EIF3G RNA-Seq in K562

General Information


RBP	EIF3G
Cell_Line	K562
Method	shRNA
Exp_Name	EIF3G-BGKLV13-K562
ENCODE_series_ID	ENCSR791UFD
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR143UET
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	EIF3G_BGKLV13_71
Rep2	EIF3G_BGKLV13_72
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	72.6
Rep2_qPCR	75.0
Rep1_WB	74.5
Rep2_WB	80.8
Antibody Cat#	A301-755A
Antibody Lot#	A301-755A
Antibody DCC ID	ENCAB042JJK
Status	Released
Project	ENCODE3
ID	383

Experiment Information (Status: Released)

	BGKLV13-71	BGKLV13-72
idx	206	207
TRCN#_or_BGC#	TRCN0000062035	TRCN0000062035
shRNA_or_gRNA_sequence	GAACAAACTCAAGGGCCAGAA	GAACAAACTCAAGGGCCAGAA
PAM
Name	EIF3G	EIF3G
Sample_ID	BGKLV13-71	BGKLV13-72
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	EIF3G	EIF3G
qPCR_result	72.6	75.0
Ave_qPCR	73.8
RT-qPCR_primer-F	CAGCTGGGCCTGTCTACTG
RT-qPCR_primer-R	CGGCACATACTTCCCTGTCT
protein_conc	1735	1646
WB_result	74.5	80.8
Ave_WB	77.7
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	224.7605	0
Rep2_TPM	208.459217	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	225	226

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

	BGKLV13-71	BGKLV13-72
Sample_ID	BGKLV13-71	BGKLV13-72
Sample Name	EIF3G_BGKLV13_71	EIF3G_BGKLV13_72
Sample Name	EIF3G_BGKLV13_71	EIF3G_BGKLV13_72
RBP	EIF3G	EIF3G
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	446	447

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-71	BGKLV13-72
Sample #
Sample Name	EIF3G-BGKLV13-71	EIF3G-BGKLV13-72
Sample_Name_Alias	EIF3G_BGKLV13_71	EIF3G_BGKLV13_72
Index Well Position	S03	S04
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/D7.png	DNA_Library_LV13-14/set1/E7.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G3.png	RNA_Library_LV13-14-16/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-71	BGKLV13-72
RBP	EIF3G	EIF3G
Batch_ID	BGKLV13	BGKLV13
WB_result	74.500	80.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2170	2171

Sequencing Information

	BGKLV13-71	BGKLV13-72
Sample_ID	BGKLV13-71	BGKLV13-72
Sample Name	EIF3G_BGKLV13_71	EIF3G_BGKLV13_72
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	41,220,000	40,680,000
total_aligned_reads	39,479,404	38,914,748
unique_aligned_reads	36,108,746	35,566,150
percent_uniqueAligned	0.87600	0.87429
correlation_replicates	0.998460	0.998460
spikein_reads	214,148	133,690
percent_spikeins	0.00520	0.00329
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	812	813

Data Submission Information

	BGKLV13-71	BGKLV13-71
ENCODE_alias	brenton-graveley:EIF3G_BGKLV13	brenton-graveley:EIF3G-BGKLV13-K562
ENCODE_accession	ENCSR143UET	ENCSR791UFD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-71	BGKLV13-71
Sample Name	EIF3G_BGKLV13_71	EIF3G_BGKLV13_71
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2772	6686

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_BGKLV13_71_TTAGGC_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	812	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13374
EIF3G_BGKLV13_71_TTAGGC_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	812	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13426
EIF3G_BGKLV13_71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	812					GRCh38	V40	EIF3G_BGKLV13_71_TTAGGC_L007_R1_001.fastq.gz,EIF3G_BGKLV13_71_TTAGGC_L007_R2_001.fastq.gz		ENCORE2	13478
EIF3G_BGKLV13_71_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	812					GRCh38	V40	EIF3G_BGKLV13_71/Aligned.sortedByCoord.out.bam		ENCORE2	13530
EIF3G_BGKLV13_71_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	812					GRCh38	V40	EIF3G_BGKLV13_71/Aligned.sortedByCoord.out.bam		ENCORE2	13582
EIF3G_BGKLV13_71_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	812					GRCh38	V40	EIF3G_BGKLV13_71/Aligned.sortedByCoord.out.bam		ENCORE2	13634
EIF3G_BGKLV13_71_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	812					GRCh38	V40	EIF3G_BGKLV13_71/Aligned.sortedByCoord.out.bam		ENCORE2	13686
EIF3G_BGKLV13_71_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	812					GRCh38	V40	EIF3G_BGKLV13_71_TTAGGC_L007_R1_001.fastq.gz,EIF3G_BGKLV13_71_TTAGGC_L007_R2_001.fastq.gz		ENCORE2	13738
EIF3G_BGKLV13_72_TGACCA_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	813	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13375
EIF3G_BGKLV13_72_TGACCA_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	813	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13427
EIF3G_BGKLV13_72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	813					GRCh38	V40	EIF3G_BGKLV13_72_TGACCA_L007_R1_001.fastq.gz,EIF3G_BGKLV13_72_TGACCA_L007_R2_001.fastq.gz		ENCORE2	13479
EIF3G_BGKLV13_72_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	813					GRCh38	V40	EIF3G_BGKLV13_72/Aligned.sortedByCoord.out.bam		ENCORE2	13531
EIF3G_BGKLV13_72_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	813					GRCh38	V40	EIF3G_BGKLV13_72/Aligned.sortedByCoord.out.bam		ENCORE2	13583
EIF3G_BGKLV13_72_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	813					GRCh38	V40	EIF3G_BGKLV13_72/Aligned.sortedByCoord.out.bam		ENCORE2	13635
EIF3G_BGKLV13_72_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	813					GRCh38	V40	EIF3G_BGKLV13_72/Aligned.sortedByCoord.out.bam		ENCORE2	13687
EIF3G_BGKLV13_72_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	813					GRCh38	V40	EIF3G_BGKLV13_72_TGACCA_L007_R1_001.fastq.gz,EIF3G_BGKLV13_72_TGACCA_L007_R2_001.fastq.gz		ENCORE2	13739