PRPF4 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-69	BG293LV06-70
idx	0	0
TRCN#_or_BGC#	TRCN0000074772	TRCN0000074772
shRNA_or_gRNA_sequence	CCGGGCAAAGTGATGGGCCTAGATACTCGAGTATCTAGGCCCATCACTTTGCTTTTTG	CCGGGCAAAGTGATGGGCCTAGATACTCGAGTATCTAGGCCCATCACTTTGCTTTTTG
PAM
Name	PRPF4	PRPF4
Sample_ID	BG293LV06-69	BG293LV06-70
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	PRPF4	PRPF4
qPCR_result	69.1	65.6
Ave_qPCR	67.3
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	12204	12205

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-69	BG293LV06-70
Sample_ID	BG293LV06-69	BG293LV06-70
Sample Name
Sample Name	PRPF4-BG293LV06-69B	PRPF4-BG293LV06-70B
RBP	PRPF4	PRPF4
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13506	13507

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-69	BG293LV06-70
Sample #	71	72
Sample Name	PRPF4-BG293LV06-69B	PRPF4-BG293LV06-70B
Sample_Name_Alias
Index Well Position	G02	H02
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	276	285
Peak_Molarity	74.00	59.10
libSampleQC_DNA_Well	DNA_Library_set72/set1/H2.png	DNA_Library_set72/set1/G2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set72/set1/G2.png	RNA_Library_set72/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-69	BG293LV06-70
RBP	PRPF4	PRPF4
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	4496	4497

Sequencing Information

	BG293LV06-69	BG293LV06-70
Sample_ID	BG293LV06-69	BG293LV06-70
Sample Name	PRPF4-BG293LV06-69B	PRPF4-BG293LV06-70B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	31,623,135	36,165,736
total_aligned_reads	29,154,667	33,553,012
unique_aligned_reads	26,959,335	31,438,889
percent_uniqueAligned	0.85252	0.86930
correlation_replicates	0.925375	0.925375
spikein_reads	99,726	176,342
percent_spikeins	0.00315	0.00488
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3065	3066

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-BG293LV06-69B_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3065	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	29806
PRPF4-BG293LV06-69B_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3065	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	29878
PRPF4-BG293LV06-69B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3065					GRCh38	V40	PRPF4-BG293LV06-69B_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV06-69B_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29950
PRPF4-BG293LV06-69B_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	3065					GRCh38	V40	PRPF4-BG293LV06-69B_Aligned.sortedByCoord.out.bam		ENCORE2	30022
PRPF4-BG293LV06-69B_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	3065					GRCh38	V40	PRPF4-BG293LV06-69B_Aligned.sortedByCoord.out.bam		ENCORE2	30094
PRPF4-BG293LV06-69B_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	3065					GRCh38	V40	PRPF4-BG293LV06-69B_Aligned.sortedByCoord.out.bam		ENCORE2	30166
PRPF4-BG293LV06-69B_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	3065					GRCh38	V40	PRPF4-BG293LV06-69B_Aligned.sortedByCoord.out.bam		ENCORE2	30238
PRPF4-BG293LV06-69B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3065					GRCh38	V40	PRPF4-BG293LV06-69B_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV06-69B_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30310
PRPF4-BG293LV06-70B_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3066	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	29807
PRPF4-BG293LV06-70B_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3066	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	29879
PRPF4-BG293LV06-70B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3066					GRCh38	V40	PRPF4-BG293LV06-70B_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV06-70B_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29951
PRPF4-BG293LV06-70B_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	3066					GRCh38	V40	PRPF4-BG293LV06-70B_Aligned.sortedByCoord.out.bam		ENCORE2	30023
PRPF4-BG293LV06-70B_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	3066					GRCh38	V40	PRPF4-BG293LV06-70B_Aligned.sortedByCoord.out.bam		ENCORE2	30095
PRPF4-BG293LV06-70B_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	3066					GRCh38	V40	PRPF4-BG293LV06-70B_Aligned.sortedByCoord.out.bam		ENCORE2	30167
PRPF4-BG293LV06-70B_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	3066					GRCh38	V40	PRPF4-BG293LV06-70B_Aligned.sortedByCoord.out.bam		ENCORE2	30239
PRPF4-BG293LV06-70B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3066					GRCh38	V40	PRPF4-BG293LV06-70B_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BG293LV06-70B_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30311