EIF4G2 RNA-Seq in K562

General Information


RBP	EIF4G2
Cell_Line	K562
Method	shRNA
Exp_Name	EIF4G2-BGKLV25-K562
ENCODE_series_ID	ENCSR051ACD
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR040FSN
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	EIF4G2_BGKLV25-17
Rep2	EIF4G2_BGKLV25-18
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	76.4
Rep2_qPCR	80.0
Rep1_WB	88.4
Rep2_WB	85.7
Antibody Cat#	RN003P
Antibody Lot#	RN003P
Antibody DCC ID	ENCAB000BFJ
Status	Released
Project	ENCODE3
ID	616

Experiment Information (Status: Released)

	BGKLV25-17	BGKLV25-17	BGKLV25-17	BGKLV25-18	BGKLV25-18	BGKLV25-18
idx	418	0	0	419	0	0
TRCN#_or_BGC#	TRCN0000150297	TRCN0000150297	TRCN0000150297	TRCN0000150297	TRCN0000150297	TRCN0000150297
shRNA_or_gRNA_sequence	CCCTTTGGTGAAATCCTATTT			CCCTTTGGTGAAATCCTATTT
PAM
Name	EIF4G2	EIF4G2	EIF4G2	EIF4G2	EIF4G2	EIF4G2
Sample_ID	BGKLV25-17	BGKLV25-17	BGKLV25-17	BGKLV25-18	BGKLV25-18	BGKLV25-18
transduction_Date	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015	3/17/2015
days
RBP_name	EIF4G2	EIF4G2	EIF4G2	EIF4G2	EIF4G2	EIF4G2
qPCR_result	76.4	76.4	76.4	80.0	80.0	80.0
Ave_qPCR	78.2	78.2	78.2
RT-qPCR_primer-F	GGGTGCACCTCAGCACTATC	GGGTGCACCTCAGCACTATC	GGGTGCACCTCAGCACTATC
RT-qPCR_primer-R	CTTCGTGCAGGAATCCATTT	CTTCGTGCAGGAATCCATTT	CTTCGTGCAGGAATCCATTT
protein_conc	3441	3441	3441	3235	3235	3235
WB_result	88.4	92.4	91.8	85.7	91.4	86.3
Ave_WB	87.1	91.9	89.0	no more samples
WB_DONE_date	4/14/2015	4/4/2019	4/4/19,5/8/2019
MW	102kDa	102kDa	102kDa
IP	1			1
antibody_Cat#	RN003P	PA5-21377	702479	RN003P	LOT# TK2671326
Antibody DCC ID	ENCAB000BFJ	ENCAB363IRI		ENCAB000BFJ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	132.949527	0	0	0	0	0
Rep2_TPM	69.2360815	0	0	0	0	0
Action
Library_start_date	6/23/2015			6/23/2015
repeat_library
Note
ID	477	479	481	478	480	482

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
EIF4G2	Product_ID: 702479 Lot_ID: NotAvailable Source: Thermo Fisher Target Name: EIF4G2-human
EIF4G2	Product_ID: PA5-21377 Lot_ID: TK2671326 Source: Thermo Fisher Target Name: EIF4G2-human

Experiment Status

	BGKLV25-17	BGKLV25-18
Sample_ID	BGKLV25-17	BGKLV25-18
Sample Name	EIF4G2_BGKLV25-17	EIF4G2_BGKLV25-18
Sample Name	EIF4G2_BGKLV25-17	EIF4G2_BGKLV25-18
RBP	EIF4G2	EIF4G2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	912	913

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-17	BGKLV25-18
Sample #
Sample Name	EIF4G2-BGKLV25-17	EIF4G2-BGKLV25-18
Sample_Name_Alias	EIF4G2_BGKLV25-17	EIF4G2_BGKLV25-18
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/A2.png	DNA_Library_LV24-25-26/set1/B2.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C10.png	RNA_Library_LV22-23-25/set1/D10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-17	BGKLV25-18
RBP	EIF4G2	EIF4G2
Batch_ID	BGKLV25	BGKLV25
WB_result	88.400	85.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2602	2603

Sequencing Information

	BGKLV25-17	BGKLV25-18
Sample_ID	BGKLV25-17	BGKLV25-18
Sample Name	EIF4G2_BGKLV25-17	EIF4G2_BGKLV25-18
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	96,629,512	67,039,180
total_aligned_reads	99,072,486	68,176,924
unique_aligned_reads	89,987,216	62,020,188
percent_uniqueAligned	0.93126	0.92513
correlation_replicates	0.999742	0.999742
spikein_reads	696,704	412,382
percent_spikeins	0.00721	0.00615
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1244	1245

Data Submission Information

	BGKLV25-17	BGKLV25-17
ENCODE_alias	brenton-graveley:EIF4G2_BGKLV25	brenton-graveley:EIF4G2-BGKLV25-K562
ENCODE_accession	ENCSR040FSN	ENCSR051ACD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-17	BGKLV25-17
Sample Name	EIF4G2_BGKLV25-17	EIF4G2_BGKLV25-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3005	6696

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_BGKLV25-17_GTCCGC_L005_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1244	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19570
EIF4G2_BGKLV25-17_GTCCGC_L005_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1244	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19606
EIF4G2_BGKLV25-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1244					GRCh38	V40	EIF4G2_BGKLV25-17_GTCCGC_L005_001.R1.fastq.gz,EIF4G2_BGKLV25-17_GTCCGC_L005_001.R2.fastq.gz		ENCORE2	19642
EIF4G2_BGKLV25-17_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1244					GRCh38	V40	EIF4G2_BGKLV25-17/Aligned.sortedByCoord.out.bam		ENCORE2	19678
EIF4G2_BGKLV25-17_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1244					GRCh38	V40	EIF4G2_BGKLV25-17/Aligned.sortedByCoord.out.bam		ENCORE2	19714
EIF4G2_BGKLV25-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1244					GRCh38	V40	EIF4G2_BGKLV25-17/Aligned.sortedByCoord.out.bam		ENCORE2	19750
EIF4G2_BGKLV25-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1244					GRCh38	V40	EIF4G2_BGKLV25-17/Aligned.sortedByCoord.out.bam		ENCORE2	19786
EIF4G2_BGKLV25-17_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1244					GRCh38	V40	EIF4G2_BGKLV25-17_GTCCGC_L005_001.R1.fastq.gz,EIF4G2_BGKLV25-17_GTCCGC_L005_001.R2.fastq.gz		ENCORE2	19976
EIF4G2_BGKLV25-18_GTGAAA_L005_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1245	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19571
EIF4G2_BGKLV25-18_GTGAAA_L005_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1245	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19607
EIF4G2_BGKLV25-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1245					GRCh38	V40	EIF4G2_BGKLV25-18_GTGAAA_L005_001.R1.fastq.gz,EIF4G2_BGKLV25-18_GTGAAA_L005_001.R2.fastq.gz		ENCORE2	19643
EIF4G2_BGKLV25-18_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1245					GRCh38	V40	EIF4G2_BGKLV25-18/Aligned.sortedByCoord.out.bam		ENCORE2	19679
EIF4G2_BGKLV25-18_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1245					GRCh38	V40	EIF4G2_BGKLV25-18/Aligned.sortedByCoord.out.bam		ENCORE2	19715
EIF4G2_BGKLV25-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1245					GRCh38	V40	EIF4G2_BGKLV25-18/Aligned.sortedByCoord.out.bam		ENCORE2	19751
EIF4G2_BGKLV25-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1245					GRCh38	V40	EIF4G2_BGKLV25-18/Aligned.sortedByCoord.out.bam		ENCORE2	19787
EIF4G2_BGKLV25-18_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1245					GRCh38	V40	EIF4G2_BGKLV25-18_GTGAAA_L005_001.R1.fastq.gz,EIF4G2_BGKLV25-18_GTGAAA_L005_001.R2.fastq.gz		ENCORE2	19977