DDX59 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-23	BGRSLV02-24
idx	0	0
TRCN#_or_BGC#	TRCN0000050911	TRCN0000050911
shRNA_or_gRNA_sequence	CCACAGCTTTATCGTCTGCAA	CCACAGCTTTATCGTCTGCAA
PAM
Name	DDX59	DDX59
Sample_ID	BGRSLV02-23	BGRSLV02-24
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	DDX59	DDX59
qPCR_result	58.3	64.2
Ave_qPCR	61.3
RT-qPCR_primer-F	ctctgtggtgtaaagattgtgg
RT-qPCR_primer-R	caagcacttgttgttgaaaacc
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	8260	8261

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-23	BGRSLV02-24
Sample_ID	BGRSLV02-23	BGRSLV02-24
Sample Name
Sample Name	DDX59-BGRSLV02-23	DDX59-BGRSLV02-24
RBP	DDX59	DDX59
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11310	11311

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-23	BGRSLV02-24
Sample #	13	14
Sample Name	DDX59-BGRSLV02-23	DDX59-BGRSLV02-24
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	289	290
Peak_Molarity	57.90	57.30
libSampleQC_DNA_Well	DNA_Library_set57/set1/E8.png	DNA_Library_set57/set1/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set57/set1/E2.png	RNA_Library_set57/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-23	BGRSLV02-24
RBP	DDX59	DDX59
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3474	3475

Sequencing Information

	BGRSLV02-23	BGRSLV02-24
Sample_ID	BGRSLV02-23	BGRSLV02-24
Sample Name	DDX59-BGRSLV02-23	DDX59-BGRSLV02-24
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	48,019,459	45,307,097
total_aligned_reads	44,415,010	42,297,010
unique_aligned_reads	41,194,658	39,112,580
percent_uniqueAligned	0.85787	0.86328
correlation_replicates	0.996718	0.996718
spikein_reads	27,664	26,290
percent_spikeins	0.00058	0.00058
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2345	2346

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
DDX59-BGRSLV02-23_S101_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2345	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8214
DDX59-BGRSLV02-23_S101_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2345	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8260
DDX59-BGRSLV02-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2345					GRCh38	V40	DDX59-BGRSLV02-23_S101_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSLV02-23_S101_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11503
DDX59-BGRSLV02-23_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2345					GRCh38	V40	DDX59-BGRSLV02-23/Aligned.sortedByCoord.out.bam		ENCORE2	11549
DDX59-BGRSLV02-23_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2345					GRCh38	V40	DDX59-BGRSLV02-23/Aligned.sortedByCoord.out.bam		ENCORE2	11595
DDX59-BGRSLV02-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2345					GRCh38	V40	DDX59-BGRSLV02-23/Aligned.sortedByCoord.out.bam		ENCORE2	11641
DDX59-BGRSLV02-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2345					GRCh38	V40	DDX59-BGRSLV02-23/Aligned.sortedByCoord.out.bam		ENCORE2	11687
DDX59-BGRSLV02-23_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2345					GRCh38	V40	DDX59-BGRSLV02-23_S101_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSLV02-23_S101_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11733
DDX59-BGRSLV02-24_S102_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2346	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8215
DDX59-BGRSLV02-24_S102_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2346	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8261
DDX59-BGRSLV02-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2346					GRCh38	V40	DDX59-BGRSLV02-24_S102_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSLV02-24_S102_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11504
DDX59-BGRSLV02-24_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2346					GRCh38	V40	DDX59-BGRSLV02-24/Aligned.sortedByCoord.out.bam		ENCORE2	11550
DDX59-BGRSLV02-24_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2346					GRCh38	V40	DDX59-BGRSLV02-24/Aligned.sortedByCoord.out.bam		ENCORE2	11596
DDX59-BGRSLV02-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2346					GRCh38	V40	DDX59-BGRSLV02-24/Aligned.sortedByCoord.out.bam		ENCORE2	11642
DDX59-BGRSLV02-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2346					GRCh38	V40	DDX59-BGRSLV02-24/Aligned.sortedByCoord.out.bam		ENCORE2	11688
DDX59-BGRSLV02-24_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2346					GRCh38	V40	DDX59-BGRSLV02-24_S102_L003_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSLV02-24_S102_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11734