GPKOW RNA-Seq in HepG2

General Information


RBP	GPKOW
Cell_Line	HepG2
Method	shRNA
Exp_Name	GPKOW-BGHLV35-HepG2
ENCODE_series_ID	ENCSR287SRR
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR968YWY
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	GPKOW_BGHLV35-21
Rep2	GPKOW_BGHLV35-22
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	55.8
Rep2_qPCR	50.0
Rep1_WB	62.3
Rep2_WB	67.3
Antibody Cat#	GTX117716
Antibody Lot#	GTX117716
Antibody DCC ID	ENCAB445RKH
Status	Released
Project	ENCODE3
ID	734

Experiment Information (Status: Released)

	BGHLV35-21	BGHLV35-22
idx	877	878
TRCN#_or_BGC#	TRCN0000130596	TRCN0000130596
shRNA_or_gRNA_sequence	CGGAGGAGAAGGATTTCTTGA	CGGAGGAGAAGGATTTCTTGA
PAM
Name	GPKOW	GPKOW
Sample_ID	BGHLV35-21	BGHLV35-22
transduction_Date	4/29/16	4/29/16
days
RBP_name	GPKOW	GPKOW
qPCR_result	55.8	50.0
Ave_qPCR	52.9
RT-qPCR_primer-F	TGAAGATGTCCTAAGCCCAGA
RT-qPCR_primer-R	GAACCAGGGTCTCCAGCA
protein_conc	1927	2328
WB_result	62.3	67.3
Ave_WB	64.8
WB_DONE_date	5/9/2016	WES
MW	52kDa
IP	1MB	1MB
antibody_Cat#	GTX117716	GTX117716
Antibody DCC ID	ENCAB445RKH	ENCAB445RKH
submitted_to_DCC_date	10/26/16
Rep1_TPM	11	11
Rep2_TPM	15.5	15.5
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2966	2967

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GPKOW	Product_ID: GTX117716 Lot_ID: 40289 Source: GeneTex Target Name: GPKOW-human

Experiment Status

	BGHLV35-21	BGHLV35-22
Sample_ID	BGHLV35-21	BGHLV35-22
Sample Name	GPKOW_BGHLV35-21	GPKOW_BGHLV35-22
Sample Name	GPKOW_BGHLV35-21	GPKOW_BGHLV35-22
RBP	GPKOW	GPKOW
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1257	1258

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-21	BGHLV35-22
Sample #
Sample Name	GPKOW-BGHLV35-21	GPKOW-BGHLV35-22
Sample_Name_Alias	GPKOW_BGHLV35-21	GPKOW_BGHLV35-22
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set2/C2.png	DNA_Library_LV35/set2/D2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/C2.png	RNA_Library_LV35_LV36/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-21	BGHLV35-22
RBP	GPKOW	GPKOW
Batch_ID	BGHLV35	BGHLV35
WB_result	62.300	67.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2942	2943

Sequencing Information

	BGHLV35-21	BGHLV35-22
Sample_ID	BGHLV35-21	BGHLV35-22
Sample Name	GPKOW_BGHLV35-21	GPKOW_BGHLV35-22
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	70,990,472	73,465,052
total_aligned_reads	56,555,800	56,663,656
unique_aligned_reads	53,222,742	53,137,392
percent_uniqueAligned	0.74972	0.72330
correlation_replicates	0.997460	0.997460
spikein_reads	100,712	100,310
percent_spikeins	0.00142	0.00137
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1591	1592

Data Submission Information

	BGHLV35-21	BGHLV35-21
ENCODE_alias	brenton-graveley:GPKOW_BGHLV35	brenton-graveley:GPKOW-BGHLV35-HepG2
ENCODE_accession	ENCSR968YWY	ENCSR287SRR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-21	BGHLV35-21
Sample Name	GPKOW_BGHLV35-21	GPKOW_BGHLV35-21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3168	6735

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
GPKOW_BGHLV35-21_GGCTAC_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1591	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21690
GPKOW_BGHLV35-21_GGCTAC_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1591	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21716
GPKOW_BGHLV35-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1591					GRCh38	V40	GPKOW_BGHLV35-21_GGCTAC_L006_001.R1.fastq.gz,GPKOW_BGHLV35-21_GGCTAC_L006_001.R2.fastq.gz		ENCORE2	21742
GPKOW_BGHLV35-21_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1591					GRCh38	V40	GPKOW_BGHLV35-21/Aligned.sortedByCoord.out.bam		ENCORE2	21768
GPKOW_BGHLV35-21_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1591					GRCh38	V40	GPKOW_BGHLV35-21/Aligned.sortedByCoord.out.bam		ENCORE2	21794
GPKOW_BGHLV35-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1591					GRCh38	V40	GPKOW_BGHLV35-21/Aligned.sortedByCoord.out.bam		ENCORE2	21820
GPKOW_BGHLV35-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1591					GRCh38	V40	GPKOW_BGHLV35-21/Aligned.sortedByCoord.out.bam		ENCORE2	21846
GPKOW_BGHLV35-21_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1591					GRCh38	V40	GPKOW_BGHLV35-21_GGCTAC_L006_001.R1.fastq.gz,GPKOW_BGHLV35-21_GGCTAC_L006_001.R2.fastq.gz		ENCORE2	21872
GPKOW_BGHLV35-22_CTTGTA_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1592	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21691
GPKOW_BGHLV35-22_CTTGTA_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1592	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21717
GPKOW_BGHLV35-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1592					GRCh38	V40	GPKOW_BGHLV35-22_CTTGTA_L006_001.R1.fastq.gz,GPKOW_BGHLV35-22_CTTGTA_L006_001.R2.fastq.gz		ENCORE2	21743
GPKOW_BGHLV35-22_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1592					GRCh38	V40	GPKOW_BGHLV35-22/Aligned.sortedByCoord.out.bam		ENCORE2	21769
GPKOW_BGHLV35-22_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1592					GRCh38	V40	GPKOW_BGHLV35-22/Aligned.sortedByCoord.out.bam		ENCORE2	21795
GPKOW_BGHLV35-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1592					GRCh38	V40	GPKOW_BGHLV35-22/Aligned.sortedByCoord.out.bam		ENCORE2	21821
GPKOW_BGHLV35-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1592					GRCh38	V40	GPKOW_BGHLV35-22/Aligned.sortedByCoord.out.bam		ENCORE2	21847
GPKOW_BGHLV35-22_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1592					GRCh38	V40	GPKOW_BGHLV35-22_CTTGTA_L006_001.R1.fastq.gz,GPKOW_BGHLV35-22_CTTGTA_L006_001.R2.fastq.gz		ENCORE2	21873