EIF4G2 RNA-Seq in HepG2

General Information


RBP	EIF4G2
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF4G2-BGHLV23-HepG2
ENCODE_series_ID	ENCSR030SUW
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR152MON
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	EIF4G2-BGHLV23-15
Rep2	EIF4G2-BGHLV23-16
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	94.0
Rep2_qPCR	97.2
Rep1_WB	92.2
Rep2_WB	74.0
Antibody Cat#	RN003P
Antibody Lot#	RN003P
Antibody DCC ID	ENCAB000BFJ
Status	Released
Project	ENCODE3
ID	542

Experiment Information (Status: Released)

	BGHLV23-15	BGHLV23-15	BGHLV23-16	BGHLV23-16
idx	507	507	508	508
TRCN#_or_BGC#	TRCN0000150297	TRCN0000150297	TRCN0000150297	TRCN0000150297
shRNA_or_gRNA_sequence	CCCTTTGGTGAAATCCTATTT	CCCTTTGGTGAAATCCTATTT	CCCTTTGGTGAAATCCTATTT	CCCTTTGGTGAAATCCTATTT
PAM
Name	EIF4G2	EIF4G2	EIF4G2	EIF4G2
Sample_ID	BGHLV23-15	BGHLV23-15	BGHLV23-16	BGHLV23-16
transduction_Date	10/29/2014	10/29/2014	10/29/2014	10/29/2014
days
RBP_name	EIF4G2	EIF4G2	EIF4G2	EIF4G2
qPCR_result	94.0	94.0	97.2	97.2
Ave_qPCR	95.6	95.6
RT-qPCR_primer-F	GGGTGCACCTCAGCACTATC	GGGTGCACCTCAGCACTATC
RT-qPCR_primer-R	CTTCGTGCAGGAATCCATTT	CTTCGTGCAGGAATCCATTT
protein_conc	6326	6326	6112	6112
WB_result	92.2	no band on the position	74.0
Ave_WB	83.1
WB_DONE_date	4/14/2015	6/14/23,7/19/23
MW	102kd	102kd
IP	1		1
antibody_Cat#	RN003P	5169S	RN003P	lot# 1
Antibody DCC ID	ENCAB000BFJ		ENCAB000BFJ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	56	0	0	0
Rep2_TPM	66	0	0	0
Action
Library_start_date	6/10/2015		6/10/2015
repeat_library
Note
ID	2582	2584	2583	2585

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4G2	Product_ID: RN003P Lot_ID: 1 Source: MBLI Target Name: EIF4G2-human

Experiment Status

	BGHLV23-15	BGHLV23-16
Sample_ID	BGHLV23-15	BGHLV23-16
Sample Name	EIF4G2-BGHLV23-15	EIF4G2-BGHLV23-16
Sample Name	EIF4G2-BGHLV23-15	EIF4G2-BGHLV23-16
RBP	EIF4G2	EIF4G2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	820	821

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-15	BGHLV23-16
Sample #
Sample Name	EIF4G2-BGHLV23-15	EIF4G2-BGHLV23-16
Sample_Name_Alias	EIF4G2-BGHLV23-15	EIF4G2-BGHLV23-16
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set2/B2.png	DNA_Library_LV20-22-23/set2/C2.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G5.png	RNA_Library_LV22-23-25/set1/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-15	BGHLV23-16
RBP	EIF4G2	EIF4G2
Batch_ID	BGHLV23	BGHLV23
WB_result	92.200	74.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2508	2509

Sequencing Information

	BGHLV23-15	BGHLV23-16
Sample_ID	BGHLV23-15	BGHLV23-16
Sample Name	EIF4G2-BGHLV23-15	EIF4G2-BGHLV23-16
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	60,710,000	62,810,000
total_aligned_reads	53,905,674	56,290,218
unique_aligned_reads	50,706,318	52,894,990
percent_uniqueAligned	0.83522	0.84214
correlation_replicates	0.995310	0.995310
spikein_reads	407,304	337,212
percent_spikeins	0.00671	0.00537
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1130	1131

Data Submission Information

	BGHLV23-15	BGHLV23-15
ENCODE_alias	brenton-graveley:EIF4G2-BGHLV23	brenton-graveley:EIF4G2-BGHLV23-HepG2
ENCODE_accession	ENCSR152MON	ENCSR030SUW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-15	BGHLV23-15
Sample Name	EIF4G2-BGHLV23-15	EIF4G2-BGHLV23-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2942	6695

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
EIF4G2-BGHLV23-15_TTAGGC_L005_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1130	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16658
EIF4G2-BGHLV23-15_TTAGGC_L005_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1130	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16696
EIF4G2-BGHLV23-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1130					GRCh38	V40	EIF4G2-BGHLV23-15_TTAGGC_L005_R1_001.fastq.gz,EIF4G2-BGHLV23-15_TTAGGC_L005_R2_001.fastq.gz		ENCORE2	16734
EIF4G2-BGHLV23-15_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1130					GRCh38	V40	EIF4G2-BGHLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	16772
EIF4G2-BGHLV23-15_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1130					GRCh38	V40	EIF4G2-BGHLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	16810
EIF4G2-BGHLV23-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1130					GRCh38	V40	EIF4G2-BGHLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	16848
EIF4G2-BGHLV23-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1130					GRCh38	V40	EIF4G2-BGHLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	16886
EIF4G2-BGHLV23-15_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1130					GRCh38	V40	EIF4G2-BGHLV23-15_TTAGGC_L005_R1_001.fastq.gz,EIF4G2-BGHLV23-15_TTAGGC_L005_R2_001.fastq.gz		ENCORE2	16924
EIF4G2-BGHLV23-16_TGACCA_L005_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1131	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16659
EIF4G2-BGHLV23-16_TGACCA_L005_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1131	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16697
EIF4G2-BGHLV23-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1131					GRCh38	V40	EIF4G2-BGHLV23-16_TGACCA_L005_R1_001.fastq.gz,EIF4G2-BGHLV23-16_TGACCA_L005_R2_001.fastq.gz		ENCORE2	16735
EIF4G2-BGHLV23-16_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1131					GRCh38	V40	EIF4G2-BGHLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	16773
EIF4G2-BGHLV23-16_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1131					GRCh38	V40	EIF4G2-BGHLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	16811
EIF4G2-BGHLV23-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1131					GRCh38	V40	EIF4G2-BGHLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	16849
EIF4G2-BGHLV23-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1131					GRCh38	V40	EIF4G2-BGHLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	16887
EIF4G2-BGHLV23-16_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1131					GRCh38	V40	EIF4G2-BGHLV23-16_TGACCA_L005_R1_001.fastq.gz,EIF4G2-BGHLV23-16_TGACCA_L005_R2_001.fastq.gz		ENCORE2	16925