DDX59 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-11dox	BGRSDLV04-12dox
idx	0	0
TRCN#_or_BGC#	TRCN0000050911	TRCN0000050911
shRNA_or_gRNA_sequence	CCACAGCTTTATCGTCTGCAA	CCACAGCTTTATCGTCTGCAA
PAM
Name	DDX59	DDX59
Sample_ID	BGRSDLV04-11dox	BGRSDLV04-12dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	DDX59	DDX59
qPCR_result	79.28119	82.063
Ave_qPCR	80.672095
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	9375	9376

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-11dox	BGRSDLV04-12dox
Sample_ID	BGRSDLV04-11dox	BGRSDLV04-12dox
Sample Name
Sample Name	DDX59-BGRSDLV04-11dox	DDX59-BGRSDLV04-12dox
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	12656	12657

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-11dox	BGRSDLV04-12dox
Sample #	11	12
Sample Name	DDX59-BGRSDLV04-11dox	DDX59-BGRSDLV04-12dox
Sample_Name_Alias
Index Well Position	C02	D02
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	292
Peak_Molarity	35.50	35.00
libSampleQC_DNA_Well	DNA_Library_set68/set1/C2.png	DNA_Library_set68/set1/D2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/C2.png	RNA_Library_set68/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-11dox	BGRSDLV04-12dox
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	4084	4085

Sequencing Information

	BGRSDLV04-11dox	BGRSDLV04-12dox
Sample_ID	BGRSDLV04-11dox	BGRSDLV04-12dox
Sample Name	DDX59-BGRSDLV04-11dox	DDX59-BGRSDLV04-12dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	40,490,045	34,511,010
total_aligned_reads	35,670,018	30,568,808
unique_aligned_reads	33,499,098	28,710,915
percent_uniqueAligned	0.82734	0.83193
correlation_replicates	0.999417	0.999417
spikein_reads	12,890	8,190
percent_spikeins	0.00032	0.00024
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2847	2848

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-BGRSDLV04-11dox_S11_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2847	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27634
DDX59-BGRSDLV04-11dox_S11_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2847	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27698
DDX59-BGRSDLV04-11dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2847					GRCh38	V40	DDX59-BGRSDLV04-11dox_S11_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-11dox_S11_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27762
DDX59-BGRSDLV04-11dox_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	2847					GRCh38	V40	DDX59-BGRSDLV04-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	27826
DDX59-BGRSDLV04-11dox_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	2847					GRCh38	V40	DDX59-BGRSDLV04-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	27890
DDX59-BGRSDLV04-11dox_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	2847					GRCh38	V40	DDX59-BGRSDLV04-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	27954
DDX59-BGRSDLV04-11dox_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	2847					GRCh38	V40	DDX59-BGRSDLV04-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	28018
DDX59-BGRSDLV04-11dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2847					GRCh38	V40	DDX59-BGRSDLV04-11dox_S11_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-11dox_S11_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28082
DDX59-BGRSDLV04-12dox_S12_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2848	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27635
DDX59-BGRSDLV04-12dox_S12_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2848	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27699
DDX59-BGRSDLV04-12dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2848					GRCh38	V40	DDX59-BGRSDLV04-12dox_S12_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-12dox_S12_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27763
DDX59-BGRSDLV04-12dox_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	2848					GRCh38	V40	DDX59-BGRSDLV04-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	27827
DDX59-BGRSDLV04-12dox_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	2848					GRCh38	V40	DDX59-BGRSDLV04-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	27891
DDX59-BGRSDLV04-12dox_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	2848					GRCh38	V40	DDX59-BGRSDLV04-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	27955
DDX59-BGRSDLV04-12dox_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	2848					GRCh38	V40	DDX59-BGRSDLV04-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	28019
DDX59-BGRSDLV04-12dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2848					GRCh38	V40	DDX59-BGRSDLV04-12dox_S12_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGRSDLV04-12dox_S12_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28083