CPSF7 RNA-Seq in K562

General Information


RBP	CPSF7
Cell_Line	K562
Method	shRNA
Exp_Name	CPSF7-BGKLV24-K562
ENCODE_series_ID	ENCSR664RDU
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR222LRL
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	CPSF7_BGKLV24_9_17600
Rep2	CPSF7_BGKLV24_10_17601
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	54.6
Rep2_qPCR	44.7
Rep1_WB	70.7
Rep2_WB	69.7
Antibody Cat#	A301-359A
Antibody Lot#	A301-359A
Antibody DCC ID	ENCAB161FJH
Status	Archived
Project	ENCODE3
ID	557

Experiment Information (Status: Released)

	BGKLV24-9	BGKLV24-10
idx	346	347
TRCN#_or_BGC#	TRCN0000161936	TRCN0000161936
shRNA_or_gRNA_sequence	GATCCAGGTTATTCGCTCTAT	GATCCAGGTTATTCGCTCTAT
PAM
Name	CPSF7	CPSF7
Sample_ID	BGKLV24-9	BGKLV24-10
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	CPSF7	CPSF7
qPCR_result	54.6	44.7
Ave_qPCR	49.7
RT-qPCR_primer-F	agccatgtcagaaggagtgg
RT-qPCR_primer-R	gtggctgtcagcacatcatc
protein_conc	3914	3303
WB_result	70.7	69.7
Ave_WB	70.2
WB_DONE_date	4/15/2015
MW	52kDa
IP	1	1
antibody_Cat#	A301-359A	A301-359A
Antibody DCC ID	ENCAB161FJH	ENCAB161FJH
submitted_to_DCC_date	5/4/2015
Rep1_TPM	15.8886369	0
Rep2_TPM	15.5570641	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	393	394

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV24-9	BGKLV24-10
Sample_ID	BGKLV24-9	BGKLV24-10
Sample Name	CPSF7_BGKLV24_9_17600	CPSF7_BGKLV24_10_17601
Sample Name	CPSF7_BGKLV24_9_17600	CPSF7_BGKLV24_10_17601
RBP	CPSF7	CPSF7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	853	852

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-9	BGKLV24-10
Sample #
Sample Name	CPSF7-BGKLV24-9	CPSF7-BGKLV24-10
Sample_Name_Alias	CPSF7_BGKLV24_9_17600	CPSF7_BGKLV24_10_17601
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/H1.png	DNA_Library_LV21-24/set1/A2.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E1.png	RNA_Library_LV20-22-24/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-9	BGKLV24-10
RBP	CPSF7	CPSF7
Batch_ID	BGKLV24	BGKLV24
WB_result	70.700	69.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2541	2540

Sequencing Information

	BGKLV24-9	BGKLV24-10
Sample_ID	BGKLV24-9	BGKLV24-10
Sample Name	CPSF7_BGKLV24_9_17600	CPSF7_BGKLV24_10_17601
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	37,230,000	39,700,000
total_aligned_reads	34,528,230	36,452,994
unique_aligned_reads	31,651,514	33,260,752
percent_uniqueAligned	0.85016	0.83780
correlation_replicates	0.946959	0.946959
spikein_reads	166,086	141,152
percent_spikeins	0.00446	0.00356
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1075	1074

Data Submission Information

	BGKLV24-9	BGKLV24-9
ENCODE_alias	brenton-graveley:CPSF7_BGKLV24	brenton-graveley:CPSF7-BGKLV24-K562
ENCODE_accession	ENCSR222LRL	ENCSR664RDU
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-9	BGKLV24-9
Sample Name	CPSF7_BGKLV24_9_17600	CPSF7_BGKLV24_9_17600
Selected	Yes	No
Status	Released	Archived
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2977	6629

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
CPSF7_BGKLV24_9_17600_ACTGAT_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1075	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17187
CPSF7_BGKLV24_9_17600_ACTGAT_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1075	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17223
CPSF7_BGKLV24_9_17600_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1075					GRCh38	V40	CPSF7_BGKLV24_9_17600_ACTGAT_L005_R1_001.fastq.gz,CPSF7_BGKLV24_9_17600_ACTGAT_L005_R2_001.fastq.gz		ENCORE2	17259
CPSF7_BGKLV24_9_17600_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1075					GRCh38	V40	CPSF7_BGKLV24_9_17600/Aligned.sortedByCoord.out.bam		ENCORE2	17295
CPSF7_BGKLV24_9_17600_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1075					GRCh38	V40	CPSF7_BGKLV24_9_17600/Aligned.sortedByCoord.out.bam		ENCORE2	17331
CPSF7_BGKLV24_9_17600_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1075					GRCh38	V40	CPSF7_BGKLV24_9_17600/Aligned.sortedByCoord.out.bam		ENCORE2	17367
CPSF7_BGKLV24_9_17600_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1075					GRCh38	V40	CPSF7_BGKLV24_9_17600/Aligned.sortedByCoord.out.bam		ENCORE2	17403
CPSF7_BGKLV24_9_17600_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1075					GRCh38	V40	CPSF7_BGKLV24_9_17600_ACTGAT_L005_R1_001.fastq.gz,CPSF7_BGKLV24_9_17600_ACTGAT_L005_R2_001.fastq.gz		ENCORE2	17439
CPSF7_BGKLV24_10_17601_ATTCCT_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1074	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17186
CPSF7_BGKLV24_10_17601_ATTCCT_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1074	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17222
CPSF7_BGKLV24_10_17601_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1074					GRCh38	V40	CPSF7_BGKLV24_10_17601_ATTCCT_L005_R1_001.fastq.gz,CPSF7_BGKLV24_10_17601_ATTCCT_L005_R2_001.fastq.gz		ENCORE2	17258
CPSF7_BGKLV24_10_17601_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1074					GRCh38	V40	CPSF7_BGKLV24_10_17601/Aligned.sortedByCoord.out.bam		ENCORE2	17294
CPSF7_BGKLV24_10_17601_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1074					GRCh38	V40	CPSF7_BGKLV24_10_17601/Aligned.sortedByCoord.out.bam		ENCORE2	17330
CPSF7_BGKLV24_10_17601_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1074					GRCh38	V40	CPSF7_BGKLV24_10_17601/Aligned.sortedByCoord.out.bam		ENCORE2	17366
CPSF7_BGKLV24_10_17601_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1074					GRCh38	V40	CPSF7_BGKLV24_10_17601/Aligned.sortedByCoord.out.bam		ENCORE2	17402
CPSF7_BGKLV24_10_17601_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1074					GRCh38	V40	CPSF7_BGKLV24_10_17601_ATTCCT_L005_R1_001.fastq.gz,CPSF7_BGKLV24_10_17601_ATTCCT_L005_R2_001.fastq.gz		ENCORE2	17438