DDX10 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-25	BGHcLV49-26
idx	1724	1725
TRCN#_or_BGC#	BGC#0000743	BGC#0000743
shRNA_or_gRNA_sequence	AATATACTCGTGTGCACACC	AATATACTCGTGTGCACACC
PAM	AGG	AGG
Name	DDX10_75	DDX10_75
Sample_ID	BGHcLV49-25	BGHcLV49-26
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	DDX10	DDX10
qPCR_result	46.0	57.8
Ave_qPCR	51.9
RT-qPCR_primer-F	ggtcggcttcttcaacacat
RT-qPCR_primer-R	agcaaagcccatatccaaga
protein_conc	5219	5658
WB_result	91.9	82.6721
Ave_WB
WB_DONE_date	7/10/25
MW	101KD
IP	Rabbit / I
antibody_Cat#	A300-617A	LOT #1
Antibody DCC ID	ENCAB959QKK
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9913	9914

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX10	Product_ID: A300-617A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX10-human

Experiment Status

	BGHcLV49-25	BGHcLV49-26
Sample_ID	BGHcLV49-25	BGHcLV49-26
Sample Name
Sample Name	DDX10-BGHcLV49-25	DDX10-BGHcLV49-26
RBP	DDX10	DDX10
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14340	14341

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-25	BGHcLV49-26
Sample #	37	38
Sample Name	DDX10-BGHcLV49-25	DDX10-BGHcLV49-26
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	258	260
Peak_Molarity	72.80	58.00
libSampleQC_DNA_Well	DNA_Library_set81/set1/G2.png	DNA_Library_set81/set1/H2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/G5.png	RNA_Library_set81/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-25	BGHcLV49-26
RBP	DDX10	DDX10
Batch_ID	BGHcLV49	BGHcLV49
WB_result	91.900	82.672
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4782	4783

Sequencing Information

	BGHcLV49-25	BGHcLV49-26
Sample_ID	BGHcLV49-25	BGHcLV49-26
Sample Name	DDX10-BGHcLV49-25	DDX10-BGHcLV49-26
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	34,207,777	37,805,599
total_aligned_reads	28,401,681	31,066,571
unique_aligned_reads	26,747,769	29,239,877
percent_uniqueAligned	0.78192	0.77343
correlation_replicates	0.998285	0.998285
spikein_reads	103,470	133,416
percent_spikeins	0.00302	0.00353
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3509	3510

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
DDX10-BGHcLV49-25_S121_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3509	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33178
DDX10-BGHcLV49-25_S121_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3509	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33224
DDX10-BGHcLV49-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3509					GRCh38	V40	DDX10-BGHcLV49-25_S121_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGHcLV49-25_S121_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33270
DDX10-BGHcLV49-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3509					GRCh38	V40	DDX10-BGHcLV49-25_Aligned.sortedByCoord.out.bam		ENCORE2	33316
DDX10-BGHcLV49-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3509					GRCh38	V40	DDX10-BGHcLV49-25_Aligned.sortedByCoord.out.bam		ENCORE2	33362
DDX10-BGHcLV49-25_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3509					GRCh38	V40	DDX10-BGHcLV49-25_Aligned.sortedByCoord.out.bam		ENCORE2	33408
DDX10-BGHcLV49-25_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3509					GRCh38	V40	DDX10-BGHcLV49-25_Aligned.sortedByCoord.out.bam		ENCORE2	33454
DDX10-BGHcLV49-25_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3509					GRCh38	V40	DDX10-BGHcLV49-25_S121_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGHcLV49-25_S121_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33500
DDX10-BGHcLV49-26_S147_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3510	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33179
DDX10-BGHcLV49-26_S147_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3510	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33225
DDX10-BGHcLV49-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3510					GRCh38	V40	DDX10-BGHcLV49-26_S147_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGHcLV49-26_S147_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33271
DDX10-BGHcLV49-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3510					GRCh38	V40	DDX10-BGHcLV49-26_Aligned.sortedByCoord.out.bam		ENCORE2	33317
DDX10-BGHcLV49-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3510					GRCh38	V40	DDX10-BGHcLV49-26_Aligned.sortedByCoord.out.bam		ENCORE2	33363
DDX10-BGHcLV49-26_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3510					GRCh38	V40	DDX10-BGHcLV49-26_Aligned.sortedByCoord.out.bam		ENCORE2	33409
DDX10-BGHcLV49-26_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3510					GRCh38	V40	DDX10-BGHcLV49-26_Aligned.sortedByCoord.out.bam		ENCORE2	33455
DDX10-BGHcLV49-26_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3510					GRCh38	V40	DDX10-BGHcLV49-26_S147_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX10-BGHcLV49-26_S147_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33501