AKAP8L RNA-Seq in HepG2

General Information


RBP	AKAP8L
Cell_Line	HepG2
Method	shRNA
Exp_Name	AKAP8L-BGHLV31-HepG2
ENCODE_series_ID	ENCSR501SJF
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR807ODB
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	AKAP8L_BGHLV31-9
Rep2	AKAP8L_BGHLV31-10
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	19.4
Rep2_qPCR	20.1
Rep1_WB	54.9
Rep2_WB	56.3
Antibody Cat#	GTX115831
Antibody Lot#	GTX115831
Antibody DCC ID	ENCAB936VHC
Status	Released
Project	ENCODE3
ID	692

Experiment Information (Status: Released)

	BGHLV31-9	BGHLV31-10
idx	757	758
TRCN#_or_BGC#	TRCN0000037999	TRCN0000037999
shRNA_or_gRNA_sequence	CCGCAGTATTCTCAACAACAA	CCGCAGTATTCTCAACAACAA
PAM
Name	AKAP8L	AKAP8L
Sample_ID	BGHLV31-9	BGHLV31-10
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	AKAP8L	AKAP8L
qPCR_result	19.4	20.1
Ave_qPCR	19.8
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4679	4697
WB_result	54.9	56.3
Ave_WB	55.6
WB_DONE_date	11/20/2015
MW	72kDa
IP	1IP	1IP
antibody_Cat#	GTX115831	GTX115831
Antibody DCC ID	ENCAB936VHC	ENCAB936VHC
submitted_to_DCC_date	3/8/2016
Rep1_TPM	36.1	0
Rep2_TPM	53.2	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2846	2847

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

	BGHLV31-9	BGHLV31-10
Sample_ID	BGHLV31-9	BGHLV31-10
Sample Name	AKAP8L_BGHLV31-9	AKAP8L_BGHLV31-10
Sample Name	AKAP8L_BGHLV31-9	AKAP8L_BGHLV31-10
RBP	AKAP8L	AKAP8L
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1112	1111

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-9	BGHLV31-10
Sample #
Sample Name	AKAP8L-BGHLV31-9	AKAP8L-BGHLV31-10
Sample_Name_Alias	AKAP8L_BGHLV31-9	AKAP8L_BGHLV31-10
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set2/H9.png	DNA_Library_LV31-21B/set1/F5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E8.png	RNA_Library_LV29-30-31-32/set1/F8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-9	BGHLV31-10
RBP	AKAP8L	AKAP8L
Batch_ID	BGHLV31	BGHLV31
WB_result	54.900	56.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2809	2808

Sequencing Information

	BGHLV31-9	BGHLV31-10
Sample_ID	BGHLV31-9	BGHLV31-10
Sample Name	AKAP8L_BGHLV31-9	AKAP8L_BGHLV31-10
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	62,616,086	60,072,962
total_aligned_reads	54,861,130	52,720,634
unique_aligned_reads	51,651,412	49,555,116
percent_uniqueAligned	0.82489	0.82492
correlation_replicates	0.998503	0.998503
spikein_reads	271,206	261,538
percent_spikeins	0.00433	0.00435
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1458	1457

Data Submission Information

	BGHLV31-9	BGHLV31-9
ENCODE_alias	brenton-graveley:AKAP8L_BGHLV31	brenton-graveley:AKAP8L-BGHLV31-HepG2
ENCODE_accession	ENCSR807ODB	ENCSR501SJF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-9	BGHLV31-9
Sample Name	AKAP8L_BGHLV31-9	AKAP8L_BGHLV31-9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3088	6589

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_BGHLV31-9_AGTCAA_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1458	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20973
AKAP8L_BGHLV31-9_AGTCAA_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1458	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20999
AKAP8L_BGHLV31-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1458					GRCh38	V40	AKAP8L_BGHLV31-9_AGTCAA_L005_001.R1.fastq.gz,AKAP8L_BGHLV31-9_AGTCAA_L005_001.R2.fastq.gz		ENCORE2	21033
AKAP8L_BGHLV31-9_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1458					GRCh38	V40	AKAP8L_BGHLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	21059
AKAP8L_BGHLV31-9_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1458					GRCh38	V40	AKAP8L_BGHLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	21085
AKAP8L_BGHLV31-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1458					GRCh38	V40	AKAP8L_BGHLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	21111
AKAP8L_BGHLV31-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1458					GRCh38	V40	AKAP8L_BGHLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	21137
AKAP8L_BGHLV31-9_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1458					GRCh38	V40	AKAP8L_BGHLV31-9_AGTCAA_L005_001.R1.fastq.gz,AKAP8L_BGHLV31-9_AGTCAA_L005_001.R2.fastq.gz		ENCORE2	21163
AKAP8L_BGHLV31-10_AGTTCC_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1457	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20972
AKAP8L_BGHLV31-10_AGTTCC_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1457	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20998
AKAP8L_BGHLV31-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1457					GRCh38	V40	AKAP8L_BGHLV31-10_AGTTCC_L005_001.R1.fastq.gz,AKAP8L_BGHLV31-10_AGTTCC_L005_001.R2.fastq.gz		ENCORE2	21032
AKAP8L_BGHLV31-10_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1457					GRCh38	V40	AKAP8L_BGHLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	21058
AKAP8L_BGHLV31-10_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1457					GRCh38	V40	AKAP8L_BGHLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	21084
AKAP8L_BGHLV31-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1457					GRCh38	V40	AKAP8L_BGHLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	21110
AKAP8L_BGHLV31-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1457					GRCh38	V40	AKAP8L_BGHLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	21136
AKAP8L_BGHLV31-10_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1457					GRCh38	V40	AKAP8L_BGHLV31-10_AGTTCC_L005_001.R1.fastq.gz,AKAP8L_BGHLV31-10_AGTTCC_L005_001.R2.fastq.gz		ENCORE2	21162