EIF4A3 RNA-Seq in K562

General Information


RBP	EIF4A3
Cell_Line	K562
Method	shRNA
Exp_Name	EIF4A3-BGKLV08-K562
ENCODE_series_ID	ENCSR733XTT
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR961YAG
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	EIF4A3-LV08-21
Rep2	EIF4A3-LV08-22
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	47.7
Rep2_qPCR	63.0
Rep1_WB	29.4
Rep2_WB	39.0
Antibody Cat#	A302-981A
Antibody Lot#	A302-981A
Antibody DCC ID	ENCAB574DGT
Status	Archived
Project	ENCODE3
ID	287

Experiment Information (Status: Released)

	BGKLV08-21	BGKLV08-22
idx	22	23
TRCN#_or_BGC#	TRCN0000061855	TRCN0000061855
shRNA_or_gRNA_sequence	GCAATCAAGCAGATCATCAAA	GCAATCAAGCAGATCATCAAA
PAM
Name	EIF4A3	EIF4A3
Sample_ID	BGKLV08-21	BGKLV08-22
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	EIF4A3	EIF4A3
qPCR_result	47.7	63.0
Ave_qPCR	55.4
RT-qPCR_primer-F	CATCCGCATCCTCAGAGATA
RT-qPCR_primer-R	CCCACTGATCTGCTGCTTC
protein_conc	2274	2436
WB_result	29.4	39.0
Ave_WB	34.2
WB_DONE_date
MW	47kDa
IP	1	1
antibody_Cat#	A302-981A	A302-981A
Antibody DCC ID	ENCAB574DGT	ENCAB574DGT
submitted_to_DCC_date	4/2/2015
Rep1_TPM	21.7437682	0
Rep2_TPM	23.4232494	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	21	22

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4A3	Product_ID: A302-981A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF4A3-human

Experiment Status

	BGKLV08-21	BGKLV08-22
Sample_ID	BGKLV08-21	BGKLV08-22
Sample Name	EIF4A3-LV08-21	EIF4A3-LV08-22
Sample Name	EIF4A3-LV08-21	EIF4A3-LV08-22
RBP	EIF4A3	EIF4A3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	282	283

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-21	BGKLV08-22
Sample #
Sample Name	EIF4A3-BGKLV08-21	EIF4A3-BGKLV08-22
Sample_Name_Alias	EIF4A3-LV08-21	EIF4A3-LV08-22
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set2/C1.png	DNA_Library_LV08/set2/D1.png
RIN	9.7	9.2
libSample_RNA_Well	RNA_Library_LV37_38/set3/C1.png	RNA_Library_LV08/set2/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-21	BGKLV08-22
RBP	EIF4A3	EIF4A3
Batch_ID	BGKLV08	BGKLV08
WB_result	29.400	39.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1904	1905

Sequencing Information

	BGKLV08-21	BGKLV08-22
Sample_ID	BGKLV08-21	BGKLV08-22
Sample Name	EIF4A3-LV08-21	EIF4A3-LV08-22
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	46,030,000	47,720,000
total_aligned_reads	41,574,908	42,291,516
unique_aligned_reads	37,993,674	38,565,448
percent_uniqueAligned	0.82541	0.80816
correlation_replicates	0.993282	0.993282
spikein_reads	377,428	482,472
percent_spikeins	0.00820	0.01011
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	604	605

Data Submission Information

	BGKLV08-21	BGKLV08-21
ENCODE_alias	brenton-graveley:EIF4A3-LV08	brenton-graveley:EIF4A3-BGKLV08-K562
ENCODE_accession	ENCSR961YAG	ENCSR733XTT
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-21	BGKLV08-21
Sample Name	EIF4A3-LV08-21	EIF4A3-LV08-21
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2690	6690

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
EIF4A3-LV08-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	604					GRCh38	V40	EIF4A3-LV08-21_GTCCGC_L003_R1_001.fastq.gz,EIF4A3-LV08-21_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	11989
EIF4A3-LV08-21_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	604	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12045
EIF4A3-LV08-21_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	604	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12101
EIF4A3-LV08-21_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	604					GRCh38	V40	EIF4A3-LV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	12157
EIF4A3-LV08-21_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	604					GRCh38	V40	EIF4A3-LV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	12213
EIF4A3-LV08-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	604					GRCh38	V40	EIF4A3-LV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	12269
EIF4A3-LV08-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	604					GRCh38	V40	EIF4A3-LV08-21/Aligned.sortedByCoord.out.bam		ENCORE2	12325
EIF4A3-LV08-21_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	604					GRCh38	V40	EIF4A3-LV08-21_GTCCGC_L003_R1_001.fastq.gz,EIF4A3-LV08-21_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	13324
EIF4A3-LV08-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	605					GRCh38	V40	EIF4A3-LV08-22_GTGAAA_L003_R1_001.fastq.gz,EIF4A3-LV08-22_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	11990
EIF4A3-LV08-22_GTGAAA_L003_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	605	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12046
EIF4A3-LV08-22_GTGAAA_L003_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	605	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12102
EIF4A3-LV08-22_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	605					GRCh38	V40	EIF4A3-LV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	12158
EIF4A3-LV08-22_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	605					GRCh38	V40	EIF4A3-LV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	12214
EIF4A3-LV08-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	605					GRCh38	V40	EIF4A3-LV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	12270
EIF4A3-LV08-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	605					GRCh38	V40	EIF4A3-LV08-22/Aligned.sortedByCoord.out.bam		ENCORE2	12326
EIF4A3-LV08-22_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	605					GRCh38	V40	EIF4A3-LV08-22_GTGAAA_L003_R1_001.fastq.gz,EIF4A3-LV08-22_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	13325