CPSF6 RNA-Seq in K562

General Information


RBP	CPSF6
Cell_Line	K562
Method	shRNA
Exp_Name	CPSF6-BGKLV36-K562
ENCODE_series_ID	ENCSR232HNS
Batch_ID	BGKLV36
Pool ID	Pool-160912
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR384BDV
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	CPSF6_BGKLV36-11
Rep2	CPSF6_BGKLV36-12
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	73.5
Rep2_qPCR	69.6
Rep1_WB	68.0
Rep2_WB	57.2
Antibody Cat#	A301-356A
Antibody Lot#	A301-356A
Antibody DCC ID	ENCAB652TTL
Status	Released
Project	ENCODE3
ID	743

Experiment Information (Status: Released)

	BGKLV36-11	BGKLV36-11	BGKLV36-12	BGKLV36-12
idx	734	734	735	735
TRCN#_or_BGC#	TRCN0000000154	TRCN0000000154	TRCN0000000154	TRCN0000000154
shRNA_or_gRNA_sequence	ACCATAGTAGATCACGAGAAA	ACCATAGTAGATCACGAGAAA	ACCATAGTAGATCACGAGAAA	ACCATAGTAGATCACGAGAAA
PAM
Name	CPSF6	CPSF6	CPSF6	CPSF6
Sample_ID	BGKLV36-11	BGKLV36-11	BGKLV36-12	BGKLV36-12
transduction_Date	5/19/2016	5/19/2016	5/19/2016	5/19/2016
days
RBP_name	CPSF6	CPSF6	CPSF6	CPSF6
qPCR_result	73.5	73.5	69.6	69.6
Ave_qPCR	71.5	71.5
RT-qPCR_primer-F	AGAGCGCGAATATCGTCATC	AGAGCGCGAATATCGTCATC
RT-qPCR_primer-R	CCCCCATGAAGACTGTTTTG	CCCCCATGAAGACTGTTTTG
protein_conc	4275	4275	4338	4338
WB_result	68.0	67.9	57.2	78.0
Ave_WB	62.6	73.0
WB_DONE_date	6/8/16	6/28/23
MW	59kDa	59kDa
IP	1		1
antibody_Cat#	A301-356A	92879S	A301-356A	lot #1
Antibody DCC ID	ENCAB652TTL		ENCAB652TTL
submitted_to_DCC_date	11/16/17	1/8/24
Rep1_TPM	45.3	0	0	0
Rep2_TPM	38.2	0	0	0
Action
Library_start_date	07/28/16		07/28/16
repeat_library
Note
ID	823	825	824	826

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF6	Product_ID: A301-356A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF6-human
CPSF6	Product_ID: 92879S Lot_ID: 1 Source: Cell Signaling Technology Target Name: CPSF6-human

Experiment Status

	BGKLV36-11	BGKLV36-12
Sample_ID	BGKLV36-11	BGKLV36-12
Sample Name	CPSF6_BGKLV36-11	CPSF6_BGKLV36-12
Sample Name	CPSF6_BGKLV36-11	CPSF6_BGKLV36-12
RBP	CPSF6	CPSF6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1277	1278

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-11	BGKLV36-12
Sample #
Sample Name	CPSF6-BGKLV36-11	CPSF6-BGKLV36-12
Sample_Name_Alias	CPSF6_BGKLV36-11	CPSF6_BGKLV36-12
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/E1.png	DNA_Library_LV36/set1/F1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/G4.png	RNA_Library_LV35_LV36/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-11	BGKLV36-12
RBP	CPSF6	CPSF6
Batch_ID	BGKLV36	BGKLV36
WB_result	68.000	57.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2962	2963

Sequencing Information

	BGKLV36-11	BGKLV36-12
Sample_ID	BGKLV36-11	BGKLV36-12
Sample Name	CPSF6_BGKLV36-11	CPSF6_BGKLV36-12
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set36	set36
total_reads	69,200,648	86,629,088
total_aligned_reads	56,467,314	70,409,034
unique_aligned_reads	51,519,074	64,431,564
percent_uniqueAligned	0.74449	0.74376
correlation_replicates	0.997975	0.997975
spikein_reads	100,484	141,106
percent_spikeins	0.00145	0.00163
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1611	1612

Data Submission Information

	BGKLV36-11	BGKLV36-11
ENCODE_alias	brenton-graveley:CPSF6_BGKLV36	brenton-graveley:CPSF6-BGKLV36-K562
ENCODE_accession	ENCSR384BDV	ENCSR232HNS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-11	BGKLV36-11
Sample Name	CPSF6_BGKLV36-11	CPSF6_BGKLV36-11
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3178	6627

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_BGKLV36-11_AGTCAA_L008_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1611	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21892
CPSF6_BGKLV36-11_AGTCAA_L008_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1611	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21910
CPSF6_BGKLV36-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1611					GRCh38	V40	CPSF6_BGKLV36-11_AGTCAA_L008_001.R1.fastq.gz,CPSF6_BGKLV36-11_AGTCAA_L008_001.R2.fastq.gz		ENCORE2	21928
CPSF6_BGKLV36-11_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1611					GRCh38	V40	CPSF6_BGKLV36-11/Aligned.sortedByCoord.out.bam		ENCORE2	21946
CPSF6_BGKLV36-11_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1611					GRCh38	V40	CPSF6_BGKLV36-11/Aligned.sortedByCoord.out.bam		ENCORE2	21964
CPSF6_BGKLV36-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1611					GRCh38	V40	CPSF6_BGKLV36-11/Aligned.sortedByCoord.out.bam		ENCORE2	21982
CPSF6_BGKLV36-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1611					GRCh38	V40	CPSF6_BGKLV36-11/Aligned.sortedByCoord.out.bam		ENCORE2	22000
CPSF6_BGKLV36-11_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1611					GRCh38	V40	CPSF6_BGKLV36-11_AGTCAA_L008_001.R1.fastq.gz,CPSF6_BGKLV36-11_AGTCAA_L008_001.R2.fastq.gz		ENCORE2	22018
CPSF6_BGKLV36-12_AGTTCC_L008_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1612	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21893
CPSF6_BGKLV36-12_AGTTCC_L008_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1612	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21911
CPSF6_BGKLV36-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1612					GRCh38	V40	CPSF6_BGKLV36-12_AGTTCC_L008_001.R1.fastq.gz,CPSF6_BGKLV36-12_AGTTCC_L008_001.R2.fastq.gz		ENCORE2	21929
CPSF6_BGKLV36-12_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1612					GRCh38	V40	CPSF6_BGKLV36-12/Aligned.sortedByCoord.out.bam		ENCORE2	21947
CPSF6_BGKLV36-12_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1612					GRCh38	V40	CPSF6_BGKLV36-12/Aligned.sortedByCoord.out.bam		ENCORE2	21965
CPSF6_BGKLV36-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1612					GRCh38	V40	CPSF6_BGKLV36-12/Aligned.sortedByCoord.out.bam		ENCORE2	21983
CPSF6_BGKLV36-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1612					GRCh38	V40	CPSF6_BGKLV36-12/Aligned.sortedByCoord.out.bam		ENCORE2	22001
CPSF6_BGKLV36-12_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1612					GRCh38	V40	CPSF6_BGKLV36-12_AGTTCC_L008_001.R1.fastq.gz,CPSF6_BGKLV36-12_AGTTCC_L008_001.R2.fastq.gz		ENCORE2	22019