DDX59 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-9	BGRSDLV04-10
idx	0	0
TRCN#_or_BGC#	TRCN0000050911	TRCN0000050911
shRNA_or_gRNA_sequence	CCACAGCTTTATCGTCTGCAA	CCACAGCTTTATCGTCTGCAA
PAM
Name	DDX59	DDX59
Sample_ID	BGRSDLV04-9	BGRSDLV04-10
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	DDX59	DDX59
qPCR_result	74.80936	78.58847
Ave_qPCR	76.698915
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	9373	9374

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-9	BGRSDLV04-10
Sample_ID	BGRSDLV04-9	BGRSDLV04-10
Sample Name
Sample Name	DDX59-BGRSDLV04-9	DDX59-BGRSDLV04-10
RBP	DDX59	DDX59
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12654	12655

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-9	BGRSDLV04-10
Sample #	9	10
Sample Name	DDX59-BGRSDLV04-9	DDX59-BGRSDLV04-10
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	293	286
Peak_Molarity	27.10	43.50
libSampleQC_DNA_Well	DNA_Library_set68/set1/A2.png	DNA_Library_set68/set1/B2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set68/set1/A2.png	RNA_Library_set68/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-9	BGRSDLV04-10
RBP	DDX59	DDX59
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4082	4083

Sequencing Information

	BGRSDLV04-9	BGRSDLV04-10
Sample_ID	BGRSDLV04-9	BGRSDLV04-10
Sample Name	DDX59-BGRSDLV04-9	DDX59-BGRSDLV04-10
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	37,250,872	38,819,071
total_aligned_reads	31,059,957	33,136,764
unique_aligned_reads	29,098,076	31,062,844
percent_uniqueAligned	0.78114	0.80020
correlation_replicates	0.997062	0.997062
spikein_reads	20,212	14,304
percent_spikeins	0.00054	0.00037
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2845	2846

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-BGRSDLV04-9_S9_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2845	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27636
DDX59-BGRSDLV04-9_S9_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2845	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27700
DDX59-BGRSDLV04-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2845					GRCh38	V40	DDX59-BGRSDLV04-9_S9_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-9_S9_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27764
DDX59-BGRSDLV04-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2845					GRCh38	V40	DDX59-BGRSDLV04-9/Aligned.sortedByCoord.out.bam		ENCORE2	27828
DDX59-BGRSDLV04-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2845					GRCh38	V40	DDX59-BGRSDLV04-9/Aligned.sortedByCoord.out.bam		ENCORE2	27892
DDX59-BGRSDLV04-9_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2845					GRCh38	V40	DDX59-BGRSDLV04-9/Aligned.sortedByCoord.out.bam		ENCORE2	27956
DDX59-BGRSDLV04-9_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2845					GRCh38	V40	DDX59-BGRSDLV04-9/Aligned.sortedByCoord.out.bam		ENCORE2	28020
DDX59-BGRSDLV04-9_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2845					GRCh38	V40	DDX59-BGRSDLV04-9_S9_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-9_S9_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28084
DDX59-BGRSDLV04-10_S10_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2846	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27633
DDX59-BGRSDLV04-10_S10_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2846	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27697
DDX59-BGRSDLV04-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2846					GRCh38	V40	DDX59-BGRSDLV04-10_S10_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-10_S10_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27761
DDX59-BGRSDLV04-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2846					GRCh38	V40	DDX59-BGRSDLV04-10/Aligned.sortedByCoord.out.bam		ENCORE2	27825
DDX59-BGRSDLV04-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2846					GRCh38	V40	DDX59-BGRSDLV04-10/Aligned.sortedByCoord.out.bam		ENCORE2	27889
DDX59-BGRSDLV04-10_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2846					GRCh38	V40	DDX59-BGRSDLV04-10/Aligned.sortedByCoord.out.bam		ENCORE2	27953
DDX59-BGRSDLV04-10_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2846					GRCh38	V40	DDX59-BGRSDLV04-10/Aligned.sortedByCoord.out.bam		ENCORE2	28017
DDX59-BGRSDLV04-10_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2846					GRCh38	V40	DDX59-BGRSDLV04-10_S10_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-10_S10_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28081