title: Tumor15CAC6wk

description: cachectic melanoma cells 6 weeks replicate 4


title: n_ZFP_n_Rpl_Input_RZ_3

status: Public on Dec 15 2022

type: SRA

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

country: USA

institute: University of California, Los Angeles

description: Neurons Input R6/2 + ZFP replicate 3

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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: Input

tag: strain


title: PBMC-timelapse, PBMC-timelapse-plate1_89

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-plate1_89
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).

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

value: C57BL/6J mouse

tag: cell type

value: PBMC

tag: isolation method

value: ALPS


title: 3mix-timelapse, 3mix-timelapse-plate10_9

description:
3mix-timelapse-plate10_9
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: Tumor13CAC6wk

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: cachectic melanoma cells 6 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

organism: Homo sapiens

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

tag: treatment

value: cachectic melanoma cells


title: PBMC-timelapse, PBMC-timelapse-plate1_88

description:
PBMC-timelapse-plate1_88
PBMC_RNA_expression.txt


title: Tumor12CAC6wk

description: cachectic melanoma cells 6 weeks replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate10_8

description:
3mix-timelapse-plate10_8
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_RZ_2

description: Neurons Input R6/2 + ZFP replicate 2


title: n_ZFP_n_Rpl_Input_RZ_1

description: Neurons Input R6/2 + ZFP replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate10_7

description:
3mix-timelapse-plate10_7
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_87

description:
PBMC-timelapse-plate1_87
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_RD_4

description: Neurons Input R6/2 + Delta replicate 4

value: RD


title: Tumor10CAC4wk

description: cachectic melanoma cells 4 weeks replicate 5


title: 3mix-timelapse, 3mix-timelapse-plate10_6

description:
3mix-timelapse-plate10_6
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_RD_3

description: Neurons Input R6/2 + Delta replicate 3


title: Tumor11CAC6wk

description: cachectic melanoma cells 6 weeks replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate1_86

description:
PBMC-timelapse-plate1_86
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_85

description:
PBMC-timelapse-plate1_85
PBMC_RNA_expression.txt


title: Tumor8CAC4wk

description: cachectic melanoma cells 4 weeks replicate 3


title: PBMC-timelapse, PBMC-timelapse-plate1_84

description:
PBMC-timelapse-plate1_84
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_4

description:
3mix-timelapse-plate10_4
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_RD_2

description: Neurons Input R6/2 + Delta replicate 2


title: n_ZFP_n_Rpl_Input_RD_1

description: Neurons Input R6/2 + Delta replicate 1


title: Tumor9CAC4wk

description: cachectic melanoma cells 4 weeks replicate 4


title: 3mix-timelapse, 3mix-timelapse-plate10_3

description:
3mix-timelapse-plate10_3
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate10_2

description:
3mix-timelapse-plate10_2
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_NZ_4

description: Neurons Input NCAR + ZFP replicate 4

value: NZ


title: Tumor6CAC4wk

description: cachectic melanoma cells 4 weeks replicate 1


title: Tumor5CAC2wk

description: cachectic melanoma cells 2 weeks replicate 5


title: 3mix-timelapse, 3mix-timelapse-plate10_1

description:
3mix-timelapse-plate10_1
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_81

description:
PBMC-timelapse-plate1_81
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_82

description:
PBMC-timelapse-plate1_82
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_NZ_3

description: Neurons Input NCAR + ZFP replicate 3


title: n_ZFP_n_Rpl_Input_NZ_2

description: Neurons Input NCAR + ZFP replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate10_5

description:
3mix-timelapse-plate10_5
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_96

description:
3mix-timelapse-plate9_96
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_95

description:
3mix-timelapse-plate9_95
3mix_RNA_expression.txt


title: Tumor4CAC2wk

description: cachectic melanoma cells 2 weeks replicate 4


title: PBMC-timelapse, PBMC-timelapse-plate1_79

description:
PBMC-timelapse-plate1_79
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_80

description:
PBMC-timelapse-plate1_80
PBMC_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_NZ_1

description: Neurons Input NCAR + ZFP replicate 1


title: n_ZFP_n_Rpl_Input_ND_4

description: Neurons Input NCAR + Delta replicate 4

value: ND


title: Tumor3CAC2wk

description: cachectic melanoma cells 2 weeks replicate 3


title: Tumor2CAC2wk

description: cachectic melanoma cells 2 weeks replicate 2


title: Tumor7CAC4wk

description: cachectic melanoma cells 4 weeks replicate 2


title: n_ZFP_n_Rpl_Input_ND_3

description: Neurons Input NCAR + Delta replicate 3


title: 3mix-timelapse, 3mix-timelapse-plate9_94

description:
3mix-timelapse-plate9_94
3mix_RNA_expression.txt


title: Tumor1CAC2wk

description: cachectic melanoma cells 2 weeks replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate1_83

description:
PBMC-timelapse-plate1_83
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_92

description:
3mix-timelapse-plate9_92
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_ND_2

description: Neurons Input NCAR + Delta replicate 2


title: PBMC-timelapse, PBMC-timelapse-plate1_76

description:
PBMC-timelapse-plate1_76
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_78

description:
PBMC-timelapse-plate1_78
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_91

description:
3mix-timelapse-plate9_91
3mix_RNA_expression.txt


title: n_ZFP_n_Rpl_Input_ND_1

description: Neurons Input NCAR + Delta replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate1_75

description:
PBMC-timelapse-plate1_75
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_90

description:
3mix-timelapse-plate9_90
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_74

description:
PBMC-timelapse-plate1_74
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_RZ_3

description: Astrocytes IP R6/2 + ZFP replicate 3

value: Astrocytes

value: IP


title: 3mix-timelapse, 3mix-timelapse-plate9_93

description:
3mix-timelapse-plate9_93
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_89

description:
3mix-timelapse-plate9_89
3mix_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_RZ_4

description: Astrocytes IP R6/2 + ZFP replicate 4


title: PBMC-timelapse, PBMC-timelapse-plate1_73

description:
PBMC-timelapse-plate1_73
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_RZ_2

description: Astrocytes IP R6/2 + ZFP replicate 2


title: PBMC-timelapse, PBMC-timelapse-plate1_72

description:
PBMC-timelapse-plate1_72
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_77

description:
PBMC-timelapse-plate1_77
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_88

description:
3mix-timelapse-plate9_88
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_71

description:
PBMC-timelapse-plate1_71
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_RZ_1

description: Astrocytes IP R6/2 + ZFP replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate9_87

description:
3mix-timelapse-plate9_87
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_86

description:
3mix-timelapse-plate9_86
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_70

description:
PBMC-timelapse-plate1_70
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_RD_3

description: Astrocytes IP R6/2 + Delta replicate 3


title: PBMC-timelapse, PBMC-timelapse-plate1_69

description:
PBMC-timelapse-plate1_69
PBMC_RNA_expression.txt


title: Assemblage of eggs, 26 hours, Quiescent, Replicate A

city: Roskilde

first: Miguel

last: Cifuentes Acebal

state: Sjaelland

address: Universitetsvej 1

department: Department of Science and Environment

country: Denmark

institute: Roskilde university

description:
The supplementary file 2 contains the differentially expressed transcripts for all the quiescent samples against 7 and 14 subitaneous hours. The alpha value of 0.001 and fold change of 2.
see supplementary file 2
Transcriptome.annotated.fasta
coldA_S1

data_processing:
Bcl2fastq was used for both basecalling and demultiplexing
Trinity v2.13.2
The reads were assembled into a transcriptome using Trinity (settings: Forward stranded library, minimun contig length: 200, minimun k-mers to be assembled: 1)
Reads werealigned from the transcriptome and abundance estimated with Trinity
Both raw and normalized expression matrixes were built with Trinity and edgeR included with Trinity was used for differential expression analysis
Supplementary files format and content: tab-delimited text files include TMM values for each sample

organism: Acartia tonsa

source_name: Assemblage of eggs

growth_protocol: An Acartia tonsa population was kept in 60L tanks under a dark environment with salt water (32), and a temperature of 16.9ºC

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
0,3 ug RNA was used for the construction of sequencing libraries
RNA libraries were constructed using the TruSeq kit (Illumina)

treatment_protocol: Subitaneous samples were kept under the same environmentl conditions as growth protocol while quiescent samples were put at 4ºC and anoxic conditions

tag: tissue

value: Assemblage of eggs

tag: time

value: 26 Hours

tag: developmental stage

value: Gastrulation

tag: type of_development

value: Quiescent


title: Assemblage of eggs, 26 hours, Quiescent, Replicate C

description:
see supplementary file 2
Transcriptome.annotated.fasta
coldC_S1


title: 3mix-timelapse, 3mix-timelapse-plate9_85

description:
3mix-timelapse-plate9_85
3mix_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_RD_2

description: Astrocytes IP R6/2 + Delta replicate 2


title: Assemblage of eggs, 26 hours, Quiescent, Replicate D

description:
see supplementary file 2
Transcriptome.annotated.fasta
coldD_S2


title: 3mix-timelapse, 3mix-timelapse-plate9_84

description:
3mix-timelapse-plate9_84
3mix_RNA_expression.txt


title: Assemblage of eggs, 42 hours, Subitaneous, Replicate E

description:
see supplementary file
Transcriptome.annotated.fasta
42E_S21

value: 42 Hours

value: Final nauplii ready to hatch

value: Subitaneous


title: n_ZFP_a_Rpl_IP_RD_1

description: Astrocytes IP R6/2 + Delta replicate 1


title: Assemblage of eggs, 42 hours, Subitaneous, Replicate D

description:
see supplementary file
Transcriptome.annotated.fasta
42D_S20


title: PBMC-timelapse, PBMC-timelapse-plate1_67

description:
PBMC-timelapse-plate1_67
PBMC_RNA_expression.txt

value: C57BL/6J mouse

value: PBMC

value: ALPS


title: 3mix-timelapse, 3mix-timelapse-plate9_83

description:
3mix-timelapse-plate9_83
3mix_RNA_expression.txt

value: random selection


title: PBMC-timelapse, PBMC-timelapse-plate3_44

description:
PBMC-timelapse-plate3_44
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_82

description:
3mix-timelapse-plate9_82
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_66

description:
PBMC-timelapse-plate1_66
PBMC_RNA_expression.txt


title: Assemblage of eggs, 42 hours, Subitaneous, Replicate C

description:
see supplementary file
Transcriptome.annotated.fasta
42C_S19


title: n_ZFP_a_Rpl_IP_NZ_2

description: Astrocytes IP NCAR + ZFP replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate9_81

description:
3mix-timelapse-plate9_81
3mix_RNA_expression.txt


title: Assemblage of eggs, 42 hours, Subitaneous, Replicate B

description:
see supplementary file
Transcriptome.annotated.fasta
42B_S14


title: n_ZFP_a_Rpl_IP_NZ_1

description: Astrocytes IP NCAR + ZFP replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate1_65

description:
PBMC-timelapse-plate1_65
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_80

description:
3mix-timelapse-plate9_80
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_64

description:
PBMC-timelapse-plate1_64
PBMC_RNA_expression.txt


title: Assemblage of eggs, 42 hours, Subitaneous, Replicate A

description:
see supplementary file
Transcriptome.annotated.fasta
42A_S13


title: PBMC-timelapse, PBMC-timelapse-plate1_68

description:
PBMC-timelapse-plate1_68
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_79

description:
3mix-timelapse-plate9_79
3mix_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_NZ_3

description: Astrocytes IP NCAR + ZFP replicate 3


title: n_ZFP_a_Rpl_IP_NZ_4

description: Astrocytes IP NCAR + ZFP replicate 4


title: PBMC-timelapse, PBMC-timelapse-plate1_62

description:
PBMC-timelapse-plate1_62
PBMC_RNA_expression.txt


title: Assemblage of eggs, 24 hours, Subitaneous, Replicate D

description:
see supplementary file
Transcriptome.annotated.fasta
24D_S17

value: 24 Hours

value: Appendix formation


title: 3mix-timelapse, 3mix-timelapse-plate9_78

description:
3mix-timelapse-plate9_78
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_63

description:
PBMC-timelapse-plate1_63
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_IP_ND_2

description: Astrocytes IP NCAR + Delta replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate9_76

description:
3mix-timelapse-plate9_76
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_60

description:
PBMC-timelapse-plate1_60
PBMC_RNA_expression.txt


title: Assemblage of eggs, 24 hours, Subitaneous, Replicate B

description:
see supplementary file
Transcriptome.annotated.fasta
24B_S12


title: n_ZFP_a_Rpl_IP_ND_1

description: Astrocytes IP NCAR + Delta replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate1_61

description:
PBMC-timelapse-plate1_61
PBMC_RNA_expression.txt


title: Assemblage of eggs, 24 hours, Subitaneous, Replicate A

description:
see supplementary file
Transcriptome.annotated.fasta
24A_S11


title: n_ZFP_a_Rpl_Input_RZ_3

description: Astrocytes Input R6/2 + ZFP replicate 3

value: RZ

value: Input


title: 3mix-timelapse, 3mix-timelapse-plate9_75

description:
3mix-timelapse-plate9_75
3mix_RNA_expression.txt


title: Assemblage of eggs, 14 hours, Subitaneous, Replicate E

description:
see supplementary file
Transcriptome.annotated.fasta
14E_S15

value: 14 Hours

value: Organogenesis


title: n_ZFP_a_Rpl_IP_ND_4

description: Astrocytes IP NCAR + Delta replicate 4

value: Astrocytes

value: ND

value: IP


title: PBMC-timelapse, PBMC-timelapse-plate1_59

description:
PBMC-timelapse-plate1_59
PBMC_RNA_expression.txt


title: Assemblage of eggs, 24 hours, Subitaneous, Replicate C

description:
see supplementary file
Transcriptome.annotated.fasta
24C_S16

value: Assemblage of eggs


title: n_ZFP_a_Rpl_IP_ND_3

description: Astrocytes IP NCAR + Delta replicate 3


title: 3mix-timelapse, 3mix-timelapse-plate9_74

description:
3mix-timelapse-plate9_74
3mix_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_RZ_4

description: Astrocytes Input R6/2 + ZFP replicate 4


title: 3mix-timelapse, 3mix-timelapse-plate9_77

description:
3mix-timelapse-plate9_77
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_57

description:
PBMC-timelapse-plate1_57
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_RZ_1

description: Astrocytes Input R6/2 + ZFP replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate9_73

description:
3mix-timelapse-plate9_73
3mix_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_RD_2

description: Astrocytes Input R6/2 + Delta replicate 2

value: RD


title: Assemblage of eggs, 14 hours, Subitaneous, Replicate C

description:
see supplementary file
Transcriptome.annotated.fasta
14C_S13


title: Assemblage of eggs, 7 hours, Subitaneous, Replicate D

description:
see supplementary file
Transcriptome.annotated.fasta
7D_S11

value: 7 Hours

value: Gastrulation


title: PBMC-timelapse, PBMC-timelapse-plate1_54

description:
PBMC-timelapse-plate1_54
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: PBMC-timelapse, PBMC-timelapse-plate1_56

description:
PBMC-timelapse-plate1_56
PBMC_RNA_expression.txt

value: PBMC


title: 3mix-timelapse, 3mix-timelapse-plate9_72

description:
3mix-timelapse-plate9_72
3mix_RNA_expression.txt

value: ALPS


title: PBMC-timelapse, PBMC-timelapse-plate1_55

description:
PBMC-timelapse-plate1_55
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_RD_3

description: Astrocytes Input R6/2 + Delta replicate 3


title: PBMC-timelapse, PBMC-timelapse-plate1_58

description:
PBMC-timelapse-plate1_58
PBMC_RNA_expression.txt


title: Assemblage of eggs, 7 hours, Subitaneous, Replicate E

description:
see supplementary file
Transcriptome.annotated.fasta
7E_S12

value: Subitaneous


title: 3mix-timelapse, 3mix-timelapse-plate9_71

description:
3mix-timelapse-plate9_71
3mix_RNA_expression.txt

value: random selection


title: n_ZFP_a_Rpl_Input_RD_1

description: Astrocytes Input R6/2 + Delta replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate9_69

description:
3mix-timelapse-plate9_69
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_52

description:
PBMC-timelapse-plate1_52
PBMC_RNA_expression.txt


title: Assemblage of eggs, 7 hours, Subitaneous, Replicate C

description:
see supplementary file
Transcriptome.annotated.fasta
7C_S10


title: 3mix-timelapse, 3mix-timelapse-plate9_68

description:
3mix-timelapse-plate9_68
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_51

description:
PBMC-timelapse-plate1_51
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_NZ_3

description: Astrocytes Input NCAR + ZFP replicate 3

value: NZ


title: n_ZFP_a_Rpl_Input_RZ_2

description: Astrocytes Input R6/2 + ZFP replicate 2

value: RZ


title: PBMC-timelapse, PBMC-timelapse-plate1_53

description:
PBMC-timelapse-plate1_53
PBMC_RNA_expression.txt


title: Assemblage of eggs, 14 hours, Subitaneous, Replicate B

description:
see supplementary file
Transcriptome.annotated.fasta
14B_S10


title: n_ZFP_a_Rpl_Input_NZ_4

description: Astrocytes Input NCAR + ZFP replicate 4

value: Input


title: 3mix-timelapse, 3mix-timelapse-plate9_67

description:
3mix-timelapse-plate9_67
3mix_RNA_expression.txt


title: Assemblage of eggs, 7 hours, Subitaneous, Replicate B

description:
see supplementary file
Transcriptome.annotated.fasta
7B_S8


title: n_ZFP_a_Rpl_Input_NZ_2

description: Astrocytes Input NCAR + ZFP replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate9_66

description:
3mix-timelapse-plate9_66
3mix_RNA_expression.txt


title: Assemblage of eggs, 7 hours, Subitaneous, Replicate A

description:
see supplementary file
Transcriptome.annotated.fasta
7A_S7


title: Assemblage of eggs, 14 hours, Subitaneous, Replicate A

description:
see supplementary file
Transcriptome.annotated.fasta
14A_S9

value: 14 Hours


title: 3mix-timelapse, 3mix-timelapse-plate9_70

description:
3mix-timelapse-plate9_70
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_49

description:
PBMC-timelapse-plate1_49
PBMC_RNA_expression.txt


title: Assemblage of eggs, 3 Hours, Subitaneous, Replicate D

description:
see supplementary file
Transcriptome.annotated.fasta
3D_S8

value: 3 Hours

value: 4-16 cell stage


title: PBMC-timelapse, PBMC-timelapse-plate1_50

description:
PBMC-timelapse-plate1_50
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_65

description:
3mix-timelapse-plate9_65
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_64

description:
3mix-timelapse-plate9_64
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_48

description:
PBMC-timelapse-plate1_48
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_ND_3

description: Astrocytes Input NCAR + Delta replicate 3

value: Astrocytes

value: ND


title: Assemblage of eggs, 3 Hours, Subitaneous, Replicate B

description:
see supplementary file
Transcriptome.annotated.fasta
3B_S6

value: Assemblage of eggs


title: n_ZFP_a_Rpl_Input_ND_2

description: Astrocytes Input NCAR + Delta replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate9_63

description:
3mix-timelapse-plate9_63
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_46

description:
PBMC-timelapse-plate1_46
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_47

description:
PBMC-timelapse-plate1_47
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_61

description:
3mix-timelapse-plate9_61
3mix_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_ND_1

description: Astrocytes Input NCAR + Delta replicate 1


title: Assemblage of eggs, 3 Hours, Subitaneous, Replicate A

description:
The supplementary file contains the differentially expressed transcripts for all the subitaneous samples with an alpha value of 0.001 and fold change of 2.
see supplementary file
Transcriptome.annotated.fasta
3A_S5


title: 3mix-timelapse, 3mix-timelapse-plate9_60

description:
3mix-timelapse-plate9_60
3mix_RNA_expression.txt


title: Dnmt3l KO, E7.5, ExE, 3 (PBAT)

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
Fastq sequence files were quality and adaptor trimmed with trim galore v0.4.2 using default parameters. For PBAT libraries, the -clip option was used to remove the bases covered by the PBAT primer.
Mapping and methylation calling of bisulphite-seq data was performed using Bismark v0.16.3 in PBAT mode against the mouse GRCm38 genome assembly. Trimmed reads were first aligned to the genome in paired-end mode to be able to detect and discard overlapping parts of the reads while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark44 with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for positions that were covered more than once. Following methylation extraction, CpG context files from PE and SE runs were used to generate a single coverage file (the "Dirty Harry" procedure).
Assembly: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

molecule: genomic DNA

organism: Mus

source_name: Extra-embryonic ectoderm

extract_protocol:
Natural timed matings between heterozygous females and males were used for Dnmt3l, Dnmt3a, Dnmt3b and Dnmt3a/3b KO strains to generate KO and WT embryos. E7.5 epiblast, extra-embryonic ectoderm (ExE) and ectoplacental cone (EPC) for each embryo were manually separated. Single E7.5 epiblast and ExE samples were individually frozen in 10µL of buffer RLT Plus (Qiagen) for RNA-seq or PBAT; the corresponding EPC was used for genotyping.  Cells were lysed with 0.5% SDS at 37°C for 1 hour and bisulphite converted using the Imprint DNA Modification kit (Sigma). Bisulphite-converted DNA was purified using the EZ DNA Methylation Direct kit, as directed (Zymo Research). Using a biotin-conjugated adaptor containing standard Illumina adaptor sequences and 9 bp of random sequences (9N), first-strand synthesis was performed using Klenow Exo- enzyme (New England Biolabs). Following exonuclease (New England Biolabs) treatment and binding to Dynabeads M-280 Streptavidin beads (Thermo Fisher Scientific), second-strand synthesis was performed. Libraries were amplified and indexed using 10 PCR cycles with Phusion High-Fidelity DNA polymerase (New England Biolabs). Libraries were multiplexed for 75-bp paired-end sequencing on an Illumina NextSeq500.
Lysed cells were bisulphite converted using the Imprint DNA Modification kit (Sigma). Bisulphite-converted DNA was purified using the EZ DNA Methylation Direct kit, as directed (Zymo Research). Using a biotin-conjugated adaptor containing standard Illumina adaptor sequences and 9 bp of random sequences (9N), first-strand synthesis was performed using Klenow Exo- enzyme (New England Biolabs). Following exonuclease (New England Biolabs) treatment and binding to Dynabeads M-280 Streptavidin beads (Thermo Fisher Scientific), second-strand synthesis was performed. Libraries were amplified and indexed using 10 PCR cycles with Phusion High-Fidelity DNA polymerase (New England Biolabs). Libraries were multiplexed for 75-bp paired-end sequencing on an Illumina NextSeq500.
PBAT (BS-seq)

value: Extra-embryonic ectoderm

tag: genotype

value: Dnmt3l KO


title: PBMC-timelapse, PBMC-timelapse-plate1_45

description:
PBMC-timelapse-plate1_45
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_ND_4

description: Astrocytes Input NCAR + Delta replicate 4


title: Assemblage of eggs, 3 Hours, Subitaneous, Replicate E

description:
see supplementary file
Transcriptome.annotated.fasta
3E_S9


title: PBMC-timelapse, PBMC-timelapse-plate1_44

description:
PBMC-timelapse-plate1_44
PBMC_RNA_expression.txt


title: n_ZFP_a_Rpl_Input_NZ_1

description: Astrocytes Input NCAR + ZFP replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate9_59

description:
3mix-timelapse-plate9_59
3mix_RNA_expression.txt


title: Dnmt3l KO, E7.5, ExE, 2 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_43

description:
PBMC-timelapse-plate1_43
PBMC_RNA_expression.txt


title: Assemblage of eggs, 3 Hours, Subitaneous, Replicate C

description:
see supplementary file
Transcriptome.annotated.fasta
3C_S7


title: Dnmt3l KO, E7.5, ExE, 1 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_58

description:
3mix-timelapse-plate9_58
3mix_RNA_expression.txt


title: Dnmt3a KO, E7.5, ExE, 3 (PBAT)

value: Dnmt3a KO


title: 3mix-timelapse, 3mix-timelapse-plate9_62

description:
3mix-timelapse-plate9_62
3mix_RNA_expression.txt


title: hSyn_RZ_2_IP

description: Neurons IP R6/2 + ZFP replicate 2

value: Neurons

value: IP


title: hSyn_RZ_3_IP

description: Neurons IP R6/2 + ZFP replicate 3


title: hSyn_RZ_1_IP

description: Neurons IP R6/2 + ZFP replicate 1


title: Dnmt3a KO, E7.5, ExE, 2 (PBAT)


title: hSyn_RZ_4_IP

description: Neurons IP R6/2 + ZFP replicate 4


title: hSyn_RD_3_IP

description: Neurons IP R6/2 + Delta replicate 3

value: RD


title: 3mix-timelapse, 3mix-timelapse-plate9_57

description:
3mix-timelapse-plate9_57
3mix_RNA_expression.txt

value: ALPS


title: PBMC-timelapse, PBMC-timelapse-plate1_41

description:
PBMC-timelapse-plate1_41
PBMC_RNA_expression.txt

value: C57BL/6J mouse

value: PBMC


title: 3mix-timelapse, 3mix-timelapse-plate9_56

description:
3mix-timelapse-plate9_56
3mix_RNA_expression.txt

value: random selection


title: hSyn_RD_2_IP

description: Neurons IP R6/2 + Delta replicate 2


title: Dnmt3a KO, E7.5, ExE, 1 (PBAT)


title: hSyn_RD_1_IP

description: Neurons IP R6/2 + Delta replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate1_39

description:
PBMC-timelapse-plate1_39
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_55

description:
3mix-timelapse-plate9_55
3mix_RNA_expression.txt


title: hSyn_NZ_5_IP

description: Neurons IP NCAR +ZFP replicate 5

value: NZ


title: PBMC-timelapse, PBMC-timelapse-plate1_42

description:
PBMC-timelapse-plate1_42
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_54

description:
3mix-timelapse-plate9_54
3mix_RNA_expression.txt


title: Dnmt3b het, E7.5, ExE, 3 (PBAT)

value: Dnmt3b -/+, Sox2-Cre +ve


title: Dnmt3b het, E7.5, ExE, 2 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_37

description:
PBMC-timelapse-plate1_37
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_53

description:
3mix-timelapse-plate9_53
3mix_RNA_expression.txt


title: Dnmt3b chet, E7.5, ExE, 1 (PBAT)

value: Dnmt3b fl/+, Sox2-Cre +ve


title: PBMC-timelapse, PBMC-timelapse-plate1_36

description:
PBMC-timelapse-plate1_36
PBMC_RNA_expression.txt


title: hSyn_NZ_2_IP

description: Neurons IP NCAR +ZFP replicate 2


title: PBMC-timelapse, PBMC-timelapse-plate1_38

description:
PBMC-timelapse-plate1_38
PBMC_RNA_expression.txt


title: hSyn_NZ_3_IP

description: Neurons IP NCAR +ZFP replicate 3


title: Dnmt3b het, E7.5, ExE, 1 (PBAT)

value: Dnmt3b -/fl, Sox2-Cre -ve


title: PBMC-timelapse, PBMC-timelapse-plate1_40

description:
PBMC-timelapse-plate1_40
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_35

description:
PBMC-timelapse-plate1_35
PBMC_RNA_expression.txt


title: Dnmt3b cKO, E7.5, ExE, 2 (PBAT)

value: Dnmt3b -/fl, Sox2-Cre +ve


title: PBMC-timelapse, PBMC-timelapse-plate1_34

description:
PBMC-timelapse-plate1_34
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_33

description:
PBMC-timelapse-plate1_33
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_51

description:
3mix-timelapse-plate9_51
3mix_RNA_expression.txt


title: hSyn_ND_4_IP

description: Neurons IP NCAR + Delta replicate 4

value: ND


title: 3mix-timelapse, 3mix-timelapse-plate9_49

description:
3mix-timelapse-plate9_49
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_50

description:
3mix-timelapse-plate9_50
3mix_RNA_expression.txt


title: Dnmt3b het, E7.5, ExE, 4 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_48

description:
3mix-timelapse-plate9_48
3mix_RNA_expression.txt


title: hSyn_ND_2_IP

description: Neurons IP NCAR + Delta replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate9_47

description:
3mix-timelapse-plate9_47
3mix_RNA_expression.txt


title: Dnmt3b KO, E7.5, ExE, 2 (PBAT)

value: Dnmt3b KO


title: hSyn_ND_3_IP

description: Neurons IP NCAR + Delta replicate 3


title: 3mix-timelapse, 3mix-timelapse-plate9_52

description:
3mix-timelapse-plate9_52
3mix_RNA_expression.txt


title: Dnmt3b KO, E7.5, ExE, 3 (PBAT)

value: Extra-embryonic ectoderm


title: PBMC-timelapse, PBMC-timelapse-plate1_31

description:
PBMC-timelapse-plate1_31
PBMC_RNA_expression.txt


title: hSyn_ND_1_IP

description: Neurons IP NCAR + Delta replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate9_46

description:
3mix-timelapse-plate9_46
3mix_RNA_expression.txt


title: hSyn_ND_0_IP

description: Neurons IP NCAR + Delta replicate 0


title: PBMC-timelapse, PBMC-timelapse-plate1_32

description:
PBMC-timelapse-plate1_32
PBMC_RNA_expression.txt


title: Dnmt3b KO, E7.5, ExE, 1 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_45

description:
3mix-timelapse-plate9_45
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_29

description:
PBMC-timelapse-plate1_29
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_30

description:
PBMC-timelapse-plate1_30
PBMC_RNA_expression.txt


title: Dnmt3b cKO, E7.5, ExE, 1 (PBAT)


title: hSyn_RZ_4_Input

description: Neurons Input R6/2 + ZFP replicate 4

value: RZ

value: Input


title: hSyn_NZ_1_IP

description: Neurons IP NCAR +ZFP replicate 1

value: Neurons


title: Dnmt3ab DKO, E7.5, ExE, 3 (PBAT)

value: Dnmt3a/Dnmt3b DKO


title: 3mix-timelapse, 3mix-timelapse-plate9_44

description:
3mix-timelapse-plate9_44
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_28

description:
PBMC-timelapse-plate1_28
PBMC_RNA_expression.txt


title: Dnmt3ab DKO, E7.5, ExE, 2 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_27

description:
PBMC-timelapse-plate1_27
PBMC_RNA_expression.txt


title: hSyn_RZ_2_Input

description: Neurons Input R6/2 + ZFP replicate 2


title: Dnmt3ab DKO, E7.5, ExE, 1 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_43

description:
3mix-timelapse-plate9_43
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_26

description:
PBMC-timelapse-plate1_26
PBMC_RNA_expression.txt


title: Dnmt3l WT, E7.5, ExE, 3 (PBAT)

value: WT


title: hSyn_RZ_3_Input

description: Neurons Input R6/2 + ZFP replicate 3


title: 3mix-timelapse, 3mix-timelapse-plate9_42

description:
3mix-timelapse-plate9_42
3mix_RNA_expression.txt

value: ALPS


title: PBMC-timelapse, PBMC-timelapse-plate1_25

description:
PBMC-timelapse-plate1_25
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: 3mix-timelapse, 3mix-timelapse-plate9_41

description:
3mix-timelapse-plate9_41
3mix_RNA_expression.txt


title: Dnmt3l WT, E7.5, ExE, 2 (PBAT)


title: hSyn_RD_3_Input

description: Neurons Input R6/2 + Delta replicate 3

value: RD


title: hSyn_RZ_1_Input

description: Neurons Input R6/2 + ZFP replicate 1


title: Dnmt3l WT, E7.5, ExE, 1 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_24

description:
PBMC-timelapse-plate1_24
PBMC_RNA_expression.txt

value: PBMC


title: 3mix-timelapse, 3mix-timelapse-plate9_40

description:
3mix-timelapse-plate9_40
3mix_RNA_expression.txt

value: random selection


title: 3mix-timelapse, 3mix-timelapse-plate9_39

description:
3mix-timelapse-plate9_39
3mix_RNA_expression.txt


title: hSyn_RD_2_Input

description: Neurons Input R6/2 + Delta replicate 2


title: PBMC-timelapse, PBMC-timelapse-plate1_23

description:
PBMC-timelapse-plate1_23
PBMC_RNA_expression.txt


title: Dnmt3ab WT, E7.5, ExE, 3 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_22

description:
PBMC-timelapse-plate1_22
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_38

description:
3mix-timelapse-plate9_38
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_37

description:
3mix-timelapse-plate9_37
3mix_RNA_expression.txt


title: hSyn_NZ_4_Input

description: Neurons Input NCAR + ZFP replicate 4

value: NZ


title: Dnmt3ab WT, E7.5, ExE, 2 (PBAT)


title: hSyn_NZ_3_Input

description: Neurons Input NCAR + ZFP replicate 3


title: PBMC-timelapse, PBMC-timelapse-plate1_21

description:
PBMC-timelapse-plate1_21
PBMC_RNA_expression.txt


title: hSyn_RD_1_Input

description: Neurons Input R6/2 + Delta replicate 1


title: Dnmt3l KO, E7.5, Epi, 3 (PBAT)

source_name: Epiblast

value: Epiblast

value: Dnmt3l KO


title: PBMC-timelapse, PBMC-timelapse-plate1_20

description:
PBMC-timelapse-plate1_20
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_36

description:
3mix-timelapse-plate9_36
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_19

description:
PBMC-timelapse-plate1_19
PBMC_RNA_expression.txt


title: hSyn_NZ_2_Input

description: Neurons Input NCAR + ZFP replicate 2


title: 3mix-timelapse, 3mix-timelapse-plate9_35

description:
3mix-timelapse-plate9_35
3mix_RNA_expression.txt


title: Dnmt3l KO, E7.5, Epi, 2 (PBAT)


title: Dnmt3l KO, E7.5, Epi, 1 (PBAT)


title: hSyn_NZ_1_Input

description: Neurons Input NCAR + ZFP replicate 1


title: 3mix-timelapse, 3mix-timelapse-plate9_34

description:
3mix-timelapse-plate9_34
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_18

description:
PBMC-timelapse-plate1_18
PBMC_RNA_expression.txt


title: Dnmt3a KO, E7.5, Epi, 3 (PBAT)

value: Dnmt3a KO


title: hSyn_ND_4_Input

description: Neurons Input NCAR + Delta replicate 4

value: ND


title: 3mix-timelapse, 3mix-timelapse-plate9_33

description:
3mix-timelapse-plate9_33
3mix_RNA_expression.txt


title: hSyn_ND_5_Input

description: Neurons Input NCAR + Delta replicate 5


title: PBMC-timelapse, PBMC-timelapse-plate1_16

description:
PBMC-timelapse-plate1_16
PBMC_RNA_expression.txt


title: hSyn_ND_3_Input

description: Neurons Input NCAR + Delta replicate 3


title: Dnmt3a KO, E7.5, Epi, 2 (PBAT)


title: Dnmt3ab WT, E7.5, ExE, 1 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_15

description:
PBMC-timelapse-plate1_15
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_17

description:
PBMC-timelapse-plate1_17
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_31

description:
3mix-timelapse-plate9_31
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_30

description:
3mix-timelapse-plate9_30
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_29

description:
3mix-timelapse-plate9_29
3mix_RNA_expression.txt


title: hSyn_ND_2_Input

description: Neurons Input NCAR + Delta replicate 2


title: Dnmt3a KO, E7.5, Epi, 1 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_14

description:
PBMC-timelapse-plate1_14
PBMC_RNA_expression.txt


title: hSyn_ND_0_Input

description: Neurons Input NCAR + Delta replicate 0


title: MG_RZ_3_IP

description: Astrocytes R6/2 + ZFP replicate 3

value: Astrocytes

value: IP


title: 3mix-timelapse, 3mix-timelapse-plate9_32

description:
3mix-timelapse-plate9_32
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_12

description:
PBMC-timelapse-plate1_12
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_11

description:
PBMC-timelapse-plate1_11
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_13

description:
PBMC-timelapse-plate1_13
PBMC_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_10

description:
PBMC-timelapse-plate1_10
PBMC_RNA_expression.txt


title: Dnmt3b chet, E7.5, Epi, 1 (PBAT)

value: Dnmt3b fl/+, Sox2-Cre +ve


title: Dnmt3b het, E7.5, Epi, 3 (PBAT)

value: Dnmt3b -/+, Sox2-Cre +ve


title: 3mix-timelapse, 3mix-timelapse-plate9_28

description:
3mix-timelapse-plate9_28
3mix_RNA_expression.txt


title: Dnmt3b cKO, E7.5, Epi, 2 (PBAT)

value: Dnmt3b -/fl, Sox2-Cre +ve


title: PBMC-timelapse, PBMC-timelapse-plate1_9

description:
PBMC-timelapse-plate1_9
PBMC_RNA_expression.txt


title: MG_RZ_2_IP

description: Astrocytes R6/2 + ZFP replicate 2

value: RZ


title: Dnmt3b het, E7.5, Epi, 1 (PBAT)

value: Dnmt3b -/fl, Sox2-Cre -ve


title: 3mix-timelapse, 3mix-timelapse-plate9_27

description:
3mix-timelapse-plate9_27
3mix_RNA_expression.txt

value: ALPS


title: Dnmt3b cKO, E7.5, Epi, 1 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_25

description:
3mix-timelapse-plate9_25
3mix_RNA_expression.txt


title: Dnmt3b het, E7.5, Epi, 2 (PBAT)


title: PBMC-timelapse, PBMC-timelapse-plate1_8

description:
PBMC-timelapse-plate1_8
PBMC_RNA_expression.txt

value: C57BL/6J mouse


title: 3mix-timelapse, 3mix-timelapse-plate9_26

description:
3mix-timelapse-plate9_26
3mix_RNA_expression.txt


title: MG_RD_4_IP

description: Astrocytes R6/2 + Delta replicate 4

value: RD


title: MG_RZ_4_IP

description: Astrocytes R6/2 + ZFP replicate 4


title: MG_RD_3_IP

description: Astrocytes R6/2 + Delta replicate 3


title: PBMC-timelapse, PBMC-timelapse-plate1_7

description:
PBMC-timelapse-plate1_7
PBMC_RNA_expression.txt

value: PBMC


title: 3mix-timelapse, 3mix-timelapse-plate9_24

description:
3mix-timelapse-plate9_24
3mix_RNA_expression.txt

value: random selection


title: MG_RZ_1_IP

description: Astrocytes R6/2 + ZFP replicate 1


title: Dnmt3b KO, E7.5, Epi, 3 (PBAT)

value: Dnmt3b KO


title: PBMC-timelapse, PBMC-timelapse-plate1_6

description:
PBMC-timelapse-plate1_6
PBMC_RNA_expression.txt


title: MG_RD_1_IP

description: Astrocytes R6/2 + Delta replicate 1


title: PBMC-timelapse, PBMC-timelapse-plate1_5

description:
PBMC-timelapse-plate1_5
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_23

description:
3mix-timelapse-plate9_23
3mix_RNA_expression.txt


title: MG_RD_2_IP

description: Astrocytes R6/2 + Delta replicate 2


title: Dnmt3b KO, E7.5, Epi, 1 (PBAT)

value: Epiblast


title: 3mix-timelapse, 3mix-timelapse-plate9_20

description:
3mix-timelapse-plate9_20
3mix_RNA_expression.txt


title: Dnmt3ab DKO, E7.5, Epi, 2 (PBAT)

value: Dnmt3a/Dnmt3b DKO


title: PBMC-timelapse, PBMC-timelapse-plate1_4

description:
PBMC-timelapse-plate1_4
PBMC_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_21

description:
3mix-timelapse-plate9_21
3mix_RNA_expression.txt


title: MG_NZ_3_IP

description: Astrocytes NCAR + ZFP replicate 3

value: NZ


title: 3mix-timelapse, 3mix-timelapse-plate9_18

description:
3mix-timelapse-plate9_18
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_22

description:
3mix-timelapse-plate9_22
3mix_RNA_expression.txt


title: PBMC-timelapse, PBMC-timelapse-plate1_2

description:
PBMC-timelapse-plate1_2
PBMC_RNA_expression.txt


title: MG_NZ_5_IP

description: Astrocytes NCAR + ZFP replicate 5


title: Dnmt3ab DKO, E7.5, Epi, 3 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_19

description:
3mix-timelapse-plate9_19
3mix_RNA_expression.txt


title: Dnmt3ab DKO, E7.5, Epi, 1 (PBAT)


title: Dnmt3l WT, E7.5, Epi, 1 (PBAT)

value: WT


title: Dnmt3l WT, E7.5, Epi, 2 (PBAT)


title: Dnmt3b KO, E7.5, Epi, 2 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_17

description:
3mix-timelapse-plate9_17
3mix_RNA_expression.txt


title: MG_ND_4_IP

description: Astrocytes IP NCAR + Delta replicate 4

value: Astrocytes

value: ND


title: PBMC-timelapse, PBMC-timelapse-plate1_1

description:
PBMC-timelapse-plate1_1
PBMC_RNA_expression.txt


title: dms_incell_starved

city: New Haven

first: Junjie

last: Guo

state: CT

address: 295 Congress Ave, BCMM 154B

institute: Yale University School of Medicine

data_processing:
After deduplication of reads, the first six random nucleotides and the 3' adapter sequences were trimmed using FASTX tools.
The trimmed sequences were aligned to the reference transcriptome using Bowtie, requiring unique mapping and allowing one mismatch.
For each read, the nucleotide immediately upstream of the first aligned position was annotated as an RT stop.
At each position i of the transcriptome with ≥ 3 RT-stop reads, a fold-enrichment value (f) for RT stops was calculated as the ratio between the number of reads stalled at position i and the average number of reads over all positions of the same nucleotide within the same transcript (e.g. all G nucleotides) using an in-house perl script.
Assembly: hg19 RefSeq
Supplementary files format and content: Tab-delimited files containing the position of RT stop, base identity, raw RT-stop read count and fold enrichment.
Library strategy: G4-DMS-seq

molecule: polyA RNA

growth_protocol: U2OS cells were maintained at 37°C in a CO2 incubator in DMEM (Corning) supplemented with 10% FBS, 20mM HEPES (Gibco), 1% penicillin/streptomycin. To induce the oxidative stress, cells were treated with 100 uM sodium arsenite (Ars-) in regular media for an hour. Starvation stress was induced by incubating the cells in HBSS media with Ca++ and Mg++ for 2h.

extract_protocol:
Total RNA was extracted from TRIzol lysates following the manufacturer's instructions. PolyA+ mRNAs was isolated by using oligo-dT magnetic beads (Invitrogen).
Libraries were constructed as previously described (Guo and Bartel, 2016, PMID: 27708011). Poly(A)-selected RNA (1 μg) in 10 mM Tris-Cl (pH 7.5) was denatured at 95°C for 2 min, supplemented with RNA-fragmentation reagent (Ambion) and incubated at 95°C for additional 1 min before adding EDTA stop solution (Ambion). After ethanol precipitation, RNA fragments were dephosphorylated at their 3′ ends with T4 polynucleotide kinase (New England BioLabs). 60−80-nt RNA fragments were gel-purified and ligated to a pre-adenylated 3′ DNA adapter (AppTCGTATGCCGTCTTCTGCTTGddC) with T4 RNA ligase 1 (New England BioLabs) without ATP. Products of the expected size (82−102 nt) were gel-purified and resuspended in 6 μl water. For reverse transcription, 1 μl 0.2 M Tris-Cl (pH 7.5), 1 μl 1.5 M KCl (or NaCl or LiCl), 0.5 μl 60 mM MgCl2, 0.5 μl 10 mM dNTP mix and 0.5 μl 1 μM 5′-radiolabeled primer (32p-NNNNNNGATCGTCGGACTGTAGAACTCTGAACCTGTCG/iSp18/CAAGCAGAAGACGGCATACG, in which N is any nucleotide, and iSp18 is an 18-atom hexa-ethyleneglycol spacer, IDT) were added to the RNA template. The mixture was incubated at 80°C for 2 min then cooled down to 42°C and incubated for additional 2 min before adding 100 units of SuperScript III reverse transcriptase (Invitrogen). After incubation at 42°C for 10 min, the reaction was stopped with addition of 1 μl of 1 M NaOH, and the mixture was heated at 98°C for 15 min to hydrolyze the RNA. cDNAs from extension that stalled after addition of 20 to 45 nt were separated from primers and full-length cDNAs on a 10% urea gel, eluted and precipitated. Purified cDNA fragments were circularized with 50 units of CircLigase (Epicentre) at 60°C for 4 hours before inactivation at 80°C for 10 min. Circularized cDNAs were amplified with a 5′ indexed primer (AATGATACGGCGACCACCGACAGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACxxxxxxATCCGACAGGTTCAGAGTTCTACAGTCCGA, in which xxxxxx is the multiplexing index), a common 3′ primer (CAAGCAGAAGACGGCATACGA), and Platinum Taq DNA Polymerase High Fidelity (Invitrogen) for 10 to 13 cycles of PCR. Libraries were purified on an 8% formamide gel and sequenced on a HiSeq 2000 sequencing machine (Illumina; 40 cycles, single-end mode).

treatment_protocol: Dimethylsulfate (Sigma) was mixed with ethanol (1:1) and was added to U2OS cells cultured in 15 cm dishes to a final DMS concentration of 8%, and evenly distributed by slow swirling. The cells were incubated for 5 min, the media and excess DMS were decanted, and cells were washed twice with 10 mL of 25% β-mercaptoethanol (Sigma-Aldrich) in PBS to quench any residual DMS. After washing, cells were lysed in 8 mL TRIzol reagent (Invitrogen) supplemented with 5% β-mercaptoethanol, and lysates were immediately processed for mRNA isolation.

tag: cell line

value: starved cells treated with DMS, polyA+ RNA RT'ed in 150mM K+


title: PBMC-timelapse, PBMC-timelapse-plate1_3

description:
PBMC-timelapse-plate1_3
PBMC_RNA_expression.txt


title: MG_ND_3_IP

description: Astrocytes IP NCAR + Delta replicate 3

value: IP


title: MG_NZ_4_IP

description: Astrocytes NCAR + ZFP replicate 4


title: 3mix-timelapse, 3mix-timelapse-plate9_16

description:
3mix-timelapse-plate9_16
3mix_RNA_expression.txt


title: MG_ND_2_IP

description: Astrocytes IP NCAR + Delta replicate 2


title: Dnmt3ab WT, E7.5, Epi, 3 (PBAT)


title: MG_ND_1_IP

description: Astrocytes IP NCAR + Delta replicate 1


title: Dnmt3ab WT, E7.5, Epi, 2 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_15

description:
3mix-timelapse-plate9_15
3mix_RNA_expression.txt


title: dms_incell_control

value: control cells treated with DMS, polyA+ RNA RT'ed in 150mM K+


title: 3mix-timelapse, 3mix-timelapse-plate9_14

description:
3mix-timelapse-plate9_14
3mix_RNA_expression.txt


title: dms_invitro_k

value: polyA+ RNA refolded and DMS-treated in 150mM K+, RT'ed in 150mM K+


title: MG_NZ_2_IP

description: Astrocytes NCAR + ZFP replicate 2


title: Dnmt3ab WT, E7.5, Epi, 1 (PBAT)


title: 3mix-timelapse, 3mix-timelapse-plate9_13

description:
3mix-timelapse-plate9_13
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate9_12

description:
3mix-timelapse-plate9_12
3mix_RNA_expression.txt


title: no_dms_k

value: untreated polyA+ RNA, RT'ed in 150mM K+


title: no_dms_na

value: untreated polyA+ RNA, RT'ed in 150mM Na+


title: 3mix-timelapse, 3mix-timelapse-plate9_10

description:
3mix-timelapse-plate9_10
3mix_RNA_expression.txt

value: ALPS


title: tubal ectopic pregnancy rep5

city: Shanghai

first: Xiaoya

last: Zhao

state: shanghai

address: No. 910, Hengshan Rd

department: Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital

country: China

institute: School of Medicine, Shanghai Jiaotong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to genome using HISAT2 with parameters -  dta t p 4
Fragments per Kilobase per Million Mapped Fragments (FPKM) were calculated using a protocol from Trapnell, C. et al., 2010.
Genome_build: Homo_sapiens.GRCh38.87
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: placenta

extract_protocol:
placental villi were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta

tag: gestational days

tag: maternal age


title: 3mix-timelapse, 3mix-timelapse-plate9_9

description:
3mix-timelapse-plate9_9
3mix_RNA_expression.txt


title: dms_invitro_li

value: polyA+ RNA refolded and DMS-treated in 150mM Li+, RT'ed in 150mM K+


title: tubal ectopic pregnancy rep4


title: 3mix-timelapse, 3mix-timelapse-plate9_8

description:
3mix-timelapse-plate9_8
3mix_RNA_expression.txt

value: random selection


title: 3mix-timelapse, 3mix-timelapse-plate9_7

description:
3mix-timelapse-plate9_7
3mix_RNA_expression.txt


title: LibFR013_Twistmix2_STARRseq_dev_rep3

city: Wien

first: Bernardo

middle: P

last: de Almeida

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
Oligo library UMI-STARR-seq RNA and DNA input reads (150 bp) were mapped to a reference containing 249 bp long sequences containing both wildtype and mutated fragments from the Drosophila library using Bowtie v.1.2.2. We demultiplexed reads by the i5 and i7 indexes and subsequently by the oligo identity, since this library contained oligos from other experiments. Mapping reads with the correct length, strand and with no mismatches (to identify all sequence variants) were kept. Both DNA and RNA reads were collapsed by UMI (10 bp, allowing one mismatch; UMI sequences are in the sequencing read name) to ensure the counting of unique reporter transcripts.
We excluded oligos with less than 10 reads in any of the input replicates and added one read pseudocount to oligos with zero RNA counts. The enhancer activity of each oligo in each screen was calculated as the log2 fold-change over input, using both replicates, using DESeq2. We used the counts of wildtype negative regions in each library as scaling factors between samples. This normalization only changes the position of the zero and consequently does not affect the calculation of log2 fold-changes or the p-values for the statistical tests used.
Assembly: dm3 (custom oligo library)
Supplementary files format and content: Table of all Drosophila melanogaster enhancer sequences and their mutant sequences (n=34186) included in the oligo library, with genomic coordinates, oligo sequence, experiment, mutated and pasted motifs, read counts for each screen and final developmental enhancer activity (log2).

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Schneider 2 cells were grown in Schneider’s Medium supplemented with 10% heat inactivated FBS at 27ºC. Cells were passaged every 2-3 days.

extract_protocol:
24h after electroporation, total RNA was extracted using the RNeasy Maxi kit (Qiagen; cat. no. 75162), followed by polyA+ RNA isolation using Invitrogen Dynabeads Oligo(dT)25 (scaling up the manufacturer’s protocol accordingly; cat. no. 61005) and DNase treatment with Ambion Turbo DNase (cat. no. AM2239) at a concentration of at most 200 ng/µl for 30 minutes (min) at 37°C. The reactions were then subjected to Qiagen RNeasy MinElute reaction clean-up (cat. no. 74204), for Turbo DNase inactivation and RNA concentration.  After reverse transcription and second strand synthesis a unique molecular identifier (UMI) was added to each transcript. This is followed by two nested PCR steps, each with primers that are specific to the reporter transcripts such that STARR-seq does not detect endogenous cellular RNAs. See Neumayr et al., Curr. Protoc. Mol. Biol. 2019.
Oligo libraries were synthesized by Twist Bioscience including 249 bp enhancer sequence and adaptors for library cloning. Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector. To construct the dCP STARR-seq vector, the sequence between BglII and FseI from the pGL3-Promoter backbone (Promega; cat. no. E1751) was replaced with the Drosophila Synthetic Core Promoter (DSCP), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3’s SV40 late polyA-signal. The hkCP STARR-seq vector is identical to the dCP STARR-seq vector except we replaced the DSCP with the RpS12 core promoter. The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.  See Neumayr et al., Curr. Protoc. Mol. Biol. 2019.
STARR-seq

tag: sample type

value: PCR amplified cDNA (STARR-seq transcript)

tag: promoter

value: developmental (DSCP)


title: LibFR013_Twistmix2_STARRseq_dev_rep2


title: tubal ectopic pregnancy rep3


title: 3mix-timelapse, 3mix-timelapse-plate9_6

description:
3mix-timelapse-plate9_6
3mix_RNA_expression.txt


title: tubal ectopic pregnancy rep2


title: 3mix-timelapse, 3mix-timelapse-plate9_11

description:
3mix-timelapse-plate9_11
3mix_RNA_expression.txt


title: Cbl_Rep3

city: North Ryde

first: Ian

last: Paulsen

state: New South Wales

address: 14 Eastern Road

department: Molecular Sciences

country: Australia

institute: Macquarie University

data_processing:
Basecalling and adaptor sequence trimming were processed by commercial sequencing provider.
The sequence reads from the 6 RNA-Seq samples were aligned to the A. baumannii AB5075_UW reference genome and counted using EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes).
Differential gene expression between the parental and mutant samples were analysed using the DEseq2 R package.

organism: Acinetobacter baumannii

source_name: Bacterial planktonic cells grown in Müller Hinton broth

growth_protocol: Three independent A. baumannii parental AB5075_UW and AB02746 (ABUW_1016-125:T26) mutant cultures were grown overnight in 5ml Müller Hinton broth at 37°C, with shaking. The overnight cultures were diluted 1:100 in MH and grown to mid-exponential phase cultures (15 mL, OD600 ~ 0.6) at 37°C, with shaking.

extract_protocol:
Total RNA was extracted using the miRNeasy mini kit (Qiagen) and DNA digestion was performed on the total RNA using DNaseI (TURBO DNA-freeTM kit, Invitrogen).
Ribosomal RNA was depleted using Ribozero magnetic kit (Bacteria) (Illumina, Inc., USA) and the cDNA library was generated using TruSeq® stranded RNA preparation kit (Illumina, Inc., USA). The samples were then sequenced on Illumina NextSeq_500 (2x75bp high output flowcell) platform.

value: Tn mutant


title: tubal ectopic pregnancy rep1


title: plasma_2h_MIRI 2

type: RNA

city: Jiamusi

first: Zhang

last: Meng

address: No.348 Dexiang Street, Xiangyang District, Jiamusi

institute: First Hospital of Jiamusi University

description: Gene expression after 2H I/R in Rat plasma

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

organism: Rattus

source_name: plasma ，2h，MIRI

label_protocol: Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: Six adult male SD rats were selected and randomly divided into MIRI group and sham-operated group for the establishment of MIRI model, rats were anesthetized intraperitoneally, fixed on the operating table, tracheal intubation was performed with a pen-type intravenous placement needle, animal ventilator was connected, ECG equipment was connected, preoperative ECG was collected for 1-2 minutes, chest was debrided and disinfected, skin was cut between the 3rd and 4th ribs on the left side of the chest, muscles were separated to expose The rib cage was removed and disinfected, the skin was cut between the 3rd and 4th ribs on the left side of the chest, the muscle was separated under the third rib with a haemostat, the lid opener was placed, the pericardium was peeled off with a haemostat, the thymus was clamped and pulled out with a haemostat, the left anterior descending coronary artery of the rat heart was ligated with a 5-0 wire between the left auricle and the cone of the pulmonary artery, the thorax was clamped shut with a haemostat, the ECG equipment was connected again, the postoperative ECG was collected for about 5 minutes, 40 minutes after myocardial ischaemia, the silk thread was cut with ophthalmic scissors The muscle and skin were cut and sutured. After 2 hours of myocardial ischaemia reperfusion, the skin and muscle were cut and the blood was taken in the right atrium after saline rinsing, the plasma was separated by centrifuge and stored frozen in liquid nitrogen. The control group (sham-operated group) was threaded, but not ligated The rest of the operation was the same as the MIRI group. After successful modelling, venous blood was taken from the right ventricle and immediately centrifuged

value: Blood plasma

tag: gender

value: male


title: plasma_2h_MIRI 3


title: Cbl_Rep2


title: plasma_2h_MIRI 1


title: plasma_0h_MIRI 2

description: Gene expression  in Rat plasma

source_name: plasma ，0h，MIRI


title: plasma_0h_MIRI 3

description: Gene expression  in Rat plasma


title: plasma_0h_MIRI 1

description: Gene expression  in Rat plasma


title: Cbl_Rep1


title: intrauterine pregnancy rep5


title: 3mix-timelapse, 3mix-timelapse-plate9_4

description:
3mix-timelapse-plate9_4
3mix_RNA_expression.txt


title: Parental AB5075_UW Rep2

value: Parental


title: LibFR013_Twistmix2_input_dev_rep2

source_name: oligo library (in STARR-seq vector)

value: PCR amplified Plasmid library


title: intrauterine pregnancy rep4


title: C1

city: Yangling

first: Yanling

last: Yin

state: Shaanxi

address: No.22 Xinong Road

department: College of veterinary medicine

institute: Northwest A&F University

description: Gene expression of untreated HCT-8 cell at 24hr

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: We used Feature Extraction software to analyze and extract raw data, and the raw data were imported into GeneSpring GX software to obtain the original signal value. The Quantile method was used for normalization, further processed by log2 logarithms to get the normalized data.

source_name: Human colonic epithelial cells

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: 10% FBS for cell growth

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: HCT-8 cells were infectedby cryptosporidium parvum, and then the six samples from each well was rapidly sampled, washed with nuclease-free PBS. All instruments and reagents in the trial were treated with DEPC in advance and without RNase.

value: pi 24hrs

value: untreated control


title: intrauterine pregnancy rep2


title: C3


title: 3mix-timelapse, 3mix-timelapse-plate9_3

description:
3mix-timelapse-plate9_3
3mix_RNA_expression.txt


title: Parental AB5075_UW Rep3


title: LibFR013_Twistmix2_input_dev_rep3


title: O3

description: Gene expression of HCT-8 cell after infected with cryptosporidium parvum at  24hr

value: infected with cryptosporidium parvum


title: intrauterine pregnancy rep1


title: O1


title: Parental AB5075_UW Rep1


title: C2


title: BALF 6h 1

status: Public on Dec 14 2022

city: Belo Horizonte

first: GUSTAVO JOSE

middle: COTA

last: DE FREITAS

state: MG

address: Av. Presidente Antônio Carlos  6627, Instituo de Ciencias Biológicas

department: MICROBIOLOGIA

country: Brazil

institute: UNIVERSIDADE FEDERAL DE MINAS GERAIS

description: BALF 6h 1

data_processing:
Quality reads were filtered using the FastQC software, and adapters were removed by the Trimmomatic v.0.36 (Bolger, Lohse, & Usadel, 2014). Trimmed reads were mapped to the C. neoformans H99 or the Mus musculus GRCm38 reference genomes, both available on ENSEMBL, using the STAR aligner v.2.5.2b (Dobin et al., 2013). STAR aligner detects splice junctions incorporating them to align the entire read sequences and generates the BAM files. Supplementary Table S18 and S19 show the statistics of genome mapping. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2 (Liao, Smyth, & Shi, 2014), and unique reads that fell within exon regions were counted. Differentially expressed genes (DEGs) were obtained using a 5% false discovery rate (FDR), using the DESeq2 Bioconducter package (Love, Huber, & Anders, 2014).
Fungal DEGs were functionally categorized using Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes), using the FungiDB ((http://fungidb.org/fungidb/) and FungiFun2 (https://elbe.hki-jena.de/fungifun/). Mouse DEGs were categorized using the ShinyGO v0.75 database (Ge, Jung, & Yao, 2020). Highly represented categories under each condition were determined by enrichment analysis.
FastQC v0.11.7 was used to visualize the libraries quality before and after trimming.
Trimmomatic v0.36 was used to remove adapters and quality filtered setting the cutoff threshold for average base quality score at 15 over a window of 4 bases. Reads shorter than 36 bases post-trimming were excluded.
Filtered reads were mapped onto the C. neoformans h99/ mus musculus reference genomes using the STAR v2.5.2b.
Gene level read-counts were quantified using STAR’s –quantMode GeneCounts parameter.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.5 (upregulation) or <= -1.5 (downregulation) were called as differentially expressed.
Assembly: Broad C. neoformans h99/ Mus musculus GRCm38 reference genomes
Supplementary files format and content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

source_name: Bronchoalveolar lavage fluid

growth_protocol: C. neoformans H99 was cultured on Yeast extract Peptone Dextrose (YPD) for 48h/72h (stationary phase) at 37°C for experiment.

extract_protocol:
C57BL/6 mice were infected intratracheally with 1x10e5 cells the H99 strain to analyze the transcriptome. After 6h or 240h of infection, BALF obtained from 6 mice of each condition were pooled together, generating two replicates of 6h and 240h (10d). BALF was centrifuged at 1200 x g and resuspended in 1mL TRIzol Reagent (Invitrogen Life Technologies) for RNA isolation, according to the manufactures' protocol. RNA from H99 yeasts grown in YPD was used as control.
RNA quality, library preparation, sequencing reactions, and initial bioinformatics analyses were conducted at GENEWIZ Inc (South Plainfield, NJ). RNA samples were quantified by fluorometry (Qubit 2.0, Thermo Fisher Scientific–Life Technologies), and RNA integrity was checked with 2100 Bioanalyzer (Agilent Technologies). Transcriptome sequencing was performed via rRNA depletion using the Illumina HiSeq platform (Illumina, USA) in the 2 x 150 bp Paired-End configuration.

value: Bronchoalveolar lavage fluid

tag: agent

value: Cryptococcus neoformans H99

tag: time point


title: BALF10D 1

description: BALF10D 1

tag: strain

tag: cell type

value: 10 day


title: O2


title: LibFR013_Twistmix2_input_dev_rep1


title: intrauterine pregnancy rep3


title: 39_RAW_shNCOR_H3K27ac_rp2

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Supplementary_files_format_and_content: ChIP-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Supplementary_files_format_and_content: ATAC-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
4C-seq raw files (fastq, single-end) were performed by the standard 4Cseqpipe protocol. The primer sequences were trimmed from the raw reads. The trimmed reads were mapped to the mm9 reference fragmented genome. The contact intensity was normalized by the fragment counts. The cis-interacting DNA contact profiles around the baits were plotted in the same chromosome window. As the 4C-seq program only provides the heatmaps, only the list of the 4C primers which was used to amplified the signals is provided.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Supplementary_files_format_and_content: RNA-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Supplementary_files_format_and_content: CUT&TAG: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

growth_protocol:
ChIP-Seq: WT RAW264.7 cells, lentivirus-medicated knockdown cells and GPS2 CRISPR KO cells were maintained normal 10% FBS DMEM medium.
ATAC-Seq: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
4C-Seq: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
RNA-Seq: BMDM cells were maintained normal 10% FBS DMEM medium supplement with 30% L929 medium for one week.
Cut&Tag: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
ChIP-Seq: Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
ATAC-Seq: WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×105 cells one day before the experiments. Cells were harvested with IL4 1h treatment, washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
4C-Seq: Fresh cells were crosslinked with 2% formaldehyde for 10 min at room temperature. Cells were counted and aliquoted with 10x7 cells per tube. For each 4C sample, 1 ml lysis buffer was applied for 10 min. Nuclei were spined down and discarded the supernatant. The nuclei were treated with the first digestion enzyme (Dpn II) overnight. The next day, the cell nuclei were heat-inactivated at 65C for 20 min and then treated with the first ligation enzyme overnight at room temperature. The genomic DNA was extracted and followed with the second digestion enzyme (Bfa I) overnight. Then heat-inactivated the enzyme and applied with then second the ligation enzyme overnight. The genomic DNA was purified again by phenol-chloroform extraction.
4C-Seq: PCR purified DNA (by baits) was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
RNA-Seq: 2×105 WT and GPS2 KO BMDM cells were seeded one day before the treatment. The next day the cells were treatment with IL4 6h and the total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
Cut&Tag: 2×105 shGFP and shKDM1A  RAW cells were seeded one day before.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
ChIP-Seq:RAW264.7 cells were treated  with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
ATAC-Seq: RAW264.7 cells were treated IL4 (20ng/ml)  for 1h .
4C-Seq: RAW264.7 cells were treated  with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
RNA-Seq: BMDM cells were treated  with or without IL4 (20ng/ml) treatment for 6h.
Cut&Tag: No treatment

value: Macrophage

value: BALB/c

value: Control

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.


title: LibFR013_Twistmix2_STARRseq_dev_rep1

value: PCR amplified cDNA (STARR-seq transcript)


title: 3mix-timelapse, 3mix-timelapse-plate9_1

description:
3mix-timelapse-plate9_1
3mix_RNA_expression.txt

value: random selection

tag: isolation method

value: ALPS


title: 37_RAW_shGFP_H3K27ac_rp2

tag: treatment


title: 3mix-timelapse, 3mix-timelapse-plate9_5

description:
3mix-timelapse-plate9_5
3mix_RNA_expression.txt


title: BALF 6h 2

description: BALF 6h 2


title: 36_RAW_shGFP_H3K27ac_rp1


title: 3mix-timelapse, 3mix-timelapse-plate9_2

description:
3mix-timelapse-plate9_2
3mix_RNA_expression.txt


title: BALF10D 2

description: BALF10D 2


title: 38_RAW_shNCOR_H3K27ac_rp1


title: Plasma_cells_Multiple_Myeloma [T18846]

type: genomic

city: Toulouse

last: Do Souto Ferreira

address: 1 Av. Irène Joliot-Curie

country: France

institute: IUCT

hyb_protocol: Cytoscan HD arrays (Affymetrix)

scan_protocol: Scanner Affymetrix  GCS 3000 7G

data_processing: analysis with the logarithm of ChAS software

label: biotin

source_name: sorted Plasma cells, from bone marrow of newly diagnosed multiple myeloma patients

label_protocol: Cytoscan Affymetrix Label (DNA labeling reagent)

extract_protocol: Nucleospin Tissue Macherey Nagel

treatment_protocol: sorted plasma cells (CD138+) then frozen (-80°C)

tag: subject id

tag: diagnosis

value: multiple myeloma

tag: Sex

tag: age

tag: del1p32 status

value: RD

tag: tissue

value: bone marrow

value: sorted plasma cells (CD138+)


title: 35_WT_BMDM_H3K27ac_LPS_4h

value: LPS 4h


title: Plasma_cells_Multiple_Myeloma [T18879]

value: male

value: MPV


title: Plasma_cells_Multiple_Myeloma [T18761]

value: female


title: Plasma_cells_Multiple_Myeloma [T18767]


title: Plasma_cells_Multiple_Myeloma [T18862]

value: VRD-R


title: Plasma_cells_Multiple_Myeloma [T18905]


title: Plasma_cells_Multiple_Myeloma [T18901]

value: VRD-RD


title: Plasma_cells_Multiple_Myeloma [T18980]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T18836]

value: VRD


title: Plasma_cells_Multiple_Myeloma [T18679]


title: Plasma_cells_Multiple_Myeloma [T18678]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T18791]


title: Plasma_cells_Multiple_Myeloma [T18869]


title: Plasma_cells_Multiple_Myeloma [T18911]


title: Plasma_cells_Multiple_Myeloma [T18918]


title: Plasma_cells_Multiple_Myeloma [T18630]


title: Plasma_cells_Multiple_Myeloma [T19174]


title: 34_WT_BMDM_H3K27ac_LPS_1h

value: Macrophage

value: BALB/c

value: LPS 1h

value: Abcam


title: Plasma_cells_Multiple_Myeloma [T19014]

value: multiple myeloma


title: NB4 Cut&Tag PML-RARA antibody replicate 1

city: London

first: Cameron

last: Osborne

address: Guy's Hospital Campus

department: Medical and Molecular Genetics

institute: King's College London

data_processing:
Reads were trimmed of adapters and low-quality reads using Trimmomatic (Bolger et al., 2014) and aligned to the hg19 genome using Bowtie2. PCR duplicates were removed using bedtools using Samtools and blacklisted reads were removed.
Peaks were called using the SEACR peak calling algorithm. A threshold of 0.01 and the ‘norm union’ settings were used as peak calling parameters.
Assembly: hg19
Supplementary files format and content: NB4_Cut_Tag_Merged_SEACR_PR_Peaks.csv contains the final 20,086 consensus PML-RARA binding site peaks called using SEACR across both PML-RARA antibody experiments
Library strategy: Cut&Tag

growth_protocol: NB4 cells were cultured in RPMI 1640 (Thermo Fisher, A10491), supplemented with 10% fetal bovine serum (Thermo Fisher, 10082147) and incubated at 37°C, 5% CO2.

extract_protocol: Library quality was assessed using Tapestation E220 high sensitivity (Agilent), and qPCR quantitation was performed using NEB library quant kit. Libraries were sequenced using an Illumina MiSeq instrument for paired-end sequencing.

treatment_protocol: Cut&Tag was performed using the Cut&Tag kit from Active Motif using the same principles from Kaya-Okur et al 2019.  https://www.activemotif.com/catalog/1318/cut-tag-it-kit?gclid=Cj0KCQjwof6WBhD4ARIsAOi65ahv6_A9SKmEVR0YE9Gn6W2nBA6yi5e1mVACtwAtYZmAKvQILYaYt2UaAu8dEALw_wcB

tag: cell line

value: Acute Promyelocytic Leukemia cell line


title: NB4 Cut&Tag PML-RARA antibody replicate 2


title: 33_WT_BMDM_H3K27ac_Ctrl

value: Control


title: Plasma_cells_Multiple_Myeloma [T18676]

value: bone marrow

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T18562]

value: male


title: Plasma_cells_Multiple_Myeloma [T18557]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T18504]


title: Plasma_cells_Multiple_Myeloma [T19110]


title: Plasma_cells_Multiple_Myeloma [T18499]

value: female


title: Plasma_cells_Multiple_Myeloma [T18617]


title: D_F (drought applied with fullerol) rep3

city: Wuhan

first: Jun-Lan

last: Xiong

state: Hubei

address: No. 2 Xudong 2nd Road, Wuchang District, Wuhan

department: Chinese Academy of Agricultural Science

institute: Oilcrops Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Trimmed sequence reads were mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase per Million of library size (FPKM) were calculated using a protocol from Trapnell et al., Nat. Biotechnol., 2010.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Brassica napus

source_name: leaf

growth_protocol: The plants were grown in a controlled growth chamber with the photoperiod of 14 h (07:00-21:00 h BST) and the day/night temperature of 25/18 °C

extract_protocol:
Leaves were flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Brassica napus was given fullerol under drought stress

value: leaf

tag: genotype

value: wild type

value: foliar application with 100 mg L-1 fullerol under drought


title: Plasma_cells_Multiple_Myeloma [T18483]

value: RD


title: D (drought) rep3

value: drought stress (30% Field capacity)


title: D (drought) rep1


title: D_F (drought applied with fullerol) rep1


title: Plasma_cells_Multiple_Myeloma [T18596]


title: D (drought) rep2


title: Plasma_cells_Multiple_Myeloma [T18602]


title: Plasma_cells_Multiple_Myeloma [T18551]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T18480]


title: Plasma_cells_Multiple_Myeloma [T18475]


title: Plasma_cells_Multiple_Myeloma [T18474]


title: CK (well-watered) rep3

value: well-watered (80% field capacity)


title: Plasma_cells_Multiple_Myeloma [T18748]


title: Plasma_cells_Multiple_Myeloma [T19028]

value: VRD


title: Plasma_cells_Multiple_Myeloma [T18528]


title: CK (well-watered) rep2


title: Plasma_cells_Multiple_Myeloma [T18518]


title: Plasma_cells_Multiple_Myeloma [T18581]


title: Plasma_cells_Multiple_Myeloma [T18437]


title: Plasma_cells_Multiple_Myeloma [T18568]


title: D_F (drought applied with fullerol) rep2


title: Plasma_cells_Multiple_Myeloma [T18471]

value: VCD-HDM


title: CK (well-watered) rep1


title: Plasma_cells_Multiple_Myeloma [T18425]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T18433]


title: Plasma_cells_Multiple_Myeloma [T18416]


title: Plasma_cells_Multiple_Myeloma [T18355]


title: Plasma_cells_Multiple_Myeloma [T18307]


title: Plasma_cells_Multiple_Myeloma [T18366]


title: Plasma_cells_Multiple_Myeloma [T18333]


title: Plasma_cells_Multiple_Myeloma [T18325]


title: Plasma_cells_Multiple_Myeloma [T18440]


title: Plasma_cells_Multiple_Myeloma [T18287]

value: VRD-R


title: Plasma_cells_Multiple_Myeloma [T18263]


title: Plasma_cells_Multiple_Myeloma [T18390]


title: Plasma_cells_Multiple_Myeloma [T18196]


title: Plasma_cells_Multiple_Myeloma [T18242]


title: Plasma_cells_Multiple_Myeloma [T18188]


title: Plasma_cells_Multiple_Myeloma [T18249]


title: Plasma_cells_Multiple_Myeloma [T18262]


title: Plasma_cells_Multiple_Myeloma [T18193]


title: Plasma_cells_Multiple_Myeloma [T18255]


title: Plasma_cells_Multiple_Myeloma [T18214]


title: Plasma_cells_Multiple_Myeloma [T18177]


title: Plasma_cells_Multiple_Myeloma [T18241]


title: Plasma_cells_Multiple_Myeloma [T18170]


title: Plasma_cells_Multiple_Myeloma [T18148]


title: Plasma_cells_Multiple_Myeloma [T18105]


title: Plasma_cells_Multiple_Myeloma [T18129]


title: Plasma_cells_Multiple_Myeloma [T18130]


title: Plasma_cells_Multiple_Myeloma [T18092]

value: VRD-RD


title: Plasma_cells_Multiple_Myeloma [T18089]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T18072]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T18001]

value: male


title: Plasma_cells_Multiple_Myeloma [T18020]


title: Plasma_cells_Multiple_Myeloma [T18187]


title: Plasma_cells_Multiple_Myeloma [T17994]


title: Plasma_cells_Multiple_Myeloma [T17984]


title: Plasma_cells_Multiple_Myeloma [T17969]


title: Plasma_cells_Multiple_Myeloma [T18186]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T17931]


title: Plasma_cells_Multiple_Myeloma [T18065]


title: Plasma_cells_Multiple_Myeloma [T17955]

value: VD


title: Plasma_cells_Multiple_Myeloma [T17923]


title: Plasma_cells_Multiple_Myeloma [T17922]

value: female


title: Plasma_cells_Multiple_Myeloma [T17920]


title: Plasma_cells_Multiple_Myeloma [T17925]


title: Plasma_cells_Multiple_Myeloma [T17917]


title: Plasma_cells_Multiple_Myeloma [T17868]


title: Plasma_cells_Multiple_Myeloma [T17884]


title: Plasma_cells_Multiple_Myeloma [T17841]


title: Plasma_cells_Multiple_Myeloma [T17829]


title: Plasma_cells_Multiple_Myeloma [T17898]


title: Plasma_cells_Multiple_Myeloma [T17830]


title: Plasma_cells_Multiple_Myeloma [T17817]


title: Plasma_cells_Multiple_Myeloma [T17821]


title: Plasma_cells_Multiple_Myeloma [T18018]


title: Plasma_cells_Multiple_Myeloma [T18035]


title: Plasma_cells_Multiple_Myeloma [T17812]


title: Plasma_cells_Multiple_Myeloma [T17800]


title: Plasma_cells_Multiple_Myeloma [T17802]


title: Plasma_cells_Multiple_Myeloma [T17794]


title: Plasma_cells_Multiple_Myeloma [T17904]


title: Plasma_cells_Multiple_Myeloma [T17782]


title: Plasma_cells_Multiple_Myeloma [T17746]


title: Plasma_cells_Multiple_Myeloma [T17744]


title: Plasma_cells_Multiple_Myeloma [T17709]


title: Plasma_cells_Multiple_Myeloma [T17736]


title: Plasma_cells_Multiple_Myeloma [T17711]


title: Plasma_cells_Multiple_Myeloma [T17722]


title: Plasma_cells_Multiple_Myeloma [T17672]


title: Plasma_cells_Multiple_Myeloma [T17694]


title: Plasma_cells_Multiple_Myeloma [T17647]


title: Plasma_cells_Multiple_Myeloma [T17644]


title: Plasma_cells_Multiple_Myeloma [T17628]


title: Plasma_cells_Multiple_Myeloma [T17618]


title: Plasma_cells_Multiple_Myeloma [T17641]

value: Dara-MPV


title: Plasma_cells_Multiple_Myeloma [T17638]


title: Plasma_cells_Multiple_Myeloma [T17808]


title: Plasma_cells_Multiple_Myeloma [T17617]


title: Plasma_cells_Multiple_Myeloma [T17615]


title: Plasma_cells_Multiple_Myeloma [T17579]

value: VRD-Isatuximab


title: 3mix-timelapse, 3mix-timelapse-plate10_18

description:
3mix-timelapse-plate10_18
3mix_RNA_expression.txt

value: random selection

value: ALPS


title: Plasma_cells_Multiple_Myeloma [T17585]


title: Plasma_cells_Multiple_Myeloma [T17548]


title: Plasma_cells_Multiple_Myeloma [T17570]


title: Plasma_cells_Multiple_Myeloma [T17554]

value: RD


title: Plasma_cells_Multiple_Myeloma [T17546]


title: Plasma_cells_Multiple_Myeloma [T17564]


title: Plasma_cells_Multiple_Myeloma [T17531]


title: Plasma_cells_Multiple_Myeloma [T17740]


title: Plasma_cells_Multiple_Myeloma [T17526]


title: Plasma_cells_Multiple_Myeloma [T17515]


title: Plasma_cells_Multiple_Myeloma [T17511]


title: Plasma_cells_Multiple_Myeloma [T17489]


title: Plasma_cells_Multiple_Myeloma [T17492]


title: Plasma_cells_Multiple_Myeloma [T17473]


title: Plasma_cells_Multiple_Myeloma [T17466]


title: Plasma_cells_Multiple_Myeloma [T17468]


title: Plasma_cells_Multiple_Myeloma [T17444]


title: Plasma_cells_Multiple_Myeloma [T17403]

value: RCD


title: Plasma_cells_Multiple_Myeloma [T17461]


title: Plasma_cells_Multiple_Myeloma [T17467]


title: Plasma_cells_Multiple_Myeloma [T17462]


title: Plasma_cells_Multiple_Myeloma [T17405]

value: VRD


title: Plasma_cells_Multiple_Myeloma [T17336]


title: Plasma_cells_Multiple_Myeloma [T17389]


title: Plasma_cells_Multiple_Myeloma [T17299]


title: Plasma_cells_Multiple_Myeloma [T17376]


title: Plasma_cells_Multiple_Myeloma [T17285]


title: Plasma_cells_Multiple_Myeloma [T17442]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T17225]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T17205]


title: Plasma_cells_Multiple_Myeloma [T17204]


title: Plasma_cells_Multiple_Myeloma [T17379]


title: Plasma_cells_Multiple_Myeloma [T17321]


title: Plasma_cells_Multiple_Myeloma [T17296]


title: Plasma_cells_Multiple_Myeloma [T17197]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T17221]


title: Plasma_cells_Multiple_Myeloma [T17194]


title: Plasma_cells_Multiple_Myeloma [T17314]

value: VRD-R


title: Plasma_cells_Multiple_Myeloma [T17177]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T17150]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T17135]

value: male


title: Plasma_cells_Multiple_Myeloma [T17399]


title: Plasma_cells_Multiple_Myeloma [T17349]


title: Plasma_cells_Multiple_Myeloma [T17122]


title: Plasma_cells_Multiple_Myeloma [T17100]


title: Plasma_cells_Multiple_Myeloma [T17067]


title: Plasma_cells_Multiple_Myeloma [T17125]

value: VRD-RD


title: Plasma_cells_Multiple_Myeloma [T17063]


title: Plasma_cells_Multiple_Myeloma [T17050]


title: Plasma_cells_Multiple_Myeloma [T17117]


title: Plasma_cells_Multiple_Myeloma [T17048]

value: RD-HDM


title: Plasma_cells_Multiple_Myeloma [T17049]

value: female


title: Plasma_cells_Multiple_Myeloma [T17103]


title: Plasma_cells_Multiple_Myeloma [T16996]


title: Plasma_cells_Multiple_Myeloma [T16983]


title: Plasma_cells_Multiple_Myeloma [T16973]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T17012]


title: Plasma_cells_Multiple_Myeloma [T17140]


title: Plasma_cells_Multiple_Myeloma [T16964]


title: Plasma_cells_Multiple_Myeloma [T16933]

description: The .CEL file is not available for this sample.


title: Plasma_cells_Multiple_Myeloma [T16934]


title: Plasma_cells_Multiple_Myeloma [T16995]


title: Plasma_cells_Multiple_Myeloma [T16978]


title: Plasma_cells_Multiple_Myeloma [T16968]


title: Plasma_cells_Multiple_Myeloma [T16962]

value: VTD


title: Plasma_cells_Multiple_Myeloma [T17036]

value: VRD-Isatuximab


title: Plasma_cells_Multiple_Myeloma [T16952]


title: Plasma_cells_Multiple_Myeloma [T16943]


title: Plasma_cells_Multiple_Myeloma [T16969]


title: Plasma_cells_Multiple_Myeloma [T16970]


title: Plasma_cells_Multiple_Myeloma [T17032]


title: Plasma_cells_Multiple_Myeloma [T16942]


title: Plasma_cells_Multiple_Myeloma [T16891]


title: Plasma_cells_Multiple_Myeloma [T16905]


title: Plasma_cells_Multiple_Myeloma [T16893]


title: Plasma_cells_Multiple_Myeloma [T16921]


title: Plasma_cells_Multiple_Myeloma [T16892]


title: Plasma_cells_Multiple_Myeloma [T16866]


title: Plasma_cells_Multiple_Myeloma [T16860]


title: Plasma_cells_Multiple_Myeloma [T16850]


title: Plasma_cells_Multiple_Myeloma [T16903]


title: Plasma_cells_Multiple_Myeloma [T16867]


title: Plasma_cells_Multiple_Myeloma [T16848]


title: Plasma_cells_Multiple_Myeloma [T16844]


title: Plasma_cells_Multiple_Myeloma [T16845]


title: Plasma_cells_Multiple_Myeloma [T16819]


title: Plasma_cells_Multiple_Myeloma [T16837]


title: Plasma_cells_Multiple_Myeloma [T16870]


title: Plasma_cells_Multiple_Myeloma [T16790]


title: Plasma_cells_Multiple_Myeloma [T16833]


title: Plasma_cells_Multiple_Myeloma [T16750]


title: Plasma_cells_Multiple_Myeloma [T16783]


title: Plasma_cells_Multiple_Myeloma [T16730]


title: Plasma_cells_Multiple_Myeloma [T16724]


title: Plasma_cells_Multiple_Myeloma [T16824]


title: Plasma_cells_Multiple_Myeloma [T16706]


title: Plasma_cells_Multiple_Myeloma [T16694]


title: Plasma_cells_Multiple_Myeloma [T16698]


title: Plasma_cells_Multiple_Myeloma [T16629]


title: Plasma_cells_Multiple_Myeloma [T16666]


title: Plasma_cells_Multiple_Myeloma [T16653]


title: Plasma_cells_Multiple_Myeloma [T16674]


title: Plasma_cells_Multiple_Myeloma [T16699]


title: Plasma_cells_Multiple_Myeloma [T16665]


title: Plasma_cells_Multiple_Myeloma [T16622]


title: Plasma_cells_Multiple_Myeloma [T16621]


title: Plasma_cells_Multiple_Myeloma [T16690]


title: Plasma_cells_Multiple_Myeloma [T16618]


title: Plasma_cells_Multiple_Myeloma [T16687]


title: Plasma_cells_Multiple_Myeloma [T16604]


title: Plasma_cells_Multiple_Myeloma [T16589]


title: Plasma_cells_Multiple_Myeloma [T16628]


title: Plasma_cells_Multiple_Myeloma [T16555]

value: MP


title: Plasma_cells_Multiple_Myeloma [T16542]


title: Plasma_cells_Multiple_Myeloma [T16552]

value: RD


title: Plasma_cells_Multiple_Myeloma [T16614]


title: Plasma_cells_Multiple_Myeloma [T16609]


title: Plasma_cells_Multiple_Myeloma [T16459]


title: Plasma_cells_Multiple_Myeloma [T16550]


title: Plasma_cells_Multiple_Myeloma [T16531]


title: Plasma_cells_Multiple_Myeloma [T16520]


title: Plasma_cells_Multiple_Myeloma [T16451]


title: Plasma_cells_Multiple_Myeloma [T16346]


title: Plasma_cells_Multiple_Myeloma [T16494]


title: Plasma_cells_Multiple_Myeloma [T16617]


title: Plasma_cells_Multiple_Myeloma [T16372]


title: Plasma_cells_Multiple_Myeloma [T16522]


title: Plasma_cells_Multiple_Myeloma [T16327]


title: Plasma_cells_Multiple_Myeloma [T16310]


title: Plasma_cells_Multiple_Myeloma [T16400]


title: Plasma_cells_Multiple_Myeloma [T16273]


title: Plasma_cells_Multiple_Myeloma [T16414]


title: Plasma_cells_Multiple_Myeloma [T16269]


title: Plasma_cells_Multiple_Myeloma [T16278]


title: Plasma_cells_Multiple_Myeloma [T16218]


title: Plasma_cells_Multiple_Myeloma [T16175]


title: Plasma_cells_Multiple_Myeloma [T16186]


title: Plasma_cells_Multiple_Myeloma [T16196]

value: Dara-MPV


title: Plasma_cells_Multiple_Myeloma [T16229]


title: Plasma_cells_Multiple_Myeloma [T16156]


title: Plasma_cells_Multiple_Myeloma [T16344]

value: VRD


title: Plasma_cells_Multiple_Myeloma [T16404]


title: Plasma_cells_Multiple_Myeloma [T16150]

value: VCD


title: Plasma_cells_Multiple_Myeloma [T16130]

value: multiple myeloma


title: Plasma_cells_Multiple_Myeloma [T16021]


title: Plasma_cells_Multiple_Myeloma [T15991]


title: Plasma_cells_Multiple_Myeloma [T15985]


title: Plasma_cells_Multiple_Myeloma [T16868]


title: Plasma_cells_Multiple_Myeloma [T16305]


title: Plasma_cells_Multiple_Myeloma [T16292]


title: Plasma_cells_Multiple_Myeloma [T15979]


title: Plasma_cells_Multiple_Myeloma [T15984]


title: Plasma_cells_Multiple_Myeloma [T15972]


title: Plasma_cells_Multiple_Myeloma [T16009]


title: Plasma_cells_Multiple_Myeloma [T15954]


title: Plasma_cells_Multiple_Myeloma [T15945]


title: Plasma_cells_Multiple_Myeloma [T15933]


title: Plasma_cells_Multiple_Myeloma [T15915]


title: Plasma_cells_Multiple_Myeloma [T15909]

value: VCD-HDM


title: Plasma_cells_Multiple_Myeloma [T15906]


title: Plasma_cells_Multiple_Myeloma [T16151]


title: Plasma_cells_Multiple_Myeloma [T15889]


title: Plasma_cells_Multiple_Myeloma [T15886]


title: Plasma_cells_Multiple_Myeloma [T15881]


title: Plasma_cells_Multiple_Myeloma [T16027]


title: Plasma_cells_Multiple_Myeloma [T16085]


title: Plasma_cells_Multiple_Myeloma [T15865]


title: Plasma_cells_Multiple_Myeloma [T15951]


title: Plasma_cells_Multiple_Myeloma [T15810]


title: Plasma_cells_Multiple_Myeloma [T15780]


title: Plasma_cells_Multiple_Myeloma [T15784]

value: 6 VRD-MEL200-VRD-R


title: Plasma_cells_Multiple_Myeloma [T15834]

value: bone marrow


title: Plasma_cells_Multiple_Myeloma [T15811]

value: sorted plasma cells (CD138+)


title: Plasma_cells_Multiple_Myeloma [T15832]

value: male


title: Plasma_cells_Multiple_Myeloma [T15761]


title: Plasma_cells_Multiple_Myeloma [T15822]

value: VRD-R


title: Plasma_cells_Multiple_Myeloma [T15841]


title: Plasma_cells_Multiple_Myeloma [T15763]


title: Plasma_cells_Multiple_Myeloma [T15762]


title: Plasma_cells_Multiple_Myeloma [T15837]


title: Plasma_cells_Multiple_Myeloma [T15757]


title: Plasma_cells_Multiple_Myeloma [T15874]


title: Plasma_cells_Multiple_Myeloma [T15737]


title: Plasma_cells_Multiple_Myeloma [T15747]


title: Plasma_cells_Multiple_Myeloma [T15760]


title: Plasma_cells_Multiple_Myeloma [T15900]


title: Plasma_cells_Multiple_Myeloma [T15742]


title: Plasma_cells_Multiple_Myeloma [T15721]


title: Plasma_cells_Multiple_Myeloma [T15700]


title: Plasma_cells_Multiple_Myeloma [T15694]


title: Plasma_cells_Multiple_Myeloma [T15713]


title: Plasma_cells_Multiple_Myeloma [T15704]


title: Plasma_cells_Multiple_Myeloma [T15636]


title: Plasma_cells_Multiple_Myeloma [T15683]


title: Plasma_cells_Multiple_Myeloma [T15616]


title: Plasma_cells_Multiple_Myeloma [T15632]

value: VD


title: Plasma_cells_Multiple_Myeloma [T15597]

value: female


title: Plasma_cells_Multiple_Myeloma [T15595]


title: Plasma_cells_Multiple_Myeloma [T15574]


title: Plasma_cells_Multiple_Myeloma [T15581]


title: Plasma_cells_Multiple_Myeloma [T15546]


title: Plasma_cells_Multiple_Myeloma [T15519]

value: MPV


title: Plasma_cells_Multiple_Myeloma [T15523]


title: Plasma_cells_Multiple_Myeloma [T15570]


title: Plasma_cells_Multiple_Myeloma [T15563]


title: Plasma_cells_Multiple_Myeloma [T15544]


title: Plasma_cells_Multiple_Myeloma [T15514]


title: Plasma_cells_Multiple_Myeloma [T15548]


title: Plasma_cells_Multiple_Myeloma [T15490]


title: Plasma_cells_Multiple_Myeloma [T15516]

value: VRD-RD


title: Plasma_cells_Multiple_Myeloma [T15392]


title: Plasma_cells_Multiple_Myeloma [T15397]


title: Plasma_cells_Multiple_Myeloma [T15355]