DDX5 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-121	BG293LV06-122
idx	0	0
TRCN#_or_BGC#	TRCN0000272488	TRCN0000272488
shRNA_or_gRNA_sequence	CCGGGCTCCTATTCTGATTGCTACACTCGAGTGTAGCAATCAGAATAGGAGCTTTTTG	CCGGGCTCCTATTCTGATTGCTACACTCGAGTGTAGCAATCAGAATAGGAGCTTTTTG
PAM
Name	DDX5	DDX5
Sample_ID	BG293LV06-121	BG293LV06-122
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	DDX5	DDX5
qPCR_result	80.3	87.6
Ave_qPCR	84.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
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	12256	12257

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-121	BG293LV06-122
Sample_ID	BG293LV06-121	BG293LV06-122
Sample Name
Sample Name	DDX5-BG293LV06-121B	DDX5-BG293LV06-122B
RBP	DDX5	DDX5
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13558	13559

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-121	BG293LV06-122
Sample #	121	122
Sample Name	DDX5-BG293LV06-121B	DDX5-BG293LV06-122B
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	278	284
Peak_Molarity	106.00	93.20
libSampleQC_DNA_Well	DNA_Library_set72/set1/A9.png	DNA_Library_set72/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set72/set1/A9.png	RNA_Library_set72/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-121	BG293LV06-122
RBP	DDX5	DDX5
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4546	4547

Sequencing Information

	BG293LV06-121	BG293LV06-122
Sample_ID	BG293LV06-121	BG293LV06-122
Sample Name	DDX5-BG293LV06-121B	DDX5-BG293LV06-122B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	28,498,458	37,631,675
total_aligned_reads	26,786,891	35,804,502
unique_aligned_reads	24,901,253	33,592,600
percent_uniqueAligned	0.87378	0.89267
correlation_replicates	0.978945	0.978945
spikein_reads	135,548	216,178
percent_spikeins	0.00476	0.00574
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3115	3116

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
DDX5-BG293LV06-121B_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3115	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29774
DDX5-BG293LV06-121B_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3115	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29846
DDX5-BG293LV06-121B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3115					GRCh38	V40	DDX5-BG293LV06-121B_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV06-121B_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29918
DDX5-BG293LV06-121B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3115					GRCh38	V40	DDX5-BG293LV06-121B_Aligned.sortedByCoord.out.bam		ENCORE2	29990
DDX5-BG293LV06-121B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3115					GRCh38	V40	DDX5-BG293LV06-121B_Aligned.sortedByCoord.out.bam		ENCORE2	30062
DDX5-BG293LV06-121B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3115					GRCh38	V40	DDX5-BG293LV06-121B_Aligned.sortedByCoord.out.bam		ENCORE2	30134
DDX5-BG293LV06-121B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3115					GRCh38	V40	DDX5-BG293LV06-121B_Aligned.sortedByCoord.out.bam		ENCORE2	30206
DDX5-BG293LV06-121B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3115					GRCh38	V40	DDX5-BG293LV06-121B_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV06-121B_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30278
DDX5-BG293LV06-122B_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3116	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29775
DDX5-BG293LV06-122B_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3116	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29847
DDX5-BG293LV06-122B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3116					GRCh38	V40	DDX5-BG293LV06-122B_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV06-122B_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29919
DDX5-BG293LV06-122B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3116					GRCh38	V40	DDX5-BG293LV06-122B_Aligned.sortedByCoord.out.bam		ENCORE2	29991
DDX5-BG293LV06-122B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3116					GRCh38	V40	DDX5-BG293LV06-122B_Aligned.sortedByCoord.out.bam		ENCORE2	30063
DDX5-BG293LV06-122B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3116					GRCh38	V40	DDX5-BG293LV06-122B_Aligned.sortedByCoord.out.bam		ENCORE2	30135
DDX5-BG293LV06-122B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3116					GRCh38	V40	DDX5-BG293LV06-122B_Aligned.sortedByCoord.out.bam		ENCORE2	30207
DDX5-BG293LV06-122B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3116					GRCh38	V40	DDX5-BG293LV06-122B_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV06-122B_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30279