EIF3G RNA-Seq in HepG2

General Information


RBP	EIF3G
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF3G-BGHLV14-HepG2
ENCODE_series_ID	ENCSR548LCO
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR778AJO
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	EIF3G_BGHLV14-15
Rep2	EIF3G_BGHLV14-16
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	67.5
Rep2_qPCR	68.4
Rep1_WB	55.3
Rep2_WB	72.3
Antibody Cat#	A301-755A
Antibody Lot#	A301-755A
Antibody DCC ID	ENCAB042JJK
Status	Released
Project	ENCODE3
ID	390

Experiment Information (Status: Released)

	BGHLV14-15	BGHLV14-16
idx	111	112
TRCN#_or_BGC#	TRCN0000062035	TRCN0000062035
shRNA_or_gRNA_sequence	GAACAAACTCAAGGGCCAGAA	GAACAAACTCAAGGGCCAGAA
PAM
Name	EIF3G	EIF3G
Sample_ID	BGHLV14-15	BGHLV14-16
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	EIF3G	EIF3G
qPCR_result	67.5	68.4
Ave_qPCR	68.0
RT-qPCR_primer-F	CAGCTGGGCCTGTCTACTG
RT-qPCR_primer-R	CGGCACATACTTCCCTGTCT
protein_conc	4042	4174
WB_result	55.3	72.3
Ave_WB	63.8
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A301-755A	A301-755A
Antibody DCC ID	ENCAB042JJK	ENCAB042JJK
submitted_to_DCC_date	4/2/2015
Rep1_TPM	103.5	0
Rep2_TPM	129.9	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2168	2169

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3G	Product_ID: A301-755A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3G-human

Experiment Status

	BGHLV14-15	BGHLV14-16
Sample_ID	BGHLV14-15	BGHLV14-16
Sample Name	EIF3G_BGHLV14-15	EIF3G_BGHLV14-16
Sample Name	EIF3G_BGHLV14-15	EIF3G_BGHLV14-16
RBP	EIF3G	EIF3G
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	502	503

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-15	BGHLV14-16
Sample #
Sample Name	EIF3G-BGHLV14-15	EIF3G-BGHLV14-16
Sample_Name_Alias	EIF3G_BGHLV14-15	EIF3G_BGHLV14-16
Index Well Position	S20	S21
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/D9.png	DNA_Library_LV13-14/set1/E9.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G5.png	RNA_Library_LV13-14-16/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-15	BGHLV14-16
RBP	EIF3G	EIF3G
Batch_ID	BGHLV14	BGHLV14
WB_result	55.300	72.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2186	2187

Sequencing Information

	BGHLV14-15	BGHLV14-16
Sample_ID	BGHLV14-15	BGHLV14-16
Sample Name	EIF3G_BGHLV14-15	EIF3G_BGHLV14-16
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	49,760,000	45,670,000
total_aligned_reads	47,108,030	43,133,526
unique_aligned_reads	44,267,754	40,541,484
percent_uniqueAligned	0.88963	0.88770
correlation_replicates	0.998186	0.998186
spikein_reads	181,164	118,254
percent_spikeins	0.00364	0.00259
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	828	829

Data Submission Information

	BGHLV14-15	BGHLV14-15
ENCODE_alias	brenton-graveley:EIF3G_BGHLV14	brenton-graveley:EIF3G-BGHLV14-HepG2
ENCODE_accession	ENCSR778AJO	ENCSR548LCO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-15	BGHLV14-15
Sample Name	EIF3G_BGHLV14-15	EIF3G_BGHLV14-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2801	6685

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
EIF3G_BGHLV14-15_GTGGCC_L001_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	828	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	13794
EIF3G_BGHLV14-15_GTGGCC_L001_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	828	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	13856
EIF3G_BGHLV14-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	828					GRCh38	V40	EIF3G_BGHLV14-15_GTGGCC_L001_R1_001.fastq.gz,EIF3G_BGHLV14-15_GTGGCC_L001_R2_001.fastq.gz		ENCORE2	13918
EIF3G_BGHLV14-15_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	828					GRCh38	V40	EIF3G_BGHLV14-15/Aligned.sortedByCoord.out.bam		ENCORE2	13980
EIF3G_BGHLV14-15_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	828					GRCh38	V40	EIF3G_BGHLV14-15/Aligned.sortedByCoord.out.bam		ENCORE2	14042
EIF3G_BGHLV14-15_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	828					GRCh38	V40	EIF3G_BGHLV14-15/Aligned.sortedByCoord.out.bam		ENCORE2	14104
EIF3G_BGHLV14-15_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	828					GRCh38	V40	EIF3G_BGHLV14-15/Aligned.sortedByCoord.out.bam		ENCORE2	14166
EIF3G_BGHLV14-15_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	828					GRCh38	V40	EIF3G_BGHLV14-15_GTGGCC_L001_R1_001.fastq.gz,EIF3G_BGHLV14-15_GTGGCC_L001_R2_001.fastq.gz		ENCORE2	14228
EIF3G_BGHLV14-16_GTTTCG_L002_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	829	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	13795
EIF3G_BGHLV14-16_GTTTCG_L002_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	829	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	13857
EIF3G_BGHLV14-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	829					GRCh38	V40	EIF3G_BGHLV14-16_GTTTCG_L002_R1_001.fastq.gz,EIF3G_BGHLV14-16_GTTTCG_L002_R2_001.fastq.gz		ENCORE2	13919
EIF3G_BGHLV14-16_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	829					GRCh38	V40	EIF3G_BGHLV14-16/Aligned.sortedByCoord.out.bam		ENCORE2	13981
EIF3G_BGHLV14-16_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	829					GRCh38	V40	EIF3G_BGHLV14-16/Aligned.sortedByCoord.out.bam		ENCORE2	14043
EIF3G_BGHLV14-16_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	829					GRCh38	V40	EIF3G_BGHLV14-16/Aligned.sortedByCoord.out.bam		ENCORE2	14105
EIF3G_BGHLV14-16_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	829					GRCh38	V40	EIF3G_BGHLV14-16/Aligned.sortedByCoord.out.bam		ENCORE2	14167
EIF3G_BGHLV14-16_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	829					GRCh38	V40	EIF3G_BGHLV14-16_GTTTCG_L002_R1_001.fastq.gz,EIF3G_BGHLV14-16_GTTTCG_L002_R2_001.fastq.gz		ENCORE2	14229