PRPF39 RNA-Seq in K562

General Information


RBP	PRPF39
Cell_Line	K562
Method	CRISPR
Exp_Name	PRPF39-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	PRPF39-BGKcLV44-45
Rep2	PRPF39-BGKcLV44-46
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	19.0
Rep2_qPCR	0.0
Rep1_WB	67.4
Rep2_WB	71.8
Antibody Cat#	PA5-21627
Antibody Lot#	UC2743613B
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1604

Experiment Information (Status: Submitting)

	BGKcLV44-45	BGKcLV44-46
idx	0	0
TRCN#_or_BGC#	BGC#0000451	BGC#0000451
shRNA_or_gRNA_sequence	GCCCAAAGCATATGCACCAT	GCCCAAAGCATATGCACCAT
PAM	GGG	GGG
Name	PRPF39_80	PRPF39_80
Sample_ID	BGKcLV44-45	BGKcLV44-46
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	PRPF39	PRPF39
qPCR_result	19.0	0.0
Ave_qPCR	9.5
RT-qPCR_primer-F	cttgaagattttggttccgatgt
RT-qPCR_primer-R	tgtgctttcttttcctctggt
protein_conc	4220	4355
WB_result	67.4	71.8
Ave_WB	69.6
WB_DONE_date	8/12/24,8/22/24	need discussion
MW	78KD
IP
antibody_Cat#	PA5-21627	UC2743613B
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	5924	5925

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRPF39	Product_ID: PA5-21627 Lot_ID: UC2743613B Source: Thermo Fisher Target Name: PRPF39-human

Experiment Status

	BGKcLV44-45	BGKcLV44-46
Sample_ID	BGKcLV44-45	BGKcLV44-46
Sample Name
Sample Name	PRPF39-BGKcLV44-45	PRPF39-BGKcLV44-46
RBP	PRPF39	PRPF39
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13600	13601

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-45	BGKcLV44-46
Sample #	29	30
Sample Name	PRPF39-BGKcLV44-45	PRPF39-BGKcLV44-46
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	300	291
Peak_Molarity	67.30	67.80
libSampleQC_DNA_Well	DNA_Library_set75/set1/E9.png	DNA_Library_set75/set1/F9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/E3.png	RNA_Library_set75/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-45	BGKcLV44-46
RBP	PRPF39	PRPF39
Batch_ID	BGKcLV44	BGKcLV44
WB_result	67.400	71.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4588	4589

Sequencing Information

	BGKcLV44-45	BGKcLV44-46
Sample_ID	BGKcLV44-45	BGKcLV44-46
Sample Name	PRPF39-BGKcLV44-45	PRPF39-BGKcLV44-46
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	41,584,202	35,860,243
total_aligned_reads	39,759,731	33,604,783
unique_aligned_reads	36,870,689	31,250,602
percent_uniqueAligned	0.88665	0.87146
correlation_replicates	0.997235	0.997235
spikein_reads	67,570	47,280
percent_spikeins	0.00162	0.00132
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3299	3300

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
PRPF39-BGKcLV44-45_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3299	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30956
PRPF39-BGKcLV44-45_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3299	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30998
PRPF39-BGKcLV44-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3299					GRCh38	V40	PRPF39-BGKcLV44-45_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGKcLV44-45_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31040
PRPF39-BGKcLV44-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3299					GRCh38	V40	PRPF39-BGKcLV44-45_Aligned.sortedByCoord.out.bam		ENCORE2	31082
PRPF39-BGKcLV44-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3299					GRCh38	V40	PRPF39-BGKcLV44-45_Aligned.sortedByCoord.out.bam		ENCORE2	31124
PRPF39-BGKcLV44-45_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3299					GRCh38	V40	PRPF39-BGKcLV44-45_Aligned.sortedByCoord.out.bam		ENCORE2	31166
PRPF39-BGKcLV44-45_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3299					GRCh38	V40	PRPF39-BGKcLV44-45_Aligned.sortedByCoord.out.bam		ENCORE2	31208
PRPF39-BGKcLV44-45_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3299					GRCh38	V40	PRPF39-BGKcLV44-45_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGKcLV44-45_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31250
PRPF39-BGKcLV44-46_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3300	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30957
PRPF39-BGKcLV44-46_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3300	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30999
PRPF39-BGKcLV44-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3300					GRCh38	V40	PRPF39-BGKcLV44-46_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGKcLV44-46_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31041
PRPF39-BGKcLV44-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3300					GRCh38	V40	PRPF39-BGKcLV44-46_Aligned.sortedByCoord.out.bam		ENCORE2	31083
PRPF39-BGKcLV44-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3300					GRCh38	V40	PRPF39-BGKcLV44-46_Aligned.sortedByCoord.out.bam		ENCORE2	31125
PRPF39-BGKcLV44-46_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3300					GRCh38	V40	PRPF39-BGKcLV44-46_Aligned.sortedByCoord.out.bam		ENCORE2	31167
PRPF39-BGKcLV44-46_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3300					GRCh38	V40	PRPF39-BGKcLV44-46_Aligned.sortedByCoord.out.bam		ENCORE2	31209
PRPF39-BGKcLV44-46_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3300					GRCh38	V40	PRPF39-BGKcLV44-46_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGKcLV44-46_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31251