PRPF40A RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-107	BG293LV06-108
idx	0	0
TRCN#_or_BGC#	TRCN0000247663	TRCN0000247663
shRNA_or_gRNA_sequence	CCGGGCGATAATCAGTTCAACTAAACTCGAGTTTAGTTGAACTGATTATCGCTTTTTG	CCGGGCGATAATCAGTTCAACTAAACTCGAGTTTAGTTGAACTGATTATCGCTTTTTG
PAM
Name	PRPF40A	PRPF40A
Sample_ID	BG293LV06-107	BG293LV06-108
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	PRPF40A	PRPF40A
qPCR_result	85.9	84.3
Ave_qPCR	85.1
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	12242	12243

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-107	BG293LV06-107	BG293LV06-108	BG293LV06-108
Sample_ID	BG293LV06-107	BG293LV06-107	BG293LV06-108	BG293LV06-108
Sample Name
Sample Name	PRPF40A-BG293LV06-107B	PRPF40A-BG293LV06-107B	PRPF40A-BG293LV06-108B	PRPF40A-BG293LV06-108B
RBP	PRPF40A	PRPF40A	PRPF40A	PRPF40A
Cell_Line	293T	293T	293T	293T
Exp UID
Status	Released	Released	Released	Released
Status_date	2025-04-21	2025-04-21	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13544	13578	13545	13579

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-107	BG293LV06-107	BG293LV06-108	BG293LV06-108
Sample #	107	7	108	8
Sample Name	PRPF40A-BG293LV06-107B	PRPF40A-BG293LV06-107C	PRPF40A-BG293LV06-108B	PRPF40A-BG293LV06-108C
Sample_Name_Alias
Index Well Position	C07	G10	D07	H10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	274	288	277	282
Peak_Molarity	19.70	74.60	86.50	97.90
libSampleQC_DNA_Well	DNA_Library_set72/set1/C7.png	DNA_Library_set72/set1/C7.png	DNA_Library_set72/set1/D7.png	DNA_Library_set72/set1/D7.png
RIN	10.0	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_set72/set1/C7.png	RNA_Library_set72/set1/C7.png	RNA_Library_set72/set1/D7.png	RNA_Library_set72/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04	2024-10-04	2024-10-04
Sample_ID	BG293LV06-107	BG293LV06-107	BG293LV06-108	BG293LV06-108
RBP	PRPF40A	PRPF40A	PRPF40A	PRPF40A
Batch_ID	BG293LV06	BG293LV06	BG293LV06	BG293LV06
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	C	B	C
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	4532	4566	4533	4567

Sequencing Information

	BG293LV06-107	BG293LV06-107	BG293LV06-108	BG293LV06-108
Sample_ID	BG293LV06-107	BG293LV06-107	BG293LV06-108	BG293LV06-108
Sample Name	PRPF40A-BG293LV06-107B	PRPF40A-BG293LV06-107C	PRPF40A-BG293LV06-108B	PRPF40A-BG293LV06-108C
Pool ID	Pool-241004	Pool-241004	Pool-241004	Pool-241004
LocalServer_folder	set72	set72	set72	set72
total_reads	27,328,758	23,340,715	34,686,411	26,293,211
total_aligned_reads	24,853,569	21,712,813	30,806,337	24,354,163
unique_aligned_reads	23,147,578	20,172,398	28,683,053	22,688,270
percent_uniqueAligned	0.84700	0.86426	0.82692	0.86289
correlation_replicates	0.997677	0.997804	0.997677	0.997804
spikein_reads	129,930	51,424	144,324	57,066
percent_spikeins	0.00475	0.00220	0.00416	0.00217
original_ReadLength	101	101	101	101
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	3101	3135	3102	3136

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-BG293LV06-107B_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3101	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	29804
PRPF40A-BG293LV06-107B_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3101	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	29876
PRPF40A-BG293LV06-107B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3101					GRCh38	V40	PRPF40A-BG293LV06-107B_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV06-107B_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29948
PRPF40A-BG293LV06-107B_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	3101					GRCh38	V40	PRPF40A-BG293LV06-107B_Aligned.sortedByCoord.out.bam		ENCORE2	30020
PRPF40A-BG293LV06-107B_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	3101					GRCh38	V40	PRPF40A-BG293LV06-107B_Aligned.sortedByCoord.out.bam		ENCORE2	30092
PRPF40A-BG293LV06-107B_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	3101					GRCh38	V40	PRPF40A-BG293LV06-107B_Aligned.sortedByCoord.out.bam		ENCORE2	30164
PRPF40A-BG293LV06-107B_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	3101					GRCh38	V40	PRPF40A-BG293LV06-107B_Aligned.sortedByCoord.out.bam		ENCORE2	30236
PRPF40A-BG293LV06-107B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3101					GRCh38	V40	PRPF40A-BG293LV06-107B_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV06-107B_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30308
PRPF40A-BG293LV06-108B_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3102	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	29805
PRPF40A-BG293LV06-108B_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3102	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	29877
PRPF40A-BG293LV06-108B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3102					GRCh38	V40	PRPF40A-BG293LV06-108B_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV06-108B_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29949
PRPF40A-BG293LV06-108B_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	3102					GRCh38	V40	PRPF40A-BG293LV06-108B_Aligned.sortedByCoord.out.bam		ENCORE2	30021
PRPF40A-BG293LV06-108B_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	3102					GRCh38	V40	PRPF40A-BG293LV06-108B_Aligned.sortedByCoord.out.bam		ENCORE2	30093
PRPF40A-BG293LV06-108B_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	3102					GRCh38	V40	PRPF40A-BG293LV06-108B_Aligned.sortedByCoord.out.bam		ENCORE2	30165
PRPF40A-BG293LV06-108B_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	3102					GRCh38	V40	PRPF40A-BG293LV06-108B_Aligned.sortedByCoord.out.bam		ENCORE2	30237
PRPF40A-BG293LV06-108B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3102					GRCh38	V40	PRPF40A-BG293LV06-108B_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF40A-BG293LV06-108B_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30309