DDX50 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-35	BGHcLV49-36
idx	1734	1735
TRCN#_or_BGC#	BGC#0000901	BGC#0000901
shRNA_or_gRNA_sequence	GCTCCATAATGTCCCCCCAG	GCTCCATAATGTCCCCCCAG
PAM	agg	agg
Name	DDX50_74	DDX50_74
Sample_ID	BGHcLV49-35	BGHcLV49-36
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	DDX50	DDX50
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	tgccatccccttaattgaaa
RT-qPCR_primer-R	gccacgctgagtttcctagt
protein_conc	5016	5827
WB_result	50.5	49.6
Ave_WB
WB_DONE_date	6/19/25,6/27/25
MW	83KD
IP
antibody_Cat#	A301-312A	lot # 1
Antibody DCC ID	ENCAB756NJZ
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9923	9924

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX50	Product_ID: A301-312A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX50-human

Experiment Status

	BGHcLV49-35	BGHcLV49-36
Sample_ID	BGHcLV49-35	BGHcLV49-36
Sample Name
Sample Name	DDX50-BGHcLV49-35	DDX50-BGHcLV49-36
RBP	DDX50	DDX50
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14342	14343

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-35	BGHcLV49-36
Sample #	39	40
Sample Name	DDX50-BGHcLV49-35	DDX50-BGHcLV49-36
Sample_Name_Alias
Index Well Position	A06	B06
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	261	273
Peak_Molarity	78.20	65.70
libSampleQC_DNA_Well	DNA_Library_set81/set1/A3.png	DNA_Library_set81/set1/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/A6.png	RNA_Library_set81/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-35	BGHcLV49-36
RBP	DDX50	DDX50
Batch_ID	BGHcLV49	BGHcLV49
WB_result	50.500	49.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4784	4785

Sequencing Information

	BGHcLV49-35	BGHcLV49-36
Sample_ID	BGHcLV49-35	BGHcLV49-36
Sample Name	DDX50-BGHcLV49-35	DDX50-BGHcLV49-36
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	34,436,164	23,385,151
total_aligned_reads	29,397,805	19,983,292
unique_aligned_reads	27,672,079	18,869,330
percent_uniqueAligned	0.80358	0.80689
correlation_replicates	0.996083	0.996083
spikein_reads	134,974	79,672
percent_spikeins	0.00392	0.00341
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3511	3512

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
DDX50-BGHcLV49-35_S133_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3511	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	33180
DDX50-BGHcLV49-35_S133_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3511	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	33226
DDX50-BGHcLV49-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3511					GRCh38	V40	DDX50-BGHcLV49-35_S133_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGHcLV49-35_S133_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33272
DDX50-BGHcLV49-35_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	3511					GRCh38	V40	DDX50-BGHcLV49-35_Aligned.sortedByCoord.out.bam		ENCORE2	33318
DDX50-BGHcLV49-35_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	3511					GRCh38	V40	DDX50-BGHcLV49-35_Aligned.sortedByCoord.out.bam		ENCORE2	33364
DDX50-BGHcLV49-35_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	3511					GRCh38	V40	DDX50-BGHcLV49-35_Aligned.sortedByCoord.out.bam		ENCORE2	33410
DDX50-BGHcLV49-35_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	3511					GRCh38	V40	DDX50-BGHcLV49-35_Aligned.sortedByCoord.out.bam		ENCORE2	33456
DDX50-BGHcLV49-35_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3511					GRCh38	V40	DDX50-BGHcLV49-35_S133_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGHcLV49-35_S133_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33502
DDX50-BGHcLV49-36_S142_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3512	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	33181
DDX50-BGHcLV49-36_S142_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3512	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	33227
DDX50-BGHcLV49-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3512					GRCh38	V40	DDX50-BGHcLV49-36_S142_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGHcLV49-36_S142_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33273
DDX50-BGHcLV49-36_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	3512					GRCh38	V40	DDX50-BGHcLV49-36_Aligned.sortedByCoord.out.bam		ENCORE2	33319
DDX50-BGHcLV49-36_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	3512					GRCh38	V40	DDX50-BGHcLV49-36_Aligned.sortedByCoord.out.bam		ENCORE2	33365
DDX50-BGHcLV49-36_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	3512					GRCh38	V40	DDX50-BGHcLV49-36_Aligned.sortedByCoord.out.bam		ENCORE2	33411
DDX50-BGHcLV49-36_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	3512					GRCh38	V40	DDX50-BGHcLV49-36_Aligned.sortedByCoord.out.bam		ENCORE2	33457
DDX50-BGHcLV49-36_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3512					GRCh38	V40	DDX50-BGHcLV49-36_S142_L008_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGHcLV49-36_S142_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33503