EEF2 RNA-Seq in K562

General Information


RBP	EEF2
Cell_Line	K562
Method	shRNA
Exp_Name	EEF2-BGKLV19-K562
ENCODE_series_ID	ENCSR396EPO
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR181RLB
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	EEF2_BGKLV19_21B
Rep2	EEF2_BGKLV19_22B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	97.6
Rep2_qPCR	97.2
Rep1_WB	62.7
Rep2_WB	68.9
Antibody Cat#	A301-688A
Antibody Lot#	A301-688A
Antibody DCC ID	ENCAB334DWC
Status	Released
Project	ENCODE3
ID	470

Experiment Information (Status: Released)

	BGKLV19-21	BGKLV19-21	BGKLV19-21	BGKLV19-21	BGKLV19-22	BGKLV19-22	BGKLV19-22	BGKLV19-22
idx	228	0	0	0	229	0	0	0
TRCN#_or_BGC#	TRCN0000047908	TRCN0000047908	TRCN0000047908	TRCN0000047908	TRCN0000047908	TRCN0000047908	TRCN0000047908	TRCN0000047908
shRNA_or_gRNA_sequence	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA
PAM
Name	EEF2	EEF2	EEF2	EEF2	EEF2	EEF2	EEF2	EEF2
Sample_ID	BGKLV19-21	BGKLV19-21	BGKLV19-21	BGKLV19-21	BGKLV19-22	BGKLV19-22	BGKLV19-22	BGKLV19-22
transduction_Date	9/4/2014	9/4/2014	9/4/2014	9/4/2014	9/4/2014	9/4/2014	9/4/2014	9/4/2014
days
RBP_name	EEF2	EEF2	EEF2	EEF2	EEF2	EEF2	EEF2	EEF2
qPCR_result	97.6	97.6	97.6	97.6	97.2	97.2	97.2	97.2
Ave_qPCR	97.4	97.4	97.4	97.4
RT-qPCR_primer-F	aacggcaagttcagcaagtc	aacggcaagttcagcaagtc	aacggcaagttcagcaagtc	aacggcaagttcagcaagtc
RT-qPCR_primer-R	cgcatcaaacaccttgaaga	cgcatcaaacaccttgaaga	cgcatcaaacaccttgaaga	cgcatcaaacaccttgaaga
protein_conc	1876	1876	1876	1876	2339	2339	2339	2339
WB_result	62.7	59.0	62.8	29.6	68.9	69.2	64.6	26.0
Ave_WB	65.8	64.1	63.7	27.8
WB_DONE_date	12/5/2014	3/27/2019	5/6/2019	9/27/2019		WES	WES	WES
MW		95kd	95kd	95kd
IP	1				1
antibody_Cat#	A301-688A	702807	711842	711843	A301-688A	LOT# 2000400	LOT# 1931156
Antibody DCC ID	ENCAB334DWC	ENCAB828EJY	ENCAB559BYO		ENCAB334DWC
submitted_to_DCC_date	4/2/2015	4/17/2019	4/17/2019
Rep1_TPM	1003.71034	0	0	0	0	0	0	0
Rep2_TPM	1827.85123	0	0	0	0	0	0	0
Action
Library_start_date	10/2/2014				10/2/2014
repeat_library
Note
ID	247	249	251	253	248	250	252	254

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EEF2	Product_ID: A301-688A Lot_ID: 1 Source: Bethyl Labs Target Name: EEF2-human
EEF2	Product_ID: 702807 Lot_ID: 2000400 Source: Thermo Fisher Target Name: EEF2-human
EEF2	Product_ID: 711842 Lot_ID: 1931156 Source: Thermo Fisher Target Name: EEF2-human

Experiment Status

	BGKLV19-21	BGKLV19-22
Sample_ID	BGKLV19-21	BGKLV19-22
Sample Name	EEF2_BGKLV19_21B	EEF2_BGKLV19_22B
Sample Name	EEF2_BGKLV19_21B	EEF2_BGKLV19_22B
RBP	EEF2	EEF2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	670	671

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-21	BGKLV19-22
Sample #
Sample Name	EEF2-BGKLV19-21B	EEF2-BGKLV19-22B
Sample_Name_Alias	EEF2_BGKLV19_21B	EEF2_BGKLV19_22B
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C8.png	DNA_Library_LV18-19/set1/D8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G2.png	RNA_Library_LV19-21-24/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-21	BGKLV19-22
RBP	EEF2	EEF2
Batch_ID	BGKLV19	BGKLV19
WB_result	62.700	68.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2356	2357

Sequencing Information

	BGKLV19-21	BGKLV19-22
Sample_ID	BGKLV19-21	BGKLV19-22
Sample Name	EEF2_BGKLV19_21B	EEF2_BGKLV19_22B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	63,030,000	40,640,000
total_aligned_reads	59,203,074	38,164,828
unique_aligned_reads	54,051,186	34,707,562
percent_uniqueAligned	0.85755	0.85402
correlation_replicates	0.997156	0.997156
spikein_reads	435,182	192,066
percent_spikeins	0.00690	0.00473
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	998	999

Data Submission Information

	BGKLV19-21	BGKLV19-21
ENCODE_alias	brenton-graveley:EEF2_BGKLV19	brenton-graveley:EEF2-BGKLV19-K562
ENCODE_accession	ENCSR181RLB	ENCSR396EPO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-21	BGKLV19-21
Sample Name	EEF2_BGKLV19_21B	EEF2_BGKLV19_21B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2884	6675

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
EEF2_BGKLV19_21B_GGCTAC_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	998	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15110
EEF2_BGKLV19_21B_GGCTAC_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	998	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15168
EEF2_BGKLV19_21B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	998					GRCh38	V40	EEF2_BGKLV19_21B_GGCTAC_L003_R1_001.fastq.gz,EEF2_BGKLV19_21B_GGCTAC_L003_R2_001.fastq.gz		ENCORE2	15226
EEF2_BGKLV19_21B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	998					GRCh38	V40	EEF2_BGKLV19_21B/Aligned.sortedByCoord.out.bam		ENCORE2	15297
EEF2_BGKLV19_21B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	998					GRCh38	V40	EEF2_BGKLV19_21B/Aligned.sortedByCoord.out.bam		ENCORE2	15355
EEF2_BGKLV19_21B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	998					GRCh38	V40	EEF2_BGKLV19_21B/Aligned.sortedByCoord.out.bam		ENCORE2	15413
EEF2_BGKLV19_21B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	998					GRCh38	V40	EEF2_BGKLV19_21B/Aligned.sortedByCoord.out.bam		ENCORE2	15471
EEF2_BGKLV19_21B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	998					GRCh38	V40	EEF2_BGKLV19_21B_GGCTAC_L003_R1_001.fastq.gz,EEF2_BGKLV19_21B_GGCTAC_L003_R2_001.fastq.gz		ENCORE2	16368
EEF2_BGKLV19_22B_CTTGTA_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	999	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15111
EEF2_BGKLV19_22B_CTTGTA_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	999	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15169
EEF2_BGKLV19_22B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	999					GRCh38	V40	EEF2_BGKLV19_22B_CTTGTA_L003_R1_001.fastq.gz,EEF2_BGKLV19_22B_CTTGTA_L003_R2_001.fastq.gz		ENCORE2	15227
EEF2_BGKLV19_22B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	999					GRCh38	V40	EEF2_BGKLV19_22B/Aligned.sortedByCoord.out.bam		ENCORE2	15298
EEF2_BGKLV19_22B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	999					GRCh38	V40	EEF2_BGKLV19_22B/Aligned.sortedByCoord.out.bam		ENCORE2	15356
EEF2_BGKLV19_22B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	999					GRCh38	V40	EEF2_BGKLV19_22B/Aligned.sortedByCoord.out.bam		ENCORE2	15414
EEF2_BGKLV19_22B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	999					GRCh38	V40	EEF2_BGKLV19_22B/Aligned.sortedByCoord.out.bam		ENCORE2	15472
EEF2_BGKLV19_22B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	999					GRCh38	V40	EEF2_BGKLV19_22B_CTTGTA_L003_R1_001.fastq.gz,EEF2_BGKLV19_22B_CTTGTA_L003_R2_001.fastq.gz		ENCORE2	16369