title: PBMC-timelapse, PBMC-timelapse-plate4_33

description:
PBMC-timelapse-plate4_33
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_34

status: Public on Dec 15 2022

type: SRA

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

description:
PBMC-timelapse-plate4_34
PBMC_RNA_expression.txt

library_source: transcriptomic

data_processing:
Basecalls performed by Illumina MiSeq or Hiseq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq or using bcl2fastq for Illumina Hiseq resultes
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA molecules per cell for each gene is listed (cells which were not filtered out are shown).

molecule: total RNA

organism: Mus musculus

source_name: Murine PBMCs

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Murine T cells, leukemia cells, hematopoietic progenitor cells, and PBMCs were isolated by ALPS or FACS

tag: strain

value: C57BL/6J mouse

tag: cell type

value: PBMC

tag: isolation method

value: ALPS


title: Hypothalamusollicular Lib8

city: Zaragoza

first: Kenza

last: Lakhssassi

state: Zaragoza

address: Av Montañana, 930,

country: Spain

institute: CITA

data_processing:
Checking quality control of the sequence with FastQC v0.11.5
Triming with Trimmomatic v0.38 with parameters LEADING:20 SLIDINGWINDOW:40:20 MINLEN:35
Alignment with HISAT2 v2.1.0 using default parameters except the options –k 2 –max seed 30
Converting files to sorted bam files with Samtools v1.7
Quantifying gene features from aligned reads with StringTie v1.3.5 using the “-G” option for annotation
Identification of differentially expressed genes with DESeq2 package in R v3.5.1 statistical environment.
Genome_build: GCA_000298735.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ovis aries

source_name: Hypothalamus

extract_protocol:
Samples from HT and PT tissues were isolated and rapidly frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from approximately 0.5 g of tissue using RNeasy Lipid Tissue mini kit from Qiagen following the manufacturer’s instructions.
Only RNA samples with a RIN > 7 were used for library construction. Sequencing was carried out at the CNAG through the Illumina Hi-Seq 2000 platform.

tag: tissue

value: Hypothalamus

tag: phase

value: Follicular

tag: breed

value: Rasa Aragonesa

tag: Sex

value: female

tag: developmental stage

value: adult ewe


title: Hypothalamusollicular Lib9


title: PBMC-timelapse, PBMC-timelapse-plate4_32

description:
PBMC-timelapse-plate4_32
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_93

description:
3mix-timelapse-plate11_93
3mix_RNA_expression.txt

source_name: Cell line mixture of murine T cell, murine leukemia cell, and murine hematopoietic progenitor cell

value: random selection


title: PBMC-timelapse, PBMC-timelapse-plate4_28

description:
PBMC-timelapse-plate4_28
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_26

description:
PBMC-timelapse-plate4_26
PBMC_RNA_expression.txt


title: Hypothalamus Luteal Lib6

value: Luteal


title: PBMC-timelapse, PBMC-timelapse-plate4_30

description:
PBMC-timelapse-plate4_30
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_31

description:
PBMC-timelapse-plate4_31
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_92

description:
3mix-timelapse-plate11_92
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_29

description:
PBMC-timelapse-plate4_29
PBMC_RNA_expression.txt


title: Hypothalamus Luteal Lib5


title: 3mix-timelapse, 3mix-timelapse-plate11_91

description:
3mix-timelapse-plate11_91
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_88

description:
3mix-timelapse-plate11_88
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_24

description:
PBMC-timelapse-plate4_24
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_22

description:
PBMC-timelapse-plate4_22
PBMC_RNA_expression.txt


title: Hypothalamus Luteal Lib7


title: PBMC-timelapse, PBMC-timelapse-plate4_27

description:
PBMC-timelapse-plate4_27
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_95

description:
3mix-timelapse-plate11_95
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_90

description:
3mix-timelapse-plate11_90
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_87

description:
3mix-timelapse-plate11_87
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_89

description:
3mix-timelapse-plate11_89
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_20

description:
PBMC-timelapse-plate4_20
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_23

description:
PBMC-timelapse-plate4_23
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate12_10

description:
3mix-timelapse-plate12_10
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_19

description:
PBMC-timelapse-plate4_19
PBMC_RNA_expression.txt


title: Hypothalamus Luteal Lib4


title: Hypothalamus Luteal Lib3


title: PBMC-timelapse, PBMC-timelapse-plate4_21

description:
PBMC-timelapse-plate4_21
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_25

description:
PBMC-timelapse-plate4_25
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_17

description:
PBMC-timelapse-plate4_17
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_86

description:
3mix-timelapse-plate11_86
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_85

description:
3mix-timelapse-plate11_85
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_18

description:
PBMC-timelapse-plate4_18
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_84

description:
3mix-timelapse-plate11_84
3mix_RNA_expression.txt


title: Hypothalamus Luteal Lib2


title: PBMC-timelapse, PBMC-timelapse-plate4_16

description:
PBMC-timelapse-plate4_16
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_83

description:
3mix-timelapse-plate11_83
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_13

description:
PBMC-timelapse-plate4_13
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_15

description:
PBMC-timelapse-plate4_15
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_14

description:
PBMC-timelapse-plate4_14
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_82

description:
3mix-timelapse-plate11_82
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_11

description:
PBMC-timelapse-plate4_11
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_10

description:
PBMC-timelapse-plate4_10
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_81

description:
3mix-timelapse-plate11_81
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_12

description:
PBMC-timelapse-plate4_12
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_9

description:
PBMC-timelapse-plate4_9
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_6

description:
PBMC-timelapse-plate4_6
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_3

description:
PBMC-timelapse-plate4_3
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_8

description:
PBMC-timelapse-plate4_8
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_7

description:
PBMC-timelapse-plate4_7
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_1

description:
PBMC-timelapse-plate4_1
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_80

description:
3mix-timelapse-plate11_80
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_95

description:
PBMC-timelapse-plate3_95
PBMC_RNA_expression.txt


title: Col0_seedling_pretreated_w_Brz_treated_w_DMSO_3hr_rep3

type: RNA

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 14-day seedlings treated with brassinazole followed by DMSO

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Qick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on MS-based agar media in growth chamber at 22 Celsius degree in 16h/8h day/night cycle.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: Seedling was treated pretreated with 1 micro M brassinazole for 14 days and then treated with 1 micro M brassinolide or DMSO for 3 hours.

tag: genotype

value: Wild type

tag: ecotype

tag: treatment

value: brassinazole followed by DMSO

tag: treatment duration

value: 14 days followed by 3 hours


title: PBMC-timelapse, PBMC-timelapse-plate3_96

description:
PBMC-timelapse-plate3_96
PBMC_RNA_expression.txt


title: Hypothalamus Luteal Lib1


title: Col0_seedling_pretreated_w_Brz_treated_w_DMSO_3hr_rep4


title: PBMC-timelapse, PBMC-timelapse-plate4_4

description:
PBMC-timelapse-plate4_4
PBMC_RNA_expression.txt


title: Col0_seedling_pretreated_w_Brz_treated_w_DMSO_3hr_rep1


title: 3mix-timelapse, 3mix-timelapse-plate11_79

description:
3mix-timelapse-plate11_79
3mix_RNA_expression.txt


title: Col0_seedling_pretreated_w_Brz_treated_w_DMSO_3hr_rep2


title: PBMC-timelapse, PBMC-timelapse-plate4_5

description:
PBMC-timelapse-plate4_5
PBMC_RNA_expression.txt


title: bil1_seedling_pretreated_w_Brz_treated_w_BL_3hr_rep3

source_name: Arabidopsis bil1-1D/bzr1-1D 14-day seedlings treated with brassinazole followed by brassinolide

value: brassinazole followed by brassinolide


title: 3mix-timelapse, 3mix-timelapse-plate11_77

description:
3mix-timelapse-plate11_77
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_76

description:
3mix-timelapse-plate11_76
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_78

description:
3mix-timelapse-plate11_78
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_94

description:
PBMC-timelapse-plate3_94
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_93

description:
PBMC-timelapse-plate3_93
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate4_2

description:
PBMC-timelapse-plate4_2
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_92

description:
PBMC-timelapse-plate3_92
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_75

description:
3mix-timelapse-plate11_75
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_91

description:
PBMC-timelapse-plate3_91
PBMC_RNA_expression.txt


title: Bai_Exp_2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

data_processing:
BCL Convert (v3.9.3)
CutAdapt (v2.3)
FastQC (v0.11.8)
RSEM (v1.3.3) / STAR (v2.7.8a)
DESeq2 (v1.34)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text of raw counts

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: breast cancer

value: baicalein treated


title: Bai_Exp_1


title: 3mix-timelapse, 3mix-timelapse-plate11_74

description:
3mix-timelapse-plate11_74
3mix_RNA_expression.txt


title: bil1_seedling_pretreated_w_Brz_treated_w_BL_3hr_rep2


title: bil1_seedling_pretreated_w_Brz_treated_w_BL_3hr_rep4


title: PBMC-timelapse, PBMC-timelapse-plate3_90

description:
PBMC-timelapse-plate3_90
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_73

description:
3mix-timelapse-plate11_73
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_89

description:
PBMC-timelapse-plate3_89
PBMC_RNA_expression.txt


title: Bai_Control_2


title: PBMC-timelapse, PBMC-timelapse-plate3_88

description:
PBMC-timelapse-plate3_88
PBMC_RNA_expression.txt


title: Bai_Control_1


title: 3mix-timelapse, 3mix-timelapse-plate11_71

description:
3mix-timelapse-plate11_71
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_85

description:
PBMC-timelapse-plate3_85
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_87

description:
PBMC-timelapse-plate3_87
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_86

description:
PBMC-timelapse-plate3_86
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_72

description:
3mix-timelapse-plate11_72
3mix_RNA_expression.txt


title: bil1_seedling_pretreated_w_Brz_treated_w_BL_3hr_rep1


title: PBMC-timelapse, PBMC-timelapse-plate3_84

description:
PBMC-timelapse-plate3_84
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_70

description:
3mix-timelapse-plate11_70
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_69

description:
3mix-timelapse-plate11_69
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_82

description:
PBMC-timelapse-plate3_82
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_80

description:
PBMC-timelapse-plate3_80
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_68

description:
3mix-timelapse-plate11_68
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_79

description:
PBMC-timelapse-plate3_79
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_78

description:
PBMC-timelapse-plate3_78
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_77

description:
PBMC-timelapse-plate3_77
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_67

description:
3mix-timelapse-plate11_67
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_75

description:
PBMC-timelapse-plate3_75
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_76

description:
PBMC-timelapse-plate3_76
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_66

description:
3mix-timelapse-plate11_66
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_73

description:
PBMC-timelapse-plate3_73
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_83

description:
PBMC-timelapse-plate3_83
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_65

description:
3mix-timelapse-plate11_65
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_71

description:
PBMC-timelapse-plate3_71
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_74

description:
PBMC-timelapse-plate3_74
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_64

description:
3mix-timelapse-plate11_64
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_81

description:
PBMC-timelapse-plate3_81
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_70

description:
PBMC-timelapse-plate3_70
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_68

description:
PBMC-timelapse-plate3_68
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_69

description:
PBMC-timelapse-plate3_69
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_63

description:
3mix-timelapse-plate11_63
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_67

description:
PBMC-timelapse-plate3_67
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate12_2

description:
3mix-timelapse-plate12_2
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_64

description:
PBMC-timelapse-plate3_64
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_63

description:
PBMC-timelapse-plate3_63
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_61

description:
3mix-timelapse-plate11_61
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_65

description:
PBMC-timelapse-plate3_65
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_59

description:
3mix-timelapse-plate11_59
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_61

description:
PBMC-timelapse-plate3_61
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_58

description:
3mix-timelapse-plate11_58
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_62

description:
PBMC-timelapse-plate3_62
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_59

description:
PBMC-timelapse-plate3_59
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_58

description:
PBMC-timelapse-plate3_58
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_57

description:
PBMC-timelapse-plate3_57
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_57

description:
3mix-timelapse-plate11_57
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_55

description:
PBMC-timelapse-plate3_55
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_56

description:
PBMC-timelapse-plate3_56
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_54

description:
PBMC-timelapse-plate3_54
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_66

description:
PBMC-timelapse-plate3_66
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_62

description:
3mix-timelapse-plate11_62
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_53

description:
PBMC-timelapse-plate3_53
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_55

description:
3mix-timelapse-plate11_55
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_56

description:
3mix-timelapse-plate11_56
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_50

description:
PBMC-timelapse-plate3_50
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_60

description:
3mix-timelapse-plate11_60
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_54

description:
3mix-timelapse-plate11_54
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_72

description:
PBMC-timelapse-plate3_72
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_60

description:
PBMC-timelapse-plate3_60
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_52

description:
PBMC-timelapse-plate3_52
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_48

description:
PBMC-timelapse-plate3_48
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_51

description:
PBMC-timelapse-plate3_51
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_53

description:
3mix-timelapse-plate11_53
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_49

description:
PBMC-timelapse-plate3_49
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_51

description:
3mix-timelapse-plate11_51
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_47

description:
PBMC-timelapse-plate3_47
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_43

description:
PBMC-timelapse-plate3_43
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_46

description:
PBMC-timelapse-plate3_46
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_45

description:
PBMC-timelapse-plate3_45
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_42

description:
PBMC-timelapse-plate3_42
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_50

description:
3mix-timelapse-plate11_50
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_41

description:
PBMC-timelapse-plate3_41
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_49

description:
3mix-timelapse-plate11_49
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_40

description:
PBMC-timelapse-plate3_40
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_39

description:
PBMC-timelapse-plate3_39
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_37

description:
PBMC-timelapse-plate3_37
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_48

description:
3mix-timelapse-plate11_48
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_31

description:
PBMC-timelapse-plate3_31
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_32

description:
PBMC-timelapse-plate3_32
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_44

description:
3mix-timelapse-plate11_44
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_46

description:
3mix-timelapse-plate11_46
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_43

description:
3mix-timelapse-plate11_43
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_47

description:
3mix-timelapse-plate11_47
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_28

description:
PBMC-timelapse-plate3_28
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_52

description:
3mix-timelapse-plate11_52
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_29

description:
PBMC-timelapse-plate3_29
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_33

description:
PBMC-timelapse-plate3_33
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_30

description:
PBMC-timelapse-plate3_30
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_25

description:
PBMC-timelapse-plate3_25
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_27

description:
PBMC-timelapse-plate3_27
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_35

description:
PBMC-timelapse-plate3_35
PBMC_RNA_expression.txt


title: H9

city: San Francisco

first: Akira

last: Kunitomi

state: CA

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description: Primed embryonic stem cells

data_processing:
FASTQ files were generated from bcl files using bcl2fastq v2.17.1.14 (illumina) and processed using ENCODE long-rna-seq-pipeline v2.3.4.
Sequenced reads were mapped to the human reference genome (GRCh38) using STAR 2.5.1b with GENCODE v24 gene annotations.
Normalized gene expression data was calculated using RSEM 1.2.23.
Gene count data was obtained using featureCounts bundled in Subread 1.5.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Human embryonic stem cells

growth_protocol: Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö medium. Feeder-free naive iPSCs were maintained on Matrigel (hESC-qualified, Corning)

extract_protocol:
Total RNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primed embryonic stem cells

tag: gender

value: Female


title: PBMC-timelapse, PBMC-timelapse-plate3_26

description:
PBMC-timelapse-plate3_26
PBMC_RNA_expression.txt

value: C57BL/6J mouse

value: PBMC


title: 3mix-timelapse, 3mix-timelapse-plate11_42

description:
3mix-timelapse-plate11_42
3mix_RNA_expression.txt

value: ALPS


title: PBMC-timelapse, PBMC-timelapse-plate3_38

description:
PBMC-timelapse-plate3_38
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_40

description:
3mix-timelapse-plate11_40
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_41

description:
3mix-timelapse-plate11_41
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_34

description:
PBMC-timelapse-plate3_34
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_24

description:
PBMC-timelapse-plate3_24
PBMC_RNA_expression.txt


title: 201B7

description: Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

source_name: Human induced pluripotent stem cells

value: Primed induced pluripotent stem cells


title: PBMC-timelapse, PBMC-timelapse-plate3_36

description:
PBMC-timelapse-plate3_36
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_45

description:
3mix-timelapse-plate11_45
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_39

description:
3mix-timelapse-plate11_39
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_38

description:
3mix-timelapse-plate11_38
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_36

description:
3mix-timelapse-plate11_36
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_23

description:
PBMC-timelapse-plate3_23
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_20

description:
PBMC-timelapse-plate3_20
PBMC_RNA_expression.txt


title: OSKL_3

description: Primed induced pluripotent stem cells derived from adult periferal blood mononuclear cells


title: OSKL_2


title: OSKL_4


title: 3mix-timelapse, 3mix-timelapse-plate11_37

description:
3mix-timelapse-plate11_37
3mix_RNA_expression.txt


title: OSKL_1


title: PBMC-timelapse, PBMC-timelapse-plate3_21

description:
PBMC-timelapse-plate3_21
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_35

description:
3mix-timelapse-plate11_35
3mix_RNA_expression.txt


title: nH9

description: Naive embryonic stem cells which were reset from the primed to naive state

value: Naive embryonic stem cells


title: nOSKL_4

description: Naive induced pluripotent stem cells derived from  adult periferal blood mononuclear cells

value: Naive induced pluripotent stem cells


title: 3mix-timelapse, 3mix-timelapse-plate11_33

description:
3mix-timelapse-plate11_33
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_16

description:
PBMC-timelapse-plate3_16
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_34

description:
3mix-timelapse-plate11_34
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_15

description:
PBMC-timelapse-plate3_15
PBMC_RNA_expression.txt


title: nOSKL_2

description: Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: PBMC-timelapse, PBMC-timelapse-plate3_17

description:
PBMC-timelapse-plate3_17
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_31

description:
3mix-timelapse-plate11_31
3mix_RNA_expression.txt


title: nOSKL_1


title: PBMC-timelapse, PBMC-timelapse-plate3_14

description:
PBMC-timelapse-plate3_14
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_22

description:
PBMC-timelapse-plate3_22
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_30

description:
3mix-timelapse-plate11_30
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_13

description:
PBMC-timelapse-plate3_13
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_29

description:
3mix-timelapse-plate11_29
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_18

description:
PBMC-timelapse-plate3_18
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_12

description:
PBMC-timelapse-plate3_12
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_11

description:
PBMC-timelapse-plate3_11
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_19

description:
PBMC-timelapse-plate3_19
PBMC_RNA_expression.txt


title: nOSKL_3

description: Naive induced pluripotent stem cells derived from adult periferal blood mononuclear cells


title: 3mix-timelapse, 3mix-timelapse-plate11_27

description:
3mix-timelapse-plate11_27
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_28

description:
3mix-timelapse-plate11_28
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_26

description:
3mix-timelapse-plate11_26
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_32

description:
3mix-timelapse-plate11_32
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_25

description:
3mix-timelapse-plate11_25
3mix_RNA_expression.txt


title: 67_S2

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

description:
CTRL female human glia
counts_AD-astro_hsa.txt.gz
counts_AD-astro_mmu.txt.gz

data_processing:
Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to human genome hg38 and mouse genome mm10 using STAR aligner (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Assembly: hg38; mm10
Supplementary files format and content: Tab delimeted text files (2) containing unnormalized (raw) read counts per feature, separately for unique human and mouse alignments.

organism:
Homo sapiens
Mus musculus

source_name: Mouse hippocampus containing hiPSC-derived glia

growth_protocol: The generation of PSEN1 ΔE9 mutant and isogenic CTRL iPSC lines and the astrosphere differentiation protocol were described previously (Stem Cell Reports. 2017;9:1885-1897).  Glial progenitors were grown in astrocyte differentiation medium in suspension for 6.5-7.5 months before the transplantation. For transplantation, astrospheres were dissociated with Accutase and the cells were resuspended at the concentration of 100,000 cells/µL in phosphate-buffered saline (PBS).  A total of 200,000 cells were injected intracerebroventricularly into cryoanestethized newborn pups (P0-P1) at 4 different injection sites (M/L ± 0.8 mm; A/P 1.0 mm, 2.0 mm; D/V −1.5 mm from lambda point; 0.5 μL each) using a 33 G needle cut at 30° angle (Hamilton) at rate 3 μL/min. Further, 100,000 cells in 1 μL PBS were injected into the middle of the cerebellum by freehand. After the injections, the pups were placed in a +37 °C chamber for 5 min to recover from cold anesthesia before being returned to the dams.

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Sigma). Trace amounts of the leftover DNA were removed by DNAse I treatment (molecular biology grade, Thermo Fisher Scientific) for 30 min at 37 °C. RNA was further purified using RNeasy Mini Kit (Qiagen). The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.

treatment_protocol: The transplanted mice underwent a panel of behavioral tests at the ages of 8, 12 and 16 months. At the age of 18 months, the mice were terminally anesthetized with Avertin and transcardially perfused with heparinizedd saline. The right hippocampi were quickly dissected out, frozen in the liquid nitrogen and stored at -80 C before the RNA extraction.

tag: hipsc source

value: skin fibroblasts

tag: group status

value: CTRL, AD3

tag: patient age_(years)

tag: patient gender

value: female

tag: mouse strain

tag: mouse age_(months)

tag: mouse sex

value: male


title: 69_S11

description:
PSEN1 ΔE9 female human glia
counts_AD-astro_hsa.txt.gz
counts_AD-astro_mmu.txt.gz

tag: tissue

value: Mouse hippocampus containing hiPSC-derived glia

value: PSEN1 ΔE9, AD3


title: 68_S1


title: 73_S3

description:
PSEN1 ΔE9 male human glia
counts_AD-astro_hsa.txt.gz
counts_AD-astro_mmu.txt.gz

value: PSEN1 ΔE9, AD2


title: 60_S9


title: 62_S5

description:
CTRL male human glia
counts_AD-astro_hsa.txt.gz
counts_AD-astro_mmu.txt.gz

value: CTRL, AD2


title: oe_TFAP4_bio rep c

city: BOSTON

first: William

middle: C

last: Hahn

state: Massachusetts

address: 450 Brookline Avenue

institute: DANA-FARBER CANCER INSTITUTE

description:
H36_317TFAP4_c
Overexpression_Compiled.txt

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to hg38 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output
Assembly: hg38
Supplementary files format and content: txt files contain TPM values for each sample

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
Libraries were prepared using Kapa mRNA Hyper prep kit (Roche)

tag: disease

value: pancreatic adenocarcinoma

value: TFAP4 overexpression


title: PBMC-timelapse, PBMC-timelapse-plate3_8

description:
PBMC-timelapse-plate3_8
PBMC_RNA_expression.txt

tag: strain

tag: cell type

tag: isolation method


title: 3mix-timelapse, 3mix-timelapse-plate11_24

description:
3mix-timelapse-plate11_24
3mix_RNA_expression.txt

value: random selection


title: oe_TFAP4_bio rep a

description:
H36_317TFAP4_a
Overexpression_Compiled.txt

tag: genotype


title: PBMC-timelapse, PBMC-timelapse-plate3_7

description:
PBMC-timelapse-plate3_7
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: oe_eGFP_bio rep c

description:
H36_317eGFP_c
Overexpression_Compiled.txt

value: WT (eGFP overexpression)


title: 58_S8


title: PBMC-timelapse, PBMC-timelapse-plate3_6

description:
PBMC-timelapse-plate3_6
PBMC_RNA_expression.txt

value: PBMC

value: ALPS


title: PBMC-timelapse, PBMC-timelapse-plate3_10

description:
PBMC-timelapse-plate3_10
PBMC_RNA_expression.txt


title: 57_S7


title: oe_eGFP_bio rep b

description:
H36_317eGFP_b
Overexpression_Compiled.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_23

description:
3mix-timelapse-plate11_23
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_21

description:
3mix-timelapse-plate11_21
3mix_RNA_expression.txt


title: 56_S6


title: 3mix-timelapse, 3mix-timelapse-plate11_22

description:
3mix-timelapse-plate11_22
3mix_RNA_expression.txt


title: oe_TFAP4_bio rep b

description:
H36_317TFAP4_b
Overexpression_Compiled.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_5

description:
PBMC-timelapse-plate3_5
PBMC_RNA_expression.txt


title: oe_eGFP_bio rep a

description:
H36_317eGFP_a
Overexpression_Compiled.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_9

description:
PBMC-timelapse-plate3_9
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_3

description:
PBMC-timelapse-plate3_3
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_19

description:
3mix-timelapse-plate11_19
3mix_RNA_expression.txt


title: 54_S4

description:
CTRL male human glia
counts_AD-astro_hsa.txt.gz
counts_AD-astro_mmu.txt.gz


title: VO_R3

city: Shanghai

first: Qing

last: Cui

state: Shanghai

address: Dongfang Lu No.1678

country: China

institute: Shanghai Children′s Medical Center Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)   in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  wascorrected.We used clusterProfiler R package to test the  statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were  filtered with GATK standard filter method and other parameters (cluster:3;  WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to  annotation for the Variablesite).
Genome_build: GCA_000001895.4
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: RV free wall myocardium

extract_protocol:
Myocardium of RV and LV free wall was rapidly removed from executed rat and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: SD

value: myocardium

tag: treatment method

value: volume overload(AVF)

tag: treatment  age

value: postnatal day 1

tag: test age

value: postnatal day 7


title: PBMC-timelapse, PBMC-timelapse-plate3_4

description:
PBMC-timelapse-plate3_4
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_20

description:
3mix-timelapse-plate11_20
3mix_RNA_expression.txt


title: sg_TFAP4_guide 2_bio rep b

description:
TFAP4_sg2_b
Knockout_Compiled.txt

tag: cell line

value: TFAP4 knockdown


title: 61_S10

value: Mouse hippocampus containing hiPSC-derived glia

tag: hipsc source

value: skin fibroblasts

value: male


title: sg_TFAP4_guide 2_bio rep c

description:
TFAP4_sg2_c
Knockout_Compiled.txt


title: PBMC-timelapse, PBMC-timelapse-plate3_2

description:
PBMC-timelapse-plate3_2
PBMC_RNA_expression.txt


title: VO_R2


title: PBMC-timelapse, PBMC-timelapse-plate3_1

description:
PBMC-timelapse-plate3_1
PBMC_RNA_expression.txt


title: VO_R1


title: VO_L3

source_name: LV free wall myocardium


title: sg_TFAP4_guide 1_bio rep b

description:
TFAP4_sg1_b
Knockout_Compiled.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_96

description:
PBMC-timelapse-plate2_96
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_17

description:
3mix-timelapse-plate11_17
3mix_RNA_expression.txt


title: VO_L2


title: 3mix-timelapse, 3mix-timelapse-plate11_16

description:
3mix-timelapse-plate11_16
3mix_RNA_expression.txt


title: sg_TFAP4_guide 1_bio rep a

description:
TFAP4_sg1_a
Knockout_Compiled.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_18

description:
3mix-timelapse-plate11_18
3mix_RNA_expression.txt


title: sg_TFAP4_guide 2_bio rep a

description:
TFAP4_sg2_a
Knockout_Compiled.txt


title: VO_L1


title: PBMC-timelapse, PBMC-timelapse-plate2_95

description:
PBMC-timelapse-plate2_95
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_94

description:
PBMC-timelapse-plate2_94
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_14

description:
3mix-timelapse-plate11_14
3mix_RNA_expression.txt


title: sg_TFAP4_guide 1_bio rep c

description:
TFAP4_sg1_c
Knockout_Compiled.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_15

description:
3mix-timelapse-plate11_15
3mix_RNA_expression.txt


title: sg_Control_guide 4_bio rep c

description:
Control_4_c
Knockout_Compiled.txt

value: WT (intergenic guide)


title: sham_R3

value: operated-sham


title: PBMC-timelapse, PBMC-timelapse-plate2_92

description:
PBMC-timelapse-plate2_92
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_93

description:
PBMC-timelapse-plate2_93
PBMC_RNA_expression.txt


title: sham_R2


title: 3mix-timelapse, 3mix-timelapse-plate11_11

description:
3mix-timelapse-plate11_11
3mix_RNA_expression.txt


title: sg_Control_guide 4_bio rep b

description:
Control_4_b
Knockout_Compiled.txt

value: pancreatic adenocarcinoma


title: 3mix-timelapse, 3mix-timelapse-plate11_13

description:
3mix-timelapse-plate11_13
3mix_RNA_expression.txt

value: random selection


title: sham_L3


title: 3mix-timelapse, 3mix-timelapse-plate11_12

description:
3mix-timelapse-plate11_12
3mix_RNA_expression.txt


title: sg_Control_guide 2_bio rep c

description:
Control_2_c
Knockout_Compiled.txt


title: sg_Control_guide 4_bio rep a

description:
Control_4_a
Knockout_Compiled.txt


title: sg_Control_guide 2_bio rep b

description:
Control_2_b
Knockout_Compiled.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_9

description:
3mix-timelapse-plate11_9
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_91

description:
PBMC-timelapse-plate2_91
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: 3mix-timelapse, 3mix-timelapse-plate11_10

description:
3mix-timelapse-plate11_10
3mix_RNA_expression.txt


title: NCO2_AK2292Me_24h_3

first: Shaomeng

last: Wang

state: Michigan

address: 1600 Huron Parkway, Building 520 Rm 352

description:
NCO2_AK2292Me_24h_3
NCO2_gene_FPKM.csv

data_processing:
RTA version 1.18.66.3 (HCS  version 2.2.68 ) was used for basecalling
bcl2fastq version 2.17.1.14 was used for generating fastq files
Reads were mapped to the reference genome GRCh38 (ENSEMBL) using STAR v2.7.8a
Gene abundance estimation was done using RSEM v1.3.3.
Transcriptome annotation: GENCODE v24 basic.
Assembly: NCBI GRCh38
Supplementary files format and content: FPKM values of each cell line treated with DMSO, AK2292 and AK2292Me

source_name: Hematopoietic/Lymphoid tissue

growth_protocol: KU812 and NCO2 human chronic myelogenous leukemiacells were maintained in RPMI supplemented with 10% heat-inactivated fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was purified by RNeasy Mini Kit (Qiagen, #74104) following the manufacturer’s instructions. RNA quality was checked using the TapeStation (Agilent).
Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs (NEB), # E7760L), NEBNext rRNA Depletion kit v2 (NEB, # E7400X) and NEBNext Multiplex Oligos for Illumina (NEB, # E6440L). About 320 ng of total RNA was ribosomal depleted using the rRNA Depletion module. The rRNA-depleted RNA is then fragmented for 10 min determined by RIN (RNA Integrity Number) of input RNA as per protocol and copied into first-strand cDNA using mixed reverse transcriptase and dUTP. Samples undergo end repair and dA-Tailing step followed by ligation of NEBNext adapters. The products were purified and enriched by PCR to create the final cDNA library. The final libraries were checked for quality and quantity by TapeStation (Agilent) and Qubit (Fisher Scientific).

treatment_protocol: Cells were treated with DMSO, 1 µM of AK2292 and 5µM of AK-2292Me for 8 or 24 hours respectively.

value: Hematopoietic/Lymphoid tissue

tag: agent

tag: treatment


title: 279-LN: Lymph Node Of AITL-Carrying NSG Mouse #279

city: New Haven

first: Elias

last: Lolis

state: Connecticut

address: PO Box 208066, 333 Cedar St.

department: Pharmacology

institute: Yale University

data_processing:
Reads were filtered for quality and aligned to hg38 with Ensembl Transcripts release 100 and mm10 with Ensembl Transcripts release 100 using Partek Flow (v10.0.21.0509)
Aligned reads were separated into mouse and human reads using XenofilteR v1.6
Reads were then quantified and analyzed again with Partek Flow. Transcripts with £10 reads were removed and separated aligned reads were normalized to the total number of counts per sample.
Transcripts were used for Gene Specific Analysis and Alternative Splicing Detection using Partek Flow (v10.0.21.0509)
Genome_build: hg38, mm10
Supplementary_files_format_and_content: csv files containing the differential gene expressions, fold change, p-values, and corrected p-values
Supplementary_files_format_and_content: tab-delimited txt files containing the differential splice variant expressions, fold change, p-values, and corrected p-values
Supplementary_files_format_and_content: Filtered BED files containig human-only and mouse-only transcripts.

source_name: Lymph Node

extract_protocol:
Lymph nodes were excised and formalin-fixed/paraffin-embedded. Slices of tissue were deparaffinized and rRNA was depleted.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated twice daily by oral gavage at 40mg/kg of compound with 4.7% DMSO in PBS as the vehicle or an equivalent volume of vehicle

value: Angioimmunoblastic T-cell Lymphoma Xenograft

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG)

tag: xenograft number


title: PBMC-timelapse, PBMC-timelapse-plate2_90

description:
PBMC-timelapse-plate2_90
PBMC_RNA_expression.txt

value: PBMC

value: ALPS


title: 277-LN: Lymph Node Of AITL-Carrying NSG Mouse #277

tag: mouse strain


title: sham_R1

value: SD

value: myocardium


title: PBMC-timelapse, PBMC-timelapse-plate2_88

description:
PBMC-timelapse-plate2_88
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_7

description:
3mix-timelapse-plate11_7
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_87

description:
PBMC-timelapse-plate2_87
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_8

description:
3mix-timelapse-plate11_8
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_89

description:
PBMC-timelapse-plate2_89
PBMC_RNA_expression.txt


title: sham_L1

value: postnatal day 1

value: postnatal day 7


title: sg_Control_guide 2_bio rep a

description:
Control_2_a
Knockout_Compiled.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_6

description:
3mix-timelapse-plate11_6
3mix_RNA_expression.txt


title: sham_L2


title: 274-LN: Lymph Node Of AITL-Carrying NSG Mouse #274

value: Vehicle


title: NCO2_AK2292_8h_3

description:
NCO2_AK2292_8h_3
NCO2_gene_FPKM.csv

value: 8 h


title: NCO2_AK2292Me_24h_1

description:
NCO2_AK2292Me_24h_1
NCO2_gene_FPKM.csv


title: PBMC-timelapse, PBMC-timelapse-plate2_86

description:
PBMC-timelapse-plate2_86
PBMC_RNA_expression.txt


title: NCO2_AK2292Me_24h_2

description:
NCO2_AK2292Me_24h_2
NCO2_gene_FPKM.csv


title: NCO2_AK2292_8h_2

description:
NCO2_AK2292_8h_2
NCO2_gene_FPKM.csv


title: 267-LN: Lymph Node Of AITL-Carrying NSG Mouse #267


title: 3mix-timelapse, 3mix-timelapse-plate11_4

description:
3mix-timelapse-plate11_4
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_85

description:
PBMC-timelapse-plate2_85
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_84

description:
PBMC-timelapse-plate2_84
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_3

description:
3mix-timelapse-plate11_3
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_82

description:
PBMC-timelapse-plate2_82
PBMC_RNA_expression.txt


title: NCO2_DMSO_3

description:
NCO2_DMSO_3
NCO2_gene_FPKM.csv

value: DMSO


title: NCO2_DMSO_1

description:
NCO2_DMSO_1
NCO2_gene_FPKM.csv


title: 3mix-timelapse, 3mix-timelapse-plate10_96

description:
3mix-timelapse-plate10_96
3mix_RNA_expression.txt


title: 262-LN: Lymph Node Of AITL-Carrying NSG Mouse #262


title: H3F3A-specific siRNA, replicate 3

city: Singapore

first: Reshma

last: Taneja

address: 10 Medical Dr

country: Singapore

institute: NUS

data_processing:
Raw image data file from sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
Bcl2fastq was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.5 with parameters mismatch=2. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis between two condition/groups (three biological replicates per condition) was performed using the DESeq2 R package (v2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg19
Supplementary files format and content: ReadsPerGene file

growth_protocol: Rh41 cells were cultured in RPMI media supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin

extract_protocol:
Total RNA extraction with Trizol. RNA purity and integrity were assessed with Nanodrop and agarose gel electrophoresis. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was first fragmented randomly by addition of fragmentation buffer. The first strand of cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-).
RNA libraries were prepared for sequencing using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Control(siscr) and H3F3A-knockdown (siH3F3A) cells were transfected with scrambled siRNA and H3F3A-specific siRNA respectively using Lipofectamine RNAiMAX.

value: ARMS

value: FP-RMS

value: H3F3A-specific siRNA


title: PBMC-timelapse, PBMC-timelapse-plate2_79

description:
PBMC-timelapse-plate2_79
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_2

description:
3mix-timelapse-plate11_2
3mix_RNA_expression.txt

value: random selection


title: NCO2_AK2292_8h_1

description:
NCO2_AK2292_8h_1
NCO2_gene_FPKM.csv


title: PBMC-timelapse, PBMC-timelapse-plate2_80

description:
PBMC-timelapse-plate2_80
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: PBMC-timelapse, PBMC-timelapse-plate2_83

description:
PBMC-timelapse-plate2_83
PBMC_RNA_expression.txt


title: NCO2_DMSO_2

description:
NCO2_DMSO_2
NCO2_gene_FPKM.csv

value: Hematopoietic/Lymphoid tissue


title: 3mix-timelapse, 3mix-timelapse-plate11_1

description:
3mix-timelapse-plate11_1
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate11_5

description:
3mix-timelapse-plate11_5
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_94

description:
3mix-timelapse-plate10_94
3mix_RNA_expression.txt


title: H3F3A-specific siRNA, replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate2_78

description:
PBMC-timelapse-plate2_78
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_95

description:
3mix-timelapse-plate10_95
3mix_RNA_expression.txt


title: H3F3A-specific siRNA, replicate 2


title: scrambled siRNA, replicate 3

value: scrambled siRNA


title: 264-LN: Lymph Node Of AITL-Carrying NSG Mouse #264

value: Angioimmunoblastic T-cell Lymphoma Xenograft

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG)


title: KU812_AK2292Me_24h_1

description:
KU812_AK2292Me_24h_1
KU812_gene_FPKM.csv


title: 3mix-timelapse, 3mix-timelapse-plate10_93

description:
3mix-timelapse-plate10_93
3mix_RNA_expression.txt

value: ALPS


title: PBMC-timelapse, PBMC-timelapse-plate2_81

description:
PBMC-timelapse-plate2_81
PBMC_RNA_expression.txt

value: PBMC


title: 3mix-timelapse, 3mix-timelapse-plate10_92

description:
3mix-timelapse-plate10_92
3mix_RNA_expression.txt


title: H3.3 ChIP, replicate 1

library_source: genomic

data_processing:
Raw base call files from HiSeq PE150 were demultiplex with bcl2fastq v2.20 and fastq files were subjected to QC with FastQC
The fastq files were mapped to the human genome GRCh38.p13 with Bowtie2 and the BAM files from the mapping were passed into MACS2 for peak calling.
The BED files for the broad peaks, gapped peaks, narrow peaks and peak submits, along with the BigWig track for the peaks were imported into Integrative Genomics Viewer (IGV) for visualisation.
Assembly: Hg19

molecule: genomic DNA

extract_protocol:
Cells were fixed with formaldehyde. After quenching and cell lysis, sonication was performed (Bioruptor Pico)
Performed by Novogene, included  terminal repair, add A, add adapter, length filter, PCR amplification

value: ChIP

tag: chip antibody


title: KU812_AK2292Me_24h_3

description:
KU812_AK2292Me_24h_3
KU812_gene_FPKM.csv


title: 3mix-timelapse, 3mix-timelapse-plate10_91

description:
3mix-timelapse-plate10_91
3mix_RNA_expression.txt


title: Input, replicate 2

value: No pulldown


title: PBMC-timelapse, PBMC-timelapse-plate2_75

description:
PBMC-timelapse-plate2_75
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_90

description:
3mix-timelapse-plate10_90
3mix_RNA_expression.txt


title: KU812_AK2292_8h_2

description:
KU812_AK2292_8h_2
KU812_gene_FPKM.csv


title: scrambled siRNA, replicate 1


title: KU812_AK2292_8h_3

description:
KU812_AK2292_8h_3
KU812_gene_FPKM.csv


title: PBMC-timelapse, PBMC-timelapse-plate2_76

description:
PBMC-timelapse-plate2_76
PBMC_RNA_expression.txt


title: KU812_AK2292Me_24h_2

description:
KU812_AK2292Me_24h_2
KU812_gene_FPKM.csv


title: PBMC-timelapse, PBMC-timelapse-plate2_77

description:
PBMC-timelapse-plate2_77
PBMC_RNA_expression.txt


title: H3.3 ChIP, replicate 2


title: Input, replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate2_74

description:
PBMC-timelapse-plate2_74
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_72

description:
PBMC-timelapse-plate2_72
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_88

description:
3mix-timelapse-plate10_88
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_89

description:
3mix-timelapse-plate10_89
3mix_RNA_expression.txt


title: Neuronal RNA-seq, N-ZFP, zQ175-4

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Striatum, Neuronal RNA-seq, N-ZFP, zQ175-4
Q175_N_ZFP_Str_N_IP_4

data_processing:
Aligned to mouse genome (mm10) using STAR spliced read aligner
Count the reads with htseq-count
Normalization and differential expression analysis using Bioconductor packages
Assembly: mm10
Supplementary files format and content: xlsx file with counts for each sample

source_name: Striatum

extract_protocol:
RNA from R6/2 and NCAR mice striatum was extracted using RNeasy mini plus kit (Qiagen). RNA from Q175 and WT mice was extracted using Rneasy plus micro kit (Qiagen) following manufacturer's protocol.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: R6/2 and NCAR mice were injected with astrocytic PHP.eB AAVs (A-ZFP, A-Delta) at 4 weeks of old and RNA extracted from the striatum at 11 weeks old. Similarly, R6/2 and NCAR mice were injected with astrocytic PHP.eB AAVs (N-ZFP, N-Delta) at 4 weeks of old and RNA extracted from the striatum at 11 weeks old. ZQ175 and WT mice were injected intrastriatal with neuronal AAVs (N-ZFP, N-Delta) at 6 months old and RNA extracted from the striatum at 12 months old.

value: Striatum

value: N-ZFP

value: neuron


title: PBMC-timelapse, PBMC-timelapse-plate2_73

description:
PBMC-timelapse-plate2_73
PBMC_RNA_expression.txt


title: KU812_AK2292_8h_1

description:
KU812_AK2292_8h_1
KU812_gene_FPKM.csv

value: 8 h


title: 3mix-timelapse, 3mix-timelapse-plate10_87

description:
3mix-timelapse-plate10_87
3mix_RNA_expression.txt


title: KU812_DMSO_2

description:
KU812_DMSO_2
KU812_gene_FPKM.csv

value: DMSO


title: KU812_DMSO_3

description:
KU812_DMSO_3
KU812_gene_FPKM.csv


title: KU812_DMSO_1

description:
KU812_DMSO_1
KU812_gene_FPKM.csv


title: Neuronal RNA-seq, N-ZFP, zQ175-2

description:
Striatum, Neuronal RNA-seq, N-ZFP, zQ175-2
Q175_N_ZFP_Str_N_IP_2


title: Neuronal RNA-seq, N-ZFP, zQ175-3

description:
Striatum, Neuronal RNA-seq, N-ZFP, zQ175-3
Q175_N_ZFP_Str_N_IP_3


title: PBMC-timelapse, PBMC-timelapse-plate2_70

description:
PBMC-timelapse-plate2_70
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_69

description:
PBMC-timelapse-plate2_69
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_71

description:
PBMC-timelapse-plate2_71
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_86

description:
3mix-timelapse-plate10_86
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_68

description:
PBMC-timelapse-plate2_68
PBMC_RNA_expression.txt


title: Target_293T_EEF1A1_18S_RPS6_gCtrl_CMC

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

data_processing:
Trim_galore (version0.6.6 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20. The remaining reads were further processed by removing the random barcode. Processed reads were mapped to hg19 or mm10.
For CeU-seq, the data processing requires multiple input and treatment samples (including replicates) that are sequencing separately to give multiple fastq files; the processed data were calculated based on these multiple input and treatment groups data to give a single summarized table. Similarly for Target-seq, each target contains input and treatment groups that produced multiple fastq files; the processed data requires calculating the signal in both input and treatment of multiple data, and all results of all targets were summarized in a single table file.
Assembly: hg19/mm10
Library strategy: Target-seq

source_name: human embryonic kidney cell (HEK293T)

growth_protocol: HEK293T cells and primary mouse embryonic fibroblasts (MEFs) were maintained under 5% CO2 at 37 °C in DMEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco). The primary human dermal fibroblasts (HDF) and primary human bronchial epithelial cells (HBE) were cultured in Fibroblast Growth Medium (iXCells, MD-0011) and Bronchial Epithelial Cell Growth Basal Medium (Lonza, CC-3171), respectively. Both media were supplemented with 1% penicillin–streptomycin. The B-Lymphocytes were cultured in 1640 (Corning) with 15% FBS and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Life Technologies). The selection of polyA(+) RNA was performed using Dynabeads™ Oligo(dT)25 (Invitrogen).
RNA-seq of transfected HEK293T cells were performed with TRACE-seq method. For CeU-seq and Target-seq, the RNA pellet was dissolved in 20 μl 5 mM EDTA, incubated at 80°C for 5 minutes, and quickly chilled on ice. Next, 10 μl denatured RNA was transferred into 100 μl in BEU buffer (50 mM Bicine, pH 8.5, 4 mM EDTA, 7 M urea) with 0.2 M CMC (Sigma, Cat#C106402, 95%) as the CMC+ sample, or into 100 μl BEU buffer as the CMC- control sample. Both CMC+ and CMC- samples were then incubated at 37 °C for 20 min, followed by purification with ethanol precipitation. The RNA pellets were then dissolved in 50 μl Na2CO3 buffer (50 mM Na2CO3 pH 10.4, 2 mM EDTA) and incubated at 37 °C for 6 h, followed by ethanol precipitation.

treatment_protocol: HEK293T cells were seeded in six-well plates and incubated for 24 h, followed by transfection. 72 h post transfection, total RNA was extracted from cells. For AAV-mediated cell transduction, 24 hours after seeding, HDF, HBE and B-Lymphocytes were transduced by AAV6.2 (EEF2-U1570/EEF2-U2881/PPIB-U272/CFTR-W1282X), and MEFs were transduced by AAVDJ (mIdua-W392X). 7 days after transduction, cells were collected.

value: human embryonic kidney cell

tag: passages


title: Target_Bcell_CFTR_RESTART

source_name: B-Lymphocyte GM04345

value: B-Lymphocyte GM04345


title: 3mix-timelapse, 3mix-timelapse-plate10_84

description:
3mix-timelapse-plate10_84
3mix_RNA_expression.txt

value: random selection


title: Target_Bcell_CFTR_mock


title: Neuronal RNA-seq, N-ZFP, zQ175-1

description:
Striatum, Neuronal RNA-seq, N-ZFP, zQ175-1
Q175_N_ZFP_Str_N_IP_1

tag: tissue


title: Neuronal RNA-seq, N-Delta, zQ175-3

description:
Striatum, Neuronal RNA-seq, N-Delta, zQ175-3
Q175_N_Delta_Str_N_IP_3

value: N-Delta


title: 3mix-timelapse, 3mix-timelapse-plate10_82

description:
3mix-timelapse-plate10_82
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_83

description:
3mix-timelapse-plate10_83
3mix_RNA_expression.txt


title: Neuronal RNA-seq, N-Delta, zQ175-1

description:
Striatum, Neuronal RNA-seq, N-Delta, zQ175-1
Q175_N_Delta_Str_N_IP_1


title: PBMC-timelapse, PBMC-timelapse-plate2_67

description:
PBMC-timelapse-plate2_67
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: Target_293T_EEF1A1_18S_RPS6_gCtrl_BEU


title: PBMC-timelapse, PBMC-timelapse-plate2_66

description:
PBMC-timelapse-plate2_66
PBMC_RNA_expression.txt


title: Neuronal RNA-seq, N-Delta, zQ175-2

description:
Striatum, Neuronal RNA-seq, N-Delta, zQ175-2
Q175_N_Delta_Str_N_IP_2


title: Target_293T_RPL5_EEF2_PPIB_gCtrl_BEU


title: 3mix-timelapse, 3mix-timelapse-plate10_81

description:
3mix-timelapse-plate10_81
3mix_RNA_expression.txt


title: Neuronal RNA-seq, N-ZFP, WT-4

description:
Striatum, Neuronal RNA-seq, N-ZFP, WT-4
WT_N_ZFP_Str_N_IP_4

value: WT


title: Target_293T_RPL5_EEF2_PPIB_gCtrl_CMC


title: 3mix-timelapse, 3mix-timelapse-plate10_80

description:
3mix-timelapse-plate10_80
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_64

description:
PBMC-timelapse-plate2_64
PBMC_RNA_expression.txt


title: Target_293T_ACTB_EEF2_gCtrl_CMC


title: 3mix-timelapse, 3mix-timelapse-plate10_85

description:
3mix-timelapse-plate10_85
3mix_RNA_expression.txt


title: Neuronal RNA-seq, N-Delta, zQ175-4

description:
Striatum, Neuronal RNA-seq, N-Delta, zQ175-4
Q175_N_Delta_Str_N_IP_4


title: Neuronal RNA-seq, N-ZFP, WT-3

description:
Striatum, Neuronal RNA-seq, N-ZFP, WT-3
WT_N_ZFP_Str_N_IP_3


title: PBMC-timelapse, PBMC-timelapse-plate2_63

description:
PBMC-timelapse-plate2_63
PBMC_RNA_expression.txt


title: Target_293T_ACTB_EEF2_gCtrl_BEU


title: 3mix-timelapse, 3mix-timelapse-plate10_79

description:
3mix-timelapse-plate10_79
3mix_RNA_expression.txt


title: Neuronal RNA-seq, N-ZFP, WT-2

description:
Striatum, Neuronal RNA-seq, N-ZFP, WT-2
WT_N_ZFP_Str_N_IP_2


title: 3mix-timelapse, 3mix-timelapse-plate10_78

description:
3mix-timelapse-plate10_78
3mix_RNA_expression.txt


title: Target_293T_EEF1A1_18S_RPS6_gACA19_CMC


title: PBMC-timelapse, PBMC-timelapse-plate2_62

description:
PBMC-timelapse-plate2_62
PBMC_RNA_expression.txt


title: Neuronal RNA-seq, N-ZFP, WT-1

description:
Striatum, Neuronal RNA-seq, N-ZFP, WT-1
WT_N_ZFP_Str_N_IP_1


title: PBMC-timelapse, PBMC-timelapse-plate2_61

description:
PBMC-timelapse-plate2_61
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_65

description:
PBMC-timelapse-plate2_65
PBMC_RNA_expression.txt


title: Neuronal RNA-seq, N-Delta, WT-4

description:
Striatum, Neuronal RNA-seq, N-Delta, WT-4
WT_N_Delta_Str_N_IP_4


title: Target_293T_EEF1A1_18S_RPS6_gACA19_BEU


title: 3mix-timelapse, 3mix-timelapse-plate10_76

description:
3mix-timelapse-plate10_76
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_60

description:
PBMC-timelapse-plate2_60
PBMC_RNA_expression.txt


title: Target_293T_RPL5_EEF2_PPIB_gACA19_CMC


title: 3mix-timelapse, 3mix-timelapse-plate10_75

description:
3mix-timelapse-plate10_75
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_59

description:
PBMC-timelapse-plate2_59
PBMC_RNA_expression.txt


title: Target_293T_RPL5_EEF2_PPIB_gACA19_BEU


title: Neuronal RNA-seq, N-Delta, WT-2

description:
Striatum, Neuronal RNA-seq, N-Delta, WT-2
WT_N_Delta_Str_N_IP_2


title: PBMC-timelapse, PBMC-timelapse-plate2_58

description:
PBMC-timelapse-plate2_58
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_74

description:
3mix-timelapse-plate10_74
3mix_RNA_expression.txt


title: Neuronal RNA-seq, N-Delta, WT-1

description:
Striatum, Neuronal RNA-seq, N-Delta, WT-1
WT_N_Delta_Str_N_IP_1


title: 3mix-timelapse, 3mix-timelapse-plate10_73

description:
3mix-timelapse-plate10_73
3mix_RNA_expression.txt


title: Target_293T_ACTB_EEF2_gACA19_CMC


title: PBMC-timelapse, PBMC-timelapse-plate2_57

description:
PBMC-timelapse-plate2_57
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_72

description:
3mix-timelapse-plate10_72
3mix_RNA_expression.txt


title: Target_293T_EEF1A1_18S_RPS6_gACA19_DKC1_CMC


title: 3mix-timelapse, 3mix-timelapse-plate10_77

description:
3mix-timelapse-plate10_77
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-ZFP, zQ175-4

description:
Striatum, Bulk RNA-seq, N-ZFP, zQ175-4
zQ175_N_ZFP_Str_Input_4


title: Target_293T_ACTB_EEF2_gACA19_BEU


title: 3mix-timelapse, 3mix-timelapse-plate10_71

description:
3mix-timelapse-plate10_71
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-ZFP, zQ175-2

description:
Striatum, Bulk RNA-seq, N-ZFP, zQ175-2
zQ175_N_ZFP_Str_Input_2


title: Neuronal RNA-seq, N-Delta, WT-3

description:
Striatum, Neuronal RNA-seq, N-Delta, WT-3
WT_N_Delta_Str_N_IP_3


title: 3mix-timelapse, 3mix-timelapse-plate10_70

description:
3mix-timelapse-plate10_70
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_55

description:
PBMC-timelapse-plate2_55
PBMC_RNA_expression.txt


title: Target_293T_EEF1A1_18S_RPS6_gACA19_DKC1_BEU


title: 3mix-timelapse, 3mix-timelapse-plate10_69

description:
3mix-timelapse-plate10_69
3mix_RNA_expression.txt


title: Target_293T_RPL5_EEF2_PPIB_gACA19_DKC1_CMC


title: Striatum, Bulk RNA-seq, N-ZFP, zQ175-1

description:
Striatum, Bulk RNA-seq, N-ZFP, zQ175-1
zQ175_N_ZFP_Str_Input_1


description:
Striatum, Bulk RNA-seq, N-Delta, zQ175-4
zQ175_N_Delta_Str_Input_4


title: PBMC-timelapse, PBMC-timelapse-plate2_53

description:
PBMC-timelapse-plate2_53
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_52

description:
PBMC-timelapse-plate2_52
PBMC_RNA_expression.txt


title: Target_293T_RPL5_EEF2_PPIB_gACA19_DKC1_BEU


title: PBMC-timelapse, PBMC-timelapse-plate2_54

description:
PBMC-timelapse-plate2_54
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_68

description:
3mix-timelapse-plate10_68
3mix_RNA_expression.txt


title: Target_293T_ACTB_EEF2_gACA19_DKC1_BEU


title: 3mix-timelapse, 3mix-timelapse-plate10_66

description:
3mix-timelapse-plate10_66
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_67

description:
3mix-timelapse-plate10_67
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_56

description:
PBMC-timelapse-plate2_56
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_51

description:
PBMC-timelapse-plate2_51
PBMC_RNA_expression.txt


description:
Striatum, Bulk RNA-seq, N-Delta, zQ175-3
zQ175_N_Delta_Str_Input_3


description:
Striatum, Bulk RNA-seq, N-Delta, zQ175-2
zQ175_N_Delta_Str_Input_2


title: Striatum, Bulk RNA-seq, N-ZFP, zQ175-3

description:
Striatum, Bulk RNA-seq, N-ZFP, zQ175-3
zQ175_N_ZFP_Str_Input_3


title: PBMC-timelapse, PBMC-timelapse-plate2_50

description:
PBMC-timelapse-plate2_50
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_49

description:
PBMC-timelapse-plate2_49
PBMC_RNA_expression.txt


title: Target_293T_PPIB_RPS6_mock_CMC


title: PBMC-timelapse, PBMC-timelapse-plate2_48

description:
PBMC-timelapse-plate2_48
PBMC_RNA_expression.txt


title: Target_293T_ACTB_EEF2_gACA19_DKC1_CMC


title: Striatum, Bulk RNA-seq, N-ZFP, WT-4

description:
Striatum, Bulk RNA-seq, N-ZFP, WT-4
WT_N_ZFP_Str_Input_4


title: Target_293T_ACTB_EEF2_PPIB_mock_CMC


title: Target_293T_PPIB_RPS6_mock_BEU


title: Striatum, Bulk RNA-seq, N-ZFP, WT-3

description:
Striatum, Bulk RNA-seq, N-ZFP, WT-3
WT_N_ZFP_Str_Input_3


description:
Striatum, Bulk RNA-seq, N-Delta, zQ175-1
zQ175_N_Delta_Str_Input_1


title: Target_293T_ACTB_EEF2_PPIB_mock_BEU


title: PBMC-timelapse, PBMC-timelapse-plate2_47

description:
PBMC-timelapse-plate2_47
PBMC_RNA_expression.txt


title: Target_293T_ACTB_EEF2_RPL5_RPS6_mock_CMC


title: 3mix-timelapse, 3mix-timelapse-plate10_62

description:
3mix-timelapse-plate10_62
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-Delta, WT-4

description:
Striatum, Bulk RNA-seq, N-Delta, WT-4
WT_N_Delta_Str_Input_4


title: Striatum, Bulk RNA-seq, N-ZFP, WT-1

description:
Striatum, Bulk RNA-seq, N-ZFP, WT-1
WT_N_ZFP_Str_Input_1


title: PBMC-timelapse, PBMC-timelapse-plate2_46

description:
PBMC-timelapse-plate2_46
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_61

description:
3mix-timelapse-plate10_61
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_45

description:
PBMC-timelapse-plate2_45
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-Delta, WT-3

description:
Striatum, Bulk RNA-seq, N-Delta, WT-3
WT_N_Delta_Str_Input_3


title: 3mix-timelapse, 3mix-timelapse-plate10_65

description:
3mix-timelapse-plate10_65
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_60

description:
3mix-timelapse-plate10_60
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_44

description:
PBMC-timelapse-plate2_44
PBMC_RNA_expression.txt


title: Target_293T_ACTB_EEF2_RPL5_RPS6_mock_BEU


title: Target_reporter_TGA_gACA19_CMC


title: 3mix-timelapse, 3mix-timelapse-plate10_59

description:
3mix-timelapse-plate10_59
3mix_RNA_expression.txt


title: Target_reporter_TGA_gACA19_BEU


title: PBMC-timelapse, PBMC-timelapse-plate2_43

description:
PBMC-timelapse-plate2_43
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-Delta, WT-1

description:
Striatum, Bulk RNA-seq, N-Delta, WT-1
WT_N_Delta_Str_Input_1


title: 3mix-timelapse, 3mix-timelapse-plate10_58

description:
3mix-timelapse-plate10_58
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_42

description:
PBMC-timelapse-plate2_42
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_63

description:
3mix-timelapse-plate10_63
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_57

description:
3mix-timelapse-plate10_57
3mix_RNA_expression.txt


title: Target_reporter_TAG_gACA19_BEU


title: PBMC-timelapse, PBMC-timelapse-plate2_41

description:
PBMC-timelapse-plate2_41
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-ZFP, R6/2-3

description:
Striatum, Bulk RNA-seq, N-ZFP, R6/2-3
PHP_Str_Bulk_N_ZFP_R62_3


title: PBMC-timelapse, PBMC-timelapse-plate2_40

description:
PBMC-timelapse-plate2_40
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-ZFP, R6/2-2

description:
Striatum, Bulk RNA-seq, N-ZFP, R6/2-2
PHP_Str_Bulk_N_ZFP_R62_2


title: Target_reporter_TAA_gACA19_BEU


title: Striatum, Bulk RNA-seq, N-ZFP, R6/2-1

description:
Striatum, Bulk RNA-seq, N-ZFP, R6/2-1
PHP_Str_Bulk_N_ZFP_R62_1


title: Striatum, Bulk RNA-seq, N-Delta, WT-2

description:
Striatum, Bulk RNA-seq, N-Delta, WT-2
WT_N_Delta_Str_Input_2


title: PBMC-timelapse, PBMC-timelapse-plate2_38

description:
PBMC-timelapse-plate2_38
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_39

description:
PBMC-timelapse-plate2_39
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_55

description:
3mix-timelapse-plate10_55
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-Delta, R6/2-4

description:
Striatum, Bulk RNA-seq, N-Delta, R6/2-4
PHP_Str_Bulk_N_Delta_R62_4


title: 3mix-timelapse, 3mix-timelapse-plate10_54

description:
3mix-timelapse-plate10_54
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_64

description:
3mix-timelapse-plate10_64
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_37

description:
PBMC-timelapse-plate2_37
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-ZFP, R6/2-4

description:
Striatum, Bulk RNA-seq, N-ZFP, R6/2-4
PHP_Str_Bulk_N_ZFP_R62_4


title: Target_reporter_TAG_gACA19_CMC


title: Striatum, Bulk RNA-seq, N-Delta, R6/2-3

description:
Striatum, Bulk RNA-seq, N-Delta, R6/2-3
PHP_Str_Bulk_N_Delta_R62_3


title: RNA_Maltonis_rep2

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

data_processing:
Reads are aligned by Tophat/bowtie2
Reads are counted at gene level by HTseq-count
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count at gene level for each Sample

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% of fetal bovine serum (FBS, Gibco, Paisley, UK), 1% of L-glutamine (Lonza, Verviers, Belgium) and 1% of penicillin/streptomycin (Euroclone, Pero, MI, Italy) in a humidified atmosphere at 37° C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), following manufacture's instructions. 1.5 μg of  RNA was used for the generation of sequencing libraries.
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, San Diego, CA, USA, Cat #: 20020599)

treatment_protocol: Maltonis was synthesised as already described (Amatori S. et al. JOC 2012) and used for the treatments of NB4 cells (stock solution of 10 mM diluted in distilled water) at the reported concentrations for 24 hours

value: Acute promyelocytic leukemia

value: 24 hours with maltonis 10 μM in vitro


title: 3mix-timelapse, 3mix-timelapse-plate10_53

description:
3mix-timelapse-plate10_53
3mix_RNA_expression.txt

value: ALPS


title: RNA_Maltonis_rep3


title: PBMC-timelapse, PBMC-timelapse-plate2_36

description:
PBMC-timelapse-plate2_36
PBMC_RNA_expression.txt

value: PBMC


title: Striatum, Bulk RNA-seq, N-Delta, R6/2-2

description:
Striatum, Bulk RNA-seq, N-Delta, R6/2-2
PHP_Str_Bulk_N_Delta_R62_2


title: 3mix-timelapse, 3mix-timelapse-plate10_56

description:
3mix-timelapse-plate10_56
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_51

description:
3mix-timelapse-plate10_51
3mix_RNA_expression.txt


title: Target_reporter_TAA_gACA19_CMC


title: 3mix-timelapse, 3mix-timelapse-plate10_50

description:
3mix-timelapse-plate10_50
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-Delta, R6/2-1

description:
Striatum, Bulk RNA-seq, N-Delta, R6/2-1
PHP_Str_Bulk_N_Delta_R62_1


title: 3mix-timelapse, 3mix-timelapse-plate10_52

description:
3mix-timelapse-plate10_52
3mix_RNA_expression.txt


title: RNA_Nt_rep3


title: RNA_Nt_rep2


title: 3mix-timelapse, 3mix-timelapse-plate10_49

description:
3mix-timelapse-plate10_49
3mix_RNA_expression.txt


title: RNA_Nt_rep1


title: Striatum, Bulk RNA-seq, N-ZFP, NCAR-4

description:
Striatum, Bulk RNA-seq, N-ZFP, NCAR-4
PHP_Str_Bulk_N_ZFP_NCAR_4

value: NCAR


title: RNA_Maltonis_rep1


title: PBMC-timelapse, PBMC-timelapse-plate2_33

description:
PBMC-timelapse-plate2_33
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_35

description:
PBMC-timelapse-plate2_35
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-ZFP, NCAR-3

description:
Striatum, Bulk RNA-seq, N-ZFP, NCAR-3
PHP_Str_Bulk_N_ZFP_NCAR_3


title: Striatum, Bulk RNA-seq, N-ZFP, NCAR-2

description:
Striatum, Bulk RNA-seq, N-ZFP, NCAR-2
PHP_Str_Bulk_N_ZFP_NCAR_2


title: 3mix-timelapse, 3mix-timelapse-plate10_47

description:
3mix-timelapse-plate10_47
3mix_RNA_expression.txt


title: H3K27ac_Maltonis_rep2

data_processing:
Reads were aligned to hg19 using ‘bwa’
Unmapped reads, reads with a MAPQ smaller then 1, duplicate reads and those that mapped outside of chr 1-19 and Chr X were removed using ‘samtools
Peak calling was performed using MACS2 for H3K4me3 while epic2 is used for H3K27ac and H3K9me3
Assembly: hg19
Supplementary files format and content: Text file (bed and broadPeak) containing enriched regions coordinates

extract_protocol:
NB4 cells were cross-linked for 10 min at 37 °C by adding, directly to the cell culture medium, 1/10 of cross-linking solution [50 mM Hepes (pH 7.5), 11% FA, 1 mM Na2EDTA, and 0.1 M NaCl]. The cross-linking reaction was stopped by addition of glycine at a final concentration of 0.125 M. Cells were then washed twice with ice-cold PBS and finally resuspended in 0.5 ml of lysis buffer (10 mM Tris-HCl pH 7.4, 0.15 M NaCl, 3 mM CaCl2, 2 mM MgCl2, 0.5% Tween20, 1 mM PMSF, and 10 μg/mL RNase A—Roche, Mannheim, Germany) and incubated 30 min at room temperature on a rotating platform. When not specified, all centrifugations were performed at 17,860×g for 3 min at +4 °C. After resuspension in 0.3 ml of extraction buffer (10 mM Tris-HCl pH 7.4, 0.15 M NaCl, 3 mM CaCl2, 2 mM MgCl2, 0.1% SDS), samples were sonicated with three pulses of 30 s each with an amplitude of 40% (using a − 20 °C refrigerated thermoblock), interrupted by 60 s pauses, using the EpiShear sonicator (Active Motif, Carlsbad, CA, USA). After being cleared by centrifugation, at 9,500× g for 5 min at room temperature, supernatants containing chromatin were saved.
Libraries were prepared for sequencing using standard Illumina protocols

value: H3K27ac (ab4729, Abcam)


title: 3mix-timelapse, 3mix-timelapse-plate10_46

description:
3mix-timelapse-plate10_46
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_31

description:
PBMC-timelapse-plate2_31
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_29

description:
PBMC-timelapse-plate2_29
PBMC_RNA_expression.txt


title: H3K27ac_Maltonis_rep1


title: H3K27ac_Maltonis_rep3


title: PBMC-timelapse, PBMC-timelapse-plate2_34

description:
PBMC-timelapse-plate2_34
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-ZFP, NCAR-1

description:
Striatum, Bulk RNA-seq, N-ZFP, NCAR-1
PHP_Str_Bulk_N_ZFP_NCAR_1

value: Striatum


title: PBMC-timelapse, PBMC-timelapse-plate2_30

description:
PBMC-timelapse-plate2_30
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_44

description:
3mix-timelapse-plate10_44
3mix_RNA_expression.txt


title: H3K27ac_Nt_rep3


title: 3mix-timelapse, 3mix-timelapse-plate10_45

description:
3mix-timelapse-plate10_45
3mix_RNA_expression.txt


title: H3K27ac_Nt_rep2


title: Striatum, Bulk RNA-seq, N-Delta, NCAR-3

description:
Striatum, Bulk RNA-seq, N-Delta, NCAR-3
PHP_Str_Bulk_N_Delta_NCAR_3


title: Striatum, Bulk RNA-seq, N-Delta, NCAR-2

description:
Striatum, Bulk RNA-seq, N-Delta, NCAR-2
PHP_Str_Bulk_N_Delta_NCAR_2


title: PBMC-timelapse, PBMC-timelapse-plate2_32

description:
PBMC-timelapse-plate2_32
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_43

description:
3mix-timelapse-plate10_43
3mix_RNA_expression.txt


title: H3K27ac_Nt_rep1


title: 3mix-timelapse, 3mix-timelapse-plate10_48

description:
3mix-timelapse-plate10_48
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_27

description:
PBMC-timelapse-plate2_27
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, N-Delta, NCAR-1

description:
Striatum, Bulk RNA-seq, N-Delta, NCAR-1
PHP_Str_Bulk_N_Delta_NCAR_1


title: Striatum, Bulk RNA-seq, N-Delta, NCAR-4

description:
Striatum, Bulk RNA-seq, N-Delta, NCAR-4
PHP_Str_Bulk_N_Delta_NCAR_4


title: 3mix-timelapse, 3mix-timelapse-plate10_41

description:
3mix-timelapse-plate10_41
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-ZFP, R6/2-3

description:
Striatum, Bulk RNA-seq, A-ZFP, R6/2-3
PHP_Str_Bulk_A_ZFP_R62_3

value: A-ZFP

value: astrocyte


title: PBMC-timelapse, PBMC-timelapse-plate2_28

description:
PBMC-timelapse-plate2_28
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_42

description:
3mix-timelapse-plate10_42
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_26

description:
PBMC-timelapse-plate2_26
PBMC_RNA_expression.txt


title: H3K9me3_Maltonis_rep3

value: H3K9me3 (#39766, Active Motif)


title: 3mix-timelapse, 3mix-timelapse-plate10_40

description:
3mix-timelapse-plate10_40
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-ZFP, R6/2-2

description:
Striatum, Bulk RNA-seq, A-ZFP, R6/2-2
PHP_Str_Bulk_A_ZFP_R62_2


title: PBMC-timelapse, PBMC-timelapse-plate2_24

description:
PBMC-timelapse-plate2_24
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_23

description:
PBMC-timelapse-plate2_23
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_39

description:
3mix-timelapse-plate10_39
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-ZFP, R6/2-1

description:
Striatum, Bulk RNA-seq, A-ZFP, R6/2-1
PHP_Str_Bulk_A_ZFP_R62_1


title: H3K9me3_Maltonis_rep2


title: 3mix-timelapse, 3mix-timelapse-plate10_38

description:
3mix-timelapse-plate10_38
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_22

description:
PBMC-timelapse-plate2_22
PBMC_RNA_expression.txt


title: H3K9me3_Nt_rep3


title: H3K9me3_Maltonis_rep1


title: 3mix-timelapse, 3mix-timelapse-plate10_37

description:
3mix-timelapse-plate10_37
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-Delta, R6/2-3

description:
Striatum, Bulk RNA-seq, A-Delta, R6/2-3
PHP_Str_Bulk_A_Delta_R62_3

value: A-Delta


title: H3K9me3_Nt_rep2


title: Striatum, Bulk RNA-seq, A-Delta, R6/2-2

description:
Striatum, Bulk RNA-seq, A-Delta, R6/2-2
PHP_Str_Bulk_A_Delta_R62_2


title: H3K9me3_Nt_rep1


title: 3mix-timelapse, 3mix-timelapse-plate10_36

description:
3mix-timelapse-plate10_36
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_21

description:
PBMC-timelapse-plate2_21
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_20

description:
PBMC-timelapse-plate2_20
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_25

description:
PBMC-timelapse-plate2_25
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-Delta, R6/2-1

description:
Striatum, Bulk RNA-seq, A-Delta, R6/2-1
PHP_Str_Bulk_A_Delta_R62_1


title: 3mix-timelapse, 3mix-timelapse-plate10_34

description:
3mix-timelapse-plate10_34
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_19

description:
PBMC-timelapse-plate2_19
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_35

description:
3mix-timelapse-plate10_35
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_18

description:
PBMC-timelapse-plate2_18
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-ZFP, NCAR-4

description:
Striatum, Bulk RNA-seq, A-ZFP, NCAR-4
PHP_Str_Bulk_A_ZFP_NCAR_4


title: H3K4me3_Maltonis_rep1

value: H3K4me3 (#39159, Active Motif)


title: H3K4me3_Maltonis_rep2


title: Striatum, Bulk RNA-seq, A-Delta, R6/2-4

description:
Striatum, Bulk RNA-seq, A-Delta, R6/2-4
PHP_Str_Bulk_A_Delta_R62_4


title: PBMC-timelapse, PBMC-timelapse-plate2_17

description:
PBMC-timelapse-plate2_17
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_32

description:
3mix-timelapse-plate10_32
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_16

description:
PBMC-timelapse-plate2_16
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_33

description:
3mix-timelapse-plate10_33
3mix_RNA_expression.txt


title: H3K4me3_Nt_rep3


title: Striatum, Bulk RNA-seq, A-ZFP, NCAR-3

description:
Striatum, Bulk RNA-seq, A-ZFP, NCAR-3
PHP_Str_Bulk_A_ZFP_NCAR_3


title: H3K4me3_Nt_rep2


title: H3K4me3_Maltonis_rep3


title: H3K4me3_Nt_rep1


title: 3mix-timelapse, 3mix-timelapse-plate10_31

description:
3mix-timelapse-plate10_31
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_15

description:
PBMC-timelapse-plate2_15
PBMC_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-ZFP, NCAR-1

description:
Striatum, Bulk RNA-seq, A-ZFP, NCAR-1
PHP_Str_Bulk_A_ZFP_NCAR_1


title: PBMC-timelapse, PBMC-timelapse-plate2_14

description:
PBMC-timelapse-plate2_14
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_30

description:
3mix-timelapse-plate10_30
3mix_RNA_expression.txt


title: Striatum, Bulk RNA-seq, A-Delta, NCAR-3

description:
Striatum, Bulk RNA-seq, A-Delta, NCAR-3
PHP_Str_Bulk_A_Delta_NCAR_3


title: 3mix-timelapse, 3mix-timelapse-plate10_29

description:
3mix-timelapse-plate10_29
3mix_RNA_expression.txt


title: LQS-KO-3: NSG injected MTF1-KO HCT116 tumor rep3

city: Hefei

first: qiangsheng

last: li

state: Anhui

address: Huangshan Road 443

department: Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
Bcl2fastq(v2.17.1.14)software used for basecalling.
Cutadapt（version 1.9.1）software used for trim adapter sequence and  low-quality sequence , after removing trim, the reads length was less than 75 bp also abandoned
Hisat2(v2.0.1) software used for comparison of short reads
StringTie(v1.3.3b) and Cufflinks(V2.2.1) software used for new transcript prediction
Genome_build: GRCh.38.101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human colon cancer tumor cell

extract_protocol:
Tumor tissue：after the tumor tissue was separated from the mouse, it was frozen and stored.and RNA was harvested using Trizol reagent. Cells:RNA was harvested using FastPure Cell/Tissue Tatal RNA Isolation Kit V2(Cat#RC112)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mus Tumor

tag: host

value: NSG mouse


title: PBMC-timelapse, PBMC-timelapse-plate2_13

description:
PBMC-timelapse-plate2_13
PBMC_RNA_expression.txt

data_processing:
Basecalls performed by Illumina MiSeq or Hiseq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq or using bcl2fastq for Illumina Hiseq resultes
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA molecules per cell for each gene is listed (cells which were not filtered out are shown).

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

tag: strain


title: LQS-KO-2: NSG injected MTF1-KO HCT116 tumor rep2


title: PBMC-timelapse, PBMC-timelapse-plate2_12

description:
PBMC-timelapse-plate2_12
PBMC_RNA_expression.txt

tag: cell type


title: Striatum, Bulk RNA-seq, A-Delta, NCAR-2

description:
Striatum, Bulk RNA-seq, A-Delta, NCAR-2
PHP_Str_Bulk_A_Delta_NCAR_2


title: LQS-KO-1: NSG injected MTF1-KO HCT116 tumor rep1


title: 3mix-timelapse, 3mix-timelapse-plate10_28

description:
3mix-timelapse-plate10_28
3mix_RNA_expression.txt

value: random selection

tag: isolation method


title: Striatum, Bulk RNA-seq, A-ZFP, NCAR-2

description:
Striatum, Bulk RNA-seq, A-ZFP, NCAR-2
PHP_Str_Bulk_A_ZFP_NCAR_2

tag: genotype


title: Striatum, Bulk RNA-seq, A-Delta, NCAR-1

description:
Striatum, Bulk RNA-seq, A-Delta, NCAR-1
PHP_Str_Bulk_A_Delta_NCAR_1


title: PBMC-timelapse, PBMC-timelapse-plate2_11

description:
PBMC-timelapse-plate2_11
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: 3mix-timelapse, 3mix-timelapse-plate10_27

description:
3mix-timelapse-plate10_27
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_RZ_4

description: Neurons IP R6/2 + ZFP replicate 4

data_processing:
Aligned to mouse genome (mm10) using STAR spliced read aligner
Count the reads with htseq-count
Normalization (TMM), quantitation and differential expression analysis using Bioconductor packages
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts

extract_protocol:
RiboTag-HA based immunoprecipitation and RNA extraction
Sequencing libraries were prepared using Illumina TruSeq RNA sample prep kit following manufacturer's protocol

treatment_protocol: Cell-type specific AAVs for ZFP or Delta (Control) in astrocytes and neurons.

tag: celltype

value: Neurons

tag: condition

value: RZ

tag: fraction

value: IP


title: LQS-WT-3: NSG injected WT HCT116 tumor rep3


title: LQS-WT-2: NSG injected WT HCT116 tumor rep2


title: PBMC-timelapse, PBMC-timelapse-plate2_10

description:
PBMC-timelapse-plate2_10
PBMC_RNA_expression.txt

value: ALPS


title: n_ZFP_n_Rpl_IP_RZ_3

description: Neurons IP R6/2 + ZFP replicate 3


title: Striatum, Bulk RNA-seq, A-Delta, NCAR-4

description:
Striatum, Bulk RNA-seq, A-Delta, NCAR-4
PHP_Str_Bulk_A_Delta_NCAR_4


title: 3mix-timelapse, 3mix-timelapse-plate10_25

description:
3mix-timelapse-plate10_25
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_26

description:
3mix-timelapse-plate10_26
3mix_RNA_expression.txt


title: LQS-WT-1: NSG injected WT HCT116 tumor rep1


title: 3mix-timelapse, 3mix-timelapse-plate10_24

description:
3mix-timelapse-plate10_24
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_8

description:
PBMC-timelapse-plate2_8
PBMC_RNA_expression.txt

value: PBMC


title: PBMC-timelapse, PBMC-timelapse-plate2_9

description:
PBMC-timelapse-plate2_9
PBMC_RNA_expression.txt


title: LQS-116-KO: MTF1-KO HCT116 cells

source_name: Human colon cancer tumor cellline

value: MTF1-KO cells

value: n/a (cultured cells)


title: n_ZFP_n_Rpl_IP_RZ_2

description: Neurons IP R6/2 + ZFP replicate 2


title: n_ZFP_n_Rpl_IP_RZ_1

description: Neurons IP R6/2 + ZFP replicate 1


title: n_ZFP_n_Rpl_IP_RD_4

description: Neurons IP R6/2 + Delta replicate 4

value: RD


title: 3mix-timelapse, 3mix-timelapse-plate10_23

description:
3mix-timelapse-plate10_23
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_7

description:
PBMC-timelapse-plate2_7
PBMC_RNA_expression.txt

source_name: Murine PBMCs


title: 3mix-timelapse, 3mix-timelapse-plate10_22

description:
3mix-timelapse-plate10_22
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_6

description:
PBMC-timelapse-plate2_6
PBMC_RNA_expression.txt


title: Tumor49NCAC8wk

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: non-cachectic melanoma cells 8 weeks replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence; after removing mouse-specific reads, the reads were mapped to hg38 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all 26 samples

source_name: human melanoma cells and associated mouse stroma

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from the  time points of 3 week post LLC cell injection
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina NovaSeq 6000 platform.

value: tumor cell

tag: age

value: 2 months

value: cachectic melanoma cells


title: n_ZFP_n_Rpl_IP_RD_3

description: Neurons IP R6/2 + Delta replicate 3


title: 3mix-timelapse, 3mix-timelapse-plate10_21

description:
3mix-timelapse-plate10_21
3mix_RNA_expression.txt

source_name: Cell line mixture of murine T cell, murine leukemia cell, and murine hematopoietic progenitor cell


title: Tumor48NCAC8wk

description: non-cachectic melanoma cells 8 weeks replicate 2


title: n_ZFP_n_Rpl_IP_RD_2

description: Neurons IP R6/2 + Delta replicate 2


title: Tumor47NCAC8wk

description: non-cachectic melanoma cells 8 weeks replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate10_20

description:
3mix-timelapse-plate10_20
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_RD_1

description: Neurons IP R6/2 + Delta replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate10_19

description:
3mix-timelapse-plate10_19
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_4

description:
PBMC-timelapse-plate2_4
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_3

description:
PBMC-timelapse-plate2_3
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_NZ_4

description: Neurons IP NCAR + ZFP replicate 4

value: NZ


title: Tumor41NCAC6wk

description: non-cachectic melanoma cells 6 weeks replicate 1


title: Tumor30CAC8wk

description: cachectic melanoma cells 8 weeks replicate 7


title: n_ZFP_n_Rpl_IP_NZ_3

description: Neurons IP NCAR + ZFP replicate 3


title: LQS-116-WT: WT HCT116 cells

value: WT cells


title: PBMC-timelapse, PBMC-timelapse-plate2_2

description:
PBMC-timelapse-plate2_2
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_17

description:
3mix-timelapse-plate10_17
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_NZ_2

description: Neurons IP NCAR + ZFP replicate 2


title: Tumor28CAC8wk

description: cachectic melanoma cells 8 weeks replicate 6


title: 3mix-timelapse, 3mix-timelapse-plate10_16

description:
3mix-timelapse-plate10_16
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_96

description:
PBMC-timelapse-plate1_96
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_NZ_1

description: Neurons IP NCAR + ZFP replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate2_5

description:
PBMC-timelapse-plate2_5
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_ND_4

description: Neurons IP NCAR + Delta replicate 4

value: ND


title: Tumor24CAC8wk

description: cachectic melanoma cells 8 weeks replicate 4


title: PBMC-timelapse, PBMC-timelapse-plate1_95

description:
PBMC-timelapse-plate1_95
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_15

description:
3mix-timelapse-plate10_15
3mix_RNA_expression.txt


title: Tumor27CAC8wk

description: cachectic melanoma cells 8 weeks replicate 5


title: 3mix-timelapse, 3mix-timelapse-plate10_14

description:
3mix-timelapse-plate10_14
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_94

description:
PBMC-timelapse-plate1_94
PBMC_RNA_expression.txt


title: Tumor23CAC8wk

description: cachectic melanoma cells 8 weeks replicate 3


title: Tumor21CAC8wk

description: cachectic melanoma cells 8 weeks replicate 2


title: PBMC-timelapse, PBMC-timelapse-plate1_93

description:
PBMC-timelapse-plate1_93
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_13

description:
3mix-timelapse-plate10_13
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate2_1

description:
PBMC-timelapse-plate2_1
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_ND_2

description: Neurons IP NCAR + Delta replicate 2


title: PBMC-timelapse, PBMC-timelapse-plate1_92

description:
PBMC-timelapse-plate1_92
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_ND_3

description: Neurons IP NCAR + Delta replicate 3


title: 3mix-timelapse, 3mix-timelapse-plate10_12

description:
3mix-timelapse-plate10_12
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_IP_ND_1

description: Neurons IP NCAR + Delta replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate10_11

description:
3mix-timelapse-plate10_11
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_91

description:
PBMC-timelapse-plate1_91
PBMC_RNA_expression.txt


title: Tumor16CAC6wk

description: cachectic melanoma cells 6 weeks replicate 5


title: Tumor19CAC8wk

description: cachectic melanoma cells 8 weeks replicate 1


title: n_ZFP_n_Rpl_Input_RZ_4

description: Neurons Input R6/2 + ZFP replicate 4

value: Input


title: 3mix-timelapse, 3mix-timelapse-plate10_10

description:
3mix-timelapse-plate10_10
3mix_RNA_expression.txt

value: random selection


title: PBMC-timelapse, PBMC-timelapse-plate1_90

description:
PBMC-timelapse-plate1_90
PBMC_RNA_expression.txt

value: C57BL/6J mouse