PRPF4 RNA-Seq in K562

General Information


RBP	PRPF4
Cell_Line	K562
Method	shRNA
Exp_Name	PRPF4-BGKLV38-K562
ENCODE_series_ID	ENCSR810PUY
Batch_ID	BGKLV38
Pool ID	Pool-180316
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR363QIA
ENCODE_CN_Exp_ID	ENCSR260BQC
Rep1	PRPF4-BGKLV38-63C
Rep2	PRPF4-BGKLV38-64C
CN1	NT-BGKLV38-1C
CN2	NT-BGKLV38-2C
Rep1_qPCR	76.9
Rep2_qPCR	76.0
Rep1_WB	71.0
Rep2_WB	63.1
Antibody Cat#	RN093PW
Antibody Lot#	RN093PW
Antibody DCC ID	ENCAB624FBH
Status	Released
Project	ENCODE4
ID	277

Experiment Information (Status: Released)

	BGKLV38-63	BGKLV38-64
idx	834	835
TRCN#_or_BGC#	TRCN0000074770	TRCN0000074770
shRNA_or_gRNA_sequence	CCTATCTCCTACTGTCACTTT	CCTATCTCCTACTGTCACTTT
PAM
Name	PRPF4	PRPF4
Sample_ID	BGKLV38-63	BGKLV38-64
transduction_Date	9/15/16	9/15/16
days
RBP_name	PRPF4	PRPF4
qPCR_result	76.9	76.0
Ave_qPCR	76.4
RT-qPCR_primer-F	ctgcatcaggaaggccatag
RT-qPCR_primer-R	aaactcgaccaaatgcatcc
protein_conc	2780	3634
WB_result	71.0	63.1
Ave_WB	67.0
WB_DONE_date	9/30/16	WES
MW	60kDa
IP	1	1
antibody_Cat#	RN093PW	RN093PW
Antibody DCC ID	ENCAB624FBH	ENCAB624FBH
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	12/19/17	12/19/17
repeat_library
Note
ID	931	932

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRPF4	Product_ID: RN093PW Lot_ID: 1 Source: MBLI Target Name: PRPF4-human

Experiment Status

	BGKLV38-63	BGKLV38-64
Sample_ID	BGKLV38-63	BGKLV38-64
Sample Name
Sample Name	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-64C
RBP	PRPF4	PRPF4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6479	6480

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-63	BGKLV38-64
Sample #	63	64
Sample Name	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-64C
Sample_Name_Alias
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	300	298
Peak_Molarity	16.40	18.20
libSampleQC_DNA_Well	DNA_Library_set40/set1/A10.png	DNA_Library_set40/set1/B10.png
RIN	8.8	8.9
libSample_RNA_Well	RNA_Library_set40/set1/A5.png	RNA_Library_set40/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV38-63	BGKLV38-64
RBP	PRPF4	PRPF4
Batch_ID	BGKLV38	BGKLV38
WB_result	71.000	63.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	986	987

Sequencing Information

	BGKLV38-63	BGKLV38-63	BGKLV38-64	BGKLV38-64
Sample_ID	BGKLV38-63	BGKLV38-63	BGKLV38-64	BGKLV38-64
Sample Name	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-64C	PRPF4-BGKLV38-64C
Pool ID	Pool-180109	Pool-180316	Pool-180109	Pool-180316
LocalServer_folder	set40_K	set40_K	set40_K	set40_K
total_reads	28,205,384	28,209,164	24,556,878	43,887,006
total_aligned_reads	19,444,494	19,411,704	18,105,742	32,265,642
unique_aligned_reads	17,692,296	17,682,196	16,445,638	29,406,828
percent_uniqueAligned	0.62727	0.62682	0.66970	0.67006
correlation_replicates	0.998890		0.998890
spikein_reads	9,536	9,382	13,524	24,000
percent_spikeins	0.00034	0.00033	0.00055	0.00055
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	389	408	390	409

Data Submission Information

	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-64	BGKLV38-64	BGKLV38-64	BGKLV38-64	BGKLV38-64	BGKLV38-64
ENCODE_alias	brenton-graveley:PRPF4-BGKLV38-C	brenton-graveley:PRPF4-BGKLV38-63C	brenton-graveley:L-PRPF4-BGKLV38-63C	brenton-graveley:PRPF4-BGKLV38-63C_GTCCGC_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:PRPF4-BGKLV38-63C_GTCCGC_AHFKCFBCX2_L001_001.R1.fastq.gz	brenton-graveley:PRPF4-BGKLV38-63C_GTCCGC_ACBYWVANXX_L005_001.R2.fastq.gz	brenton-graveley:PRPF4-BGKLV38-63C_GTCCGC_AHFKCFBCX2_L001_001.R2.fastq.gz	brenton-graveley:PRPF4-BGKLV38-K562	brenton-graveley:PRPF4-BGKLV38-64C	brenton-graveley:L-PRPF4-BGKLV38-64C	brenton-graveley:PRPF4-BGKLV38-64C_GTGAAA_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:PRPF4-BGKLV38-64C_GTGAAA_AHFKCFBCX2_L002_001.R1.fastq.gz	brenton-graveley:PRPF4-BGKLV38-64C_GTGAAA_ACBYWVANXX_L005_001.R2.fastq.gz	brenton-graveley:PRPF4-BGKLV38-64C_GTGAAA_AHFKCFBCX2_L002_001.R2.fastq.gz
ENCODE_accession	ENCSR363QIA	ENCBS780VTX	ENCLB331KSX	ENCFF404SZI	ENCFF698IDD	ENCFF582UDO	ENCFF489FFV	ENCSR810PUY	ENCBS437ESZ	ENCLB717XEG	ENCFF594HCT	ENCFF235UVM	ENCFF937SOU	ENCFF061CJM
object_type	experiment	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-63	BGKLV38-64	BGKLV38-64	BGKLV38-64	BGKLV38-64	BGKLV38-64	BGKLV38-64
Sample Name	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-63C	PRPF4-BGKLV38-64C	PRPF4-BGKLV38-64C	PRPF4-BGKLV38-64C	PRPF4-BGKLV38-64C	PRPF4-BGKLV38-64C	PRPF4-BGKLV38-64C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol						LV40_biosample_protocol	LV40_library_protocol
protocol_URL		PRPF4-BGKLV38-63C.pdf	L-PRPF4-BGKLV38-63C.pdf						PRPF4-BGKLV38-64C.pdf	L-PRPF4-BGKLV38-64C.pdf
ID	1448	1494	1550	1665	1666	1698	1699	7290	1495	1551	1667	1668	1700	1701

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-BGKLV38-63C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	389	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	23455
PRPF4-BGKLV38-63C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	389	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	23464
PRPF4-BGKLV38-63C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	389					GRCh38	V40	PRPF4-BGKLV38-63C_L001_001.R1.fastq.gz,PRPF4-BGKLV38-63C_L001_001.R2.fastq.gz		ENCORE2	23490
PRPF4-BGKLV38-63C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	389					GRCh38	V40	PRPF4-BGKLV38-63C/Aligned.sortedByCoord.out.bam		ENCORE2	23524
PRPF4-BGKLV38-63C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	389					GRCh38	V40	PRPF4-BGKLV38-63C/Aligned.sortedByCoord.out.bam		ENCORE2	23558
PRPF4-BGKLV38-63C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	389					GRCh38	V40	PRPF4-BGKLV38-63C/Aligned.sortedByCoord.out.bam		ENCORE2	23592
PRPF4-BGKLV38-63C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	389					GRCh38	V40	PRPF4-BGKLV38-63C/Aligned.sortedByCoord.out.bam		ENCORE2	23626
PRPF4-BGKLV38-63C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	389					GRCh38	V40	PRPF4-BGKLV38-63C_L001_001.R1.fastq.gz,PRPF4-BGKLV38-63C_L001_001.R2.fastq.gz		ENCORE2	23660
PRPF4-BGKLV38-64C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	390	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	23456
PRPF4-BGKLV38-64C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	390	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	23465
PRPF4-BGKLV38-64C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	390					GRCh38	V40	PRPF4-BGKLV38-64C_L001_001.R1.fastq.gz,PRPF4-BGKLV38-64C_L001_001.R2.fastq.gz		ENCORE2	23491
PRPF4-BGKLV38-64C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	390					GRCh38	V40	PRPF4-BGKLV38-64C/Aligned.sortedByCoord.out.bam		ENCORE2	23525
PRPF4-BGKLV38-64C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	390					GRCh38	V40	PRPF4-BGKLV38-64C/Aligned.sortedByCoord.out.bam		ENCORE2	23559
PRPF4-BGKLV38-64C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	390					GRCh38	V40	PRPF4-BGKLV38-64C/Aligned.sortedByCoord.out.bam		ENCORE2	23593
PRPF4-BGKLV38-64C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	390					GRCh38	V40	PRPF4-BGKLV38-64C/Aligned.sortedByCoord.out.bam		ENCORE2	23627
PRPF4-BGKLV38-64C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	390					GRCh38	V40	PRPF4-BGKLV38-64C_L001_001.R1.fastq.gz,PRPF4-BGKLV38-64C_L001_001.R2.fastq.gz		ENCORE2	23661