CPSF6 RNA-Seq in K562

General Information


RBP	CPSF6
Cell_Line	K562
Method	shRNA
Exp_Name	CPSF6-BGKLV08-K562
ENCODE_series_ID
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR895BTE
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	CPSF6-LV08-7
Rep2	CPSF6-LV08-8
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	57.2
Rep2_qPCR	50.7
Rep1_WB	0.0
Rep2_WB	12.2
Antibody Cat#	A301-356A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB652TTL
Status	Archived
Project	ENCODE3
ID	282

Experiment Information (Status: Released)

	BGKLV08-7	BGKLV08-8
idx	8	9
TRCN#_or_BGC#	TRCN0000000151	TRCN0000000151
shRNA_or_gRNA_sequence	CTGGTGATTATGGGAGTGCTA	CTGGTGATTATGGGAGTGCTA
PAM
Name	CPSF6	CPSF6
Sample_ID	BGKLV08-7	BGKLV08-8
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	CPSF6	CPSF6
qPCR_result	57.2	50.7
Ave_qPCR	54.0
RT-qPCR_primer-F	TCTTTGCAAGATTGCCTTCA
RT-qPCR_primer-R	TCGTGATCTACTATGGTCCCTC
protein_conc	2650	2719
WB_result	0.0	12.2
Ave_WB	6.1
WB_DONE_date	4/17/2015
MW	59kDa
IP	1	1
antibody_Cat#	A301-356A	A301-356A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	45.3293322	0
Rep2_TPM	38.1645852	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	7	8

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-7	BGKLV08-8
Sample_ID	BGKLV08-7	BGKLV08-8
Sample Name	CPSF6-LV08-7	CPSF6-LV08-8
Sample Name	CPSF6-LV08-7	CPSF6-LV08-8
RBP	CPSF6	CPSF6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	272	273

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-7	BGKLV08-8
Sample #
Sample Name	CPSF6-BGKLV08-7	CPSF6-BGKLV08-8
Sample_Name_Alias	CPSF6-LV08-7	CPSF6-LV08-8
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set1/H1.png	DNA_Library_LV08/set1/A2.png
RIN	9.3	9.0
libSample_RNA_Well	RNA_Library_LV08/set1/G1.png	RNA_Library_LV08/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-7	BGKLV08-8
RBP	CPSF6	CPSF6
Batch_ID	BGKLV08	BGKLV08
WB_result	0.000	12.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1894	1895

Sequencing Information

	BGKLV08-7	BGKLV08-8
Sample_ID	BGKLV08-7	BGKLV08-8
Sample Name	CPSF6-LV08-7	CPSF6-LV08-8
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	60,200,000	50,880,000
total_aligned_reads	51,439,734	44,134,016
unique_aligned_reads	46,806,204	40,192,350
percent_uniqueAligned	0.77751	0.78994
correlation_replicates	0.998265	0.998265
spikein_reads	455,202	371,962
percent_spikeins	0.00756	0.00731
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	594	595

Data Submission Information

	BGKLV08-7
ENCODE_alias	brenton-graveley:CPSF6-LV08
ENCODE_accession	ENCSR895BTE
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKLV08-7
Sample Name	CPSF6-LV08-7
Selected	Yes
Status	Released
Status_Date	2014-08-13
Project	ENCODE3

protocol_URL
ID	2685

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
CPSF6-LV08-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	594					GRCh38	V40	CPSF6-LV08-7_CAGATC_L001_R1_001.fastq.gz,CPSF6-LV08-7_CAGATC_L001_R2_001.fastq.gz		ENCORE2	11979
CPSF6-LV08-7_CAGATC_L001_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	594	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12035
CPSF6-LV08-7_CAGATC_L001_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	594	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12091
CPSF6-LV08-7_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	594					GRCh38	V40	CPSF6-LV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	12147
CPSF6-LV08-7_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	594					GRCh38	V40	CPSF6-LV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	12203
CPSF6-LV08-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	594					GRCh38	V40	CPSF6-LV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	12259
CPSF6-LV08-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	594					GRCh38	V40	CPSF6-LV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	12315
CPSF6-LV08-7_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	594					GRCh38	V40	CPSF6-LV08-7_CAGATC_L001_R1_001.fastq.gz,CPSF6-LV08-7_CAGATC_L001_R2_001.fastq.gz		ENCORE2	13314
CPSF6-LV08-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	595					GRCh38	V40	CPSF6-LV08-8_ACTTGA_L002_R1_001.fastq.gz,CPSF6-LV08-8_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	11980
CPSF6-LV08-8_ACTTGA_L002_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	595	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12036
CPSF6-LV08-8_ACTTGA_L002_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	595	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12092
CPSF6-LV08-8_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	595					GRCh38	V40	CPSF6-LV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	12148
CPSF6-LV08-8_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	595					GRCh38	V40	CPSF6-LV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	12204
CPSF6-LV08-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	595					GRCh38	V40	CPSF6-LV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	12260
CPSF6-LV08-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	595					GRCh38	V40	CPSF6-LV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	12316
CPSF6-LV08-8_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	595					GRCh38	V40	CPSF6-LV08-8_ACTTGA_L002_R1_001.fastq.gz,CPSF6-LV08-8_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	13315