AKAP1 RNA-Seq in HepG2

General Information


RBP	AKAP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	AKAP1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR220SFY
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR016IDR
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	AKAP1-BGHLV12-3
Rep2	AKAP1-BGHLV12-4
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	97.2
Rep2_qPCR	97.1
Rep1_WB	83.2
Rep2_WB	86.8
Antibody Cat#	A301-379A
Antibody Lot#	A301-379A
Antibody DCC ID	ENCAB496QKB
Status	Released
Project	ENCODE3
ID	329

Experiment Information (Status: Released)

	BGHLV12-3	BGHLV12-4
idx	3	4
TRCN#_or_BGC#	TRCN0000013159	TRCN0000013159
shRNA_or_gRNA_sequence	GCTCAGATTCTTTCAGCACTT	GCTCAGATTCTTTCAGCACTT
PAM
Name	AKAP1	AKAP1
Sample_ID	BGHLV12-3	BGHLV12-4
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	AKAP1	AKAP1
qPCR_result	97.2	97.1
Ave_qPCR	97.2
RT-qPCR_primer-F	CTTCCTCTGATTCAGCTGTGG
RT-qPCR_primer-R	GTCTACCCACTGGGCAAGG
protein_conc	2555	2556
WB_result	83.2	86.8
Ave_WB	85.0
WB_DONE_date	9/13/18-2	WES
MW	97kDa
IP	1	1
antibody_Cat#	A301-379A	A301-379A
Antibody DCC ID	ENCAB496QKB
submitted_to_DCC_date	2/22/2019
Rep1_TPM	26.3	0
Rep2_TPM	28.5	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2050	2051

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AKAP1	Product_ID: A301-379A Lot_ID: 1 Source: Bethyl Labs Target Name: AKAP1-human

Experiment Status

	BGHLV12-3	BGHLV12-4
Sample_ID	BGHLV12-3	BGHLV12-4
Sample Name	AKAP1-BGHLV12-3	AKAP1-BGHLV12-4
Sample Name	AKAP1-BGHLV12-3	AKAP1-BGHLV12-4
RBP	AKAP1	AKAP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	372	373

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-3	BGHLV12-4
Sample #
Sample Name	AKAP1-BGHLV12-3	AKAP1-BGHLV12-4
Sample_Name_Alias	AKAP1-BGHLV12-3	AKAP1-BGHLV12-4
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set1/C1.png	DNA_Library_LV12/set1/D1.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/B11.png	RNA_Library_LV12/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-3	BGHLV12-4
RBP	AKAP1	AKAP1
Batch_ID	BGHLV12	BGHLV12
WB_result	83.200	86.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1994	1995

Sequencing Information

	BGHLV12-3	BGHLV12-4
Sample_ID	BGHLV12-3	BGHLV12-4
Sample Name	AKAP1-BGHLV12-3	AKAP1-BGHLV12-4
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	70,060,000	70,620,000
total_aligned_reads	64,358,740	65,000,748
unique_aligned_reads	61,155,640	61,697,330
percent_uniqueAligned	0.87290	0.87365
correlation_replicates	0.991906	0.991906
spikein_reads	586,676	610,862
percent_spikeins	0.00837	0.00865
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	694	695

Data Submission Information

	BGHLV12-3	BGHLV12-3
ENCODE_alias	brenton-graveley:AKAP1-BGHLV12	brenton-graveley:AKAP1-BGHLV12-HepG2
ENCODE_accession	ENCSR016IDR	ENCSR220SFY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-3	BGHLV12-3
Sample Name	AKAP1-BGHLV12-3	AKAP1-BGHLV12-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2735	6585

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-BGHLV12-3_TTAGGC_L001_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	694	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12751
AKAP1-BGHLV12-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	694					GRCh38	V40	AKAP1-BGHLV12-3_TTAGGC_L001_R1_001.fastq.gz,AKAP1-BGHLV12-3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	12890
AKAP1-BGHLV12-3_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	694					GRCh38	V40	AKAP1-BGHLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	12960
AKAP1-BGHLV12-3_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	694					GRCh38	V40	AKAP1-BGHLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	13030
AKAP1-BGHLV12-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	694					GRCh38	V40	AKAP1-BGHLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	13100
AKAP1-BGHLV12-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	694					GRCh38	V40	AKAP1-BGHLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	13170
AKAP1-BGHLV12-3_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	694					GRCh38	V40	AKAP1-BGHLV12-3_TTAGGC_L001_R1_001.fastq.gz,AKAP1-BGHLV12-3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	13240
AKAP1-BGHLV12-4_TGACCA_L001_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	695	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12752
AKAP1-BGHLV12-4_TGACCA_L001_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	695	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12821
AKAP1-BGHLV12-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	695					GRCh38	V40	AKAP1-BGHLV12-4_TGACCA_L001_R1_001.fastq.gz,AKAP1-BGHLV12-4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	12891
AKAP1-BGHLV12-4_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	695					GRCh38	V40	AKAP1-BGHLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	12961
AKAP1-BGHLV12-4_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	695					GRCh38	V40	AKAP1-BGHLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	13031
AKAP1-BGHLV12-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	695					GRCh38	V40	AKAP1-BGHLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	13101
AKAP1-BGHLV12-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	695					GRCh38	V40	AKAP1-BGHLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	13171
AKAP1-BGHLV12-4_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	695					GRCh38	V40	AKAP1-BGHLV12-4_TGACCA_L001_R1_001.fastq.gz,AKAP1-BGHLV12-4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	13241