AKAP8 RNA-Seq in HepG2

General Information


RBP	AKAP8
Cell_Line	HepG2
Method	shRNA
Exp_Name	AKAP8-BGHLV27-HepG2
ENCODE_series_ID	ENCSR969FIX
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR958KSY
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	AKAP8_BGHLV27-5
Rep2	AKAP8_BGHLV27-6
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	57.7
Rep2_qPCR	64.6
Rep1_WB	66.5
Rep2_WB	62.9
Antibody Cat#	A301-061A
Antibody Lot#	A301-061A
Antibody DCC ID	ENCAB124CAD
Status	Released
Project	ENCODE3
ID	639

Experiment Information (Status: Released)

	BGHLV27-5	BGHLV27-6
idx	625	626
TRCN#_or_BGC#	TRCN0000037944	TRCN0000037944
shRNA_or_gRNA_sequence	GCAGAGTCTAAAGACGCTGTT	GCAGAGTCTAAAGACGCTGTT
PAM
Name	AKAP8	AKAP8
Sample_ID	BGHLV27-5	BGHLV27-6
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	AKAP8	AKAP8
qPCR_result	57.7	64.6
Ave_qPCR	61.1
RT-qPCR_primer-F	acgaggacgaggatgtgaag
RT-qPCR_primer-R	tcaaagctacggaacttgcat
protein_conc	4313	3981
WB_result	66.5	62.9
Ave_WB	64.7
WB_DONE_date	8/26/2015
MW	76kDa
IP	1	1
antibody_Cat#	A301-061A	A301-061A
Antibody DCC ID	ENCAB124CAD	ENCAB124CAD
submitted_to_DCC_date	12/7/2015
Rep1_TPM	11	0
Rep2_TPM	11.3	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	x	x
ID	2712	2713

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

	BGHLV27-5	BGHLV27-6
Sample_ID	BGHLV27-5	BGHLV27-6
Sample Name	AKAP8_BGHLV27-5	AKAP8_BGHLV27-6
Sample Name	AKAP8_BGHLV27-5	AKAP8_BGHLV27-6
RBP	AKAP8	AKAP8
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	962	963

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-5	BGHLV27-6
Sample #
Sample Name	AKAP8-BGHLV27-5	AKAP8-BGHLV27-6
Sample_Name_Alias	AKAP8_BGHLV27-5	AKAP8_BGHLV27-6
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2015-09-28
Lib_ID	Lib-150928	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set1/C1.png	DNA_Library_LV27/set1/D1.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/C4.png	RNA_Library_LV26-27-28-29/set1/D4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-5	BGHLV27-6
RBP	AKAP8	AKAP8
Batch_ID	BGHLV27	BGHLV27
WB_result	66.500	62.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2654	2655

Sequencing Information

	BGHLV27-5	BGHLV27-6
Sample_ID	BGHLV27-5	BGHLV27-6
Sample Name	AKAP8_BGHLV27-5	AKAP8_BGHLV27-6
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	82,895,844	63,115,998
total_aligned_reads	74,443,990	54,482,080
unique_aligned_reads	70,107,708	51,312,160
percent_uniqueAligned	0.84573	0.81298
correlation_replicates	0.997018	0.997018
spikein_reads	318,444	236,716
percent_spikeins	0.00384	0.00375
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1296	1297

Data Submission Information

	BGHLV27-5	BGHLV27-5
ENCODE_alias	brenton-graveley:AKAP8_BGHLV27	brenton-graveley:AKAP8-BGHLV27-HepG2
ENCODE_accession	ENCSR958KSY	ENCSR969FIX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-5	BGHLV27-5
Sample Name	AKAP8_BGHLV27-5	AKAP8_BGHLV27-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3028	6587

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_BGHLV27-5_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1296	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20004
AKAP8_BGHLV27-5_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1296	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20026
AKAP8_BGHLV27-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1296					GRCh38	V40	AKAP8_BGHLV27-5_1.fastq.gz,AKAP8_BGHLV27-5_2.fastq.gz		ENCORE2	20048
AKAP8_BGHLV27-5_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1296					GRCh38	V40	AKAP8_BGHLV27-5/Aligned.sortedByCoord.out.bam		ENCORE2	20070
AKAP8_BGHLV27-5_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1296					GRCh38	V40	AKAP8_BGHLV27-5/Aligned.sortedByCoord.out.bam		ENCORE2	20092
AKAP8_BGHLV27-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1296					GRCh38	V40	AKAP8_BGHLV27-5/Aligned.sortedByCoord.out.bam		ENCORE2	20114
AKAP8_BGHLV27-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1296					GRCh38	V40	AKAP8_BGHLV27-5/Aligned.sortedByCoord.out.bam		ENCORE2	20136
AKAP8_BGHLV27-5_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1296					GRCh38	V40	AKAP8_BGHLV27-5_1.fastq.gz,AKAP8_BGHLV27-5_2.fastq.gz		ENCORE2	20676
AKAP8_BGHLV27-6_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1297	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20005
AKAP8_BGHLV27-6_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1297	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20027
AKAP8_BGHLV27-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1297					GRCh38	V40	AKAP8_BGHLV27-6_1.fastq.gz,AKAP8_BGHLV27-6_2.fastq.gz		ENCORE2	20049
AKAP8_BGHLV27-6_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1297					GRCh38	V40	AKAP8_BGHLV27-6/Aligned.sortedByCoord.out.bam		ENCORE2	20071
AKAP8_BGHLV27-6_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1297					GRCh38	V40	AKAP8_BGHLV27-6/Aligned.sortedByCoord.out.bam		ENCORE2	20093
AKAP8_BGHLV27-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1297					GRCh38	V40	AKAP8_BGHLV27-6/Aligned.sortedByCoord.out.bam		ENCORE2	20115
AKAP8_BGHLV27-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1297					GRCh38	V40	AKAP8_BGHLV27-6/Aligned.sortedByCoord.out.bam		ENCORE2	20137
AKAP8_BGHLV27-6_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1297					GRCh38	V40	AKAP8_BGHLV27-6_1.fastq.gz,AKAP8_BGHLV27-6_2.fastq.gz		ENCORE2	20677