PRPF40A RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-35	BG293LV02-36
idx	0	0
TRCN#_or_BGC#	TRCN0000247663	TRCN0000247663
shRNA_or_gRNA_sequence	CCGGGCGATAATCAGTTCAACTAAACTCGAGTTTAGTTGAACTGATTATCGCTTTTTG	CCGGGCGATAATCAGTTCAACTAAACTCGAGTTTAGTTGAACTGATTATCGCTTTTTG
PAM
Name	PRPF40A	PRPF40A
Sample_ID	BG293LV02-35	BG293LV02-36
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	PRPF40A	PRPF40A
qPCR_result	90.9	82.1
Ave_qPCR	86.5
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	9830	9831

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-35	BG293LV02-36
Sample_ID	BG293LV02-35	BG293LV02-36
Sample Name
Sample Name	PRPF40A-BG293LV02-35	PRPF40A-BG293LV02-36
RBP	PRPF40A	PRPF40A
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11588	11589

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-35	BG293LV02-36
Sample #	31	32
Sample Name	PRPF40A-BG293LV02-35	PRPF40A-BG293LV02-36
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	284	284
Peak_Molarity	103.00	83.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/G4.png	DNA_Library_set60-62/set2/H4.png
RIN	9.8	9.4
libSample_RNA_Well	RNA_Library_set60-62/set1/G4.png	RNA_Library_set60-62/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-35	BG293LV02-36
RBP	PRPF40A	PRPF40A
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3618	3619

Sequencing Information

	BG293LV02-35	BG293LV02-36
Sample_ID	BG293LV02-35	BG293LV02-36
Sample Name	PRPF40A-BG293LV02-35	PRPF40A-BG293LV02-36
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	38,486,578	41,854,576
total_aligned_reads	34,177,649	34,605,860
unique_aligned_reads	31,887,348	32,113,877
percent_uniqueAligned	0.82853	0.76727
correlation_replicates	0.997377	0.997377
spikein_reads	61,478	87,200
percent_spikeins	0.00160	0.00208
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2489	2490

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
PRPF40A-BG293LV02-35_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2489	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7992
PRPF40A-BG293LV02-35_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2489	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8036
PRPF40A-BG293LV02-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2489					GRCh38	V40	PRPF40A-BG293LV02-35_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV02-35_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10785
PRPF40A-BG293LV02-35_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2489					GRCh38	V40	PRPF40A-BG293LV02-35/Aligned.sortedByCoord.out.bam		ENCORE2	10829
PRPF40A-BG293LV02-35_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2489					GRCh38	V40	PRPF40A-BG293LV02-35/Aligned.sortedByCoord.out.bam		ENCORE2	10873
PRPF40A-BG293LV02-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2489					GRCh38	V40	PRPF40A-BG293LV02-35/Aligned.sortedByCoord.out.bam		ENCORE2	10917
PRPF40A-BG293LV02-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2489					GRCh38	V40	PRPF40A-BG293LV02-35/Aligned.sortedByCoord.out.bam		ENCORE2	10961
PRPF40A-BG293LV02-35_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2489					GRCh38	V40	PRPF40A-BG293LV02-35_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV02-35_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11005
PRPF40A-BG293LV02-36_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2490	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7993
PRPF40A-BG293LV02-36_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2490	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8037
PRPF40A-BG293LV02-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2490					GRCh38	V40	PRPF40A-BG293LV02-36_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV02-36_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10786
PRPF40A-BG293LV02-36_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2490					GRCh38	V40	PRPF40A-BG293LV02-36/Aligned.sortedByCoord.out.bam		ENCORE2	10830
PRPF40A-BG293LV02-36_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2490					GRCh38	V40	PRPF40A-BG293LV02-36/Aligned.sortedByCoord.out.bam		ENCORE2	10874
PRPF40A-BG293LV02-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2490					GRCh38	V40	PRPF40A-BG293LV02-36/Aligned.sortedByCoord.out.bam		ENCORE2	10918
PRPF40A-BG293LV02-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2490					GRCh38	V40	PRPF40A-BG293LV02-36/Aligned.sortedByCoord.out.bam		ENCORE2	10962
PRPF40A-BG293LV02-36_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2490					GRCh38	V40	PRPF40A-BG293LV02-36_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV02-36_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11006