DDX17 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-115	BG293LV06-116
idx	0	0
TRCN#_or_BGC#	TRCN0000074389	TRCN0000074389
shRNA_or_gRNA_sequence	CCACAAGTTGATCCAACTAATCTCGAGATTAGTTGGATCAACTTGTGG	CCACAAGTTGATCCAACTAATCTCGAGATTAGTTGGATCAACTTGTGG
PAM
Name	DDX17	DDX17
Sample_ID	BG293LV06-115	BG293LV06-116
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	DDX17	DDX17
qPCR_result	95.5	95.6
Ave_qPCR	95.6
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	12250	12251

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-115	BG293LV06-116
Sample_ID	BG293LV06-115	BG293LV06-116
Sample Name
Sample Name	DDX17-BG293LV06-115B	DDX17-BG293LV06-116B
RBP	DDX17	DDX17
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13552	13553

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-115	BG293LV06-116
Sample #	115	116
Sample Name	DDX17-BG293LV06-115B	DDX17-BG293LV06-116B
Sample_Name_Alias
Index Well Position	C08	D08
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	287	293
Peak_Molarity	79.40	87.60
libSampleQC_DNA_Well	DNA_Library_set72/set1/C8.png	DNA_Library_set72/set1/D8.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set72/set1/C8.png	RNA_Library_set72/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-115	BG293LV06-116
RBP	DDX17	DDX17
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	4540	4541

Sequencing Information

	BG293LV06-115	BG293LV06-116
Sample_ID	BG293LV06-115	BG293LV06-116
Sample Name	DDX17-BG293LV06-115B	DDX17-BG293LV06-116B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	46,102,028	55,870,145
total_aligned_reads	42,848,156	52,935,601
unique_aligned_reads	39,995,249	49,638,671
percent_uniqueAligned	0.86754	0.88847
correlation_replicates	0.975947	0.975947
spikein_reads	179,136	202,798
percent_spikeins	0.00389	0.00363
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3109	3110

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
DDX17-BG293LV06-115B_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3109	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	29772
DDX17-BG293LV06-115B_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3109	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	29844
DDX17-BG293LV06-115B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3109					GRCh38	V40	DDX17-BG293LV06-115B_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV06-115B_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29916
DDX17-BG293LV06-115B_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	3109					GRCh38	V40	DDX17-BG293LV06-115B_Aligned.sortedByCoord.out.bam		ENCORE2	29988
DDX17-BG293LV06-115B_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	3109					GRCh38	V40	DDX17-BG293LV06-115B_Aligned.sortedByCoord.out.bam		ENCORE2	30060
DDX17-BG293LV06-115B_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	3109					GRCh38	V40	DDX17-BG293LV06-115B_Aligned.sortedByCoord.out.bam		ENCORE2	30132
DDX17-BG293LV06-115B_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	3109					GRCh38	V40	DDX17-BG293LV06-115B_Aligned.sortedByCoord.out.bam		ENCORE2	30204
DDX17-BG293LV06-115B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3109					GRCh38	V40	DDX17-BG293LV06-115B_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV06-115B_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30276
DDX17-BG293LV06-116B_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3110	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	29773
DDX17-BG293LV06-116B_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3110	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	29845
DDX17-BG293LV06-116B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3110					GRCh38	V40	DDX17-BG293LV06-116B_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV06-116B_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29917
DDX17-BG293LV06-116B_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	3110					GRCh38	V40	DDX17-BG293LV06-116B_Aligned.sortedByCoord.out.bam		ENCORE2	29989
DDX17-BG293LV06-116B_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	3110					GRCh38	V40	DDX17-BG293LV06-116B_Aligned.sortedByCoord.out.bam		ENCORE2	30061
DDX17-BG293LV06-116B_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	3110					GRCh38	V40	DDX17-BG293LV06-116B_Aligned.sortedByCoord.out.bam		ENCORE2	30133
DDX17-BG293LV06-116B_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	3110					GRCh38	V40	DDX17-BG293LV06-116B_Aligned.sortedByCoord.out.bam		ENCORE2	30205
DDX17-BG293LV06-116B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3110					GRCh38	V40	DDX17-BG293LV06-116B_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV06-116B_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30277