AKAP8 RNA-Seq in K562

General Information


RBP	AKAP8
Cell_Line	K562
Method	shRNA
Exp_Name	AKAP8-BGKLV32-K562
ENCODE_series_ID	ENCSR437DYW
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR000YYN
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	AKAP8_BGKLV32-7
Rep2	AKAP8_BGKLV32-8
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	37.2
Rep2_qPCR	39.6
Rep1_WB	55.7
Rep2_WB	67.9
Antibody Cat#	A301-061A
Antibody Lot#	A301-061A
Antibody DCC ID	ENCAB124CAD
Status	Released
Project	ENCODE3
ID	703

Experiment Information (Status: Released)

	BGKLV32-7	BGKLV32-8
idx	606	607
TRCN#_or_BGC#	TRCN0000037944	TRCN0000037944
shRNA_or_gRNA_sequence	GCAGAGTCTAAAGACGCTGTT	GCAGAGTCTAAAGACGCTGTT
PAM
Name	AKAP8	AKAP8
Sample_ID	BGKLV32-7	BGKLV32-8
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	AKAP8	AKAP8
qPCR_result	37.2	39.6
Ave_qPCR	38.4
RT-qPCR_primer-F	acgaggacgaggatgtgaag
RT-qPCR_primer-R	tcaaagctacggaacttgcat
protein_conc	2830	2798
WB_result	55.7	67.9
Ave_WB	61.8
WB_DONE_date	2/8/2016
MW	76kDa	wes
IP	1	1
antibody_Cat#	A301-061A	A301-061A
Antibody DCC ID	ENCAB124CAD	ENCAB124CAD
submitted_to_DCC_date	3/8/2016
Rep1_TPM	15.41849335	0
Rep2_TPM	13.26950507	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	687	688

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AKAP8	Product_ID: A301-061A Lot_ID: 1 Source: Bethyl Labs Target Name: AKAP8-human

Experiment Status

	BGKLV32-7	BGKLV32-8
Sample_ID	BGKLV32-7	BGKLV32-8
Sample Name	AKAP8_BGKLV32-7	AKAP8_BGKLV32-8
Sample Name	AKAP8_BGKLV32-7	AKAP8_BGKLV32-8
RBP	AKAP8	AKAP8
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1155	1156

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-7	BGKLV32-8
Sample #
Sample Name	AKAP8-BGKLV32-7	AKAP8-BGKLV32-8
Sample_Name_Alias	AKAP8_BGKLV32-7	AKAP8_BGKLV32-8
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/E6.png	DNA_Library_LV33-34-25B-32/set1/F6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E11.png	RNA_Library_LV29-30-31-32/set1/F11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-7	BGKLV32-8
RBP	AKAP8	AKAP8
Batch_ID	BGKLV32	BGKLV32
WB_result	55.700	67.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2840	2841

Sequencing Information

	BGKLV32-7	BGKLV32-8
Sample_ID	BGKLV32-7	BGKLV32-8
Sample Name	AKAP8_BGKLV32-7	AKAP8_BGKLV32-8
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	84,002,440	83,922,940
total_aligned_reads	71,968,354	72,455,114
unique_aligned_reads	65,513,340	66,303,430
percent_uniqueAligned	0.77990	0.79005
correlation_replicates	0.990380	0.990380
spikein_reads	331,736	349,044
percent_spikeins	0.00395	0.00416
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1489	1490

Data Submission Information

	BGKLV32-7	BGKLV32-7
ENCODE_alias	brenton-graveley:AKAP8_BGKLV32	brenton-graveley:AKAP8-BGKLV32-K562
ENCODE_accession	ENCSR000YYN	ENCSR437DYW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-7	BGKLV32-7
Sample Name	AKAP8_BGKLV32-7	AKAP8_BGKLV32-7
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3117	6588

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
AKAP8_BGKLV32-7_ACAGTG_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1489	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21188
AKAP8_BGKLV32-7_ACAGTG_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1489	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21218
AKAP8_BGKLV32-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1489					GRCh38	V40	AKAP8_BGKLV32-7_ACAGTG_L001_001.R1.fastq.gz,AKAP8_BGKLV32-7_ACAGTG_L001_001.R2.fastq.gz		ENCORE2	21248
AKAP8_BGKLV32-7_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1489					GRCh38	V40	AKAP8_BGKLV32-7/Aligned.sortedByCoord.out.bam		ENCORE2	21278
AKAP8_BGKLV32-7_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1489					GRCh38	V40	AKAP8_BGKLV32-7/Aligned.sortedByCoord.out.bam		ENCORE2	21308
AKAP8_BGKLV32-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1489					GRCh38	V40	AKAP8_BGKLV32-7/Aligned.sortedByCoord.out.bam		ENCORE2	21338
AKAP8_BGKLV32-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1489					GRCh38	V40	AKAP8_BGKLV32-7/Aligned.sortedByCoord.out.bam		ENCORE2	21368
AKAP8_BGKLV32-7_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1489					GRCh38	V40	AKAP8_BGKLV32-7_ACAGTG_L001_001.R1.fastq.gz,AKAP8_BGKLV32-7_ACAGTG_L001_001.R2.fastq.gz		ENCORE2	21398
AKAP8_BGKLV32-8_GCCAAT_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1490	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21189
AKAP8_BGKLV32-8_GCCAAT_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1490	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21219
AKAP8_BGKLV32-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1490					GRCh38	V40	AKAP8_BGKLV32-8_GCCAAT_L001_001.R1.fastq.gz,AKAP8_BGKLV32-8_GCCAAT_L001_001.R2.fastq.gz		ENCORE2	21249
AKAP8_BGKLV32-8_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1490					GRCh38	V40	AKAP8_BGKLV32-8/Aligned.sortedByCoord.out.bam		ENCORE2	21279
AKAP8_BGKLV32-8_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1490					GRCh38	V40	AKAP8_BGKLV32-8/Aligned.sortedByCoord.out.bam		ENCORE2	21309
AKAP8_BGKLV32-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1490					GRCh38	V40	AKAP8_BGKLV32-8/Aligned.sortedByCoord.out.bam		ENCORE2	21339
AKAP8_BGKLV32-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1490					GRCh38	V40	AKAP8_BGKLV32-8/Aligned.sortedByCoord.out.bam		ENCORE2	21369
AKAP8_BGKLV32-8_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1490					GRCh38	V40	AKAP8_BGKLV32-8_GCCAAT_L001_001.R1.fastq.gz,AKAP8_BGKLV32-8_GCCAAT_L001_001.R2.fastq.gz		ENCORE2	21399