AGO1 RNA-Seq in HepG2

General Information


RBP	AGO1
Cell_Line	HepG2
Method	shRNA
Exp_Name	AGO1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR213SDO
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR533HXS
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	EIF2C1_BGHLV14-13
Rep2	EIF2C1_BGHLV14-14
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	86.1
Rep2_qPCR	85.1
Rep1_WB	93.1
Rep2_WB	94.1
Antibody Cat#	RN028PW
Antibody Lot#	RN028PW
Antibody DCC ID	ENCAB179WCQ
Status	Released
Project	ENCODE3
ID	389

Experiment Information (Status: Released)

	BGHLV14-13	BGHLV14-13	BGHLV14-14	BGHLV14-14
idx	107	109	108	110
TRCN#_or_BGC#	TRCN0000007860	TRCN0000007860	TRCN0000007860	TRCN0000007860
shRNA_or_gRNA_sequence	GCTGACAAGAATGAGCGAATT	GCTGACAAGAATGAGCGAATT	GCTGACAAGAATGAGCGAATT	GCTGACAAGAATGAGCGAATT
PAM
Name	EIF2C1	EIF2C1	EIF2C1	EIF2C1
Sample_ID	BGHLV14-13	BGHLV14-13	BGHLV14-14	BGHLV14-14
transduction_Date	7/4/2014	7/4/2014	7/4/2014	7/4/2014
days
RBP_name	AGO1	AGO1	AGO1	AGO1
qPCR_result	86.1	86.1	85.1	85.1
Ave_qPCR	85.6	85.6
RT-qPCR_primer-F	CGCATCATCTTCTACCGAGA	CGCATCATCTTCTACCGAGA
RT-qPCR_primer-R	TTTCCAGTTTGATGCAGGC	TTTCCAGTTTGATGCAGGC
protein_conc	4355	4355	4068	4068
WB_result	93.1	86.4	94.1	87.8
Ave_WB	93.6	87.1
WB_DONE_date	2/25/2016	2/25/2016
MW	97kDa	97kDa	WES	WES
IP	1		1	FU'S
antibody_Cat#	RN028PW	#5053	RN028PW	#5053
Antibody DCC ID	ENCAB179WCQ	ENCAB189GDE		ENCAB189GDE
submitted_to_DCC_date	3/8/2016	3/8/2016
Rep1_TPM	2.4	2.4	0	0
Rep2_TPM	1.4	1.4	0	0
Action
Library_start_date	7/30/2014		7/30/2014
repeat_library
Note
ID	2164	2166	2165	2167

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AGO1	Product_ID: RN028PW Lot_ID: 2 Source: MBLI Target Name: AGO1-human
AGO1	Product_ID: 5053 Lot_ID: 1 Source: Cell Signaling Technology Target Name: AGO1-human

Experiment Status

	BGHLV14-13	BGHLV14-14
Sample_ID	BGHLV14-13	BGHLV14-14
Sample Name	EIF2C1_BGHLV14-13	EIF2C1_BGHLV14-14
Sample Name	EIF2C1_BGHLV14-13	EIF2C1_BGHLV14-14
RBP	EIF2C1	EIF2C1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	500	501

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-13	BGHLV14-14
Sample #
Sample Name	AGO1-BGHLV14-13	AGO1-BGHLV14-14
Sample_Name_Alias	EIF2C1_BGHLV14-13	EIF2C1_BGHLV14-14
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/B9.png	DNA_Library_LV13-14/set1/C9.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E5.png	RNA_Library_LV13-14-16/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-13	BGHLV14-14
RBP	AGO1	AGO1
Batch_ID	BGHLV14	BGHLV14
WB_result	93.100	94.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2184	2185

Sequencing Information

	BGHLV14-13	BGHLV14-14
Sample_ID	BGHLV14-13	BGHLV14-14
Sample Name	EIF2C1_BGHLV14-13	EIF2C1_BGHLV14-14
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	51,620,000	47,580,000
total_aligned_reads	48,983,662	44,786,554
unique_aligned_reads	46,279,474	42,234,552
percent_uniqueAligned	0.89654	0.88765
correlation_replicates	0.996004	0.996004
spikein_reads	234,004	196,844
percent_spikeins	0.00453	0.00414
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	826	827

Data Submission Information

	BGHLV14-13	BGHLV14-13
ENCODE_alias	brenton-graveley:EIF2C1_BGHLV14	brenton-graveley:AGO1-BGHLV14-HepG2
ENCODE_accession	ENCSR533HXS	ENCSR213SDO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-13	BGHLV14-13
Sample Name	EIF2C1_BGHLV14-13	EIF2C1_BGHLV14-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2800	6583

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
EIF2C1_BGHLV14-13_GTCCGC_L001_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	826	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13792
EIF2C1_BGHLV14-13_GTCCGC_L001_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	826	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13854
EIF2C1_BGHLV14-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	826					GRCh38	V40	EIF2C1_BGHLV14-13_GTCCGC_L001_R1_001.fastq.gz,EIF2C1_BGHLV14-13_GTCCGC_L001_R2_001.fastq.gz		ENCORE2	13916
EIF2C1_BGHLV14-13_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	826					GRCh38	V40	EIF2C1_BGHLV14-13/Aligned.sortedByCoord.out.bam		ENCORE2	13978
EIF2C1_BGHLV14-13_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	826					GRCh38	V40	EIF2C1_BGHLV14-13/Aligned.sortedByCoord.out.bam		ENCORE2	14040
EIF2C1_BGHLV14-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	826					GRCh38	V40	EIF2C1_BGHLV14-13/Aligned.sortedByCoord.out.bam		ENCORE2	14102
EIF2C1_BGHLV14-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	826					GRCh38	V40	EIF2C1_BGHLV14-13/Aligned.sortedByCoord.out.bam		ENCORE2	14164
EIF2C1_BGHLV14-13_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	826					GRCh38	V40	EIF2C1_BGHLV14-13_GTCCGC_L001_R1_001.fastq.gz,EIF2C1_BGHLV14-13_GTCCGC_L001_R2_001.fastq.gz		ENCORE2	14226
EIF2C1_BGHLV14-14_GTGAAA_L001_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	827	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13793
EIF2C1_BGHLV14-14_GTGAAA_L001_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	827	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13855
EIF2C1_BGHLV14-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	827					GRCh38	V40	EIF2C1_BGHLV14-14_GTGAAA_L001_R1_001.fastq.gz,EIF2C1_BGHLV14-14_GTGAAA_L001_R2_001.fastq.gz		ENCORE2	13917
EIF2C1_BGHLV14-14_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	827					GRCh38	V40	EIF2C1_BGHLV14-14/Aligned.sortedByCoord.out.bam		ENCORE2	13979
EIF2C1_BGHLV14-14_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	827					GRCh38	V40	EIF2C1_BGHLV14-14/Aligned.sortedByCoord.out.bam		ENCORE2	14041
EIF2C1_BGHLV14-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	827					GRCh38	V40	EIF2C1_BGHLV14-14/Aligned.sortedByCoord.out.bam		ENCORE2	14103
EIF2C1_BGHLV14-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	827					GRCh38	V40	EIF2C1_BGHLV14-14/Aligned.sortedByCoord.out.bam		ENCORE2	14165
EIF2C1_BGHLV14-14_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	827					GRCh38	V40	EIF2C1_BGHLV14-14_GTGAAA_L001_R1_001.fastq.gz,EIF2C1_BGHLV14-14_GTGAAA_L001_R2_001.fastq.gz		ENCORE2	14227