PRPF4 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-39	BG293LV05-40
idx	0	0
TRCN#_or_BGC#	TRCN0000074772	TRCN0000074772
shRNA_or_gRNA_sequence	CCGGGCAAAGTGATGGGCCTAGATACTCGAGTATCTAGGCCCATCACTTTGCTTTTTG	CCGGGCAAAGTGATGGGCCTAGATACTCGAGTATCTAGGCCCATCACTTTGCTTTTTG
PAM
Name	PRPF4	PRPF4
Sample_ID	BG293LV05-39	BG293LV05-40
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	PRPF4	PRPF4
qPCR_result	66.5	72.9
Ave_qPCR	69.7
RT-qPCR_primer-F	ctgcatcaggaaggccatag
RT-qPCR_primer-R	aaactcgaccaaatgcatcc
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	10011	10012

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-39	BG293LV05-40
Sample_ID	BG293LV05-39	BG293LV05-40
Sample Name
Sample Name	PRPF4-BG293LV05-39	PRPF4-BG293LV05-40
RBP	PRPF4	PRPF4
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12852	12853

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-39	BG293LV05-40
Sample #	19	20
Sample Name	PRPF4-BG293LV05-39	PRPF4-BG293LV05-40
Sample_Name_Alias
Index Well Position	C09	D09
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	277	271
Peak_Molarity	107.00	82.40
libSampleQC_DNA_Well	DNA_Library_set69/set1/C3.png	DNA_Library_set69/set1/D3.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set69/set1/D8.png	RNA_Library_set69/set1/E8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-39	BG293LV05-40
RBP	PRPF4	PRPF4
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	4200	4201

Sequencing Information

	BG293LV05-39	BG293LV05-40
Sample_ID	BG293LV05-39	BG293LV05-40
Sample Name	PRPF4-BG293LV05-39	PRPF4-BG293LV05-40
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	20,618,814	16,767,154
total_aligned_reads	17,670,770	14,352,476
unique_aligned_reads	16,467,945	13,334,446
percent_uniqueAligned	0.79869	0.79527
correlation_replicates	0.992713	0.992713
spikein_reads	3,300	1,342
percent_spikeins	0.00016	0.00008
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2919	2920

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
PRPF4-BG293LV05-39_S151_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2919	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	28517
PRPF4-BG293LV05-39_S151_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2919	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	28561
PRPF4-BG293LV05-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2919					GRCh38	V40	PRPF4-BG293LV05-39_S151_L002_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV05-39_S151_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28605
PRPF4-BG293LV05-39_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	2919					GRCh38	V40	PRPF4-BG293LV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	28649
PRPF4-BG293LV05-39_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	2919					GRCh38	V40	PRPF4-BG293LV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	28693
PRPF4-BG293LV05-39_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	2919					GRCh38	V40	PRPF4-BG293LV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	28737
PRPF4-BG293LV05-39_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	2919					GRCh38	V40	PRPF4-BG293LV05-39/Aligned.sortedByCoord.out.bam		ENCORE2	28781
PRPF4-BG293LV05-39_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2919					GRCh38	V40	PRPF4-BG293LV05-39_S151_L002_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV05-39_S151_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28825
PRPF4-BG293LV05-40_S152_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2920	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	28518
PRPF4-BG293LV05-40_S152_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2920	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	28562
PRPF4-BG293LV05-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2920					GRCh38	V40	PRPF4-BG293LV05-40_S152_L002_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV05-40_S152_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28606
PRPF4-BG293LV05-40_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	2920					GRCh38	V40	PRPF4-BG293LV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	28650
PRPF4-BG293LV05-40_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	2920					GRCh38	V40	PRPF4-BG293LV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	28694
PRPF4-BG293LV05-40_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	2920					GRCh38	V40	PRPF4-BG293LV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	28738
PRPF4-BG293LV05-40_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	2920					GRCh38	V40	PRPF4-BG293LV05-40/Aligned.sortedByCoord.out.bam		ENCORE2	28782
PRPF4-BG293LV05-40_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2920					GRCh38	V40	PRPF4-BG293LV05-40_S152_L002_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV05-40_S152_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28826