DDX17 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV03-9	BG293LV03-10
idx	0	0
TRCN#_or_BGC#	TRCN0000074389	TRCN0000074389
shRNA_or_gRNA_sequence	CCACAAGTTGATCCAACTAATCTCGAGATTAGTTGGATCAACTTGTGG	CCACAAGTTGATCCAACTAATCTCGAGATTAGTTGGATCAACTTGTGG
PAM
Name	DDX17	DDX17
Sample_ID	BG293LV03-9	BG293LV03-10
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	DDX17	DDX17
qPCR_result	78.1	79.1
Ave_qPCR	78.6
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	9859	9860

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV03-9	BG293LV03-10
Sample_ID	BG293LV03-9	BG293LV03-10
Sample Name
Sample Name	DDX17-BG293LV03-9	DDX17-BG293LV03-10
RBP	DDX17	DDX17
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11740	11741

Library-Prep
Sequencing

Library-Prep Information

	BG293LV03-9	BG293LV03-10
Sample #	5	6
Sample Name	DDX17-BG293LV03-9	DDX17-BG293LV03-10
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	292	288
Peak_Molarity	41.50	47.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/E1.png	DNA_Library_set60-62/set4/F1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/E1.png	RNA_Library_set60-62/set2/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BG293LV03-9	BG293LV03-10
RBP	DDX17	DDX17
Batch_ID	BG293LV03	BG293LV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3688	3689

Sequencing Information

	BG293LV03-9	BG293LV03-10
Sample_ID	BG293LV03-9	BG293LV03-10
Sample Name	DDX17-BG293LV03-9	DDX17-BG293LV03-10
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_W	set62_W
total_reads	48,182,704	36,735,870
total_aligned_reads	36,573,640	28,477,948
unique_aligned_reads	34,113,151	26,473,511
percent_uniqueAligned	0.70800	0.72064
correlation_replicates	0.996973	0.996973
spikein_reads	97,172	68,182
percent_spikeins	0.00202	0.00186
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2559	2560

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-BG293LV03-9_S5_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2559	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7845
DDX17-BG293LV03-9_S5_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2559	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7861
DDX17-BG293LV03-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2559					GRCh38	V40	DDX17-BG293LV03-9_S5_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV03-9_S5_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10086
DDX17-BG293LV03-9_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2559					GRCh38	V40	DDX17-BG293LV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	10102
DDX17-BG293LV03-9_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2559					GRCh38	V40	DDX17-BG293LV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	10118
DDX17-BG293LV03-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2559					GRCh38	V40	DDX17-BG293LV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	10134
DDX17-BG293LV03-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2559					GRCh38	V40	DDX17-BG293LV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	10150
DDX17-BG293LV03-9_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2559					GRCh38	V40	DDX17-BG293LV03-9_S5_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV03-9_S5_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10166
DDX17-BG293LV03-10_S6_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2560	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7844
DDX17-BG293LV03-10_S6_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2560	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7860
DDX17-BG293LV03-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2560					GRCh38	V40	DDX17-BG293LV03-10_S6_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV03-10_S6_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10085
DDX17-BG293LV03-10_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2560					GRCh38	V40	DDX17-BG293LV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	10101
DDX17-BG293LV03-10_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2560					GRCh38	V40	DDX17-BG293LV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	10117
DDX17-BG293LV03-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2560					GRCh38	V40	DDX17-BG293LV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	10133
DDX17-BG293LV03-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2560					GRCh38	V40	DDX17-BG293LV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	10149
DDX17-BG293LV03-10_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2560					GRCh38	V40	DDX17-BG293LV03-10_S6_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX17-BG293LV03-10_S6_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10165