EEF2 RNA-Seq in HepG2

General Information


RBP	EEF2
Cell_Line	HepG2
Method	shRNA
Exp_Name	EEF2-BGHLV16-HepG2
ENCODE_series_ID	ENCSR471OBZ
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR477TRX
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	EEF2_BGHLV16_19
Rep2	EEF2_BGHLV16_20
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	80.9
Rep2_qPCR	80.4
Rep1_WB	69.9
Rep2_WB	59.3
Antibody Cat#	A301-688A
Antibody Lot#	A301-688A
Antibody DCC ID	ENCAB334DWC
Status	Released
Project	ENCODE3
ID	415

Experiment Information (Status: Released)

	BGHLV16-19	BGHLV16-20
idx	187	188
TRCN#_or_BGC#	TRCN0000047908	TRCN0000047908
shRNA_or_gRNA_sequence	GCGATCATGAATTTCAAGAAA	GCGATCATGAATTTCAAGAAA
PAM
Name	EEF2	EEF2
Sample_ID	BGHLV16-19	BGHLV16-20
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	EEF2	EEF2
qPCR_result	80.9	80.4
Ave_qPCR	80.7
RT-qPCR_primer-F	aacggcaagttcagcaagtc
RT-qPCR_primer-R	cgcatcaaacaccttgaaga
protein_conc	2343	2116
WB_result	69.9	59.3
Ave_WB	64.6
WB_DONE_date	12/22/2014
MW	95kDa
IP	1	1
antibody_Cat#	A301-688A	A301-688A
Antibody DCC ID	ENCAB334DWC	ENCAB334DWC
submitted_to_DCC_date	4/2/2015
Rep1_TPM	1137.8	0
Rep2_TPM	1631.9	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2254	2255

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

Experiment Status

	BGHLV16-19	BGHLV16-20
Sample_ID	BGHLV16-19	BGHLV16-20
Sample Name	EEF2_BGHLV16_19	EEF2_BGHLV16_20
Sample Name	EEF2_BGHLV16_19	EEF2_BGHLV16_20
RBP	EEF2	EEF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	554	555

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-19	BGHLV16-20
Sample #
Sample Name	EEF2-BGHLV16-19	EEF2-BGHLV16-20
Sample_Name_Alias	EEF2_BGHLV16_19	EEF2_BGHLV16_20
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/E6.png	DNA_Library_LV16-17/set1/F6.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C12.png	RNA_Library_LV13-14-16/set1/D12.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-19	BGHLV16-20
RBP	EEF2	EEF2
Batch_ID	BGHLV16	BGHLV16
WB_result	69.900	59.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2238	2239

Sequencing Information

	BGHLV16-19	BGHLV16-20
Sample_ID	BGHLV16-19	BGHLV16-20
Sample Name	EEF2_BGHLV16_19	EEF2_BGHLV16_20
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	67,610,000	75,370,000
total_aligned_reads	59,403,790	67,665,096
unique_aligned_reads	56,078,698	63,976,318
percent_uniqueAligned	0.82944	0.84883
correlation_replicates	0.997837	0.997837
spikein_reads	99,744	129,370
percent_spikeins	0.00148	0.00172
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	880	881

Data Submission Information

	BGHLV16-19	BGHLV16-19
ENCODE_alias	brenton-graveley:EEF2_BGHLV16	brenton-graveley:EEF2-BGHLV16-HepG2
ENCODE_accession	ENCSR477TRX	ENCSR471OBZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-19	BGHLV16-19
Sample Name	EEF2_BGHLV16_19	EEF2_BGHLV16_19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2845	6674

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_BGHLV16_19_ACAGTG_L006_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	880	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14280
EEF2_BGHLV16_19_ACAGTG_L006_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	880	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14306
EEF2_BGHLV16_19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	880					GRCh38	V40	EEF2_BGHLV16_19_ACAGTG_L006_R1_001.fastq.gz,EEF2_BGHLV16_19_ACAGTG_L006_R2_001.fastq.gz		ENCORE2	14332
EEF2_BGHLV16_19_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	880					GRCh38	V40	EEF2_BGHLV16_19/Aligned.sortedByCoord.out.bam		ENCORE2	14358
EEF2_BGHLV16_19_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	880					GRCh38	V40	EEF2_BGHLV16_19/Aligned.sortedByCoord.out.bam		ENCORE2	14384
EEF2_BGHLV16_19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	880					GRCh38	V40	EEF2_BGHLV16_19/Aligned.sortedByCoord.out.bam		ENCORE2	14410
EEF2_BGHLV16_19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	880					GRCh38	V40	EEF2_BGHLV16_19/Aligned.sortedByCoord.out.bam		ENCORE2	14436
EEF2_BGHLV16_19_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	880					GRCh38	V40	EEF2_BGHLV16_19_ACAGTG_L006_R1_001.fastq.gz,EEF2_BGHLV16_19_ACAGTG_L006_R2_001.fastq.gz		ENCORE2	14462
EEF2_BGHLV16_20_GCCAAT_L006_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	881	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14281
EEF2_BGHLV16_20_GCCAAT_L006_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	881	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14307
EEF2_BGHLV16_20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	881					GRCh38	V40	EEF2_BGHLV16_20_GCCAAT_L006_R1_001.fastq.gz,EEF2_BGHLV16_20_GCCAAT_L006_R2_001.fastq.gz		ENCORE2	14333
EEF2_BGHLV16_20_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	881					GRCh38	V40	EEF2_BGHLV16_20/Aligned.sortedByCoord.out.bam		ENCORE2	14359
EEF2_BGHLV16_20_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	881					GRCh38	V40	EEF2_BGHLV16_20/Aligned.sortedByCoord.out.bam		ENCORE2	14385
EEF2_BGHLV16_20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	881					GRCh38	V40	EEF2_BGHLV16_20/Aligned.sortedByCoord.out.bam		ENCORE2	14411
EEF2_BGHLV16_20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	881					GRCh38	V40	EEF2_BGHLV16_20/Aligned.sortedByCoord.out.bam		ENCORE2	14437
EEF2_BGHLV16_20_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	881					GRCh38	V40	EEF2_BGHLV16_20_GCCAAT_L006_R1_001.fastq.gz,EEF2_BGHLV16_20_GCCAAT_L006_R2_001.fastq.gz		ENCORE2	14463