AKAP1 RNA-Seq in K562

General Information


RBP	AKAP1
Cell_Line	K562
Method	shRNA
Exp_Name	AKAP1-BGKLV08-K562
ENCODE_series_ID	ENCSR533CRH
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR338CON
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	AKAP1-LV08-3
Rep2	AKAP1-LV08-4
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	80.0
Rep2_qPCR	86.8
Rep1_WB	99.9
Rep2_WB	99.8
Antibody Cat#	A301-379A
Antibody Lot#	A301-379A
Antibody DCC ID	ENCAB496QKB
Status	Released
Project	ENCODE3
ID	280

Experiment Information (Status: Released)

	BGKLV08-3	BGKLV08-4
idx	4	5
TRCN#_or_BGC#	TRCN0000013159	TRCN0000013159
shRNA_or_gRNA_sequence	GCTCAGATTCTTTCAGCACTT	GCTCAGATTCTTTCAGCACTT
PAM
Name	AKAP1	AKAP1
Sample_ID	BGKLV08-3	BGKLV08-4
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	AKAP1	AKAP1
qPCR_result	80.0	86.8
Ave_qPCR	83.4
RT-qPCR_primer-F	CTTCCTCTGATTCAGCTGTGG
RT-qPCR_primer-R	GTCTACCCACTGGGCAAGG
protein_conc	2805	2552
WB_result	99.9	99.8
Ave_WB	99.9
WB_DONE_date	3/3/2016
MW	97kDa	wes
IP	1	1
antibody_Cat#	A301-379A	A301-379A
Antibody DCC ID	ENCAB496QKB
submitted_to_DCC_date
Rep1_TPM	17.646059	0
Rep2_TPM	10.9895272	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	3	4

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-3	BGKLV08-4
Sample_ID	BGKLV08-3	BGKLV08-4
Sample Name	AKAP1-LV08-3	AKAP1-LV08-4
Sample Name	AKAP1-LV08-3	AKAP1-LV08-4
RBP	AKAP1	AKAP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	268	269

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-3	BGKLV08-4
Sample #
Sample Name	AKAP1-BGKLV08-3	AKAP1-BGKLV08-4
Sample_Name_Alias	AKAP1-LV08-3	AKAP1-LV08-4
Index Well Position	S03	S04
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/D1.png	DNA_Library_LV08/set1/E1.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_LV08/set1/C1.png	RNA_Library_LV08/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-3	BGKLV08-4
RBP	AKAP1	AKAP1
Batch_ID	BGKLV08	BGKLV08
WB_result	99.900	99.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1890	1891

Sequencing Information

	BGKLV08-3	BGKLV08-4
Sample_ID	BGKLV08-3	BGKLV08-4
Sample Name	AKAP1-LV08-3	AKAP1-LV08-4
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	47,830,000	49,730,000
total_aligned_reads	41,074,954	42,403,288
unique_aligned_reads	37,448,696	38,652,596
percent_uniqueAligned	0.78295	0.77725
correlation_replicates	0.998396	0.998396
spikein_reads	402,376	418,872
percent_spikeins	0.00841	0.00842
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	590	591

Data Submission Information

	BGKLV08-3	BGKLV08-3
ENCODE_alias	brenton-graveley:AKAP1-LV08	brenton-graveley:AKAP1-BGKLV08-K562
ENCODE_accession	ENCSR338CON	ENCSR533CRH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-3	BGKLV08-3
Sample Name	AKAP1-LV08-3	AKAP1-LV08-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2683	6586

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
AKAP1-LV08-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	590					GRCh38	V40	AKAP1-LV08-3_TTAGGC_L001_R1_001.fastq.gz,AKAP1-LV08-3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	11975
AKAP1-LV08-3_TTAGGC_L001_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	590	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	12031
AKAP1-LV08-3_TTAGGC_L001_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	590	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	12087
AKAP1-LV08-3_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	590					GRCh38	V40	AKAP1-LV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	12143
AKAP1-LV08-3_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	590					GRCh38	V40	AKAP1-LV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	12199
AKAP1-LV08-3_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	590					GRCh38	V40	AKAP1-LV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	12255
AKAP1-LV08-3_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	590					GRCh38	V40	AKAP1-LV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	12311
AKAP1-LV08-3_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	590					GRCh38	V40	AKAP1-LV08-3_TTAGGC_L001_R1_001.fastq.gz,AKAP1-LV08-3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	13310
AKAP1-LV08-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	591					GRCh38	V40	AKAP1-LV08-4_TGACCA_L001_R1_001.fastq.gz,AKAP1-LV08-4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	11976
AKAP1-LV08-4_TGACCA_L001_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	591	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	12032
AKAP1-LV08-4_TGACCA_L001_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	591	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	12088
AKAP1-LV08-4_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	591					GRCh38	V40	AKAP1-LV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	12144
AKAP1-LV08-4_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	591					GRCh38	V40	AKAP1-LV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	12200
AKAP1-LV08-4_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	591					GRCh38	V40	AKAP1-LV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	12256
AKAP1-LV08-4_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	591					GRCh38	V40	AKAP1-LV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	12312
AKAP1-LV08-4_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	591					GRCh38	V40	AKAP1-LV08-4_TGACCA_L001_R1_001.fastq.gz,AKAP1-LV08-4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	13311