AKAP8L RNA-Seq in K562

General Information


RBP	AKAP8L
Cell_Line	K562
Method	shRNA
Exp_Name	AKAP8L-BGKLV32-K562
ENCODE_series_ID	ENCSR819EFN
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR809ISU
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	AKAP8L_BGKLV32-9
Rep2	AKAP8L_BGKLV32-10
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	53.9
Rep2_qPCR	71.8
Rep1_WB	52.9
Rep2_WB	58.5
Antibody Cat#	GTX115831
Antibody Lot#	GTX115831
Antibody DCC ID	ENCAB936VHC
Status	Released
Project	ENCODE3
ID	704

Experiment Information (Status: Released)

	BGKLV32-9	BGKLV32-10
idx	608	609
TRCN#_or_BGC#	TRCN0000037999	TRCN0000037999
shRNA_or_gRNA_sequence	CCGCAGTATTCTCAACAACAA	CCGCAGTATTCTCAACAACAA
PAM
Name	AKAP8L	AKAP8L
Sample_ID	BGKLV32-9	BGKLV32-10
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	AKAP8L	AKAP8L
qPCR_result	53.9	71.8
Ave_qPCR	62.8
RT-qPCR_primer-F	caagaagtcctccctcatgg
RT-qPCR_primer-R	ctgtcggtgaaagggttctc
protein_conc	3544	3504
WB_result	52.9	58.5
Ave_WB	55.7
WB_DONE_date	11/9/2015
MW	72kDa
IP	1IP	1IP
antibody_Cat#	GTX115831	GTX115831
Antibody DCC ID	ENCAB936VHC	ENCAB936VHC
submitted_to_DCC_date	12/7/2015
Rep1_TPM	72.07923976	0
Rep2_TPM	84.72562207	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	689	690

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AKAP8L	Product_ID: GTX115831 Lot_ID: 40296 Source: GeneTex Target Name: AKAP8L-human

Experiment Status

	BGKLV32-9	BGKLV32-10
Sample_ID	BGKLV32-9	BGKLV32-10
Sample Name	AKAP8L_BGKLV32-10	AKAP8L_BGKLV32-9
Sample Name	AKAP8L_BGKLV32-10	AKAP8L_BGKLV32-9
RBP	AKAP8L	AKAP8L
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1157	1158

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-9	BGKLV32-10
Sample #
Sample Name	AKAP8L-BGKLV32-9	AKAP8L-BGKLV32-10
Sample_Name_Alias	AKAP8L_BGKLV32-9	AKAP8L_BGKLV32-10
Index Well Position	S07	S08
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/G6.png	DNA_Library_LV33-34-25B-32/set1/H6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G11.png	RNA_Library_LV29-30-31-32/set1/H11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-9	BGKLV32-10
RBP	AKAP8L	AKAP8L
Batch_ID	BGKLV32	BGKLV32
WB_result	52.900	58.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2843	2842

Sequencing Information

	BGKLV32-9	BGKLV32-10
Sample_ID	BGKLV32-9	BGKLV32-10
Sample Name	AKAP8L_BGKLV32-9	AKAP8L_BGKLV32-10
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	86,468,028	84,573,254
total_aligned_reads	74,006,984	73,489,496
unique_aligned_reads	66,965,064	66,510,038
percent_uniqueAligned	0.77445	0.78642
correlation_replicates	0.996151	0.996151
spikein_reads	388,026	347,978
percent_spikeins	0.00449	0.00411
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1492	1491

Data Submission Information

	BGKLV32-9	BGKLV32-9
ENCODE_alias	brenton-graveley:AKAP8L_BGKLV32	brenton-graveley:AKAP8L-BGKLV32-K562
ENCODE_accession	ENCSR809ISU	ENCSR819EFN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-9	BGKLV32-9
Sample Name	AKAP8L_BGKLV32-9	AKAP8L_BGKLV32-9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3118	6590

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
AKAP8L_BGKLV32-9_CAGATC_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1492	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21191
AKAP8L_BGKLV32-9_CAGATC_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1492	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21221
AKAP8L_BGKLV32-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1492					GRCh38	V40	AKAP8L_BGKLV32-9_CAGATC_L001_001.R1.fastq.gz,AKAP8L_BGKLV32-9_CAGATC_L001_001.R2.fastq.gz		ENCORE2	21251
AKAP8L_BGKLV32-9_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	1492					GRCh38	V40	AKAP8L_BGKLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	21281
AKAP8L_BGKLV32-9_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	1492					GRCh38	V40	AKAP8L_BGKLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	21311
AKAP8L_BGKLV32-9_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	1492					GRCh38	V40	AKAP8L_BGKLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	21341
AKAP8L_BGKLV32-9_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	1492					GRCh38	V40	AKAP8L_BGKLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	21371
AKAP8L_BGKLV32-9_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1492					GRCh38	V40	AKAP8L_BGKLV32-9_CAGATC_L001_001.R1.fastq.gz,AKAP8L_BGKLV32-9_CAGATC_L001_001.R2.fastq.gz		ENCORE2	21401
AKAP8L_BGKLV32-10_ACTTGA_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1491	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21190
AKAP8L_BGKLV32-10_ACTTGA_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1491	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21220
AKAP8L_BGKLV32-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1491					GRCh38	V40	AKAP8L_BGKLV32-10_ACTTGA_L001_001.R1.fastq.gz,AKAP8L_BGKLV32-10_ACTTGA_L001_001.R2.fastq.gz		ENCORE2	21250
AKAP8L_BGKLV32-10_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	1491					GRCh38	V40	AKAP8L_BGKLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	21280
AKAP8L_BGKLV32-10_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	1491					GRCh38	V40	AKAP8L_BGKLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	21310
AKAP8L_BGKLV32-10_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	1491					GRCh38	V40	AKAP8L_BGKLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	21340
AKAP8L_BGKLV32-10_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	1491					GRCh38	V40	AKAP8L_BGKLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	21370
AKAP8L_BGKLV32-10_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1491					GRCh38	V40	AKAP8L_BGKLV32-10_ACTTGA_L001_001.R1.fastq.gz,AKAP8L_BGKLV32-10_ACTTGA_L001_001.R2.fastq.gz		ENCORE2	21400