DDX41 RNA-Seq in HepG2

General Information


RBP	DDX41
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX41-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DDX41-BGHcLV43-13
Rep2	DDX41-BGHcLV43-14
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	78.1
Rep2_qPCR	75.7
Rep1_WB	85.0
Rep2_WB	84.2
Antibody Cat#	15076S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1573

Experiment Information (Status: Submitting)

	BGHcLV43-13	BGHcLV43-13	BGHcLV43-14	BGHcLV43-14
idx	1381	1381	1382	1382
TRCN#_or_BGC#	BGC#0001126	BGC#0001126	BGC#0001126	BGC#0001126
shRNA_or_gRNA_sequence	GACATGCTCAGAACATAACG	GACATGCTCAGAACATAACG	GACATGCTCAGAACATAACG	GACATGCTCAGAACATAACG
PAM	GGG	GGG	GGG	GGG
Name	DDX41_90	DDX41_90	DDX41_90	DDX41_90
Sample_ID	BGHcLV43-13	BGHcLV43-13	BGHcLV43-14	BGHcLV43-14
transduction_Date	6/6/24	6/6/24	6/6/24	6/6/24
days	D6	D6	D6	D6
RBP_name	DDX41	DDX41	DDX41	DDX41
qPCR_result	78.1	78.1	75.7	75.7
Ave_qPCR	76.9	76.9
RT-qPCR_primer-F	TGCTGCAGGTGCTGCATT	TGCTGCAGGTGCTGCATT
RT-qPCR_primer-R	AGTCAGTGATCCGATGACCC	AGTCAGTGATCCGATGACCC
protein_conc	3099	3099	2907	2907
WB_result	85.0	67.7	84.2	72.6535
Ave_WB	84.6	70.2
WB_DONE_date	6/13/24	6/28/24
MW	75KD	75KD
IP
antibody_Cat#	15076S	A301-050A	lot # 1	lot # 2
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	9632	9634	9633	9635

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX41	Product_ID: 15076S Lot_ID: 1 Source: Cell Signaling Technology Target Name: DDX41-human
DDX41	Product_ID: A301-050A Lot_ID: 2 Source: Bethyl Labs Target Name: DDX41-human

Experiment Status

	BGHcLV43-13	BGHcLV43-13	BGHcLV43-14	BGHcLV43-14
Sample_ID	BGHcLV43-13	BGHcLV43-13	BGHcLV43-14	BGHcLV43-14
Sample Name
Sample Name	DDX41-BGHcLV43-13		DDX41-BGHcLV43-14
RBP	DDX41	DDX41	DDX41	DDX41
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-02-11	2024-07-16	2025-02-11	2024-07-16
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13236	13286	13237	13287

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-13	BGHcLV43-14
Sample #	9	10
Sample Name	DDX41-BGHcLV43-13	DDX41-BGHcLV43-14
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	321	313
Peak_Molarity	122.00	94.40
libSampleQC_DNA_Well	DNA_Library_set74/set1/A2.png	DNA_Library_set74/set1/B2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/E7.png	RNA_Library_set74/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-13	BGHcLV43-14
RBP	DDX41	DDX41
Batch_ID	BGHcLV43	BGHcLV43
WB_result	85.000	84.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4368	4369

Sequencing Information

	BGHcLV43-13	BGHcLV43-14
Sample_ID	BGHcLV43-13	BGHcLV43-14
Sample Name	DDX41-BGHcLV43-13	DDX41-BGHcLV43-14
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	58,992,012	48,455,481
total_aligned_reads	56,138,486	45,266,235
unique_aligned_reads	52,865,188	42,595,609
percent_uniqueAligned	0.89614	0.87907
correlation_replicates	0.991238	0.991238
spikein_reads	26,644	15,566
percent_spikeins	0.00045	0.00032
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3235	3236

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
DDX41-BGHcLV43-13_S99_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3235	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30526
DDX41-BGHcLV43-13_S99_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3235	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30578
DDX41-BGHcLV43-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3235					GRCh38	V40	DDX41-BGHcLV43-13_S99_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX41-BGHcLV43-13_S99_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30630
DDX41-BGHcLV43-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3235					GRCh38	V40	DDX41-BGHcLV43-13_Aligned.sortedByCoord.out.bam		ENCORE2	30682
DDX41-BGHcLV43-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3235					GRCh38	V40	DDX41-BGHcLV43-13_Aligned.sortedByCoord.out.bam		ENCORE2	30734
DDX41-BGHcLV43-13_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3235					GRCh38	V40	DDX41-BGHcLV43-13_Aligned.sortedByCoord.out.bam		ENCORE2	30786
DDX41-BGHcLV43-13_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3235					GRCh38	V40	DDX41-BGHcLV43-13_Aligned.sortedByCoord.out.bam		ENCORE2	30838
DDX41-BGHcLV43-13_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3235					GRCh38	V40	DDX41-BGHcLV43-13_S99_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX41-BGHcLV43-13_S99_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30890
DDX41-BGHcLV43-14_S100_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3236	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30527
DDX41-BGHcLV43-14_S100_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3236	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30579
DDX41-BGHcLV43-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3236					GRCh38	V40	DDX41-BGHcLV43-14_S100_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX41-BGHcLV43-14_S100_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30631
DDX41-BGHcLV43-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3236					GRCh38	V40	DDX41-BGHcLV43-14_Aligned.sortedByCoord.out.bam		ENCORE2	30683
DDX41-BGHcLV43-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3236					GRCh38	V40	DDX41-BGHcLV43-14_Aligned.sortedByCoord.out.bam		ENCORE2	30735
DDX41-BGHcLV43-14_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3236					GRCh38	V40	DDX41-BGHcLV43-14_Aligned.sortedByCoord.out.bam		ENCORE2	30787
DDX41-BGHcLV43-14_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3236					GRCh38	V40	DDX41-BGHcLV43-14_Aligned.sortedByCoord.out.bam		ENCORE2	30839
DDX41-BGHcLV43-14_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3236					GRCh38	V40	DDX41-BGHcLV43-14_S100_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX41-BGHcLV43-14_S100_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30891