TPD52L2 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-69	BG293LV05-70
idx	0	0
TRCN#_or_BGC#	TRCN0000166214	TRCN0000166214
shRNA_or_gRNA_sequence	CCGGCTTGGAGACATGAGGAACTCTCTCGAGAGAGTTCCTCATGTCTCCAAGTTTTTTG	CCGGCTTGGAGACATGAGGAACTCTCTCGAGAGAGTTCCTCATGTCTCCAAGTTTTTTG
PAM
Name	TPD52L2	TPD52L2
Sample_ID	BG293LV05-69	BG293LV05-70
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	TPD52L2	TPD52L2
qPCR_result	98.6	97.4
Ave_qPCR	98
RT-qPCR_primer-F	aagacttcagctgccctgtc
RT-qPCR_primer-R	cttgaaggtcgcagagttcc
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	10041	10042

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-69	BG293LV05-70
Sample_ID	BG293LV05-69	BG293LV05-70
Sample Name
Sample Name	TPD52L2-BG293LV05-69	TPD52L2-BG293LV05-70
RBP	TPD52L2	TPD52L2
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12866	12867

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-69	BG293LV05-70
Sample #	33	34
Sample Name	TPD52L2-BG293LV05-69	TPD52L2-BG293LV05-70
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	267	267
Peak_Molarity	60.20	57.50
libSampleQC_DNA_Well	DNA_Library_set69/set1/A5.png	DNA_Library_set69/set1/B5.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set69/set1/C10.png	RNA_Library_set69/set1/D10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-69	BG293LV05-70
RBP	TPD52L2	TPD52L2
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4214	4215

Sequencing Information

	BG293LV05-69	BG293LV05-70
Sample_ID	BG293LV05-69	BG293LV05-70
Sample Name	TPD52L2-BG293LV05-69	TPD52L2-BG293LV05-70
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	27,214,159	19,776,597
total_aligned_reads	17,410,440	12,081,627
unique_aligned_reads	16,168,290	11,260,445
percent_uniqueAligned	0.59411	0.56938
correlation_replicates	0.983661	0.983661
spikein_reads	16,284	6,304
percent_spikeins	0.00060	0.00032
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2933	2934

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
TPD52L2-BG293LV05-69_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2933	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28527
TPD52L2-BG293LV05-69_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2933	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28571
TPD52L2-BG293LV05-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2933					GRCh38	V40	TPD52L2-BG293LV05-69_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV05-69_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28615
TPD52L2-BG293LV05-69_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2933					GRCh38	V40	TPD52L2-BG293LV05-69/Aligned.sortedByCoord.out.bam		ENCORE2	28659
TPD52L2-BG293LV05-69_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2933					GRCh38	V40	TPD52L2-BG293LV05-69/Aligned.sortedByCoord.out.bam		ENCORE2	28703
TPD52L2-BG293LV05-69_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2933					GRCh38	V40	TPD52L2-BG293LV05-69/Aligned.sortedByCoord.out.bam		ENCORE2	28747
TPD52L2-BG293LV05-69_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2933					GRCh38	V40	TPD52L2-BG293LV05-69/Aligned.sortedByCoord.out.bam		ENCORE2	28791
TPD52L2-BG293LV05-69_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2933					GRCh38	V40	TPD52L2-BG293LV05-69_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV05-69_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28835
TPD52L2-BG293LV05-70_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2934	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28528
TPD52L2-BG293LV05-70_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2934	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28572
TPD52L2-BG293LV05-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2934					GRCh38	V40	TPD52L2-BG293LV05-70_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV05-70_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28616
TPD52L2-BG293LV05-70_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2934					GRCh38	V40	TPD52L2-BG293LV05-70/Aligned.sortedByCoord.out.bam		ENCORE2	28660
TPD52L2-BG293LV05-70_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2934					GRCh38	V40	TPD52L2-BG293LV05-70/Aligned.sortedByCoord.out.bam		ENCORE2	28704
TPD52L2-BG293LV05-70_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2934					GRCh38	V40	TPD52L2-BG293LV05-70/Aligned.sortedByCoord.out.bam		ENCORE2	28748
TPD52L2-BG293LV05-70_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2934					GRCh38	V40	TPD52L2-BG293LV05-70/Aligned.sortedByCoord.out.bam		ENCORE2	28792
TPD52L2-BG293LV05-70_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2934					GRCh38	V40	TPD52L2-BG293LV05-70_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV05-70_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28836