PRPF6 RNA-Seq in K562

General Information


RBP	PRPF6
Cell_Line	K562
Method	shRNA
Exp_Name	PRPF6-BGKLV13-K562
ENCODE_series_ID	ENCSR985AIG
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR783LUA
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	PRPF6_BGKLV13_9
Rep2	PRPF6_BGKLV13_10
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	62.0
Rep2_qPCR	73.2
Rep1_WB	85.5
Rep2_WB	86.8
Antibody Cat#	A302-773A
Antibody Lot#	A302-773A
Antibody DCC ID	ENCAB729OTZ
Status	Released
Project	ENCODE3
ID	362

Experiment Information (Status: Released)

	BGKLV13-9	BGKLV13-10
idx	142	143
TRCN#_or_BGC#	TRCN0000074634	TRCN0000074634
shRNA_or_gRNA_sequence	GCGTACTTCGAGAAGAACCAT	GCGTACTTCGAGAAGAACCAT
PAM
Name	PRPF6	PRPF6
Sample_ID	BGKLV13-9	BGKLV13-10
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	PRPF6	PRPF6
qPCR_result	62.0	73.2
Ave_qPCR	67.6
RT-qPCR_primer-F	gttggggaccagatgaagaa
RT-qPCR_primer-R	gagaagaggctcccagcata
protein_conc	2006	2067
WB_result	85.5	86.8
Ave_WB	86.2
WB_DONE_date
MW	107kDa
IP	1	1
antibody_Cat#	A302-773A	A302-773A
Antibody DCC ID	ENCAB729OTZ	ENCAB729OTZ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	67.1082594	0
Rep2_TPM	75.334806	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	157	158

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRPF6	Product_ID: A302-773A Lot_ID: 1 Source: Bethyl Labs Target Name: PRPF6-human

Experiment Status

	BGKLV13-9	BGKLV13-10
Sample_ID	BGKLV13-9	BGKLV13-10
Sample Name	PRPF6_BGKLV13_9	PRPF6_BGKLV13_10
Sample Name	PRPF6_BGKLV13_9	PRPF6_BGKLV13_10
RBP	PRPF6	PRPF6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	465	464

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-9	BGKLV13-10
Sample #
Sample Name	PRPF6-BGKLV13-9	PRPF6-BGKLV13-10
Sample_Name_Alias	PRPF6_BGKLV13_9	PRPF6_BGKLV13_10
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/H1.png	DNA_Library_LV13-14/set1/A2.png
RIN	9.6	9.2
libSample_RNA_Well	RNA_Library_LV12/set1/C10.png	RNA_Library_LV12/set1/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-9	BGKLV13-10
RBP	PRPF6	PRPF6
Batch_ID	BGKLV13	BGKLV13
WB_result	85.500	86.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2126	2127

Sequencing Information

	BGKLV13-9	BGKLV13-10
Sample_ID	BGKLV13-9	BGKLV13-10
Sample Name	PRPF6_BGKLV13_9	PRPF6_BGKLV13_10
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	51,050,000	51,750,000
total_aligned_reads	47,323,190	48,342,808
unique_aligned_reads	43,569,190	44,435,224
percent_uniqueAligned	0.85346	0.85865
correlation_replicates	0.998903	0.998903
spikein_reads	220,074	192,412
percent_spikeins	0.00431	0.00372
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	768	769

Data Submission Information

	BGKLV13-9	BGKLV13-9
ENCODE_alias	brenton-graveley:PRPF6_BGKLV13	brenton-graveley:PRPF6-BGKLV13-K562
ENCODE_accession	ENCSR783LUA	ENCSR985AIG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-9	BGKLV13-9
Sample Name	PRPF6_BGKLV13_9	PRPF6_BGKLV13_9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2781	6869

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
PRPF6_BGKLV13_9_CAGATC_L001_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	768	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13393
PRPF6_BGKLV13_9_CAGATC_L001_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	768	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13445
PRPF6_BGKLV13_9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	768					GRCh38	V40	PRPF6_BGKLV13_9_CAGATC_L001_R1_001.fastq.gz,PRPF6_BGKLV13_9_CAGATC_L001_R2_001.fastq.gz		ENCORE2	13497
PRPF6_BGKLV13_9_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	768					GRCh38	V40	PRPF6_BGKLV13_9/Aligned.sortedByCoord.out.bam		ENCORE2	13549
PRPF6_BGKLV13_9_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	768					GRCh38	V40	PRPF6_BGKLV13_9/Aligned.sortedByCoord.out.bam		ENCORE2	13601
PRPF6_BGKLV13_9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	768					GRCh38	V40	PRPF6_BGKLV13_9/Aligned.sortedByCoord.out.bam		ENCORE2	13653
PRPF6_BGKLV13_9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	768					GRCh38	V40	PRPF6_BGKLV13_9/Aligned.sortedByCoord.out.bam		ENCORE2	13705
PRPF6_BGKLV13_9_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	768					GRCh38	V40	PRPF6_BGKLV13_9_CAGATC_L001_R1_001.fastq.gz,PRPF6_BGKLV13_9_CAGATC_L001_R2_001.fastq.gz		ENCORE2	13757
PRPF6_BGKLV13_10_ACTTGA_L002_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	769	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13392
PRPF6_BGKLV13_10_ACTTGA_L002_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	769	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13444
PRPF6_BGKLV13_10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	769					GRCh38	V40	PRPF6_BGKLV13_10_ACTTGA_L002_R1_001.fastq.gz,PRPF6_BGKLV13_10_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	13496
PRPF6_BGKLV13_10_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	769					GRCh38	V40	PRPF6_BGKLV13_10/Aligned.sortedByCoord.out.bam		ENCORE2	13548
PRPF6_BGKLV13_10_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	769					GRCh38	V40	PRPF6_BGKLV13_10/Aligned.sortedByCoord.out.bam		ENCORE2	13600
PRPF6_BGKLV13_10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	769					GRCh38	V40	PRPF6_BGKLV13_10/Aligned.sortedByCoord.out.bam		ENCORE2	13652
PRPF6_BGKLV13_10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	769					GRCh38	V40	PRPF6_BGKLV13_10/Aligned.sortedByCoord.out.bam		ENCORE2	13704
PRPF6_BGKLV13_10_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	769					GRCh38	V40	PRPF6_BGKLV13_10_ACTTGA_L002_R1_001.fastq.gz,PRPF6_BGKLV13_10_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	13756