TPD52L2 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-83	BG293LV06-84
idx	0	0
TRCN#_or_BGC#	TRCN0000166214	TRCN0000166214
shRNA_or_gRNA_sequence	CCGGCTTGGAGACATGAGGAACTCTCTCGAGAGAGTTCCTCATGTCTCCAAGTTTTTTG	CCGGCTTGGAGACATGAGGAACTCTCTCGAGAGAGTTCCTCATGTCTCCAAGTTTTTTG
PAM
Name	TPD52L2	TPD52L2
Sample_ID	BG293LV06-83	BG293LV06-84
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	TPD52L2	TPD52L2
qPCR_result	67.1	72.3
Ave_qPCR	69.7
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	12218	12219

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-83	BG293LV06-84
Sample_ID	BG293LV06-83	BG293LV06-84
Sample Name
Sample Name	TPD52L2-BG293LV06-83B	TPD52L2-BG293LV06-84B
RBP	TPD52L2	TPD52L2
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13520	13521

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-83	BG293LV06-84
Sample #	83	84
Sample Name	TPD52L2-BG293LV06-83B	TPD52L2-BG293LV06-84B
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	285	286
Peak_Molarity	89.00	92.10
libSampleQC_DNA_Well	DNA_Library_set72/set1/C4.png	DNA_Library_set72/set1/D4.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set72/set1/C4.png	RNA_Library_set72/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-83	BG293LV06-84
RBP	TPD52L2	TPD52L2
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4508	4509

Sequencing Information

	BG293LV06-83	BG293LV06-84
Sample_ID	BG293LV06-83	BG293LV06-84
Sample Name	TPD52L2-BG293LV06-83B	TPD52L2-BG293LV06-84B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	53,688,736	43,168,243
total_aligned_reads	49,969,305	39,486,670
unique_aligned_reads	46,987,237	37,111,394
percent_uniqueAligned	0.87518	0.85969
correlation_replicates	0.977742	0.977742
spikein_reads	240,152	168,912
percent_spikeins	0.00447	0.00391
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3077	3078

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-BG293LV06-83B_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3077	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29822
TPD52L2-BG293LV06-83B_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3077	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29894
TPD52L2-BG293LV06-83B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3077					GRCh38	V40	TPD52L2-BG293LV06-83B_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV06-83B_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29966
TPD52L2-BG293LV06-83B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3077					GRCh38	V40	TPD52L2-BG293LV06-83B_Aligned.sortedByCoord.out.bam		ENCORE2	30038
TPD52L2-BG293LV06-83B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3077					GRCh38	V40	TPD52L2-BG293LV06-83B_Aligned.sortedByCoord.out.bam		ENCORE2	30110
TPD52L2-BG293LV06-83B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3077					GRCh38	V40	TPD52L2-BG293LV06-83B_Aligned.sortedByCoord.out.bam		ENCORE2	30182
TPD52L2-BG293LV06-83B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3077					GRCh38	V40	TPD52L2-BG293LV06-83B_Aligned.sortedByCoord.out.bam		ENCORE2	30254
TPD52L2-BG293LV06-83B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3077					GRCh38	V40	TPD52L2-BG293LV06-83B_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV06-83B_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30326
TPD52L2-BG293LV06-84B_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3078	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29823
TPD52L2-BG293LV06-84B_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3078	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29895
TPD52L2-BG293LV06-84B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3078					GRCh38	V40	TPD52L2-BG293LV06-84B_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV06-84B_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29967
TPD52L2-BG293LV06-84B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3078					GRCh38	V40	TPD52L2-BG293LV06-84B_Aligned.sortedByCoord.out.bam		ENCORE2	30039
TPD52L2-BG293LV06-84B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3078					GRCh38	V40	TPD52L2-BG293LV06-84B_Aligned.sortedByCoord.out.bam		ENCORE2	30111
TPD52L2-BG293LV06-84B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3078					GRCh38	V40	TPD52L2-BG293LV06-84B_Aligned.sortedByCoord.out.bam		ENCORE2	30183
TPD52L2-BG293LV06-84B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3078					GRCh38	V40	TPD52L2-BG293LV06-84B_Aligned.sortedByCoord.out.bam		ENCORE2	30255
TPD52L2-BG293LV06-84B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3078					GRCh38	V40	TPD52L2-BG293LV06-84B_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,TPD52L2-BG293LV06-84B_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30327