DEK RNA-Seq in HepG2

General Information


RBP	DEK
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DEK-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DEK-BGHcLV45-19
Rep2	DEK-BGHcLV45-20
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	35.6
Rep2_qPCR	39.7
Rep1_WB	72.8
Rep2_WB	80.8
Antibody Cat#	720215
Antibody Lot#	SD249202
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1621

Experiment Information (Status: Submitting)

	BGHcLV45-19	BGHcLV45-20
idx	1217	1217
TRCN#_or_BGC#	BGC#0000310	BGC#0000310
shRNA_or_gRNA_sequence	GTTCTTTCTCGGACGCGGGC	GTTCTTTCTCGGACGCGGGC
PAM	tgg	tgg
Name	DEK_97	DEK_97
Sample_ID	BGHcLV45-19	BGHcLV45-20
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	DEK	DEK
qPCR_result	35.6	39.7
Ave_qPCR	37.6
RT-qPCR_primer-F	ggtcagttcagtggctttcc
RT-qPCR_primer-R	tctccaaatcaagaacctcaca
protein_conc	3609	3812
WB_result	72.8	80.8
Ave_WB
WB_DONE_date	10/10/24
MW	43kd
IP
antibody_Cat#	720215	SD249202
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9707	9708

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DEK	Product_ID: 720215 Lot_ID: SD249202 Source: Thermo Fisher Target Name: DEK-human

Experiment Status

	BGHcLV45-19	BGHcLV45-20
Sample_ID	BGHcLV45-19	BGHcLV45-20
Sample Name
Sample Name	DEK-BGHcLV45-19	DEK-BGHcLV45-20
RBP	DEK	DEK
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13700	13701

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-19	BGHcLV45-20
Sample #	15	16
Sample Name	DEK-BGHcLV45-19	DEK-BGHcLV45-20
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	291	294
Peak_Molarity	65.20	57.90
libSampleQC_DNA_Well	DNA_Library_set76/set1/G8.png	DNA_Library_set76/set1/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/G2.png	RNA_Library_set76/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-19	BGHcLV45-20
RBP	DEK	DEK
Batch_ID	BGHcLV45	BGHcLV45
WB_result	72.800	80.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4624	4625

Sequencing Information

	BGHcLV45-19	BGHcLV45-20
Sample_ID	BGHcLV45-19	BGHcLV45-20
Sample Name	DEK-BGHcLV45-19	DEK-BGHcLV45-20
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	38,319,045	41,892,792
total_aligned_reads	34,610,988	38,579,746
unique_aligned_reads	32,507,262	36,318,986
percent_uniqueAligned	0.84833	0.86695
correlation_replicates	0.999294	0.999294
spikein_reads	26,908	31,906
percent_spikeins	0.00070	0.00076
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3335	3336

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
DEK-BGHcLV45-19_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3335	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31824
DEK-BGHcLV45-19_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3335	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31866
DEK-BGHcLV45-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3335					GRCh38	V40	DEK-BGHcLV45-19_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,DEK-BGHcLV45-19_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31908
DEK-BGHcLV45-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3335					GRCh38	V40	DEK-BGHcLV45-19_Aligned.sortedByCoord.out.bam		ENCORE2	31950
DEK-BGHcLV45-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3335					GRCh38	V40	DEK-BGHcLV45-19_Aligned.sortedByCoord.out.bam		ENCORE2	31992
DEK-BGHcLV45-19_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3335					GRCh38	V40	DEK-BGHcLV45-19_Aligned.sortedByCoord.out.bam		ENCORE2	32034
DEK-BGHcLV45-19_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3335					GRCh38	V40	DEK-BGHcLV45-19_Aligned.sortedByCoord.out.bam		ENCORE2	32076
DEK-BGHcLV45-19_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3335					GRCh38	V40	DEK-BGHcLV45-19_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,DEK-BGHcLV45-19_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32118
DEK-BGHcLV45-20_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3336	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31825
DEK-BGHcLV45-20_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3336	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31867
DEK-BGHcLV45-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3336					GRCh38	V40	DEK-BGHcLV45-20_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,DEK-BGHcLV45-20_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31909
DEK-BGHcLV45-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3336					GRCh38	V40	DEK-BGHcLV45-20_Aligned.sortedByCoord.out.bam		ENCORE2	31951
DEK-BGHcLV45-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3336					GRCh38	V40	DEK-BGHcLV45-20_Aligned.sortedByCoord.out.bam		ENCORE2	31993
DEK-BGHcLV45-20_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3336					GRCh38	V40	DEK-BGHcLV45-20_Aligned.sortedByCoord.out.bam		ENCORE2	32035
DEK-BGHcLV45-20_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3336					GRCh38	V40	DEK-BGHcLV45-20_Aligned.sortedByCoord.out.bam		ENCORE2	32077
DEK-BGHcLV45-20_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3336					GRCh38	V40	DEK-BGHcLV45-20_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,DEK-BGHcLV45-20_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32119