title: B ERL Rep 1 [ERL_B_23_22_4_C13]

description:
RNAseq_20151120.C13
Sample ERL_B_23_22_4_C13

source_name: primary cardiomyocytes_Erlotinib

value: Erlotinib


title: B DAB Rep 3 [DAB_B_46_17_4_N16]

status: Public on May 13 2020

type: SRA

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
RNAseq_20151120.N16
Sample DAB_B_46_17_4_N16

library_source: transcriptomic

data_processing:
Data preparation and analysis workflow for 3'-DGE mRNA-seq dataset: https://github.com/DToxS/DGE-GEO-Depot
Aligning 3'-DGE mRNA sequence reads: https://github.com/DToxS/Sequence-Alignment
Mapping aligned 3'-DGE sequence reads to reference genes: https://github.com/DToxS/Feature-Counts
Identifying differentially expressed genes for 3'-DGE mRNA-seq dataset: https://github.com/DToxS/Differential-Comparison
Genome_build: Reference-Library.tar.gz: a compressed file containing the UCSC human genome referece library (version hg38)
Supplementary_files_format_and_content:
DGE-RNAseq-Experiment-Design-20150409.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20150409 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20150409.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20150409 dataset
Differential-Comparison-Configs-20150409.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20150409 dataset
Differential-Comparison-Params-20150409.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20150409 dataset
DEG-Calc-FDR-0.1-20150409.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20150409 dataset
DGE-RNAseq-Experiment-Design-20150503.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20150503 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20150503.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20150503 dataset
Differential-Comparison-Configs-20150503.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20150503 dataset
Differential-Comparison-Params-20150503.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20150503 dataset
DGE-RNAseq-Experiment-Design-20151120.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20151120 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20151120.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20151120 dataset
Differential-Comparison-Configs-20151120.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20151120 dataset
Differential-Comparison-Params-20151120.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20151120 dataset
DEG-Calc-FDR-0.1-20151120.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20151120 dataset
DGE-RNAseq-Experiment-Design-20161108-Cor.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Cor dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Cor.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Cor dataset
Differential-Comparison-Configs-20161108-Cor.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Cor dataset
Differential-Comparison-Params-20161108-Cor.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Cor dataset
DEG-Calc-FDR-0.1-20161108-Cor.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Cor dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Fixed.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Fixed dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Fixed.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Fixed dataset
Differential-Comparison-Configs-20161108-Spec-Fixed.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Fixed dataset
Differential-Comparison-Params-20161108-Spec-Fixed.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Fixed dataset
DEG-Calc-FDR-0.1-20161108-Spec-Fixed.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Fixed dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Var-1.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Var-1 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Var-1.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Var-1 dataset
Differential-Comparison-Configs-20161108-Spec-Var-1.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Var-1 dataset
Differential-Comparison-Params-20161108-Spec-Var-1.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Var-1 dataset
DEG-Calc-FDR-0.1-20161108-Spec-Var-1.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Var-1 dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Var-2.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Var-2 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Var-2.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Var-2 dataset
Differential-Comparison-Configs-20161108-Spec-Var-2.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Var-2 dataset
Differential-Comparison-Params-20161108-Spec-Var-2.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Var-2 dataset
DEG-Calc-FDR-0.1-20161108-Spec-Var-2.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Var-2 dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Var-3.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Var-3 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Var-3.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Var-3 dataset
Differential-Comparison-Configs-20161108-Spec-Var-3.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Var-3 dataset
Differential-Comparison-Params-20161108-Spec-Var-3.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Var-3 dataset
DEG-Calc-FDR-0.1-20161108-Spec-Var-3.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Var-3 dataset
Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment, feature counts, and differential comparison.

molecule: total RNA

organism: Homo sapiens

source_name: primary cardiomyocytes_Dabrafenib

growth_protocol: Cultured under growth conditions with antibiotic free growth media and differentiated for four weeks with antibiotic free differentiation media (see DToxS SOP CE – 1.0: PromoCell Cardiomyocyte Subculture, DToxS SOP CE – 2.0: PromoCell Cardiomyocyte Plating for Drug Test)

extract_protocol:
Total RNA was isolated using Trizol (see DToxS SOP A – 1.0: Total RNA Isolation)
Using the sample name scheme [Treatment Condition]_[Cell Line]_[Investigative Unit]_[Sample ID]_[Plate Number]_[Well Number], library was prepared using 150ng (for the samples with the plate number 1 and 2) and 200ng (for the samples with the plate number 4 and 5) of total RNA enriched for mRNA using polyA beads and the TruSeq RNA Library Prep Kit (Illumina, Cat: RS-122-2001) per manufacturer’s instructions

treatment_protocol: Fully confluent and differentiated cells were treated with drugs or vehicle (DMSO) for 48 hours (see DToxS SOP CE – 4.0: Drug Treatment and Cell Lysis)

tag: source organ

value: Heart

tag: cell type

value: cardiac myocytes

tag: treatment condition

value: Dabrafenib

tag: concentration

tag: treatment time (hrs)

tag: vendor

value: PromoCell

tag: cat #

tag: lot #

tag: well

tag: investigative unit

tag: sample id

tag: rna amount (ng)

tag: nanodrop 260/280

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: B DAB Rep 4 [DAB_B_50_13_4_P4]

description:
RNAseq_20151120.P4
Sample DAB_B_50_13_4_P4


title: B DAS Rep 4 [DAS_B_50_3_4_O19]

description:
RNAseq_20151120.O19
Sample DAS_B_50_3_4_O19

source_name: primary cardiomyocytes_Dasatinib

value: Dasatinib


title: B ERL Rep 3 [ERL_B_40_3_4_I7]

description:
RNAseq_20151120.I7
Sample ERL_B_40_3_4_I7


title: B DAS Rep 1 [DAS_B_40_5_4_I9]

description:
RNAseq_20151120.I9
Sample DAS_B_40_5_4_I9


title: B DAS Rep 2 [DAS_B_44_3_4_M3]

description:
RNAseq_20151120.M3
Sample DAS_B_44_3_4_M3


title: B ERL Rep 4 [ERL_B_40_4_4_I8]

description:
RNAseq_20151120.I8
Sample ERL_B_40_4_4_I8


title: B CTRL Rep 9 [CTRL_B_50_1_4_O18]

description:
RNAseq_20151120.O18
Sample CTRL_B_50_1_4_O18

source_name: primary cardiomyocytes_Vehicle Control

value: Vehicle Control


title: B CTRL Rep 7 [CTRL_B_44_1_4_M2]

description:
RNAseq_20151120.M2
Sample CTRL_B_44_1_4_M2


title: B DAB Rep 2 [DAB_B_44_18_4_M12]

description:
RNAseq_20151120.M12
Sample DAB_B_44_18_4_M12


title: B CTRL Rep 6 [CTRL_B_40_1_4_I6]

description:
RNAseq_20151120.I6
Sample CTRL_B_40_1_4_I6


title: B CTRL Rep 3 [CTRL_B_21_1_4_B22]

description:
RNAseq_20151120.B22
Sample CTRL_B_21_1_4_B22


title: B CTRL Rep 2 [CTRL_B_18_1_4_B14]

description:
RNAseq_20151120.B14
Sample CTRL_B_18_1_4_B14


title: B CTRL Rep 4 [CTRL_B_23_1_4_C7]

description:
RNAseq_20151120.C7
Sample CTRL_B_23_1_4_C7


title: B CTRL Rep 5 [CTRL_B_33_1_4_E23]

description:
RNAseq_20151120.E23
Sample CTRL_B_33_1_4_E23


title: B GEF Rep 2 [GEF_B_23_5_4_C9]

description:
RNAseq_20151120.C9
Sample GEF_B_23_5_4_C9

source_name: primary cardiomyocytes_Gefitinib

value: Gefitinib


title: B IMA Rep 1 [IMA_B_21_22_4_C1]

description:
RNAseq_20151120.C1
Sample IMA_B_21_22_4_C1

source_name: primary cardiomyocytes_Imatinib

value: Imatinib


title: B CRI Rep 3 [CRI_B_23_2_4_C8]

description:
RNAseq_20151120.C8
Sample CRI_B_23_2_4_C8

source_name: primary cardiomyocytes_Crizotinib

value: Crizotinib


title: B CRI Rep 4 [CRI_B_40_22_4_I23]

description:
RNAseq_20151120.I23
Sample CRI_B_40_22_4_I23


title: B DAB Rep 1 [DAB_B_40_16_4_I18]

description:
RNAseq_20151120.I18
Sample DAB_B_40_16_4_I18


title: B CRI Rep 2 [CRI_B_21_20_4_B24]

description:
RNAseq_20151120.B24
Sample CRI_B_21_20_4_B24


title: B ERL Rep 2 [ERL_B_33_10_4_E24]

description:
RNAseq_20151120.E24
Sample ERL_B_33_10_4_E24


title: B GEF Rep 1 [GEF_B_21_15_4_B23]

description:
RNAseq_20151120.B23
Sample GEF_B_21_15_4_B23


title: B CRI Rep 1 [CRI_B_12_23_4_B2]

description:
RNAseq_20151120.B2
Sample CRI_B_12_23_4_B2


title: B CTRL Rep 8 [CTRL_B_46_1_4_N4]

description:
RNAseq_20151120.N4
Sample CTRL_B_46_1_4_N4


title: B CER Rep 4 [CER_B_50_17_4_P8]

description:
RNAseq_20151120.P8
Sample CER_B_50_17_4_P8

source_name: primary cardiomyocytes_Ceritinib

value: Ceritinib


title: B CER Rep 3 [CER_B_46_21_4_N20]

description:
RNAseq_20151120.N20
Sample CER_B_46_21_4_N20


title: B CER Rep 2 [CER_B_44_23_4_M16]

description:
RNAseq_20151120.M16
Sample CER_B_44_23_4_M16


title: B CER Rep 1 [CER_B_40_21_4_I22]

description:
RNAseq_20151120.I22
Sample CER_B_40_21_4_I22


title: B CAB Rep 1 [CAB_B_40_19_4_I20]

description:
RNAseq_20151120.I20
Sample CAB_B_40_19_4_I20

source_name: primary cardiomyocytes_Cabozantinib

value: Cabozantinib


title: B CAB Rep 3 [CAB_B_46_19_4_N18]

description:
RNAseq_20151120.N18
Sample CAB_B_46_19_4_N18


title: B CAB Rep 4 [CAB_B_50_15_4_P6]

description:
RNAseq_20151120.P6
Sample CAB_B_50_15_4_P6


title: B CAB Rep 2 [CAB_B_44_20_4_M14]

description:
RNAseq_20151120.M14
Sample CAB_B_44_20_4_M14


title: B AXI Rep 4 [AXI_B_50_7_4_O21]

description:
RNAseq_20151120.O21
Sample AXI_B_50_7_4_O21

source_name: primary cardiomyocytes_Axitinib

value: Axitinib


title: B AFA Rep 4 [AFA_B_50_10_4_O24]

description:
RNAseq_20151120.O24
Sample AFA_B_50_10_4_O24

source_name: primary cardiomyocytes_Afatinib

value: Afatinib


title: B AXI Rep 1 [AXI_B_40_9_4_I12]

description:
RNAseq_20151120.I12
Sample AXI_B_40_9_4_I12


title: B AXI Rep 3 [AXI_B_46_11_4_N10]

description:
RNAseq_20151120.N10
Sample AXI_B_46_11_4_N10


title: B AFA Rep 1 [AFA_B_40_12_4_I15]

description:
RNAseq_20151120.I15
Sample AFA_B_40_12_4_I15


title: B AXI Rep 2 [AXI_B_44_12_4_M6]

description:
RNAseq_20151120.M6
Sample AXI_B_44_12_4_M6


title: A TOF Rep 4 [TOF_A_11_23_4_G15]

description:
RNAseq_20151120.G15
Sample TOF_A_11_23_4_G15

source_name: primary cardiomyocytes_Tofacitinib

value: Tofacitinib


title: B AFA Rep 2 [AFA_B_44_15_4_M9]

description:
RNAseq_20151120.M9
Sample AFA_B_44_15_4_M9


title: B AFA Rep 3 [AFA_B_46_14_4_N13]

description:
RNAseq_20151120.N13
Sample AFA_B_46_14_4_N13


title: B CTRL Rep 1 [CTRL_B_12_1_4_B1]

description:
RNAseq_20151120.B1
Sample CTRL_B_12_1_4_B1


title: B VEM Rep 3 [VEM_B_46_18_4_N17]

description:
RNAseq_20151120.N17
Sample VEM_B_46_18_4_N17

source_name: primary cardiomyocytes_Vemurafenib

value: Vemurafenib


title: A TOF Rep 3 [TOF_A_31_3_4_E11]

description:
RNAseq_20151120.E11
Sample TOF_A_31_3_4_E11


title: A TOF Rep 1 [TOF_A_11_24_4_A23]

description:
RNAseq_20151120.A23
Sample TOF_A_11_24_4_A23


title: A NIL Rep 4 [NIL_A_38_6_4_G16]

description:
RNAseq_20151120.G16
Sample NIL_A_38_6_4_G16

source_name: primary cardiomyocytes_Nilotinib

value: Nilotinib


title: A NIL Rep 3 [NIL_A_24_19_4_C15]

description:
RNAseq_20151120.C15
Sample NIL_A_24_19_4_C15


title: A NIL Rep 2 [NIL_A_22_16_4_C5]

description:
RNAseq_20151120.C5
Sample NIL_A_22_16_4_C5


title: A NIL Rep 1 [NIL_A_20_13_4_B20]

description:
RNAseq_20151120.B20
Sample NIL_A_20_13_4_B20


title: A IMA Rep 4 [IMA_A_31_4_4_E12]

description:
RNAseq_20151120.E12
Sample IMA_A_31_4_4_E12


title: A IMA Rep 2 [IMA_A_10_2_4_A9]

description:
RNAseq_20151120.A9
Sample IMA_A_10_2_4_A9


title: A IMA Rep 3 [IMA_A_11_6_4_A17]

description:
RNAseq_20151120.A17
Sample IMA_A_11_6_4_A17


title: A IMA Rep 1 [IMA_A_8_19_4_A5]

description:
RNAseq_20151120.A5
Sample IMA_A_8_19_4_A5


title: A GEF Rep 4 [GEF_A_38_3_4_G14]

description:
RNAseq_20151120.G14
Sample GEF_A_38_3_4_G14


title: A GEF Rep 3 [GEF_A_20_10_4_B19]

description:
RNAseq_20151120.B19
Sample GEF_A_20_10_4_B19


title: A DAB Rep 3 [DAB_A_49_12_4_O16]

description:
RNAseq_20151120.O16
Sample DAB_A_49_12_4_O16


title: A GEF Rep 1 [GEF_A_11_21_4_A21]

description:
RNAseq_20151120.A21
Sample GEF_A_11_21_4_A21


title: A DAB Rep 4 [DAB_A_49_13_4_O17]

description:
RNAseq_20151120.O17
Sample DAB_A_49_13_4_O17


title: A DAB Rep 1 [DAB_A_38_15_4_G18]

description:
RNAseq_20151120.G18
Sample DAB_A_38_15_4_G18


title: A CTRL Rep 9 [CTRL_A_38_1_4_G13]

description:
RNAseq_20151120.G13
Sample CTRL_A_38_1_4_G13


title: A CTRL Rep 6 [CTRL_A_22_1_4_C4]

description:
RNAseq_20151120.C4
Sample CTRL_A_22_1_4_C4


title: A CTRL Rep 2 [CTRL_A_10_1_4_A10]

description:
RNAseq_20151120.A10
Sample CTRL_A_10_1_4_A10


title: A CTRL Rep 4 [CTRL_A_14_1_4_B6]

description:
RNAseq_20151120.B6
Sample CTRL_A_14_1_4_B6


title: A CTRL Rep 1 [CTRL_A_8_1_4_A2]

description:
RNAseq_20151120.A2
Sample CTRL_A_8_1_4_A2


title: A CTRL Rep 8 [CTRL_A_31_1_4_E10]

description:
RNAseq_20151120.E10
Sample CTRL_A_31_1_4_E10


title: A CTRL Rep 7 [CTRL_A_24_1_4_C14]

description:
RNAseq_20151120.C14
Sample CTRL_A_24_1_4_C14


title: A CRI Rep 4 [CRI_A_38_23_4_G20]

description:
RNAseq_20151120.G20
Sample CRI_A_38_23_4_G20


title: A TOF Rep 2 [TOF_A_24_25_4_C17]

description:
RNAseq_20151120.C17
Sample TOF_A_24_25_4_C17


title: A CTRL Rep 5 [CTRL_A_20_1_4_B18]

description:
RNAseq_20151120.B18
Sample CTRL_A_20_1_4_B18


title: A CRI Rep 3 [CRI_A_16_21_4_B13]

description:
RNAseq_20151120.B13
Sample CRI_A_16_21_4_B13


title: A CRI Rep 2 [CRI_A_11_16_4_A20]

description:
RNAseq_20151120.A20
Sample CRI_A_11_16_4_A20


title: A CRI Rep 1 [CRI_A_8_20_4_A6]

description:
RNAseq_20151120.A6
Sample CRI_A_8_20_4_A6


title: A AXI Rep 4 [AXI_A_38_7_4_G17]

description:
RNAseq_20151120.G17
Sample AXI_A_38_7_4_G17


title: A AXI Rep 3 [AXI_A_24_20_4_C16]

description:
RNAseq_20151120.C16
Sample AXI_A_24_20_4_C16


title: D SUN Rep 2 [SUN_D_9_20_2_B8]

description:
RNAseq_20150503.B8
Sample SUN_D_9_20_2_B8

source_name: primary cardiomyocytes_Sunitinib

value: Sunitinib


title: A AXI Rep 2 [AXI_A_22_17_4_C6]

description:
RNAseq_20151120.C6
Sample AXI_A_22_17_4_C6

value: Heart


title: D SUN Rep 1 [SUN_D_9_19_2_B7]

description:
RNAseq_20150503.B7
Sample SUN_D_9_19_2_B7

value: cardiac myocytes


title: D SOR Rep 2 [SOR_D_9_16_2_B4]

description:
RNAseq_20150503.B4
Sample SOR_D_9_16_2_B4

source_name: primary cardiomyocytes_Sorafenib

value: Sorafenib


title: A DAB Rep 2 [DAB_A_38_16_4_G19]

description:
RNAseq_20151120.G19
Sample DAB_A_38_16_4_G19

value: Dabrafenib

value: PromoCell


title: A GEF Rep 2 [GEF_A_11_22_4_A22]

description:
RNAseq_20151120.A22
Sample GEF_A_11_22_4_A22


title: D IMA Rep 1 [IMA_D_9_23_2_B11]

description:
RNAseq_20150503.B11
Sample IMA_D_9_23_2_B11


title: D CTRL Rep 3 [CTRL_D_13_2_2_G9]

description:
RNAseq_20150503.G9
Sample CTRL_D_13_2_2_G9

value: Vehicle Control


title: D CTRL Rep 1 [CTRL_D_9_1_2_A1]

description:
RNAseq_20150503.A1
Sample CTRL_D_9_1_2_A1


title: B SUN Rep 2 [SUN_B_12_20_2_G3]

description:
RNAseq_20150503.G3
Sample SUN_B_12_20_2_G3


title: D CTRL Rep 2 [CTRL_D_9_2_2_A2]

description:
RNAseq_20150503.A2
Sample CTRL_D_9_2_2_A2


title: B CTRL Rep 2 [CTRL_B_12_2_2_F1]

description:
RNAseq_20150503.F1
Sample CTRL_B_12_2_2_F1


title: B CTRL Rep 3 [CTRL_B_17_1_2_H3]

description:
RNAseq_20150503.H3
Sample CTRL_B_17_1_2_H3


title: A CTRL Rep 3 [CTRL_A_11_1_4_A15]

description:
RNAseq_20151120.A15
Sample CTRL_A_11_1_4_A15


title: A TOF Rep 2 [TOF_A_11_24_2_E11]

description:
RNAseq_20150503.E11
Sample TOF_A_11_24_2_E11


title: A LAP Rep 1 [LAP_A_11_17_2_E4]

description:
RNAseq_20150503.E4
Sample LAP_A_11_17_2_E4

source_name: primary cardiomyocytes_Lapatinib

value: Lapatinib


title: A SUN Rep 1 [SUN_A_10_16_2_C12]

description:
RNAseq_20150503.C12
Sample SUN_A_10_16_2_C12


title: A LAP Rep 2 [LAP_A_11_18_2_E5]

description:
RNAseq_20150503.E5
Sample LAP_A_11_18_2_E5


title: B CRI Rep 1 [CRI_B_12_23_2_G6]

description:
RNAseq_20150503.G6
Sample CRI_B_12_23_2_G6


title: A TOF Rep 1 [TOF_A_11_23_2_E10]

description:
RNAseq_20150503.E10
Sample TOF_A_11_23_2_E10


title: B SUN Rep 1 [SUN_B_12_19_2_G2]

description:
RNAseq_20150503.G2
Sample SUN_B_12_19_2_G2


title: D SOR Rep 1 [SOR_D_9_15_2_B3]

description:
RNAseq_20150503.B3
Sample SOR_D_9_15_2_B3


title: A GEF Rep 1 [GEF_A_11_21_2_E8]

description:
RNAseq_20150503.E8
Sample GEF_A_11_21_2_E8

value: Gefitinib


title: A IMA Rep 1 [IMA_A_10_2_2_C1]

description:
RNAseq_20150503.C1
Sample IMA_A_10_2_2_C1

value: Imatinib


title: A SUN Rep 5 [SUN_A_7_14_1_F4]

description:
RNAseq_20150409.F4
Sample SUN_A_7_14_1_F4


title: A CTRL Rep 2 [CTRL_A_11_1_2_D5]

description:
RNAseq_20150503.D5
Sample CTRL_A_11_1_2_D5


title: A CTRL Rep 1 [CTRL_A_10_1_2_B12]

description:
RNAseq_20150503.B12
Sample CTRL_A_10_1_2_B12


title: A SUN Rep 4 [SUN_A_7_13_1_F3]

description:
RNAseq_20150409.F3
Sample SUN_A_7_13_1_F3


title: A SUN Rep 3 [SUN_A_6_9_1_D4]

description:
RNAseq_20150409.D4
Sample SUN_A_6_9_1_D4


title: A AXI Rep 1 [AXI_A_20_14_4_B21]

description:
RNAseq_20151120.B21
Sample AXI_A_20_14_4_B21


title: B CTRL Rep 1 [CTRL_B_12_1_2_E12]

description:
RNAseq_20150503.E12
Sample CTRL_B_12_1_2_E12


title: B LAP Rep 1 [LAP_B_12_24_2_G7]

description:
RNAseq_20150503.G7
Sample LAP_B_12_24_2_G7


title: A SOR Rep 6 [SOR_A_8_2_1_F12]

description:
RNAseq_20150409.F12
Sample SOR_A_8_2_1_F12


title: A SOR Rep 5 [SOR_A_7_4_1_E6]

description:
RNAseq_20150409.E6
Sample SOR_A_7_4_1_E6


title: A SOR Rep 3 [SOR_A_6_6_1_D1]

description:
RNAseq_20150409.D1
Sample SOR_A_6_6_1_D1


title: A SOR Rep 4 [SOR_A_7_3_1_E5]

description:
RNAseq_20150409.E5
Sample SOR_A_7_3_1_E5


title: A CTRL Rep 15 [CTRL_A_5_2_1_H10]

description:
RNAseq_20150409.H10
Sample CTRL_A_5_2_1_H10


title: A CTRL Rep 13 [CTRL_A_8_1_1_F11]

description:
RNAseq_20150409.F11
Sample CTRL_A_8_1_1_F11


title: A CTRL Rep 14 [CTRL_A_5_2_1_H9]

description:
RNAseq_20150409.H9
Sample CTRL_A_5_2_1_H9


title: A IMA Rep 1 [IMA_A_8_19_1_H4]

description:
RNAseq_20150409.H4
Sample IMA_A_8_19_1_H4


title: A CRI Rep 1 [CRI_A_11_16_2_E3]

description:
RNAseq_20150503.E3
Sample CRI_A_11_16_2_E3

value: Crizotinib


title: A SOR Rep 1 [SOR_A_5_6_1_C2]

description:
RNAseq_20150409.C2
Sample SOR_A_5_6_1_C2


title: A CTRL Rep 12 [CTRL_A_7_2_1_E4]

description:
RNAseq_20150409.E4
Sample CTRL_A_7_2_1_E4


title: A CTRL Rep 11 [CTRL_A_7_1_1_E3]

description:
RNAseq_20150409.E3
Sample CTRL_A_7_1_1_E3


title: A CTRL Rep 10 [CTRL_A_6_3_1_C11]

description:
RNAseq_20150409.C11
Sample CTRL_A_6_3_1_C11


title: A CTRL Rep 9 [CTRL_A_6_2_1_C10]

description:
RNAseq_20150409.C10
Sample CTRL_A_6_2_1_C10


title: A CTRL Rep 8 [CTRL_A_6_1_1_C9]

description:
RNAseq_20150409.C9
Sample CTRL_A_6_1_1_C9


title: A CTRL Rep 6 [CTRL_A_5_2_1_B12]

description:
RNAseq_20150409.B12
Sample CTRL_A_5_2_1_B12


title: A CTRL Rep 5 [CTRL_A_5_1_1_B11]

description:
RNAseq_20150409.B11
Sample CTRL_A_5_1_1_B11


title: A CTRL Rep 7 [CTRL_A_5_3_1_C1]

description:
RNAseq_20150409.C1
Sample CTRL_A_5_3_1_C1


title: A SUN Rep 2 [SUN_A_6_8_1_D3]

description:
RNAseq_20150409.D3
Sample SUN_A_6_8_1_D3


title: A CTRL Rep 3 [CTRL_A_4_2_1_A9]

description:
RNAseq_20150409.A9
Sample CTRL_A_4_2_1_A9


title: A CTRL Rep 1 [CTRL_A_3_5_1_A4]

description:
RNAseq_20150409.A4
Sample CTRL_A_3_5_1_A4


title: A CRI Rep 1 [CRI_A_8_20_1_H5]

description:
RNAseq_20150409.H5
Sample CRI_A_8_20_1_H5


title: A SOR Rep 2 [SOR_A_6_5_1_C12]

description:
RNAseq_20150409.C12
Sample SOR_A_6_5_1_C12


title: A CTRL Rep 4 [CTRL_A_4_3_1_A10]

description:
RNAseq_20150409.A10
Sample CTRL_A_4_3_1_A10


title: E NIN Rep 3 [NIN.E.3.3]

description:
NIN_E_3_3_TCCGCGAA_TATAGCCT
Sample77

data_processing:
Data preparation and analysis workflow for conventional mRNA-seq dataset: https://github.com/DToxS/Conv-GEO-Depot
Aligning conventional mRNA sequence reads: https://github.com/DToxS/Sequence-Alignment
Mapping aligned conventional sequence reads to reference genes: https://github.com/DToxS/Feature-Counts
Identifying differentially expressed genes for conventional mRNA-seq dataset: https://github.com/DToxS/Differential-Comparison
Genome_build: Reference-Library.tar.gz: a compressed file containing the UCSC human genome referece library (version hg38)
Supplementary_files_format_and_content: Conv-RNAseq-Experiment-Design.tsv.gz: a compressed file containing the experiment design table of all the samples from the conventional dataset to be used by the DEG-comparison pipeline
Supplementary_files_format_and_content: Conv-RNAseq-Read-Counts.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the conventional dataset
Supplementary_files_format_and_content: Differential-Comparison-Configs.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the conventional dataset
Supplementary_files_format_and_content: Differential-Comparison-Params.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the conventional dataset
Supplementary_files_format_and_content: DEG-Calc-FDR-0.1.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the conventional dataset
Supplementary_files_format_and_content: Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment, feature counts, and differential comparison.

source_name: primary cardiomyocytes_Nintedanib

extract_protocol:
Total RNA was isolated using Trizol (see DToxS SOP A – 1.0: Total RNA Isolation)
Library was prepared using 300 ng of total RNA enriched for mRNA using polyA beads and the TruSeq RNA Library Prep Kit (Illumina, Cat: RS-122-2001) per manufacturer’s instructions

value: heart

value: Nintedanib


title: E NIN Rep 1 [NIN.E.1.3]

description:
NIN_E_1_3_TAATGCGC_CAGGACGT
Sample3


title: E LEN Rep 3 [LEN.E.3.2]

description:
LEN_E_3_2_CGGCTATG_GTACTGAC
Sample72

source_name: primary cardiomyocytes_Lenvatinib

value: Lenvatinib


title: A SUN Rep 1 [SUN_A_6_7_1_D2]

description:
RNAseq_20150409.D2
Sample SUN_A_6_7_1_D2


title: E LEN Rep 1 [LEN.E.1.2]

description:
LEN_E_1_2_TAATGCGC_TAATCTTA
Sample2


title: E IBR Rep 3 [IBR.E.3.4]

description:
IBR_E_3_4_TCCGCGAA_ATAGAGGC
Sample79

source_name: primary cardiomyocytes_Ibrutinib

value: Ibrutinib


title: E IBR Rep 2 [IBR.E.2.4]

description:
IBR_E_2_4_CGGCTATG_AGGCGAAG
Sample52


title: E LEN Rep 2 [LEN.E.2.2]

description:
LEN_E_2_2_CGGCTATG_CCTATCCT
Sample48


title: E IBR Rep 4 [IBR.E.4.4]

description:
IBR_E_4_4_TCCGCGAA_CAGGACGT
Sample99


title: E LEN Rep 4 [LEN.E.4.2]

description:
LEN_E_4_2_TCCGCGAA_AGGCGAAG
Sample95


title: E CTRL Rep 4 [CTRL.E.4.1]

description:
CTRL_E_4_1_TCCGCGAA_GGCTCTGA
Sample94

source_name: primary cardiomyocytes_Control

value: Control


title: E IBR Rep 1 [IBR.E.1.4]

description:
IBR_E_1_4_TAATGCGC_GTACTGAC
Sample4


title: E CTRL Rep 2 [CTRL.E.2.1]

description:
CTRL_E_2_1_CGGCTATG_ATAGAGGC
Sample46


title: A CTRL Rep 2 [CTRL_A_4_1_1_A8]

description:
RNAseq_20150409.A8
Sample CTRL_A_4_1_1_A8

source_name: primary cardiomyocytes_Vehicle Control


title: E CER Rep 2 [CER.E.3.5]

description:
CER_E_3_5_TCCGCGAA_CCTATCCT
Sample81

source_name: primary cardiomyocytes_Ceritinb

value: Ceritinb


title: E CER Rep 3 [CER.E.4.5]

description:
CER_E_4_5_TCCGCGAA_GTACTGAC
Sample100


title: E CTRL Rep 1 [CTRL.E.1.1]

description:
CTRL_E_1_1_TAATGCGC_AGGCGAAG
Sample47


title: D NIN Rep 4 [NIN.D.4.3]

description:
NIN_D_4_3_TAATGCGC_ATAGAGGC
Sample65


title: E NIN Rep 2 [NIN.E.2.3]

description:
NIN_E_2_3_CGGCTATG_GGCTCTGA
Sample50


title: D NIN Rep 3 [NIN.D.3.3]

description:
NIN_D_3_3_CTGAAGCT_AGGCGAAG
Sample40


title: D LEN Rep 4 [LEN.D.4.2]

description:
LEN_D_4_2_TAATGCGC_TATAGCCT
Sample60


title: D NIN Rep 2 [NIN.D.2.3]

description:
NIN_D_2_3_GAATTCGT_GTACTGAC
Sample23


title: D LEN Rep 3 [LEN.D.3.2]

description:
LEN_D_3_2_CTGAAGCT_GGCTCTGA
Sample38


title: D LEN Rep 1 [LEN.D.1.2]

description:
LEN_D_1_2_GAATTCGT_ATAGAGGC
Sample7


title: D IBR Rep 2 [IBR.D.2.4]

description:
IBR_D_2_4_CTGAAGCT_TATAGCCT
Sample25


title: D IBR Rep 1 [IBR.D.1.4]

description:
IBR_D_1_4_GAATTCGT_GGCTCTGA
Sample11


title: D IBR Rep 3 [IBR.D.4.4]

description:
IBR_D_4_4_TAATGCGC_CCTATCCT
Sample67


title: D CTRL Rep 3 [CTRL.D.3.1]

description:
CTRL_D_3_1_CTGAAGCT_CCTATCCT
Sample36


title: D CTRL Rep 2 [CTRL.D.2.1]

description:
CTRL_D_2_1_GAATTCGT_TAATCTTA
Sample19


title: D CER Rep 1 [CER.D.1.5]

description:
CER_D_1_5_GAATTCGT_AGGCGAAG
Sample12


title: D CER Rep 4 [CER.D.4.5]

description:
CER_D_4_5_TAATGCGC_GGCTCTGA
Sample69


title: D CER Rep 3 [CER.D.3.5]

description:
CER_D_3_5_CTGAAGCT_CAGGACGT
Sample44


title: D CER Rep 2 [CER.D.2.5]

description:
CER_D_2_5_CTGAAGCT_ATAGAGGC
Sample29


title: D CTRL Rep 1 [CTRL.D.1.1]

description:
CTRL_D_1_1_GAATTCGT_TATAGCCT
Sample18


title: E CTRL Rep 3 [CTRL.E.3.1]

description:
CTRL_E_3_1_CGGCTATG_CAGGACGT
Sample70


title: E CER Rep 1 [CER.E.1.5]

description:
CER_E_1_5_CGGCTATG_TATAGCCT
Sample5


title: B NIN Rep 1 [NIN.B.2.3]

description:
NIN_B_2_3_GAGATTCC_GGCTCTGA
Sample84


title: B NIN Rep 2 [NIN.B.3.3]

description:
NIN_B_3_3_ATTCAGAA_TATAGCCT
Sample104


title: B LEN Rep 4 [LEN.B.4.2]

description:
LEN_B_4_2_ATTCAGAA_AGGCGAAG
Sample122


title: D NIN Rep 1 [NIN.D.1.3]

description:
NIN_D_1_3_GAATTCGT_CCTATCCT
Sample9


title: B LEN Rep 3 [LEN.B.3.2]

description:
LEN_B_3_2_GAGATTCC_GTACTGAC
Sample102


title: B DAS Rep 3 [DAS_B_46_3_4_N5]

description:
RNAseq_20151120.N5
Sample DAS_B_46_3_4_N5

source_name: primary cardiomyocytes_Dasatinib

value: Dasatinib


title: B LEN Rep 2 [LEN.B.2.2]

description:
LEN_B_2_2_GAGATTCC_CCTATCCT
Sample83


title: B LEN Rep 1 [LEN.B.1.2]

description:
LEN_B_1_2_CGCTCATT_TAATCTTA
Sample14


title: B IBR Rep 2 [IBR.B.2.4]

description:
IBR_B_2_4_GAGATTCC_AGGCGAAG
Sample85


title: D LEN Rep 2 [LEN.D.2.2]

description:
LEN_D_2_2_GAATTCGT_CAGGACGT
Sample21


title: B IBR Rep 4 [IBR.B.4.4]

description:
IBR_B_4_4_ATTCAGAA_CAGGACGT
Sample125


title: B IBR Rep 3 [IBR.B.3.4]

description:
IBR_B_3_4_ATTCAGAA_ATAGAGGC
Sample105


title: B IBR Rep 1 [IBR.B.1.4]

description:
IBR_B_1_4_CGCTCATT_GTACTGAC
Sample107


title: B CTRL Rep 3 [CTRL.B.4.1]

description:
CTRL_B_4_1_ATTCAGAA_GGCTCTGA
Sample121


title: B CTRL Rep 2 [CTRL.B.3.1]

description:
CTRL_B_3_1_GAGATTCC_CAGGACGT
Sample101


title: B CTRL Rep 1 [CTRL.B.1.1]

description:
CTRL_B_1_1_CGCTCATT_AGGCGAAG
Sample13


title: B CER Rep 2 [CER.B.2.5]

description:
CER_B_2_5_GAGATTCC_TAATCTTA
Sample87


title: A NIN Rep 3 [NIN.A.3.3]

description:
NIN_A_3_3_TCCGGAGA_AGGCGAAG
Sample118


title: A NIN Rep 2 [NIN.A.2.3]

description:
NIN_A_2_3_ATTACTCG_GTACTGAC
Sample91


title: A LEN Rep 4 [LEN.A.4.2]

description:
LEN_A_4_2_CGCTCATT_TATAGCCT
Sample128


title: A NIN Rep 1 [NIN.A.1.3]

description:
NIN_A_1_3_ATTACTCG_CCTATCCT
Sample31


title: A LEN Rep 1 [LEN.A.1.2]

description:
LEN_A_1_2_ATTACTCG_ATAGAGGC
Sample116


title: A LEN Rep 3 [LEN.A.3.2]

description:
LEN_A_3_2_TCCGGAGA_GGCTCTGA
Sample110


title: A IBR Rep 2 [IBR.A.2.4]

description:
IBR_A_2_4_TCCGGAGA_TATAGCCT
Sample92


title: A IBR Rep 1 [IBR.A.1.4]

description:
IBR_A_1_4_ATTACTCG_GGCTCTGA
Sample32


title: A IBR Rep 3 [IBR.A.3.4]

description:
IBR_A_3_4_TCCGGAGA_TAATCTTA
Sample112


title: A CTRL Rep 2 [CTRL.A.2.1]

description:
CTRL_A_2_1_ATTACTCG_TAATCTTA
Sample88


title: A CTRL Rep 4 [CTRL.A.4.1]

description:
CTRL_A_4_1_TCCGGAGA_GTACTGAC
Sample127


title: A CTRL Rep 3 [CTRL.A.3.1]

description:
CTRL_A_3_1_TCCGGAGA_CCTATCCT
Sample132


title: A CER Rep 1 [CER.A.1.5]

description:
CER_A_1_5_ATTACTCG_AGGCGAAG
Sample114


title: A CTRL Rep 1 [CTRL.A.1.1]

description:
CTRL_A_1_1_ATTACTCG_TATAGCCT
Sample89


title: A CER Rep 2 [CER.A.2.5]

description:
CER_A_2_5_TCCGGAGA_ATAGAGGC
Sample93


title: undiff_sgCX-5_R848_1

city: Vienna

first: Vitaly

last: Sedlyarov

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: Research Center for Molecular Medicine

data_processing:
basecalling: Illumina2bam, version 1.17
adapter and quality trimming: cutadapt, version 1.16
mapping: STAR, version 2.5.2b
quantification: ESAT
Genome_build: hg38

growth_protocol: THP-1 cells were purchased from ATCC. Cells were grown in RPMI supplemented with 10% (v/v) FBS and antibiotics (100 U/ml penicillin, 100 mg/ml streptomycin), all from Gibco. Cells were incubated at 37°C in 5% CO2.

extract_protocol:
RNA was isolated using the QIAGEN RNeasy Mini kit including a DNase I digest step.
RNA-Seq libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacture’s protocol.

treatment_protocol: THP1 control (sgRen) and two SLC15A4- and CXorf21-deficient cell lines (3E6 cells per point) were left untreated or stimulated for 6 hours with 5 μg/ml R848.

tag: cell line

tag: sgrna

tag: treatment


title: undiff_sgCX-5_R848_3


title: undiff_sgCX-1_R848_3


title: undiff_sgCX-5_ns_3

value: untreated


title: undiff_sgCX-5_ns_2


title: A CER Rep 3 [CER.A.3.5]

description:
CER_A_3_5_TCCGGAGA_CAGGACGT
Sample113

tag: source organ

tag: cell type

value: cardiac myocytes

tag: treatment condition


title: B CER Rep 3 [CER.B.3.5]

description:
CER_B_3_5_ATTCAGAA_CCTATCCT
Sample106

tag: concentration

tag: vendor

tag: treatment time (hrs)


title: undiff_sgCX-5_ns_1


title: B CER Rep 1 [CER.B.1.5]

description:
CER_B_1_5_GAGATTCC_TATAGCCT
Sample17

tag: cat #

tag: lot #

tag: well


title: A NIN Rep 4 [NIN.A.4.3]

description:
NIN_A_4_3_CGCTCATT_ATAGAGGC
Sample129

tag: investigative unit

tag: sample id

tag: rna amount (ng)


title: undiff_sgCX-1_R848_2


title: undiff_sgCX-1_ns_2


title: undiff_sgSLC15A4-5_R848_3


title: undiff_sgCX-1_ns_1


title: undiff_sgCX-1_R848_1


title: undiff_sgCX-5_R848_2


title: undiff_sgSLC15A4-5_ns_2


title: undiff_sgSLC15A4-5_ns_3


title: undiff_sgSLC15A4-5_ns_1


title: undiff_sgSLC15A4-2_R848_2


title: undiff_sgSLC15A4-2_R848_3


title: undiff_sgSLC15A4-2_R848_1


title: undiff_sgSLC15A4-2_ns_3


title: A LEN Rep 2 [LEN.A.2.2]

description:
LEN_A_2_2_ATTACTCG_CAGGACGT
Sample90

tag: nanodrop 260/280

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: undiff_sgSLC15A4-2_ns_1

tag: cell line

tag: sgrna


title: undiff_sgRen_R848_3

value: sgRen

tag: treatment


title: undiff_sgSLC15A4-2_ns_2


title: undiff_sgRen_R848_1


title: undiff_sgSLC15A4-5_R848_1


title: undiff_sgRen_R848_2


title: undiff_sgRen_ns_3


title: undiff_sgCX-1_ns_3


title: undiff_sgSLC15A4-5_R848_2


title: undiff_sgRen_ns_1


title: A GEF Rep 2 [GEF_A_11_22_2_E9]

description:
RNAseq_20150503.E9
Sample GEF_A_11_22_2_E9

source_name: primary cardiomyocytes_Gefitinib

tag: source organ

value: Heart

tag: cell type

tag: h2o volume (ul)


title: undiff_sgRen_ns_2


title: A IMA Rep 2 [IMA_A_11_6_2_D8]

description:
RNAseq_20150503.D8
Sample IMA_A_11_6_2_D8

source_name: primary cardiomyocytes_Imatinib

tag: treatment condition

tag: concentration

tag: vendor

value: PromoCell


title: CD8+ T cells, donor TU0085

city: San Diego

first: Mikhail

last: Pomaznoy

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1).
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
The alignment results were parsed via SAMtools to generate SAM files.
Read counts for each genomic feature were obtained with the htseq-count program (v 0.6.0) using the “union” option.
Genome_build: hg19

molecule: polyA RNA

source_name: peripheral blood

extract_protocol:
For each condition, 200 cells were collected at 4C in 8 µl of lysis buffer (0.2% Triton X-100, 2U/µl of recombinant RNase inhibitor (Clontech/Takara), 5 mM dNTP mix (Life Technologies) in a 96-well PCR plate (Bio-Rad). Immediately after sorting, plates were spun for 1 min at 3000 rpm, and stored at -80C until RNA extraction. Four microliters of each sample was amplified following the Smart-seq2 protocol.
mRNA was captured using poly-dT oligonucleotides and directly reverse transcribed into full-length cDNA (amplified by PCR for 16 cycles). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina). Whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Barcoded Illumina sequencing libraries (Nextera, Illumina) were generated using the automated platform (Biomek FXp). Libraries were sequenced on a HiSeq 2500 Illumina platform to obtain 50-bp single-end reads (TruSeq Rapid kit; Illumina).

tag: donor id

tag: disease state

value: TBneg


title: MR1tet- T cells, donor TU0085


title: CD8+ w/o MAITs T cells, donor TU0084


title: CD8+ w/o MAITs T cells, donor TU0085


title: MR1tet+ T cells, donor TU0085


title: CD8+ T cells, donor TU0084


title: MR1tet+ T cells, donor TU0084


title: MR1tet- T cells, donor TU0084


title: MR1tet+ T cells, donor TU0081

value: LTBI


title: CD8+ w/o MAITs T cells, donor TU0081


title: CD8+ T cells, donor TU0081


title: CD8+ T cells, donor TU0079


title: MR1tet- T cells, donor TU0079


title: patient no 489 tumor sample at IV grade_ biological_rep1

type: RNA

city: Kraków

first: Judyta

last: Górka

address: Gronostajowa 7

department: Department of General Biochemistry

country: Poland

institute: Jagiellonian University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48°C on Affymetrix HuGene2.1 ST Array Strp. Arrays were washed and stained in the Affymetrix Gene Atlas Fluidics Station.

scan_protocol: Affymetrix HuGene2.1 ST Array Strips were scanned using the Gene Atlas Imaging Station (S/N 91001280).

data_processing: The data were normalized with Expression Console Software 1.4.1 with RMA algorithm and analyse using Affymetrix transcriptom Analysis Console (TAC) Software 3.1 with ANOVA one-way between subject (unpaired)

label: biotin

source_name: human tumor sample in fourth stage of cancer

label_protocol: 100 ng of total RNA were used to synthesis and amplification od ss-cDNA, then samples were fragmented and labeled with biotin. Each step was performed according to Affymetrix GeneChip WT PLUS Reagent Kit Manual (2013 Affymetrix, P/N 703174 Rev. 2)

extract_protocol: patient no 241 tumor sample at II grade_ biological_rep1

tag: tissue

value: clear cell renal cell carcinoma

tag: Stage

value: fourth

tag: gender

value: female

tag: age


title: patient no 275_1 tumor sample at IV grade_ biological_rep1


title: patient no 411 tumor sample at IV grade_ biological_rep1

value: male


title: patient no 398 tumor sample at IV grade_ biological_rep1


title: patient no 452_3 tumor sample at IV grade_ biological_rep1

value: no data


title: patient no 473 tumor sample at IV grade_ biological_rep1


title: patient no 390a tumor sample at IV grade_ biological_rep1


title: MR1tet+ T cells, donor TU0079


title: patient no 415 tumor sample at IV grade_ biological_rep1


title: MR1tet+ T cells, donor TU0078


title: CD8+ T cells, donor TU0078


title: CD8+ w/o MAITs T cells, donor TU0078


title: MR1tet+ T cells, donor TU0071


title: CD8+ w/o MAITs T cells, donor TU0071


title: MR1tet- T cells, donor TU0071


title: patient no 462_1 tumor sample at IV grade_ biological_rep1


title: patient no 228 tumor sample at IV grade_ biological_rep1


title: patient no 265 tumor sample at IV grade_ biological_rep1


title: patient no 217_1 tumor sample at IV grade_ biological_rep1


title: MR1tet- T cells, donor TU0078


title: CD8+ T cells, donor TU0071


title: patient no 220_1 tumor sample at IV grade_ biological_rep1


title: patient no 204 tumor sample at IV grade_ biological_rep1


title: MR1tet+ T cells, donor TU0070


title: CD8+ w/o MAITs T cells, donor TU0070


title: patient no 474 tumor sample at III grade_ biological_rep1

source_name: human tumor sample in third stage of cancer

value: third


title: MR1tet- T cells, donor TU0063


title: CD8+ T cells, donor TU0070


title: CD8+ w/o MAITs T cells, donor TU0063


title: patient no 430_1 tumor sample at III grade_ biological_rep1


title: CD8+ T cells, donor TU0063


title: MR1tet+ T cells, donor TU0063


title: Primed state RUES-2 [RUES2-2]

type: genomic

city: Buffalo

first: Jian

last: Feng

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

hyb_protocol: Samples are resuspended and loaded into the Methylation EPIC BeadChips and hybridized overnight as per the Infinium HD Assay Methylation Protocol.

scan_protocol: Following washing, staining, and addition of a protective coating to the BeadChips as per Infinium HD Assay Methylation Protocol, the BeadChips are imaged using the Illumina iScan Reader to measure the fluorescence intensity of each probe for both methylation and unmethylated DNA.

data_processing: BeadChip data files are analyzed with Illumina's GenomeStudio (v2011.1) methylation module (v1.9.0) to report control normalization with background subtraction methylation data.

molecule: genomic DNA

source_name: embryonic stem cells

label_protocol: DNA methylation was determined using Illumina MethylationEPIC array with the Infinium HD Assay Methylation Protocol.  500ng of genomic DNA for each samples is bisulfite converted with Zymo Research EZ DNA Methylation-Gold Kit, then 200ng of each converted sample is amplified and fragmented as per the InfiniumHD Assay Methylation Protocol.

growth_protocol: Human embryonic stem cell (ESC) lines H9,RUES-2  were maintained on mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells in hESC medium (DMEM/F12 containing 20% knockout serum replacement, 2mM l-glutamine, 1% nonessential amino acids (NEAA), 100U of penicillin, 100 mg of streptomycin (all from Life Technologies), 0.1mM β-mercaptoethanol (Sigma), and 4 ng/mL bFGF (PeproTech). Cells were passaged every 6–7 days by dispase (1 mg/mL, Life Technologies) treatment.

extract_protocol: Genomic DNA was extracted and purified using QIAamp DNA Blood Mini Kit according to standard instructions

value: embryonic stem cells

tag: state

value: primed state

tag: passages

tag: qc

value: Passed


title: patient no 418 tumor sample at III grade_ biological_rep1


title: patient no 426_1 tumor sample at III grade_ biological_rep1


title: naive state RUES-2  [NRUES2-1]

growth_protocol: Naive state H9 and RUES-2 were maintained in naïve state medium(50% glucose-free DMEM/F12(Life Technologies) and 50% glucose-free Neurobasal(Life Technologies), with 5mM glucose, 1mM glutamine, 1% NEAA, 0.1mM β-mercaptoethanol, penicillin–streptomycin, 20 ng/mL recombinant human LIF (Millipore), 5 mg/mL bovine serum albumin (BSA) (Sigma), 18µg/ml human insulin (Sigma), 1 µM PD0325901 (PD, EMD Millipore), and 3 µM CHIR99021 (CH, Stemgent). Cells were passaged every 3 days by using mechanical and (or) enzymatic methods.

tag: cell line

value: naïve state


title: patient no 404 tumor sample at III grade_ biological_rep1


title: MR1tet- T cells, donor TU0053


title: Primed state RUES-2 [RUES2-3]


title: naive state RUES-2  [NRUES2-3]


title: naive state H9  [NH9-4]


title: patient no 431_1 tumor sample at III grade_ biological_rep1


title: Primed state RUES-2 [RUES2-4]


title: patient no 392_1 tumor sample at III grade_ biological_rep1


title: CD8+ w/o MAITs T cells, donor TU0053


title: naive state H9  [NH9-1 ]


title: patient no 382a tumor sample at III grade_ biological_rep1


title: MR1tet+ T cells, donor TU0054


title: patient no 318 tumor sample at III grade_ biological_rep1


title: CD8+ T cells, donor TU0053


title: patient no 477 tumor sample at III grade_ biological_rep1


title: Primed state H9  [H9-1 ]


title: MR1tet- T cells, donor TU0050


title: patient no 389 tumor sample at III grade_ biological_rep1


title: naive state H9  [NH9-3]

value: Failed in bisulfite conversion, deleted in downstream analysis


title: patient no 202 tumor sample at IV grade_ biological_rep1


title: patient no 388a tumor sample at III grade_ biological_rep1


title: CD8+ w/o MAITs T cells, donor TU0050


title: patient no 239 tumor sample at III grade_ biological_rep1


title: MR1tet+ T cells, donor TU0053


title: Primed state H9  [H9-4]


title: MR1tet+ T cells, donor TU0050


title: Primed state RUES-2 [RUES2-1]


title: naive state RUES-2  [NRUES2-4]


title: patient no 388 tumor sample at III grade_ biological_rep1


title: patient no 457 tumor sample at II grade_ biological_rep1

source_name: human tumor sample in second stage of cancer

value: second


title: CD8+ T cells, donor TU0050


title: patient no 246 tumor sample at III grade_ biological_rep1


title: naive state RUES-2  [NRUES2-2]


title: CD8+ T cells, donor TU0035


title: CD8+ w/o MAITs T cells, donor TU0035


title: CD8+ T cells, donor TU0046


title: patient no 378 tumor sample at II grade_ biological_rep1


title: MR1tet+ T cells, donor TU0046


title: Primed state H9  [H9-3]


title: CD8+ w/o MAITs T cells, donor TU0024


title: MR1tet- T cells, donor TU0046


title: patient no 472 tumor sample at II grade_ biological_rep1


title: MR1tet+ T cells, donor TU0024


title: CD8+ w/o MAITs T cells, donor TU0046


title: naive state H9  [NH9-2]


title: patient no 260 tumor sample at II grade_ biological_rep1


title: patient no 471 tumor sample at II grade_ biological_rep1


title: Primed state H9  [H9-2]


title: patient no 374 tumor sample at II grade_ biological_rep1


title: patient no 399a tumor sample at II grade_ biological_rep1


title: MR1tet+ T cells, donor TU0035


title: MR1tet- T cells, donor TU0023


title: patient no 445_2 tumor sample at II grade_ biological_rep1


title: patient no 396 tumor sample at II grade_ biological_rep1


title: patient no 268 tumor sample at II grade_ biological_rep1


title: MR1tet+ T cells, donor TU0023


title: patient no 385_2 tumor sample at II grade_ biological_rep1


title: CD8+ T cells, donor TU0024


title: MR1tet- T cells, donor TU0024


title: CD8+ T cells, donor TU0054


title: CD8+ w/o MAITs T cells, donor TU0023


title: MR1tet+ CD8+ T cells, donor TP0030

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were then aligned to GRCh38 genome using STAR aligner
Read counts for each genomic feature were obtained with the htseq-count program (v 0.6.0) with Gencode V27 for gene annotation and “union” for counting mode.
Genome_build: GRCh38

extract_protocol:
Total RNA was purified using an miRNeasy Micro Kit (QIAGEN) and quantified by quantitative PCR. Purified total RNA (1-5 ng) was amplified following the Smart-Seq2 protocol.
mRNA was captured using poly-dT oligonucleotides and directly reverse transcribed into full-length cDNA (amplified by PCR for 16 cycles). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina). Whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Barcoded Illumina sequencing libraries (Nextera, Illumina) were generated using the automated platform (Biomek FXp). Libraries were sequenced on a HiSeq 2500 Illumina platform to obtain 50-bp single-end reads (TruSeq Rapid kit; Illumina).

value: ATB


title: MR1tet+ CD8- T cells, donor TP0030


title: MR1tet+ T cells, donor TU0002


title: CD8+ w/o MAITs T cells, donor TU0013


title: CD8+ T cells, donor TU0002


title: CD8+ T cells, donor TU0023


title: MR1tet- T cells, donor TU0002


title: CD8+ T cells, donor TU0013


title: CD8+ w/o MAITs T cells, donor TU0002


title: MR1tet+ CD8+ T cells, donor TP0018


title: MR1tet+ CD8- T cells, donor TP0018


title: MR1tet+ CD8+ T cells, donor TP0005


title: MR1tet+ CD8+ T cells, donor TP0004


title: MR1tet+ CD8- T cells, donor TP0004


title: MR1tet+ CD8- T cells, donor TP0005


title: MR1tet+ CD8+ T cells, donor TP0020


title: MR1tet+ CD8- T cells, donor TP0020


title: Donor XT0134 CD8 memory T cells

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1).
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
The alignment results were parsed via SAMtools to generate SAM files.
Read counts for each genomic feature were obtained with the htseq-count program (v 0.6.0) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: TPM transformed counts

tag: sequencing batch

value: memory CD8 T cell


title: Donor XT0123 CD8 memory T cells


title: patient no 384 tumor sample at II grade_ biological_rep1


title: Donor XT0082 CD8 memory T cells


title: patient no 209 tumor sample at II grade_ biological_rep1


title: patient no 386  tumor sample at I grade_ biological_rep1

source_name: human tumor sample in first stage of cancer

value: first


title: Donor XT0106 CD8 memory T cells

value: TBneg


title: patient no 383  tumor sample at I grade_ biological_rep1


title: Donor TU0110 CD8 memory T cells


title: patient no 475  tumor sample at I grade_ biological_rep1


title: Donor TU0094 CD8 memory T cells


title: patient no 397  tumor sample at I grade_ biological_rep1


title: patient no 256  tumor sample at I grade_ biological_rep1


title: patient no 387  tumor sample at I grade_ biological_rep1


title: patient no 463  tumor sample at I grade_ biological_rep1


title: Donor TU0085 CD8 memory T cells


title: Donor TU0075 CD8 memory T cells

value: LTBI


title: patient no 465  tumor sample at I grade_ biological_rep1

value: clear cell renal cell carcinoma


title: 20890_M3_DMSO

city: Barcelona

first: Gemma

last: Moncunill

state: Please Select

address: Carrer Rosselló 153 (CEK building)

country: Spain

institute: ISGlobal

hyb_protocol: Plates were processed using the GeneTitan Hybridization, Wash and Stain kit for WT arrays (Affymetrix) in a GeneTitan multichannel instrument.

scan_protocol: GeneChip Command Console (AGCC 3.2.4., Affymetrix) was used for instrument control, first quality analysis by image inspection and generate raw intensity data. Expression Console (EC 1.2, Affymetrix) was used for quality control analysis and normalization by RMA algorithm.

data_processing: R/bioconductor

label: Biotin

source_name: Cultured PBMC

label_protocol: cDNA synthesis, fragmentation and labeling was performed starting with 125 to 200 ng total RNA, following Affymetrix protocol, using the WT Expression kit (Ambion), and WT Terminal Labeling kit (Affymetrix)

extract_protocol: Total RNA was extracted from cell pellets after RNAlater removal by centrifugation, using RNeasy Mini kits (Qiagen), either manually (batches of 24 samples) or using a QIAcube sample preparation workstation according to the manufacturer’s recommendations (batches of 12 samples). RNA concentration and quality were determined on a Nanodrop spectrophotometer (Thermo Scientific) in all samples and RNA integrity was assessed using a 2100 Bioanalyzer (Agilent) in 90% of CPS samples and 20% of the RTS,S samples.

treatment_protocol: CSP, DMSO, PfRBC or uRBC stimulations

tag: stimulation

value: DMSO

tag: subjectid

tag: vaccine

tag: site

value: Manhica

tag: immunization dose

tag: protection

value: protected

tag: timepoint

tag: Sex

value: M

value: PBMC


title: patient no 455 tumor sample at II grade_ biological_rep1

tag: tissue

value: male


title: 20889_M3_uRBC

value: uRBC

value: F


title: patient no 241_1 tumor sample at II grade_ biological_rep1

tag: Stage

value: female


title: 20889_M3_iRBC

value: iRBC


title: patient no 453  tumor sample at I grade_ biological_rep1

tag: gender


title: Donor TU0070 CD8 memory T cells

tag: donor id

tag: disease state

tag: cell type


title: Donor TU0063 CD8 memory T cells


title: 20883_M3_uRBC

value: Control

tag: age


title: patient no 470  tumor sample at I grade_ biological_rep1


title: 20883_M3_CSP

value: CSP


title: 20882_M3_DMSO

value: malaria


title: Donor TU0071 CD8 memory T cells

value: memory CD8 T cell


title: Donor TU0059 CD8 memory T cells

value: TBneg


title: 20883_M3_DMSO


title: 20889_M3_CSP


title: 20890_M3_CSP


title: 20882_M3_uRBC


title: patient no 459_1  tumor sample at I grade_ biological_rep1

value: first


title: patient no 377  tumor sample at I grade_ biological_rep1

value: clear cell renal cell carcinoma


title: Donor TU0057 CD8 memory T cells


title: 20882_M3_iRBC


title: 20889_M3_DMSO

value: DMSO


title: 20882_M3_CSP

value: Manhica


title: patient no 394_1  tumor sample at I grade_ biological_rep1


title: 20883_M3_iRBC

value: protected


title: 20881_M3_iRBC

value: M


title: Donor TU0053 CD8 memory T cells


title: Donor TU0056 CD8 memory T cells


title: patient no 207  tumor sample at I grade_ biological_rep1


title: 20881_M3_DMSO

value: PBMC


title: Donor TU0035 CD8 memory T cells

value: LTBI


title: Donor TU0050 CD8 memory T cells


title: 20881_M3_CSP


title: patient no 373  tumor sample at I grade_ biological_rep1


title: Donor TU0052 CD8 memory T cells


title: Donor TU0022 CD8 memory T cells


title: Donor TU0024 CD8 memory T cells


title: Donor TU0021 CD8 memory T cells


title: 20873_M3_uRBC

value: uRBC


title: 20881_M3_uRBC


title: Donor TU0005 CD8 memory T cells


title: Donor TU0046 CD8 memory T cells


title: Donor TU0013 CD8 memory T cells


title: 20873_M3_CSP

value: F


title: Donor TU0033 CD8 memory T cells


title: Donor TU0010 CD8 memory T cells


title: Donor TU0146 CD8 memory T cells


title: Donor TP0013 CD8 memory T cells


title: Donor XT0103 CD8 memory T cells


title: 20873_M3_iRBC


title: 20873_M3_DMSO


title: 20869_M3_uRBC


title: 20869_M3_iRBC


title: Donor TP0001 CD8 memory T cells


title: 20871_M3_uRBC


title: 20871_M3_CSP


title: Donor TP0007 CD8 memory T cells


title: 20869_M3_CSP


title: 20865_M3_uRBC


title: 20865_M3_DMSO


title: 20869_M3_DMSO


title: 20871_M3_DMSO


title: Donor XT0141 CD8 memory T cells


title: Donor XT0133 CD8 memory T cells


title: 20865_M3_iRBC


title: 20871_M3_iRBC


title: 20865_M3_CSP


title: Donor XT0131 CD8 memory T cells


title: Donor XT0127 CD8 memory T cells


title: Donor XT0130 CD8 memory T cells


title: Donor XT0115 CD8 memory T cells


title: Donor TU0119 CD8 memory T cells


title: Donor TU0137 CD8 memory T cells


title: Donor TU0079 CD8 memory T cells


title: Donor TU0081 CD8 memory T cells


title: Donor TU0078 CD8 memory T cells


title: 20863_M3_uRBC


title: 20863_M3_DMSO


title: 20863_M3_iRBC


title: Donor TU0064 CD8 memory T cells


title: Donor TU0054 CD8 memory T cells


title: Donor TU0049 CD8 memory T cells


title: Donor XT0108 CD8 memory T cells


title: Donor TU0051 CD8 memory T cells


title: 20838_M3_iRBC


title: Donor TU0040 CD8 memory T cells


title: 20838_M3_CSP


title: 20838_M3_uRBC


title: 20824_M3_uRBC


title: 20838_M3_DMSO


title: 20824_M3_CSP


title: 20824_M3_DMSO


title: Donor TU0023 CD8 memory T cells


title: Donor TU0025 CD8 memory T cells


title: 20816_M3_CSP


title: Donor TU0011 CD8 memory T cells


title: 20863_M3_CSP


title: 20822_M3_iRBC


title: 20822_M3_DMSO


title: 20816_M3_DMSO


title: 20822_M3_uRBC


title: 20822_M3_CSP


title: Donor TU0002 CD8 memory T cells


title: Donor TU0036 CD8 memory T cells


title: 20813_M3_uRBC


title: 20816_M3_iRBC


title: 20824_M3_iRBC


title: Donor XT0101 CD8 memory T cells


title: Donor TP0015 CD8 memory T cells


title: Donor TU0084 CD8 memory T cells


title: Donor TP0008 CD8 memory T cells


title: Donor TP0005 CD8 memory T cells


title: Donor TP0004 CD8 memory T cells


title: naive state RUES-2 replicate 3

data_processing:
Basecalling was performed with bcl2fastq version 2.17.1.14
Mapping to genome with TopHat (v2.1.1) with default parameters
Expression level was quantified as RPKM using Cufflink(v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM value for each sample

growth_protocol: Naive state H9 and RUES-2 were maintained in naïve state medium (50% glucose-free DMEM/F12 (Life Technologies) and 50% glucose-free Neurobasal (Life Technologies), with 5mM glucose, 1mM glutamine, 1% NEAA, 0.1mM β-mercaptoethanol, penicillin–streptomycin, 20 ng/mL recombinant human LIF (Millipore), 5 mg/mL bovine serum albumin (BSA) (Sigma), 18µg/ml human insulin (Sigma), 1 uM PD0325901 (PD, EMD Millipore), and 3 uM CHIR99021 (CH, Stemgent). Cells were passaged every 3 days by using mechanical and (or) enzymatic methods.

extract_protocol:
Total RNA Extraction with TRIZOL Reagent and Purification with QIAGEN. RNeasy Mini Kit(cat # 74104).
cDNA libraries were prepared using the TrueSeq RNA Sample Preparation Kit (Illumina)

tag: cell line

value: embryonic stem cells

tag: state

value: naïve state

tag: passages


title: naive state RUES-2 replicate 2


title: naive state RUES-2 replicate 1


title: 20816_M3_uRBC

tag: stimulation

tag: subjectid


title: Primed state RUES-2 replicate 3

growth_protocol: Human embryonic stem cell (ESC) lines H9, RUES-2  were maintained on mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells in hESC medium (DMEM/F12 containing 20% knockout serum replacement, 2mM l-glutamine, 1% nonessential amino acids (NEAA), 100U of penicillin, 100 mg of streptomycin (all from Life Technologies), 0.1mM β-mercaptoethanol (Sigma), and 4 ng/mL bFGF (PeproTech). Cells were passaged every 6–7 days by dispase (1 mg/mL, Life Technologies) treatment.

value: primed state


title: Primed state RUES-2 replicate 2


title: 20813_M3_DMSO

tag: vaccine

tag: site


title: 20809_M3_uRBC

tag: immunization dose

tag: protection


title: 20813_M3_iRBC

value: iRBC

tag: timepoint

tag: Sex


title: 20813_M3_CSP

value: CSP

value: malaria

tag: tissue


title: 20809_M3_CSP


title: naive state H9 replicate 3


title: 20809_M3_iRBC


title: naive state H9 replicate 2


title: Primed state RUES-2 replicate 1


title: 20808_M3_DMSO

value: Control


title: 20809_M3_DMSO


title: naive state H9 replicate 1


title: Donor TP0003 CD8 memory T cells

tag: sequencing batch

value: memory CD8 T cell


title: 20808_M3_CSP


title: 20793_M3_uRBC


title: 20808_M3_iRBC


title: 20793_M3_CSP


title: Primed state H9 replicate 2


title: 20808_M3_uRBC


title: 20793_M3_DMSO


title: 20793_M3_iRBC


title: 20792_M3_DMSO


title: 20792_M3_iRBC


title: 20792_M3_uRBC


title: Whole Lung_Hashtag Ab A0302

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description:
Naoki Hashing 2
ST258_24 hours
Single cell gene expression RNA-seq
processed data file: S1_B6_Ctrl_mRNA_barcodes.tsv.gz
processed data file: S1_B6_Ctrl_mRNA_features.tsv.gz
processed data file: S1_B6_Ctrl_mRNA_matrix.mtx.gz

data_processing:
10x Cellranger V.3.1.0 and V.2.1.0 were used to generate Fastq files, perform alignment, filtering, barcode counting, UMI counting and aggregation.
Seurat V.2.3.1 and V.3.0.0 for scRNA QC and further analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tsv and mtx files or H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files.

organism: Mus musculus

source_name: Lung cell

growth_protocol: All mice were obtained from Taconic farm and maintained in specific pathogen-free rooms. Experiment were performed when mice were at age of six to eight weeks.

extract_protocol:
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit.
Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v2 protocol.

treatment_protocol: Pulmonary infection of ST258 at 10e6 CFU 12 or 24 hours prior to sample collection.

tag: strain

value: Lung cell

value: 24 hr post ST258 infection

tag: treatment

value: PBS


title: Whole Lung_Hashtag Ab A0303

description:
Naoki Hashing 3
ST258_24 hours
Single cell gene expression RNA-seq
processed data file: S2_B6_FK506_mRNA_filtered_feature_bc_matrix.h5

tag: cell type


title: Whole Lung_Hashtag Ab A0301

description:
Naoki Hashing 1
ST258_24 hours
Single cell gene expression RNA-seq
processed data file: S1_B6_Ctrl_mRNA_barcodes.tsv.gz
processed data file: S1_B6_Ctrl_mRNA_features.tsv.gz
processed data file: S1_B6_Ctrl_mRNA_matrix.mtx.gz


title: Whole Lung CD45+Ly6g-_ IS#2

description:
Ivy 4
ST258_12 hours
Single cell gene expression RNA-seq
Whole Lung CD45+Ly6g- enriched
processed data file: WholeLung_CD45Ly6gnegLung_filtered_gene_bc_matrices_h5.h5

tag: genotype

value: ko/ko

value: 12 hr post ST258 infection


title: Whole Lung_ IS#2

description:
Ivy 2
ST258_12 hours
Single cell gene expression RNA-seq
Whole lung
processed data file: WholeLung_CD45Ly6gnegLung_filtered_gene_bc_matrices_h5.h5


title: Whole Lung CD45+Ly6g-_ IS#1

description:
Ivy 3
ST258_12 hours
Single cell gene expression RNA-seq
Whole Lung CD45+Ly6g- enriched
processed data file: WholeLung_CD45Ly6gnegLung_filtered_gene_bc_matrices_h5.h5


title: Primed state H9 replicate 3

tag: cell line


title: Primed state H9 replicate 1

tag: state


title: Whole Lung_Hashtag Ab A0304

description:
Naoki Hashing 4
ST258_24 hours
Single cell gene expression RNA-seq
processed data file: S2_B6_FK506_mRNA_filtered_feature_bc_matrix.h5


title: 20756_M3_iRBC

value: Manhica

tag: age

value: PBMC


title: Standard, 1/100 dilution of human DNA in mouse DNA

description:
2 replicates
PCR Amplicon

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
Per-cycle basecall (BCL) were converted to per-read FASTQ files using bcl2fastq version 2.20.0.422 using default parameters.
Forward and reverse barcode attachment sites were trimmed using cutadapt version 1.16.
Forward and reverse read-pairs were merged using vsearch fastq_mergepairs and the merged reads with greater than one expected error were filter out.
Merged reads were then classified as either human or mouse using vsearch –usearch_global with the percent identity cutoff set at 99%.
The reference sequence used for human 18S was AGCTAATACATGCCGACGGGCGCTGACCCCCTTCGCGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTCAGCCCCTCTCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCTTTGGTGACTCTAGA and the reference sequence used for mouse 18S was AGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTGGTGACTCTAGA.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: An Excel file containing the number of reads mapped to human 18S or mouse 18S in each sample.

organism:
Homo sapiens
Mus musculus

source_name: Human genomic DNA was 1:100 diluted in mouse genomic DNA.

growth_protocol: Naïve hPSCs were maintained on mitomycin C-treated mouse embryonic fibroblast (MEF) feeders (5-6 × 104/cm2) in 2iLI medium (50% glucose-free DMEM/F12 and 50% glucose-free Neurobasal, 5 mM glucose, 1 mM glutamine, 1% NEAA, 0.1 mM β-mercaptoethanol, 100 U/ml penicillin, 100 ug/ml streptomycin, 5 mg/mL bovine serum albumin to maintain osmolarity, 20 ng/mL recombinant human LIF, 18 µg/ml human insulin, 1 μM PD0325901, and 3 μM CHIR99021). Naïve hPSCs were passaged every 3 days with TrypLE. All naïve hPSCs were cultured in 5% O2 and 5% CO2.

extract_protocol:
Mouse embryos or human cells were homogenized in proteinase K solution (100 mM Tris-HCl pH8.0, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 250µg/ml Proteinase K) and incubated in the same solution at 55°C for 12-18 hours. Pheno/chloroform extraction was then used to extract genomic DNA.  The V3 regions of both human and mouse 18S ribosome genes were amplified from standard  samples or genomic DNA extracted from chimera using human/mouse universal primers containing barcode attachment sites on the 5’ ends (Forward: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGCTAATACATGCCGACGGG; Reverse: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCTAGAGTCACCAAAGCCGC; barcode attachment sites were underlined) and Hotstar plus kit (Qiagen) with an optimized PCR protocol (95°C, 5min; 94°C, 30s; 58°C, 30s; 72°C, 1min; 40 cycles; 72°C, 10min). PCR product from each sample was gel-extracted and purified with QIAquick Gel Extraction Kit (Qiagen)
Purified PCR products were barcoded and library prepared using PE150 kit (illumina)

treatment_protocol: Naive human PSCs were dissociated to single cells with TrypLE for 5-6 minutes and placed on 10 cm dishes for 45 minutes to remove MEF cells through attachment. The supernatant, which contained the hPSCs, was removed from the dish and centrifuged for 10 min at 2000 rpm. Cells in the pellet were resuspended in Mouse Blastocysts Injection Buffer (HEPES-buffered DMEM with 5% FBS). 10-12 naive hPSCs were injected to a C57BL/6J mouse blastocyst, which was obtained by superovulation from 3-4 week old C57BL/6J female mice. Injected blastocysts were transferred bilaterally to uterus of pseudopregnant CD-1 female mice at 7-9 weeks of age, with 14-18 blastocysts transferred per mouse. At Day 17.5, mouse embryos were retrieved and half of each mouse embryo cut sagittally were used in DNA extraction.

tag: sample type

value: Standard Sample


title: 20756_M3_DMSO

tag: stimulation

value: DMSO

tag: subjectid

value: F


title: 20733_M3_iRBC

tag: vaccine

tag: site

value: M


title: 20792_M3_CSP

tag: immunization dose

tag: protection

value: protected


title: Standard, 1/10 dilution of human DNA in mouse DNA

description:
2 replicates
PCR Amplicon

source_name: Human genomic DNA was 1:10 diluted in mouse genomic DNA.


title: Standard, 1/1,000 dilution of human DNA in mouse DNA

description:
2 replicates
PCR Amplicon

source_name: Human genomic DNA was 1:1,000 diluted in mouse genomic DNA.


title: Chimera 14

description:
2 replicates
PCR Amplicon

source_name: human cells in E17.5 chimeric mouse embryo

value: Chimera Sample


title: 20732_M3_DMSO

tag: timepoint

tag: Sex


title: 20756_M3_uRBC

value: uRBC

tag: tissue


title: 20733_M3_CSP

value: CSP

value: malaria


title: 20733_M3_DMSO

value: Control


title: Chimera 13

description:
2 replicates
PCR Amplicon


title: 20732_M3_iRBC

value: iRBC


title: 20733_M3_uRBC


title: 20732_M3_uRBC


title: 20732_M3_CSP


title: Chimera 11

description:
2 replicates
PCR Amplicon


title: Whole Lung_ IS#1

description:
Ivy 1
ST258_12 hours
Single cell gene expression RNA-seq
Whole lung
processed data file: WholeLung_CD45Ly6gnegLung_filtered_gene_bc_matrices_h5.h5

tag: strain

value: Lung cell


title: Chimera 12

description:
2 replicates
PCR Amplicon


title: Chimera 10

description:
2 replicates
PCR Amplicon


title: Chimera 9

description:
2 replicates
PCR Amplicon


title: Chimera 8

description:
2 replicates
PCR Amplicon


title: Chimera 7

description:
2 replicates
PCR Amplicon


title: Chimera 6

description:
2 replicates
PCR Amplicon


title: Chimera 4

description:
2 replicates
PCR Amplicon


title: Chimera 5

description:
2 replicates
PCR Amplicon


title: Chimera 2

description:
2 replicates
PCR Amplicon


title: 20756_M3_CSP


title: Chimera 1

description:
2 replicates
PCR Amplicon


title: Chimera 3

description:
2 replicates
PCR Amplicon


title: 20729_M3_DMSO


title: 20729_M3_iRBC


title: K5. Pp6N Epidermis

city: Shanghai

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were processed using Cell Ranger software provided by 10x Genomics.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files with barcodes and genes
Supplementary_files_format_and_content: mtx files with gene counts for every gene and every cell with a unique barcode

source_name: skin

extract_protocol:
Single cell suspensions were generated through enzyme digestion and dead cells were removed using FACS.
Libraries were generated using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.

treatment_protocol: C57BL/6 mice were treated with imiquimod for 5 consecutive days on the ear.

value: K5. Pp6fl/fl

value: epidermis

value: 10 week

tag: treatment


title: K5. Pp6L

value: whole skin

value: 18 week


title: 20724_M3_DMSO

value: Manhica

value: PBMC


title: C57 UT Epidermis

value: wild type


title: 20724_M3_uRBC

value: F


title: 20729_M3_uRBC

value: M


title: 5x2_D10_Granulocyte2

city: Freiburg

first: Michael

last: Schulz

address: Breisacher Straße 64

department: Institute for Neuropathology

country: Germany

institute: University Hospital Freiburg

description: 20190910_allSamples_SchulzEtal_MYTMEinBRM

data_processing:
FastQC Analysis
quality score filtering, poly-A trimming, artifact removal, removal of ‘N’ containing reads and clearing of rRNA contamination using a pipeline provided by the HUSAR platform, DKFZ.
Genomic mapping to Mouse genome M12 was performed using TopHat2 (version 2.0.14)
The number of reads per gene was determined using HTSeq count.
Paired differential analysis was performed using   ‘DESeq2’  (version 1.18.1)
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: .csv
Supplementary_files_format_and_content: processed data files contain annotated ENSEMBL IDs and gene names as well as readcounts which were annotated from HTSeq counts

source_name: mouse brain

extract_protocol:
Myeloid cells from (tumor-bearing) mice brain or peripheral blood were FACS purified, stored in Trizol LS and RNA isolated according to standard protocols (commercial processing)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Balb/C athymic nude (CAnN.Cg-Foxn1nu/Crl)

tag: cell type

value: granulocyte

tag: tumor stage

value: not stratified

tag: wbrt


title: 5x2_D10_Granulocyte1


title: 5x2_D10_Granulocyte3


title: 20729_M3_CSP

value: CSP

value: malaria


title: 20723_M3_CSP

value: protected


title: 20723_M3_uRBC

value: uRBC


title: 20722_M3_uRBC


title: 20724_M3_CSP


title: 20723_M3_iRBC

value: iRBC


title: 20722_M3_DMSO

value: DMSO


title: 20714_M3_uRBC


title: 20722_M3_iRBC


title: 20723_M3_DMSO


title: 20714_M3_iRBC


title: 5x2_D10_Monocytes2

value: inflammatory monocyte


title: 5x2_D10_Monocytes1


title: C57 UT Dermis

tag: genotype

value: dermis

value: 10 week


title: 20722_M3_CSP

value: Manhica

tag: age


title: 20714_M3_CSP

value: PBMC


title: 20699_M3_DMSO


title: 20724_M3_iRBC


title: 20699_M3_uRBC


title: 20699_M3_CSP


title: 20699_M3_iRBC


title: 20714_M3_DMSO


title: 5x2_D10_BMDM2

value: BMDM


title: 5x2_D10_Monocytes3


title: 5x2_D10_BMDM1


title: 5x2_D10_Microglia3

value: microglia


title: 5x2_D10_Microglia2


title: 5x2_D10_Microglia1


title: 20698_M3_iRBC

value: Control

value: M


title: 5x2_D5_Granulocyte3

value: Balb/C athymic nude (CAnN.Cg-Foxn1nu/Crl)

value: granulocyte

value: 5x2 Gy, D5


title: 5x2_D5_Granulocyte4

value: not stratified


title: 5x2_D5_Granulocyte2


title: 5x2_D10_BMDM3


title: 20698_M3_CSP

value: CSP

value: protected


title: 20698_M3_uRBC

value: uRBC


title: 5x2_D5_Granulocyte1


title: 5x2_D5_Monocytes4


title: 20698_M3_DMSO

value: DMSO


title: 5x2_D5_Monocytes3

value: inflammatory monocyte


title: 20695_M3_uRBC


title: 20695_M3_DMSO


title: 20695_M3_iRBC

value: iRBC


title: 20693_M3_CSP


title: 5x2_D5_Monocytes2


title: 5x2_D5_BMDM4


title: 20693_M3_uRBC


title: 20693_M3_DMSO


title: 5x2_D5_BMDM3


title: 5x2_D5_BMDM2


title: 20691_M3_CSP


title: 5x2_D5_Monocytes1


title: 20695_M3_CSP


title: 20693_M3_iRBC


title: 20691_M3_uRBC


title: 20691_M3_iRBC


title: 5x2_D5_Microglia4


title: 5x2_D5_Microglia2


title: 5x2_D5_Microglia1


title: 20685_M3_iRBC

value: F


title: 5x2_D5_Microglia3


title: 1x10_D3_Granulocyte2


title: 1x10_D3_Granulocyte3


title: 5x2_D5_BMDM1


title: 1x10_D3_Granulocyte1


title: 20691_M3_DMSO

value: Manhica


title: 20665_M3_CSP

value: PBMC


title: 1x10_D3_Monocyte3


title: 20662_M3_CSP


title: 20665_M3_DMSO


title: 1x10_D3_Monocyte2


title: 20665_M3_uRBC


title: 20685_M3_DMSO


title: 20685_M3_uRBC


title: 1x10_D3_BMDM3

value: BMDM


title: 1x10_D3_Monocyte1


title: 1x10_D3_BMDM2


title: 1x10_D3_BMDM1


title: 20662_M3_iRBC


title: 1x10_D3_Microglia1

value: microglia


title: 1x10_D3_Microglia3


title: 5x2_D3_Granulocyte4

value: 5x2 Gy, D3


title: 20661_M3_CSP

value: Control


title: 20661_M3_iRBC


title: 20662_M3_uRBC

value: M


title: 5x2_D3_Granulocyte2

value: Balb/C athymic nude (CAnN.Cg-Foxn1nu/Crl)

value: granulocyte


title: 5x2_D3_Granulocyte1

value: not stratified


title: 20662_M3_DMSO


title: 5x2_D3_Monocytes4


title: 5x2_D3_Granulocyte3


title: 20661_M3_uRBC


title: 20665_M3_iRBC


title: 5x2_D3_Monocytes2


title: 20654_M3_uRBC


title: 20653_M3_iRBC


title: 5x2_D3_Monocytes3


title: 5x2_D3_Monocytes1


title: 5x2_D3_BMDM3


title: 20654_M3_CSP

value: CSP


title: 5x2_D3_BMDM2


title: 5x2_D3_BMDM4


title: 5x2_D3_Microglia4


title: 5x2_D3_BMDM1


title: 20651_M3_CSP

value: protected


title: 5x2_D3_Microglia3


title: 5x2_D3_Microglia2


title: 5x2_D3_Microglia1


title: large_Granulocyte5

value: large


title: 1x10_D3_Microglia2


title: 20653_M3_uRBC

value: uRBC


title: 20654_M3_iRBC


title: 20651_M3_DMSO

value: DMSO


title: large_Granulocyte3


title: large_Monocyte3

value: inflammatory monocyte


title: large_Granulocyte2


title: large_Granulocyte1


title: large_Granulocyte4


title: large_Monocyte5


title: large_Monocyte1


title: large_Monocyte2


title: 20641_M3_iRBC

value: iRBC

value: F


title: large_BMDM5


title: large_Monocyte4


title: large_BMDM4


title: large_BMDM3


title: 20641_M3_DMSO

value: Manhica

value: PBMC


title: 20651_M3_iRBC


title: 20645_M3_CSP


title: 20685_M3_CSP


title: 20653_M3_DMSO


title: 20641_M3_CSP


title: 20640_M3_CSP


title: 20640_M3_DMSO


title: 20645_M3_DMSO


title: 20639_M3_iRBC


title: 20640_M3_uRBC


title: 20638_M3_DMSO


title: 20638_M3_iRBC


title: large_BMDM2

value: BMDM


title: 20651_M3_uRBC


title: 20639_M3_uRBC


title: 20628_M3_DMSO


title: large_BMDM1


title: 20625_M3_CSP


title: large_Microglia5

value: microglia


title: large_Microglia4


title: 20654_M3_DMSO


title: large_Microglia3


title: 20653_M3_CSP

value: Control


title: large_Microglia2


title: 20611_M3_DMSO


title: large_Microglia1


title: small_Granulocyte3

value: small


title: small_Granulocyte4

value: Balb/C athymic nude (CAnN.Cg-Foxn1nu/Crl)


title: 20639_M3_CSP

value: M


title: 20638_M3_CSP


title: 20625_M3_DMSO


title: 20611_M3_iRBC


title: 20628_M3_CSP


title: small_Granulocyte1

value: granulocyte


title: 20640_M3_iRBC


title: 20609_M3_CSP

value: CSP


title: small_Granulocyte2


title: 20611_M3_uRBC

value: protected


title: small_Monocyte3


title: 20611_M3_CSP


title: 20638_M3_uRBC


title: 20639_M3_DMSO


title: 20609_M3_uRBC


title: 20609_M3_DMSO


title: small_Monocyte2


title: 20609_M3_iRBC


title: 20599_M3_CSP


title: 20599_M3_DMSO


title: small_Monocyte1


title: small_Monocyte4


title: small_BMDM3


title: small_BMDM5


title: small_BMDM4


title: small_BMDM2


title: small_Microglia2


title: small_Microglia3


title: 20585_M3_iRBC


title: 20585_M3_uRBC


title: Control_BloodMonocyte4

source_name: mouse peripheral blood

value: blood monocyte


title: 20582_M3_CSP

value: malaria


title: 20599_M3_uRBC

value: uRBC


title: 20582_M3_iRBC


title: 20561_M3_uRBC


title: Control_BloodMonocyte3


title: 20585_M3_CSP


title: 20559_M3_uRBC


title: 20561_M3_iRBC


title: 20582_M3_uRBC


title: 20582_M3_DMSO

value: DMSO


title: small_BMDM1

value: bone marrow-derived macrophage (BMDM)


title: Control_BloodMonocyte1


title: 20599_M3_iRBC

value: iRBC

value: F


title: 20561_M3_DMSO

value: Manhica

value: PBMC


title: Control_BloodMonocyte2


title: small_Microglia5

value: microglia


title: small_Microglia4


title: 20561_M3_CSP

value: Control


title: Control_MG_5x2_D5_3


title: 20559_M3_DMSO


title: Control_MG_5x2_D5_2


title: 20559_M3_iRBC


title: 20559_M3_CSP


title: Control_MG_5x2_D5_1


title: 20558_M3_CSP


title: 20558_M3_DMSO


title: 20557_M3_iRBC


title: 20557_M3_uRBC


title: 20557_M3_DMSO


title: 20557_M3_CSP


title: Control_MG2


title: Control_MG_5x2_D3_3


title: Control_MG4


title: Control_MG1


title: Control_MG_5x2_D3_2


title: Control_MG_5x2_D3_1


title: Control_MG3


title: RPHD19DM

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

data_processing:
Illumina BaseCalling pipeline
RNA-Seq reads were first mapped to the human genome GRCh38 using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2). Raw read counts for each gene were quantified by using featureCounts software. Then RNA-seq counts were obtained by using GENCODE v.27 Gene Transfer Format (GTF) file as a transcript reference (GENCODE annotation).
Genes with raw read counts below 5 for more than 50% of samples within each condition were first filtered out.
Count data were normalized using Trimmed Mean of M-values (TMM) method.  R package EdgeR was used for testing differential expression between conditions.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts

source_name: T cells

growth_protocol: Human T cells were isolated from healthy donor (HD) PBMCs (n=4) by negative selection. T cells were stimulated with CD3/CD28 Dynabeadsbeads treated with vehicle (DMSO) or PRMT5 inhibtor C220 (PRT) for 48hrs, RNA isolated and RNA-seq performed.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and treated with DNase (Qiagen, Hilden, Germany).
RNA quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and the RNA integrity number values were greater than 7 for all samples. Sequencing libraries were generated with polyA+ RNA using the TruSeq RNA sample prep kit (Illumina, San Diego, CA). Libraries underwent paired end 50bp sequencing using the Illumina HiSeq2500 sequencer to a depth of 17 – 20 million passed filter clusters per sample. Demultiplexed and quality-filtered reads were mapped to the human genome GRCh38 using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2)(35). Raw read counts for each gene were quantified using featureCounts software, with GENCODE v.27 transcript reference (GENCODE annotation)(36). RNAs with less than twenty read counts on average across all samples were excluded from further analysis.

treatment_protocol: T cells were stimulated with CD3/CD28 Dynabeadsbeads  for 48 hrs in the presence of PRMT5 inhibitor ( C220, PRT, PR) or DMSO (DMS, DM).

value: RPHD19 T cells CD3/CD28 +DMSO


title: RPHD19PR

value: RPHD19 T cells CD3/CD28 +PRMT5 INHIBITOR


title: U87PbR

first: Markus

last: Siegelin

state: New York

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Galaxy (from fasq file to bigwig file)
Integrated Genome Brower (compared peak between control and treated samples)
Genome_build: hg38

source_name: Glioblastoma cell line

extract_protocol:
DNA was extracted using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell Signalling
Next generation sequencing (NGS) from Genewiz, New Jersey

treatment_protocol: The U87 PbR cells were exposed with 100 nM panobinostat in DMEM containing 10%FBS and primocinfor a week

value: Panobinostat

tag: chip antibody

value: H3k27me3 (Cell Signalling 9733)


title: RPHD18DM

value: RPHD18 T cells CD3/CD28 +DMSO


title: U87-DMSO


title: RPHD17PR

value: RPHD17 T cells CD3/CD28 +PRMT5 INHIBITOR


title: RPHD17DM

value: RPHD17 T cells CD3/CD28 +DMSO


title: RPHD7DMS

value: RPHD7 T cells CD3/CD28 +DMSO


title: RPHD18PR

value: RPHD18 T cells CD3/CD28 +PRMT5 INHIBITOR


title: 20541_M3_DMSO

tag: stimulation

value: DMSO

value: protected


title: 20543_M3_uRBC

value: uRBC

tag: subjectid

value: M


title: 20547_M3_CSP

value: CSP

tag: vaccine

value: Manhica

value: F


title: 20541_M3_CSP

tag: site

value: PBMC


title: 20547_M3_uRBC

tag: immunization dose


title: 20543_M3_iRBC

value: iRBC

tag: protection


title: 20541_M3_uRBC

tag: timepoint


title: 20531_M3_CSP

tag: Sex


title: 20541_M3_iRBC

tag: tissue


title: 20531_M3_iRBC


title: 20531_M3_DMSO


title: 20543_M3_CSP


title: 20543_M3_DMSO


title: 20530_M3_iRBC


title: WT-6

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

institute: Stanford University

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: hg38 for human samples, mm10 for mouse samples
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: HAP1 cells

extract_protocol:
RNA extracted using a PureLink RNA Mini Kit (Ambion)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

tag: cell line

value: HAP1 cells

tag: genotype/treatment

value: WT


title: 20530_M3_DMSO


title: RPHD7 PRT

tag: treatment

value: RPHD7 T cells CD3/CD28 +PRMT5 INHIBITOR


title: WT-3


title: 20531_M3_uRBC


title: 20547_M3_iRBC


title: 20547_M3_DMSO


title: WT-2


title: 20530_M3_uRBC


title: WT-1


title: WT-5


title: S252-5

value: RPS25-HA addback2


title: S252-3


title: S252-2


title: S252-4


title: S251-6

value: RPS25-HA addback1


title: S252-1


title: S251-3


title: S251-5


title: S251-4


title: S252-6


title: S251-2


title: S251-1


title: 20530_M3_CSP


title: 20528_M3_iRBC

value: Control

value: malaria


title: 20524_M3_CSP


title: KO2-6

value: RPS25 KO2


title: 20528_M3_DMSO

value: DMSO


title: KO2-4


title: 20524_M3_uRBC

value: protected


title: 20528_M3_uRBC

value: uRBC


title: KO2-3


title: KO2-5


title: 20524_M3_iRBC


title: 20520_M3_DMSO

value: M


title: 20520_M3_iRBC


title: 20528_M3_CSP

value: CSP


title: KO2-2


title: KO2-1


title: 20520_M3_uRBC

value: Manhica


title: KO1-6

value: RPS25 KO1


title: 20524_M3_DMSO

value: F

value: PBMC


title: 20514_M3_DMSO


title: KO1-5

value: HAP1 cells


title: 20520_M3_CSP


title: 20514_M3_iRBC

value: iRBC


title: 20511_M3_DMSO


title: KO1-2


title: small_Microglia1

tag: strain

value: Balb/C athymic nude (CAnN.Cg-Foxn1nu/Crl)

tag: cell type

value: microglia

tag: tumor stage

value: small


title: 20514_M3_CSP

tag: age


title: 20511_M3_CSP

value: Control


title: KO1-1


title: 20509_M3_DMSO


title: 20514_M3_uRBC


title: 20511_M3_iRBC


title: 20488_M3_CSP


title: 20488_M3_DMSO


title: 20511_M3_uRBC


title: 20488_M3_uRBC


title: KO1-3


title: 20462_M3_DMSO


title: 20509_M3_CSP


title: 20462_M3_CSP


title: 20462_M3_uRBC


title: SAMP8 0.96mg/kg/day

city: Cornella de Llobregat

first: Tamara

last: Maes

state: Barcelona

address: Carrer Sant Ferran 74

department: R&D

institute: Oryzon Genomics S.A.

description:
SI-104
Agilent design ID 017498

hyb_protocol: Cy3 and Cy5 labeled cRNA for the control probes (Zea mays Zmmyb42 and Expansin) were added to the Cy3- and Cy5-labelled sample cRNA mixes and hybridized to microarrays according to the manufacturer’s instruction.

scan_protocol: Raw data were obtained using Agilent's DNA Microarray Scanner G2505B. Images were quantified using Agilent Feature Extraction software (v10.1).

data_processing: The raw fluorescence intensity data were processed using proprietary Oryzon Genomics SA Polyphemus software, which involves the following steps: 1. Spatial data compensation of the signals in the 2 channels based on the spike probes distributed over the array and generating signal at several discrete levels. 2. Noise filtering based on negative controls.  3. Data normalization by modified nonlinear Q-splines normalization method (Workman et al., 2002) and Log2(sample/control) value calculation without background correction. Differential expression assessment using robust statistics on the average of 3 technical replicates per gene oligo after removal of eventual outlier points (caused by dust or array imperfections). Criteria for outlier elimination are established automatically based on the intra-array technical variability of the signal distribution of the controls probes. The p-values are calculated after outlier elimination based on the absolute value of the regularized t-statistics (Baldi et al., 2001), which uses a Bayesian framework to derive the algorithm. Control probes have SPOTID ORY_C* and each is present in 2103 copies; gene oligos have SPOTID ORY_P* and each is present in triplicate, respectively, in the crossref file. The Agilent design file and AgilentOryzonRrossRef file are provided.

source_name: SAMP8-ORY-2001 0.96mg/kg/day

label_protocol: Total RNA (0.5 μg) amplification and labeling with Cy3 or Cy5 was carried out using a modified Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems).

extract_protocol: Total RNA was extracted using the Qiagen RNeasy extraction kit. Evaluation of RNA quality was performed with the Agilent 2100 bioanalyzer and NanoDrop™ ND-1000 (Thermo Scientific).

treatment_protocol: 5-month old SAMP8 mice (male and females) were treated for several weeks (6, 8 or 16) with vehicle or ORY-2001. Vehicle-treated SAMR1 mice were included as a control. All drugs were administered via drinking water and diluted in vehicle.

tag: gender

value: Female

value: Hippocampus


title: 20462_M3_iRBC

tag: stimulation


title: 20454_M3_CSP

tag: subjectid


title: 20454_M3_DMSO

value: DMSO

tag: vaccine


title: SAMR1 Vehicle

description:
SI-104
Agilent design ID 017498


title: 20454_M3_iRBC

tag: site

value: protected


title: D4_C3

city: Durban

first: Alex

last: Sigal

state: -- SELECT --

address: 719 Umbilo Road, Congella

country: South Africa

institute: Africa Health Research Institute (AHRI)

description:
Reverse transcriptase region of HIV provirus
~ 300bp amplicon of the Reverse trancriptase region of HIV containing all the Efavirenz resistant mutants

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (minimum mapping quality Q30), then mapped to HIV NL4-3 using Geneious v 11.1.4
For SNP detection in cell population experiments: minimum variant frequency of 0.01 and maximum variant p-value 0.0001
For SNP detection in single experiments: minimum variant frequency of 0.05 and maximum variant p-value 0.0001
Genome_build: AF324493.2
Supplementary_files_format_and_content: comma separated files (csv) containing the variant raw frequency of mutants, the quality score, coverage as wells as the unique identifiers for each read that has a SNP in it

organism: Human immunodeficiency virus 1

source_name: RevCEM E7 cells infected with NL4-3

growth_protocol: Cell culture and experiments were performed in complete RPMI 1640 medium supplemented with L-Glutamine, sodium pyruvate, HEPES, non-essential amino acids (Lonza), and 10\% heat-inactivated FBS (Hyclone).

extract_protocol:
For infected single cells, the cells were lysed and DNA was kept suspended in the lysis buffer. For infected cell populations, genomic DNA was extracted using the QIAamp DNA mini kit (Qiagen)
Phusion hot start II DNA polymerase (New England Biolabs) PCR reaction mix (10$ul 5 x Phusion HF buffer, 1ul dNTPs, 2.5ul of the forward primer, 2.5ul of the reverse primer, 0.5ul Phusion hot start II DNA polymerase, 2.5ul of DMSO and molecular biology grade water to 50ul reaction volume) was added to the lysed single cells or extracted genomic DNA of cell populations. Two rounds of PCR were performed. The first-round reaction amplified a region of the RT gene in the proviral DNA using the forward primer 5’ tcgtcggcagcgtcagatgtgtataagagacagTTAATAAGAGAACTCAAGATTTC 3’ and reverse primer 5’ gtctcgtgggctcggagatgtgtataagagacagCCCCACCTCAACAGATGTTGTC 3’. Non-capitalized portion of the primers represent the Nextera XT Index Kit adaptors. Cycling program was 98C for 30 seconds, then 35 cycles of 98C for 10 seconds, 50C for 30 seconds and 72C for 15 seconds with a final extension of 72C for 5 minutes. 1$\mu l$ of the first round product was then transferred into a PCR mix as above, with second round Nextera XT Index Kit adaptor primers (forward 5’ tcgtcggcagcgtcagatgtgtataagagacag 3’, reverse 5’ gtctcgtgggctcggagatgtgtataagagacag 3’). The second round PCR amplified a 400bp product which was then visualized on a 1% agarose gel. The PCR amplicon was gel extracted using the QIAquick gel extraction kit (Qiagen). Illumina indices were attached to the amplicon with the Nextera XT Index Kit and deep sequenced using the Illumina Miseq. Fast-q files were analysed in Geneious.
amplicon sequencing using illumina MiSeq with adaptors from Nextera kit

treatment_protocol: Experiments were initiated with a cell-free infection, where 10^6 cells/ml RevCEM E7 were infected with 2 x 10^8 NL4-3 viral copies/ml (approximately 20ng p24 equivalent) for 2 days. Infected cells from the cell-free infection were used as the donors and cocultured with 10^6 cells/ml target cells. After two days of infection, 2% of the infected cells were added to uninfected target cells and cocultured for a 2-day cycle (day 0). Thereafter, 2% of resuspended infected cells were added to uninfected targets in the presence of EFV and co-cultured for each 2-day cycle.

value: RevCEM E7 cells

value: Cells treated every 2 days with Efavirenz

tag: time

value: Second run_Day 4

tag: population/single cell

value: single cells


title: D4_C5


title: D4_C2


title: D4_C6


title: Basal SAMP8 0.96mg/kg/day

description:
SI-182
Agilent design ID 017498

value: Male

value: Prefrontal Cortex

source_name: SAMP8-vehicle-treated-basal conditions


title: SAMP8 3.2mg/kg/day

description:
SI-104
Agilent design ID 017498

source_name: SAMP8-ORY-2001 3.2mg/kg/day


title: 20446_M3_uRBC

value: uRBC

value: Manhica

tag: immunization dose

tag: protection

tag: timepoint

value: F

value: PBMC


title: 20488_M3_iRBC

value: iRBC

tag: Sex

value: M

tag: tissue


title: 20454_M3_uRBC

value: Control


title: SAMP8 Vehicle

description:
SI-104
Agilent design ID 017498

value: Female


title: 20446_M3_DMSO


title: D4_C4

tag: cell line

tag: treatment


title: Basal SAMR1 Vehicle

description:
SI-182
Agilent design ID 017498

source_name: SAMR1-vehicle-treated-basal conditions

tag: strain


title: 20447_M3_DMSO

source_name: Cultured PBMC


title: 20446_M3_CSP

value: CSP


title: Basal SAMP8 Vehicle

description:
SI-182
Agilent design ID 017498


title: 20435_M3_iRBC

value: malaria


title: D4_B9


title: D4_C1


title: 20446_M3_iRBC

value: protected


title: D4_B8

value: RevCEM E7 cells


title: 20435_M3_CSP


title: D4_B6

value: Cells treated every 2 days with Efavirenz


title: D4_B7

value: Second run_Day 4


title: D4_B5

value: single cells


title: D4_B4


title: D4_B11


title: D4_B3


title: D4_B10


title: D4_B12


title: D4_B2


title: D4_A9


title: D4_B1


title: 20447_M3_CSP


title: WT-4

value: HAP1 cells

tag: genotype/treatment

value: WT


title: 20435_M3_uRBC

value: uRBC

tag: age


title: 20377_M3_uRBC

value: Manhica


title: 20377_M3_DMSO

value: DMSO


title: 20366_M3_DMSO

value: F

value: PBMC


title: 20377_M3_iRBC

value: iRBC

value: M


title: D4_A8


title: 20366_M3_CSP


title: D4_A7


title: D4_A6


title: D4_A3


title: D4_A5


title: D4_A2


title: 20377_M3_CSP


title: D4_A12


title: Basal SAMP8 0.32mg/kg/day

description:
SI-182
Agilent design ID 017498

tag: gender

value: Male

value: Prefrontal Cortex


title: 20365_M3_CSP

tag: stimulation

value: CSP


title: 20365_M3_iRBC

tag: subjectid

value: protected


title: 20365_M3_uRBC

tag: vaccine


title: 20365_M3_DMSO

tag: site


title: 20361_M3_DMSO

value: Control


title: D4_A10

value: RevCEM E7 cells

value: Cells treated every 2 days with Efavirenz

tag: time


title: D4_A11

value: Second run_Day 4

tag: population/single cell

value: single cells


title: D4_A1


title: 20361_M3_CSP

tag: immunization dose


title: D18_C5

value: Second run_Day 18


title: 20361_M3_iRBC

tag: protection


title: 20350_M3_DMSO

tag: timepoint


title: D18_C4


title: D18_C6


title: 20350_M3_uRBC

value: uRBC

tag: Sex


title: D18_C3


title: D18_C2


title: D18_C1


title: 20350_M3_CSP

value: Manhica

tag: tissue


title: 20347_M3_uRBC


title: 20347_M3_DMSO

value: DMSO


title: 20347_M3_CSP


title: 20361_M3_uRBC

value: F


title: 20345_M3_CSP

value: malaria

value: PBMC


title: 20345_M3_iRBC

value: iRBC

value: M


title: D18_B7

tag: cell line


title: 20345_M3_uRBC


title: 20338_M3_CSP


title: 20347_M3_iRBC


title: 20292_M3_uRBC


title: KO1-4

value: HAP1 cells

value: RPS25 KO1


title: D18_B6

tag: treatment


title: D18_B5


title: D18_B4


title: D18_B9


title: D18_B3


title: 20350_M3_iRBC

value: protected


title: 20292_M3_DMSO

value: Control


title: D18_B8

value: RevCEM E7 cells


title: D18_B2

value: Cells treated every 2 days with Efavirenz


title: 20338_M3_DMSO


title: D18_B10


title: D18_B1


title: D18_B11


title: D18_A9


title: 20292_M3_iRBC


title: D18_A7


title: D18_B12


title: D18_A8


title: D18_A6


title: 19941_M3_DMSO


title: 19941_M3_CSP

value: CSP


title: 19941_M0_CSP


title: 19941_M0_DMSO


title: 19941_M0_uRBC


title: 19930_M0_iRBC


title: D18_A4

value: single cells


title: D18_A5

value: Second run_Day 18


title: 19930_M0_uRBC

value: uRBC


title: D18_A3


title: 19930_M0_DMSO

value: Manhica


title: 19941_M0_iRBC


title: D18_A12


title: D18_A2


title: 19929_M3_uRBC


title: D18_A11


title: 19930_M0_CSP


title: 19929_M3_iRBC


title: 19929_M3_DMSO

value: DMSO


title: 19915_M0_uRBC


title: D4_A4

value: Second run_Day 4


title: 19929_M3_CSP


title: 19915_M0_iRBC

value: malaria


title: D18_A10


title: D18_A1


title: 19915_M0_CSP

value: PBMC


title: 19900_M0_CSP

value: F


title: 19900_M0_DMSO


title: D10_C4

value: Second run_Day 10


title: D10_B9


title: D10_C5


title: D10_B8


title: D10_B7


title: 19889_M0_CSP

value: M


title: D10_C3


title: 19889_M0_DMSO


title: D10_B5


title: 19900_M0_uRBC


title: D10_C2


title: 19915_M0_DMSO


title: D10_B6


title: D10_B4


title: D10_B3


title: D10_C1


title: 19881_M0_DMSO


title: D10_C6


title: 19900_M0_iRBC

value: iRBC


title: 19857_M3_iRBC

value: protected


title: D10_B2


title: D10_B12


title: 19867_M0_CSP

value: Control


title: 19881_M0_CSP


title: 19867_M0_DMSO


title: D10_B10

value: RevCEM E7 cells


title: 19857_M3_uRBC


title: 19857_M3_CSP


title: D10_B1

value: Cells treated every 2 days with Efavirenz


title: D10_B11


title: 19831_M0_uRBC


title: D10_A9


title: D10_A7


title: 19855_M0_DMSO


title: 19857_M3_DMSO


title: 19855_M0_CSP

value: CSP


title: D10_A8

value: single cells


title: D10_A6


title: D10_A5


title: 20292_M3_CSP


title: 19831_M0_CSP


title: 19826_M3_DMSO


title: 19831_M0_iRBC


title: 19820_M3_iRBC

value: Bagamoyo


title: 19826_M3_CSP


title: 19831_M0_DMSO


title: D10_A3


title: D10_A2


title: D10_A12


title: D10_A11


title: 19820_M3_CSP


title: D10_A1


title: D10_A4


title: 19732_M0_CSP


title: first run_D18_C7

value: First run_Day 18


title: 19820_M3_uRBC

value: uRBC


title: first run_D18_C8


title: 19717_M0_CSP

value: Manhica


title: first run_D18_C6


title: D10_A10


title: 19706_M0_DMSO

value: DMSO


title: first run_D18_C3


title: first run_D18_C2


title: 19706_M0_CSP


title: 19732_M0_DMSO


title: first run_D18_B9


title: 19717_M0_DMSO


title: 19508_M0_iRBC

value: malaria


title: 19667_M0_CSP

value: PBMC


title: 19667_M0_DMSO

value: F


title: 19508_M0_DMSO


title: first run_D18_B8


title: 19508_M0_CSP


title: 19489_M0_DMSO


title: 19489_M0_CSP


title: first run_D18_B7


title: first run_D18_B5


title: first run_D18_C4


title: first run_D18_B6


title: 19820_M3_DMSO


title: first run_D18_B3


title: first run_D18_B4


title: first run_D18_B2


title: 6469_M3_uRBC

value: Lamba


title: 6469_M3_CSP


title: 6469_M3_DMSO


title: first run_D18_B11


title: 6602_M3_CSP


title: first run_D18_B12


title: first run_D18_A9


title: first run_D18_B1


title: first run_D18_B10


title: first run_D18_A8


title: 6469_M3_iRBC


title: first run_D18_A6


title: first run_D18_A5


title: first run_D18_A7


title: first run_D18_A2


title: first run_D18_A4


title: first run_D18_A3


title: first run_D18_A12


title: first run_D18_A11


title: first run_D18_A10


title: 6329_M0_DMSO

value: M


title: 6267_M0_iRBC

value: iRBC


title: 6267_M0_uRBC

value: protected


title: 6266_M0_DMSO

value: Control


title: 6448_M3_uRBC


title: 6448_M3_CSP


title: first run_D12_C8

value: RevCEM E7 cells

value: First run_Day 12


title: first run_D18_A1

value: Cells treated every 2 days with Efavirenz


title: 6329_M0_CSP

value: CSP


title: first run_D12_C7

value: single cells


title: 6266_M0_uRBC


title: first run_D12_C6


title: 6267_M0_CSP


title: first run_D12_C5


title: first run_D12_C4


title: first run_D12_C3


title: first run_D12_C1


title: first run_D12_C2


title: first run_D12_B9


title: first run_D12_B7


title: 6266_M0_iRBC


title: 6267_M0_DMSO


title: 6290_M3_CSP


title: 6251_M0_DMSO


title: 6266_M0_CSP


title: 6237_M0_uRBC


title: 6251_M0_iRBC


title: 6236_M0_iRBC


title: 6239_M0_iRBC


title: 6239_M0_CSP


title: 6251_M0_uRBC


title: 6448_M3_DMSO


title: first run_D12_B6


title: 6290_M3_DMSO


title: first run_D12_B8