNcell VM treated with 10 uM a443654

description:
RNA-seq of ReNcell VM treated with 10 uM a443654
barcode: TGTAAA batch: dge1


title: whole blood, DU09-02S0000141

value: Black/African American


title: whole blood, DU09-02S0000143

value: Male


title: GP-SLIT 1 (12m)


title: GP-SLIT 2 (12m)


title: whole blood, 105791


title: dge1_E23 RNA-seq of ReNcell VM treated with 10 uM sb202190

description:
RNA-seq of ReNcell VM treated with 10 uM sb202190
barcode: TGATTT batch: dge1


title: whole blood, 105824

value: Asian


title: whole blood, 434619


title: whole blood, DU09-02S0000142


title: PL-SLIT 2 (12m)

value: Placebo


title: PL-SLIT 1 (12m)


title: dge1_E22 RNA-seq of ReNcell VM treated with 10 uM fccp

description:
RNA-seq of ReNcell VM treated with 10 uM fccp
barcode: TGAAAT batch: dge1

value: 10 uM fccp

value: fccp


title: dge1_E21 RNA-seq of ReNcell VM treated with 1 uM sb202190

description:
RNA-seq of ReNcell VM treated with 1 uM sb202190
barcode: TCTTAA batch: dge1


title: whole blood, DU10-01S0000709

value: White


title: dge1_E20 RNA-seq of ReNcell VM treated with 3 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 3 uM r 59-022
barcode: TCATTA batch: dge1

value: in-vitro differentiated neural and glial cells


title: whole blood, DU18-02S0011633

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt

value: early

value: Yes


title: whole blood, DU18-02S0011631

value: middle


title: GP-SLIT 1 (24m) [RNA-Seq]

value: Grass pollen sublingual immunotherapy


title: GP-SLIT 2 (24m) [RNA-Seq]

value: 24 months


title: dge1_E18 RNA-seq of ReNcell VM treated with 1 uM entinostat

description:
RNA-seq of ReNcell VM treated with 1 uM entinostat
barcode: TATTTG batch: dge1

value: 1 uM entinostat

value: ReNcell VM

value: entinostat


title: dge1_E19 RNA-seq of ReNcell VM treated with 10 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 10 uM ruxolitinib
barcode: TCATAT batch: dge1

value: 10 uM ruxolitinib

value: ruxolitinib


title: whole blood, 105861

value: Male

value: Influenza

value: whole blood


title: whole blood, DU18-02S0011654


title: GP-SLIT 1 (12m) [RNA-Seq]

value: Innate lymphoid cells


title: GP-SLIT 2 (12m) [RNA-Seq]


title: PL-SLIT 2 (12m) [RNA-Seq]

value: Placebo


title: whole blood, 105929

value: Female

value: Black/African American


title: whole blood, 95996

value: White

value: Bacterial


title: whole blood, 105841


title: whole blood, 95997


title: whole blood, 95994

value: Unknown/Not reported


title: whole blood, 95986


title: whole blood, 97407


title: dge1_E15 RNA-seq of ReNcell VM treated with 1 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 1 uM tofacitinib
barcode: TATGAA batch: dge1

value: in-vitro differentiated neural and glial cells

value: 1 uM tofacitinib

value: tofacitinib


title: whole blood, 97406


title: PL-SLIT 1 (12m) [RNA-Seq]


title: whole blood, 96004


title: dge1_E14 RNA-seq of ReNcell VM treated with 0.3 uM a443654

description:
RNA-seq of ReNcell VM treated with 0.3 uM a443654
barcode: TATATC batch: dge1

value: ReNcell VM


title: whole blood, 95982


title: KCNQ1enh KO3 B

city: La Jolla

first: Kyle

last: Gaulton

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

data_processing:
Alignment: STAR v2.5.3a aligned to hg19 allowing for up to 10 mismatches.
Filtering: Reads mapping to one genomic location.
Counts: Counts matrix created with HTSeq v.0.9.0.
Differential expression: DESeq2 v1.10.1 with differentiation batch as a covariate.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: KCNQ1enh_deletion.counts.txt: Counts matrix.
Supplementary_files_format_and_content: KCNQ1enh_deletion.DESeq2_results.txt: Differential expression results

source_name: ES-derived beta cells

growth_protocol: KCNQ1 enhancer-deleted hESC lines were differentiated in a suspension-based format using rotational culture with some modifications to a published protocol. Undifferentiated hESCs were aggregated by preparing a single cell suspension in mTeSR media and overnight culture in six-well ultra-low attachment plates with 5.5ml per well on an orbital rotator at 100 rpm. The following day, undifferentiated aggregates were washed in DMEM/F12 and differentiated using a multistep protocol with daily media changes and continued orbital rotation at either 100 rpm or at 108 rpm from days 8 to 28. In addition to 1% GlutaMAX and 15 mM (days 0-10) or 20 mM (days 11-28) glucose, MCDB 131 media was supplemented with 0.5% (days 0-5) or 2% (days 6-14) fatty acid-free BSA, 1.5 g/L (days 0-5 and days 11-28) or 2.5 g/L (days 6-10) NaHCO3, and 0.25 mM (days 3-10) ascorbic acid.

extract_protocol:
For each KCNQ1 enhancer-deleted hESC clone, we collected aggregates from two independent batches of differentiation and lysed them in RLT Buffer. We then extracted total RNA using the RNeasy Micro Kit following the manufacturer’s instructions.
RNA libraries were prepared using KAPA mRNA Hyper Prep kit.

treatment_protocol: To generate clonal homozygous KCNQ1 enhancer deletion hESC lines, two sgRNAs targeting the enhancer were designed and cloned into Px333-GFP, a modified version of Px333. The plasmid was transfected into H1 hESCs with XtremeGene 9. 24 hours later, 5000 GFP+ cells were sorted into a well of six-well plate. Individual colonies that emerged within 5-7 days after transfection were subsequently transferred manually into 48-well plates for expansion, genomic DNA extraction, PCR genotyping, and Sanger sequencing. For control clones, we transfected the Px333-GFP plasmid into H1 hESCs and subjected the cells to the same workflow as H1 hESCs transfected with sgRNAs.

value: ES-derived beta cells

value: male

tag: genotype/variation

value: KCNQ1 enhancer deletion


title: KCNQ1enh KO1 B


title: whole blood, 95981

value: Male


title: dge1_E17 RNA-seq of ReNcell VM treated with 10 uM rotenone

description:
RNA-seq of ReNcell VM treated with 10 uM rotenone
barcode: TATTGT batch: dge1

value: 10 uM rotenone

value: rotenone


title: whole blood, DU09-03S19475

value: whole blood


title: whole blood, 00943

value: CoV other


title: Scrambled control B

value: Control


title: whole blood, 95971

value: Female

value: Black/African American


title: whole blood, 97395

value: Bacterial


title: whole blood, 97403


title: dge1_E12 RNA-seq of ReNcell VM treated with 1 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 1 uM hg-9-91-01
barcode: TAGTTT batch: dge1


title: whole blood, 95970


title: dge1_E11 RNA-seq of ReNcell VM treated with 10 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 10 uM gsk1070916
barcode: TAGTAA batch: dge1


title: KCNQ1enh KO2 A


title: whole blood, 97394


title: dge1_E16 RNA-seq of ReNcell VM treated with 1 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 1 uM r 59-022
barcode: TATGTT batch: dge1


title: dge1_E10 RNA-seq of ReNcell VM treated with 1 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 1 uM fedratinib
barcode: TACTTA batch: dge1

value: 1 uM fedratinib

value: fedratinib


title: KCNQ1enh KO3 A


title: dge1_E09 RNA-seq of ReNcell VM treated with 1 uM brivanib

description:
RNA-seq of ReNcell VM treated with 1 uM brivanib
barcode: TACTAT batch: dge1

value: in-vitro differentiated neural and glial cells

value: 1 uM brivanib

value: brivanib


title: whole blood, 94486


title: KCNQ1enh KO1 A

value: ES-derived beta cells


title: KCNQ1enh KO2 B

value: male


title: whole blood, 95968


title: whole blood, 95969


title: dge1_E13 RNA-seq of ReNcell VM treated with lipopolysaccharide

description:
RNA-seq of ReNcell VM treated with lipopolysaccharide
barcode: TATAGA batch: dge1

value: lipopolysaccharide

value: ReNcell VM

tag: stimulant


title: whole blood, 95967


title: Scrambled control A

tag: Sex


title: dge1_E08 RNA-seq of ReNcell VM treated with 1 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 1 uM bortezomib
barcode: TAATTC batch: dge1

value: 1 uM bortezomib

value: bortezomib


title: whole blood, 97392

value: whole blood


title: whole blood, 94478

description:
excluded from analyses for poor data quality
counts_key.csv
counts.csv


title: whole blood, DU09-03S19498


title: dge1_E06 RNA-seq of ReNcell VM treated with 0.3 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 0.3 uM zm-447439
barcode: TAAGTA batch: dge1


title: whole blood, 97389

value: Male

value: Unknown/Not reported


title: dge1_E05 RNA-seq of ReNcell VM treated with 0.3 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 0.3 uM plx-4720
barcode: TAAGAT batch: dge1


title: dge1_E04 RNA-seq of ReNcell VM treated with 0.3 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 0.3 uM (+)-jq1
barcode: TAAATG batch: dge1


title: whole blood, DU18-02S0011612

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt

value: White

value: middle

value: Yes


title: whole blood, DU10-01S0000032

value: Female

value: Black/African American

value: CoV other


title: GemR_siSTIM1_Thap_rep3

city: Rochester

first: Steven

last: Johnsen

state: MN

address: 200 First Street SW

department: Gastroenterology Research

institute: Mayo Clinic

data_processing:
The fastq files were mapped to the human genome (hg38) using STAR (version 2.6.0c) followed by HTSeq-count (version 0.11.1), which was used to obtain the read counts. DESeq2 was used for differential analysis as well as to obtain normalized read counts for each condition.
Genome_build: hg38
Supplementary_files_format_and_content: The text files contain the differential analysis obtained from DESeq2.
Supplementary_files_format_and_content: The normalized read counts for each replicate of each condition obtained from DESeq2 can be found in a separate text file.

source_name: Pancreatic cancer

growth_protocol: The cells were cultured in Minimum Essential Medium Eagle (MEM) supplemented with 10% FBS, 1% Penicillin and Streptomycin and 1% L-Glutamine. GemR cells were maintained in 64nM gemcitabine.

extract_protocol:
RNA was harvested using QIAzol (Qiagen) and following manufacturer’s instructions.
mRNA-Seq libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) and 500ng of RNA.

treatment_protocol: Gene knockdowns were performed for 48h using RNAiMax (Invitrogen) and following manufacturer's instructions. 3h prior to harvesting, the cells were submitted to vehicle (DMSO) or 500nM thapsigargin treatment.

value: Gemcitabine resistant L3.6pl

value: siSTIM1 (48h), 500nM thapsigargin (3h)


title: whole blood, DU18-02S0011676

value: early


title: whole blood, DU18-02S0011675


title: GoPDX13_Veh

data_processing:
The fastq files were mapped to the human genome (hg38) using STAR (version 2.6.0c) followed by HTSeq-count (version 0.11.1), which was used to obtain the read counts. DESeq2 was used to obtain normalized read counts.
Genome_build: hg38
Supplementary_files_format_and_content: The normalized read counts obtained from DESeq2 can be found in a separate text file.

value: Patient-drived xenograft

value: Veh (0.9% saline)


title: GemR_siSTIM1_Thap_rep2


title: dge1_E03 RNA-seq of ReNcell VM treated with 0.3 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 0.3 uM hg-9-91-01
barcode: TAAAGT batch: dge1

source_name: in-vitro differentiated neural and glial cells

value: ReNcell VM


title: whole blood, DU18-02S0011668


title: whole blood, DU18-02S0011662


title: GemR_siSTIM1_Veh_rep3

value: siSTIM1 (48h), Veh. (3h)


title: whole blood, DU18-02S0011669


title: dge1_E07 RNA-seq of ReNcell VM treated with 10 uM bx-912

description:
RNA-seq of ReNcell VM treated with 10 uM bx-912
barcode: TAATGA batch: dge1

value: in-vitro differentiated neural and glial cells


title: dge1_E02 RNA-seq of ReNcell VM treated with 1 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 1 uM pha-665752
barcode: GTTTTA batch: dge1


title: whole blood, DU18-02S0011670

value: whole blood


title: whole blood, DU18-02S0011664

value: late

value: No


title: whole blood, DU18-02S0011618

value: Male

value: Unknown/Not reported


title: GoPDX13_Gem_Pac

value: Gemcitabine (100mg/kg) and nab-Paclitaxel (30mg/kg)


title: dge1_E01 RNA-seq of ReNcell VM treated with 10 uM metformin

description:
RNA-seq of ReNcell VM treated with 10 uM metformin
barcode: GTTTAT batch: dge1

value: 10 uM metformin

value: metformin


title: dge1_D24 RNA-seq of ReNcell VM treated with dsRNA

description:
RNA-seq of ReNcell VM treated with dsRNA
barcode: GTTATT batch: dge1

value: dsRNA


title: whole blood, DU18-02S0011666

value: White


title: GemR_siSTIM1_Veh_rep2

value: Gemcitabine resistant L3.6pl


title: whole blood, DU18-02S0011613

value: Female

value: Asian

value: early


title: GemR_siSTIM1_Veh_rep1


title: dge1_D23 RNA-seq of ReNcell VM treated with 1 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 1 uM (+)-jq1
barcode: GTTAAA batch: dge1

value: ReNcell VM


title: whole blood, DU18-02S0011652

value: Black/African American

value: middle

value: Yes


title: whole blood, DU18-02S0011651

value: whole blood


title: GemR_siCont_Thap_rep3

value: siCont. (48h), 500nM thapsigargin (3h)


title: dge1_D22 RNA-seq of ReNcell VM treated with 10 uM brivanib

description:
RNA-seq of ReNcell VM treated with 10 uM brivanib
barcode: GTAAAT batch: dge1

value: in-vitro differentiated neural and glial cells

value: 10 uM brivanib

value: brivanib


title: GemR_siCont_Thap_rep2


title: dge1_D21 RNA-seq of ReNcell VM treated with 3 uM barasertib

description:
RNA-seq of ReNcell VM treated with 3 uM barasertib
barcode: GATTAA batch: dge1

value: 3 uM barasertib

value: barasertib


title: GemR_siSTIM1_Thap_rep1

value: siSTIM1 (48h), 500nM thapsigargin (3h)


title: whole blood, DU18-02S0011648

value: Male

value: Native Hawaiian/Pacific Islander

value: No


title: GemR_siCont_Thap_rep1

value: Gemcitabine resistant L3.6pl


title: whole blood, DU18-02S0011653

value: Asian

value: late


title: whole blood, DU18-02S0011610

value: White


title: whole blood, DU18-02S0011661

value: early


title: GemR_siCont_Veh_rep3

value: siCont. (48h), Veh. (3h)


title: whole blood, DU18-02S0011667

value: Female

value: whole blood


title: whole blood, DU18-02S0011647

value: middle


title: whole blood, DU18-02S0011646


title: GemR_siCont_Veh_rep2


title: GemR_siCont_Veh_rep1


title: dge1_D19 RNA-seq of ReNcell VM treated with 3 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 3 uM pha-665752
barcode: GAATAT batch: dge1

value: in-vitro differentiated neural and glial cells

value: ReNcell VM


title: dge1_D18 RNA-seq of ReNcell VM treated with 0.3 uM kw2449

description:
RNA-seq of ReNcell VM treated with 0.3 uM kw2449
barcode: CTTATA batch: dge1


title: Par_siCont_Thap_rep3

value: siCont. (48h), 500nM thapsigargin (3h)


title: whole blood, DU18-02S0011663


title: whole blood, DU18-02S0011645


title: whole blood, DU18-02S0011659


title: whole blood, DU18-02S0011650


title: whole blood, DU18-02S0011644


title: whole blood, DU18-02S0011649


title: dge1_D20 RNA-seq of ReNcell VM treated with 1 uM metformin

description:
RNA-seq of ReNcell VM treated with 1 uM metformin
barcode: GAATTA batch: dge1

value: 1 uM metformin

value: metformin


title: whole blood, DU18-02S0011655

value: Male


title: Par_siCont_Thap_rep1


title: dge1_D15 RNA-seq of ReNcell VM treated with 3 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 3 uM tofacitinib
barcode: CTAAAA batch: dge1

value: 3 uM tofacitinib

value: tofacitinib


title: whole blood, DU18-02S0011615

value: No


title: dge1_D14 RNA-seq of ReNcell VM treated with 0.3 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM fedratinib
barcode: CATATT batch: dge1

value: 0.3 uM fedratinib

value: fedratinib


title: whole blood, DU18-02S0011643

value: White


title: whole blood, DU18-02S0011614

value: late


title: whole blood, DU18-02S0011642


title: Par_siCont_Veh_rep3

value: siCont. (48h), Veh. (3h)


title: whole blood, DU18-02S0011641

value: Female

value: early


title: whole blood, DU18-02S0011640

value: Asian

value: middle

value: whole blood


title: dge1_D13 RNA-seq of ReNcell VM treated with 10 uM barasertib

description:
RNA-seq of ReNcell VM treated with 10 uM barasertib
barcode: CATAAA batch: dge1

value: in-vitro differentiated neural and glial cells

value: 10 uM barasertib

value: ReNcell VM

value: barasertib


title: whole blood, DU18-02S0011665

value: Male


title: whole blood, DU18-02S0011639


title: dge1_D12 RNA-seq of ReNcell VM treated with 3 uM metformin

description:
RNA-seq of ReNcell VM treated with 3 uM metformin
barcode: CAAAAT batch: dge1

value: 3 uM metformin

value: metformin


title: whole blood, DU18-02S0011660

value: No


title: Par_siCont_Thap_rep2

value: siCont. (48h), 500nM thapsigargin (3h)


title: Par_siCont_Veh_rep1


title: dge1_D11 RNA-seq of ReNcell VM treated with 1 uM a443654

description:
RNA-seq of ReNcell VM treated with 1 uM a443654
barcode: ATTTTG batch: dge1


title: whole blood, DU18-02S0011638

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt

value: White


title: whole blood, DU18-02S0011637


title: dge1_D16 RNA-seq of ReNcell VM treated with 3 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 3 uM cabozantinib
barcode: CTAATT batch: dge1

value: 3 uM cabozantinib

value: cabozantinib


title: GemR_rep3

description:
mRNAseq_Par_GemR_normalized_counts.txt
DESeq2_GemR_vs_Par.txt

data_processing:
The fastq files were mapped to the human genome (hg38) using STAR (version 2.6.0c) followed by HTSeq-count (version 0.11.1), which was used to obtain the read counts. DESeq2 was used for differential analysis as well as to obtain normalized read counts for each condition.
Genome_build: hg38
Supplementary_files_format_and_content: The differential analysis obtained from DESeq2 can be found in a text file.
Supplementary_files_format_and_content: The normalized read counts for each replicate of each condition obtained from DESeq2 can be found in a separate text file.

treatment_protocol: The cells were vehicle (DMSO) treated for 24h prior to harvesting.

value: Gemcitabine resistant L3.6pl


title: whole blood, DU18-02S0011636


title: dge1_D10 RNA-seq of ReNcell VM treated with 10 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 10 uM ruxolitinib
barcode: ATTTAC batch: dge1

value: 10 uM ruxolitinib

value: ruxolitinib


title: whole blood, DU18-02S0011674

value: Female

value: late


title: Par_siCont_Veh_rep2

value: siCont. (48h), Veh. (3h)


title: whole blood, DU18-02S0011635

value: middle

value: whole blood


title: whole blood, DU18-02S0011673


title: dge1_D09 RNA-seq of ReNcell VM treated with 3 uM torin1

description:
RNA-seq of ReNcell VM treated with 3 uM torin1
barcode: ATTGTT batch: dge1

value: in-vitro differentiated neural and glial cells

value: 3 uM torin1

value: ReNcell VM


title: GemR_rep2


title: GemR_rep1


title: whole blood, DU18-02S0011608


title: whole blood, DU18-02S0011634


title: dge1_D07 RNA-seq of ReNcell VM treated with 3 uM bx-912

description:
RNA-seq of ReNcell VM treated with 3 uM bx-912
barcode: ATTATC batch: dge1


title: Par_rep3


title: whole blood, DU18-02S0011680


title: Par_rep2


title: whole blood, DU18-02S0011658


title: whole blood, DU18-02S0011607


title: whole blood, DU18-02S0011679

value: Black/African American


title: Par_rep1


title: dge1_D06 RNA-seq of ReNcell VM treated with 0.3 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 0.3 uM nvp-tae684
barcode: ATTAAG batch: dge1

value: 0.3 uM nvp-tae684


title: ATF4_Par_siCont_Thap_rep2

data_processing:
Bowtie2 (version 2.3.4.1) with a very sensitive read alignment setting was used to map fastq files to the human genome (hg38). Bam files for each condition were merged and their PCR duplicates removed using Samtools (version 1.9). Bamcoverage from deeptools (version 3.0.1) was used to normalize the ChIPseq signal to RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using bamcoverage from deeptools (version 3.0.1) and represent the ChIPseq signal normalized to RPKM. H3K27ac bigwigs were scaled to an equal background intensity. The scaling factor of each condition was individually defined as the the ratio of the median signal intensity of control (vehicle treated Par) across all TSSs +/- 1kb divided by the median signal intensity of each individual condition across all TSSs +/- 1kb.

extract_protocol:
The ChIP was performed by crosslinking protein to DNA using 1% formaldehyde in PBS for 20min followed by chromatin shearing and immunoprecipitation overnight with 1µg of antibody. The immunocomplexes were captured by protein A sepharose for 2h and washed. Crosslinking was reversed and the DNA extracted using phenol-chloroform-isoamyl.
ChIP-Seq libraries were prepared using the KAPA HyperPrep kit and 2.5ng DNA.

tag: chip antibody

value: ATF4 (Cell Signaling #11815)


title: whole blood, DU18-02S0011677

value: Asian

value: No


title: whole blood, DU18-02S0011656

value: Male

value: White


title: whole blood, DU18-02S0011678


title: whole blood, DU18-02S0011604


title: whole blood, DU18-02S0011632


title: ATF4_Par_siCont_Thap_rep1


title: H3K27ac_GemR_siSTIM1_Thap_rep2

value: Gemcitabine resistant L3.6pl

value: siSTIM1 (48h), 500nM thapsigargin (3h)

value: H3K27ac (Diagenode #C15410196)


title: dge1_D02 RNA-seq of ReNcell VM treated with 10 uM rotenone

description:
RNA-seq of ReNcell VM treated with 10 uM rotenone
barcode: ATATTC batch: dge1

data_processing:
Raw RNA reads were aligned against the reference genome and quantified using the bcbio-nextgen single cell/DGE RNA-seq analysis pipeline (https://bcbio-nextgen.readthedocs.io/). The pipeline consists of the following steps:
Well barcodes and unique molecular identifiers (UMIs) were extracted from the first read. All reads not within the edit distance of a single nucleotide from a predefined well barcode were discarded.
Each extant read was quasialigned to the human transcriptome (version GRCh38) using RapMap.
Reads per well were counted using the UMIs, discarding reads originating from the same original RNA molecule with duplicate UMI, weighting multi-mapped reads by the number of transcripts they aligned to and collapsing transcript counts to gene level by summing. across all transcripts of a gene.
Counts were normalized using the size factor method in DESeq2. Replicates with fewer than 30k total counts were excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: deduplicated_counts.csv.gz: CSV file of UMI-deduplicated counts of all 765 samples with Ensembl gene IDs.
Supplementary_files_format_and_content: normalized_counts.csv.gz: CSV file of UMI-deduplicated and normalized counts of all 765 samples with HUGO gene symbols.

value: 10 uM rotenone

value: rotenone


title: whole blood, DU18-02S0011617

value: late


title: dge1_D17 RNA-seq of ReNcell VM treated with 1 uM r 59949

description:
RNA-seq of ReNcell VM treated with 1 uM r 59949
barcode: CTTAAT batch: dge1


title: whole blood, DU18-02S0011657

value: Female

value: whole blood


title: whole blood, DU18-02S0011630

value: early


title: whole blood, DU18-02S0011606

value: middle


title: H3K27ac_GemR_siSTIM1_Thap_rep1


title: dge1_D01 RNA-seq of ReNcell VM treated with 10 uM barasertib

description:
RNA-seq of ReNcell VM treated with 10 uM barasertib
barcode: ATATGA batch: dge1

value: in-vitro differentiated neural and glial cells

value: 10 uM barasertib

value: ReNcell VM

value: barasertib


title: H3K27ac_GemR_siSTIM1_Veh_rep2

value: siSTIM1 (48h), Veh. (3h)


title: dge1_C24 RNA-seq of ReNcell VM treated with 3 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 3 uM pazopanib
barcode: GTATAA batch: dge1

value: 3 uM pazopanib

value: pazopanib


title: whole blood, DU18-02S0011609

value: White

value: No


title: dge1_D05 RNA-seq of ReNcell VM treated with 0.3 uM a443654

description:
RNA-seq of ReNcell VM treated with 0.3 uM a443654
barcode: ATGTAA batch: dge1


title: dge1_D03 RNA-seq of ReNcell VM treated with 10 uM brivanib

description:
RNA-seq of ReNcell VM treated with 10 uM brivanib
barcode: ATCTAT batch: dge1

value: 10 uM brivanib

value: brivanib


title: whole blood, DU18-02S0011629


title: dge1_D08 RNA-seq of ReNcell VM treated with 3 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 3 uM cabozantinib
barcode: ATTCAT batch: dge1

value: 3 uM cabozantinib

value: cabozantinib