DDX5 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-23	BG293LV04-24
idx	0	0
TRCN#_or_BGC#	TRCN0000272488	TRCN0000272488
shRNA_or_gRNA_sequence	CCGGGCTCCTATTCTGATTGCTACACTCGAGTGTAGCAATCAGAATAGGAGCTTTTTG	CCGGGCTCCTATTCTGATTGCTACACTCGAGTGTAGCAATCAGAATAGGAGCTTTTTG
PAM
Name	DDX5	DDX5
Sample_ID	BG293LV04-23	BG293LV04-24
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	DDX5	DDX5
qPCR_result	90.5	85.1
Ave_qPCR	87.8
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	9910	9911

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-23	BG293LV04-24
Sample_ID	BG293LV04-23	BG293LV04-24
Sample Name
Sample Name	DDX5-BG293LV04-23	DDX5-BG293LV04-24
RBP	DDX5	DDX5
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12520	12521

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-23	BG293LV04-24
Sample #	7	8
Sample Name	DDX5-BG293LV04-23	DDX5-BG293LV04-24
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-10	2023-10-10
Lib_ID	Lib-231010	Lib-231010
Tecan_Location
Tecan
Tecan_date
Size_bp	271	273
Peak_Molarity	65.30	52.40
libSampleQC_DNA_Well	DNA_Library_set64/set1/G9.png	DNA_Library_set64/set1/H9.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set64/set1/G5.png	RNA_Library_set64/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-23	BG293LV04-24
RBP	DDX5	DDX5
Batch_ID	BG293LV04	BG293LV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4012	4013

Sequencing Information

	BG293LV04-23	BG293LV04-24
Sample_ID	BG293LV04-23	BG293LV04-24
Sample Name	DDX5-BG293LV04-23	DDX5-BG293LV04-24
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	26,175,834	33,489,200
total_aligned_reads	24,022,935	31,369,296
unique_aligned_reads	22,285,240	29,224,003
percent_uniqueAligned	0.85137	0.87264
correlation_replicates	0.989145	0.989145
spikein_reads	15,796	20,862
percent_spikeins	0.00060	0.00062
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2621	2622

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
DDX5-BG293LV04-23_S7_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2621	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8684
DDX5-BG293LV04-23_S7_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2621	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8712
DDX5-BG293LV04-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2621					GRCh38	V40	DDX5-BG293LV04-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV04-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9761
DDX5-BG293LV04-23_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2621					GRCh38	V40	DDX5-BG293LV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	9789
DDX5-BG293LV04-23_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2621					GRCh38	V40	DDX5-BG293LV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	9817
DDX5-BG293LV04-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2621					GRCh38	V40	DDX5-BG293LV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	9845
DDX5-BG293LV04-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2621					GRCh38	V40	DDX5-BG293LV04-23/Aligned.sortedByCoord.out.bam		ENCORE2	9873
DDX5-BG293LV04-23_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2621					GRCh38	V40	DDX5-BG293LV04-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV04-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9901
DDX5-BG293LV04-24_S8_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2622	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8685
DDX5-BG293LV04-24_S8_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2622	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8713
DDX5-BG293LV04-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2622					GRCh38	V40	DDX5-BG293LV04-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV04-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9762
DDX5-BG293LV04-24_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2622					GRCh38	V40	DDX5-BG293LV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	9790
DDX5-BG293LV04-24_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2622					GRCh38	V40	DDX5-BG293LV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	9818
DDX5-BG293LV04-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2622					GRCh38	V40	DDX5-BG293LV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	9846
DDX5-BG293LV04-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2622					GRCh38	V40	DDX5-BG293LV04-24/Aligned.sortedByCoord.out.bam		ENCORE2	9874
DDX5-BG293LV04-24_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2622					GRCh38	V40	DDX5-BG293LV04-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BG293LV04-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9902