EIF3A RNA-Seq in K562

General Information


RBP	EIF3A
Cell_Line	K562
Method	shRNA
Exp_Name	EIF3A-BGKLV24-K562
ENCODE_series_ID	ENCSR475GEI
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR258VGD
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	EIF3A_BGKLV24_21_17613
Rep2	EIF3A_BGKLV24_22_17614
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	66.5
Rep2_qPCR	63.6
Rep1_WB	67.4
Rep2_WB	87.8
Antibody Cat#	A302-002A
Antibody Lot#	A302-002A
Antibody DCC ID	ENCAB265WCJ
Status	Released
Project	ENCODE3
ID	563

Experiment Information (Status: Released)

	BGKLV24-21	BGKLV24-21	BGKLV24-21	BGKLV24-22	BGKLV24-22	BGKLV24-22
idx	358	358	358	359	359	359
TRCN#_or_BGC#	TRCN0000074805	TRCN0000074805	TRCN0000074805	TRCN0000074805	TRCN0000074805	TRCN0000074805
shRNA_or_gRNA_sequence	CGTGCTGATGATGATCGGTTT	CGTGCTGATGATGATCGGTTT	CGTGCTGATGATGATCGGTTT	CGTGCTGATGATGATCGGTTT	CGTGCTGATGATGATCGGTTT	CGTGCTGATGATGATCGGTTT
PAM
Name	EIF3A	EIF3A	EIF3A	EIF3A	EIF3A	EIF3A
Sample_ID	BGKLV24-21	BGKLV24-21	BGKLV24-21	BGKLV24-22	BGKLV24-22	BGKLV24-22
transduction_Date	2/27/2015	2/27/2015	2/27/2015	2/27/2015	2/27/2015	2/27/2015
days
RBP_name	EIF3A	EIF3A	EIF3A	EIF3A	EIF3A	EIF3A
qPCR_result	66.5	66.5	66.5	63.6	63.6	63.6
Ave_qPCR	65.1	65.1	65.1
RT-qPCR_primer-F	atggatgatgatcgcctttc	atggatgatgatcgcctttc	atggatgatgatcgcctttc
RT-qPCR_primer-R	ccacctggcttgactaatgg	ccacctggcttgactaatgg	ccacctggcttgactaatgg
protein_conc	1961	1961	1961	2089	2089	2089
WB_result	67.4	56.0	59.2	87.8	50.0	61.2
Ave_WB	77.6	53.0	60.2
WB_DONE_date	5/19/2015	6/26/2023	6/14/2023
MW	167kDa	167kDa	167kDa
IP	1			1
antibody_Cat#	A302-002A	A302-003A	3411S	A302-002A	LOT # 2	LOT# 3
Antibody DCC ID	ENCAB265WCJ	SUBMITTED	SUBMITTED	ENCAB265WCJ	10/18/23	10/18/23
submitted_to_DCC_date	8/6/2015
Rep1_TPM	120.106804	0	0	0	0	0
Rep2_TPM	108.640926	0	0	0	0	0
Action
Library_start_date	5/22/2015			5/22/2015
repeat_library
Note
ID	407	409	411	408	410	412

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3A	Product_ID: A302-002A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3A-human
EIF3A	Product_ID: 3411S Lot_ID: 3 Source: Cell Signaling Technology Target Name: EIF3A-human
EIF3A	Product_ID: A302-003A Lot_ID: 2 Source: Bethyl Labs Target Name: EIF3A-human

Experiment Status

	BGKLV24-21	BGKLV24-22
Sample_ID	BGKLV24-21	BGKLV24-22
Sample Name	EIF3A_BGKLV24_21_17613	EIF3A_BGKLV24_22_17614
Sample Name	EIF3A_BGKLV24_21_17613	EIF3A_BGKLV24_22_17614
RBP	EIF3A	EIF3A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	864	865

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-21	BGKLV24-22
Sample #
Sample Name	EIF3A-BGKLV24-21	EIF3A-BGKLV24-22
Sample_Name_Alias	EIF3A_BGKLV24_21_17613	EIF3A_BGKLV24_22_17614
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/D3.png	DNA_Library_LV21-24/set2/B1.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A3.png	RNA_Library_LV20-22-24/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-21	BGKLV24-22
RBP	EIF3A	EIF3A
Batch_ID	BGKLV24	BGKLV24
WB_result	67.400	87.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2552	2553

Sequencing Information

	BGKLV24-21	BGKLV24-22
Sample_ID	BGKLV24-21	BGKLV24-22
Sample Name	EIF3A_BGKLV24_21_17613	EIF3A_BGKLV24_22_17614
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	36,220,000	29,660,000
total_aligned_reads	34,140,634	24,912,546
unique_aligned_reads	31,271,868	22,837,072
percent_uniqueAligned	0.86339	0.76996
correlation_replicates	0.988036	0.988036
spikein_reads	210,704	155,624
percent_spikeins	0.00582	0.00525
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1086	1087

Data Submission Information

	BGKLV24-21	BGKLV24-21
ENCODE_alias	brenton-graveley:EIF3A_BGKLV24	brenton-graveley:EIF3A-BGKLV24-K562
ENCODE_accession	ENCSR258VGD	ENCSR475GEI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-21	BGKLV24-21
Sample Name	EIF3A_BGKLV24_21_17613	EIF3A_BGKLV24_21_17613
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2983	6682

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
EIF3A_BGKLV24_21_17613_GGCTAC_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1086	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17198
EIF3A_BGKLV24_21_17613_GGCTAC_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1086	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17234
EIF3A_BGKLV24_21_17613_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1086					GRCh38	V40	EIF3A_BGKLV24_21_17613_GGCTAC_L007_R1_001.fastq.gz,EIF3A_BGKLV24_21_17613_GGCTAC_L007_R2_001.fastq.gz		ENCORE2	17270
EIF3A_BGKLV24_21_17613_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1086					GRCh38	V40	EIF3A_BGKLV24_21_17613/Aligned.sortedByCoord.out.bam		ENCORE2	17306
EIF3A_BGKLV24_21_17613_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1086					GRCh38	V40	EIF3A_BGKLV24_21_17613/Aligned.sortedByCoord.out.bam		ENCORE2	17342
EIF3A_BGKLV24_21_17613_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1086					GRCh38	V40	EIF3A_BGKLV24_21_17613/Aligned.sortedByCoord.out.bam		ENCORE2	17378
EIF3A_BGKLV24_21_17613_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1086					GRCh38	V40	EIF3A_BGKLV24_21_17613/Aligned.sortedByCoord.out.bam		ENCORE2	17414
EIF3A_BGKLV24_21_17613_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1086					GRCh38	V40	EIF3A_BGKLV24_21_17613_GGCTAC_L007_R1_001.fastq.gz,EIF3A_BGKLV24_21_17613_GGCTAC_L007_R2_001.fastq.gz		ENCORE2	17450
EIF3A_BGKLV24_22_17614_CTTGTA_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1087	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17199
EIF3A_BGKLV24_22_17614_CTTGTA_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1087	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17235
EIF3A_BGKLV24_22_17614_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1087					GRCh38	V40	EIF3A_BGKLV24_22_17614_CTTGTA_L007_R1_001.fastq.gz,EIF3A_BGKLV24_22_17614_CTTGTA_L007_R2_001.fastq.gz		ENCORE2	17271
EIF3A_BGKLV24_22_17614_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1087					GRCh38	V40	EIF3A_BGKLV24_22_17614/Aligned.sortedByCoord.out.bam		ENCORE2	17307
EIF3A_BGKLV24_22_17614_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1087					GRCh38	V40	EIF3A_BGKLV24_22_17614/Aligned.sortedByCoord.out.bam		ENCORE2	17343
EIF3A_BGKLV24_22_17614_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1087					GRCh38	V40	EIF3A_BGKLV24_22_17614/Aligned.sortedByCoord.out.bam		ENCORE2	17379
EIF3A_BGKLV24_22_17614_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1087					GRCh38	V40	EIF3A_BGKLV24_22_17614/Aligned.sortedByCoord.out.bam		ENCORE2	17415
EIF3A_BGKLV24_22_17614_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1087					GRCh38	V40	EIF3A_BGKLV24_22_17614_CTTGTA_L007_R1_001.fastq.gz,EIF3A_BGKLV24_22_17614_CTTGTA_L007_R2_001.fastq.gz		ENCORE2	17451