EIF4G1 RNA-Seq in HepG2

General Information


RBP	EIF4G1
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF4G1-BGHLV23-HepG2
ENCODE_series_ID	ENCSR885LXL
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR509LIV
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	EIF4G1-BGHLV23-13
Rep2	EIF4G1-BGHLV23-14
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	75.2
Rep2_qPCR	83.5
Rep1_WB	93.5
Rep2_WB	99.9
Antibody Cat#	RN002P
Antibody Lot#	RN002P
Antibody DCC ID	ENCAB000BFI
Status	Released
Project	ENCODE3
ID	541

Experiment Information (Status: Released)

	BGHLV23-13	BGHLV23-14
idx	505	506
TRCN#_or_BGC#	TRCN0000061769	TRCN0000061769
shRNA_or_gRNA_sequence	GCCCTTGTAGTGACCTTAGAA	GCCCTTGTAGTGACCTTAGAA
PAM
Name	EIF4G1_69	EIF4G1_69
Sample_ID	BGHLV23-13	BGHLV23-14
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	EIF4G1	EIF4G1
qPCR_result	75.2	83.5
Ave_qPCR	79.3
RT-qPCR_primer-F	caacctgagtgagcagcaga
RT-qPCR_primer-R	cggaggggagtctcaaaaat
protein_conc	5722	5403
WB_result	93.5	99.9
Ave_WB	96.7
WB_DONE_date	3/9/2015
MW
IP	1	1
antibody_Cat#	RN002P	RN002P
Antibody DCC ID	ENCAB000BFI	ENCAB000BFI
submitted_to_DCC_date	5/4/2015
Rep1_TPM	79.6	0
Rep2_TPM	79.2	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2580	2581

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4G1	Product_ID: RN002P Lot_ID: 2 Source: MBLI Target Name: EIF4G1-human

Experiment Status

	BGHLV23-13	BGHLV23-14
Sample_ID	BGHLV23-13	BGHLV23-14
Sample Name	EIF4G1-BGHLV23-13	EIF4G1-BGHLV23-14
Sample Name	EIF4G1-BGHLV23-13	EIF4G1-BGHLV23-14
RBP	EIF4G1	EIF4G1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	818	819

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-13	BGHLV23-14
Sample #
Sample Name	EIF4G1-BGHLV23-13	EIF4G1-BGHLV23-14
Sample_Name_Alias	EIF4G1-BGHLV23-13	EIF4G1-BGHLV23-14
Index Well Position	S01	S02
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/set1/A12.png	DNA_Library_LV20-22-23/set1/B12.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/E5.png	RNA_Library_LV19-21-24/set2/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-13	BGHLV23-14
RBP	EIF4G1	EIF4G1
Batch_ID	BGHLV23	BGHLV23
WB_result	93.500	99.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2506	2507

Sequencing Information

	BGHLV23-13	BGHLV23-14
Sample_ID	BGHLV23-13	BGHLV23-14
Sample Name	EIF4G1-BGHLV23-13	EIF4G1-BGHLV23-14
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	60,410,000	71,330,000
total_aligned_reads	52,582,752	63,962,432
unique_aligned_reads	49,289,332	59,928,064
percent_uniqueAligned	0.81591	0.84015
correlation_replicates	0.997192	0.997192
spikein_reads	355,160	419,280
percent_spikeins	0.00588	0.00588
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1128	1129

Data Submission Information

	BGHLV23-13	BGHLV23-13
ENCODE_alias	brenton-graveley:EIF4G1-BGHLV23	brenton-graveley:EIF4G1-BGHLV23-HepG2
ENCODE_accession	ENCSR509LIV	ENCSR885LXL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-13	BGHLV23-13
Sample Name	EIF4G1-BGHLV23-13	EIF4G1-BGHLV23-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2941	6693

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
EIF4G1-BGHLV23-13_ATCACG_L005_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1128	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	16656
EIF4G1-BGHLV23-13_ATCACG_L005_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1128	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	16694
EIF4G1-BGHLV23-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1128					GRCh38	V40	EIF4G1-BGHLV23-13_ATCACG_L005_R1_001.fastq.gz,EIF4G1-BGHLV23-13_ATCACG_L005_R2_001.fastq.gz		ENCORE2	16732
EIF4G1-BGHLV23-13_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	1128					GRCh38	V40	EIF4G1-BGHLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	16770
EIF4G1-BGHLV23-13_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	1128					GRCh38	V40	EIF4G1-BGHLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	16808
EIF4G1-BGHLV23-13_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	1128					GRCh38	V40	EIF4G1-BGHLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	16846
EIF4G1-BGHLV23-13_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	1128					GRCh38	V40	EIF4G1-BGHLV23-13/Aligned.sortedByCoord.out.bam		ENCORE2	16884
EIF4G1-BGHLV23-13_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1128					GRCh38	V40	EIF4G1-BGHLV23-13_ATCACG_L005_R1_001.fastq.gz,EIF4G1-BGHLV23-13_ATCACG_L005_R2_001.fastq.gz		ENCORE2	16922
EIF4G1-BGHLV23-14_CGATGT_L005_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1129	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	16657
EIF4G1-BGHLV23-14_CGATGT_L005_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1129	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	16695
EIF4G1-BGHLV23-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1129					GRCh38	V40	EIF4G1-BGHLV23-14_CGATGT_L005_R1_001.fastq.gz,EIF4G1-BGHLV23-14_CGATGT_L005_R2_001.fastq.gz		ENCORE2	16733
EIF4G1-BGHLV23-14_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	1129					GRCh38	V40	EIF4G1-BGHLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	16771
EIF4G1-BGHLV23-14_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	1129					GRCh38	V40	EIF4G1-BGHLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	16809
EIF4G1-BGHLV23-14_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	1129					GRCh38	V40	EIF4G1-BGHLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	16847
EIF4G1-BGHLV23-14_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	1129					GRCh38	V40	EIF4G1-BGHLV23-14/Aligned.sortedByCoord.out.bam		ENCORE2	16885
EIF4G1-BGHLV23-14_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1129					GRCh38	V40	EIF4G1-BGHLV23-14_CGATGT_L005_R1_001.fastq.gz,EIF4G1-BGHLV23-14_CGATGT_L005_R2_001.fastq.gz		ENCORE2	16923