EFTUD2 RNA-Seq in HepG2

General Information


RBP	EFTUD2
Cell_Line	HepG2
Method	shRNA
Exp_Name	EFTUD2-BGHLV16-HepG2
ENCODE_series_ID	ENCSR669NXJ
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR620OKS
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	EFTUD2_BGHLV16_21
Rep2	EFTUD2_BGHLV16_22
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	65.4
Rep2_qPCR	69.6
Rep1_WB	46.2
Rep2_WB	34.6
Antibody Cat#	A300-957A
Antibody Lot#	A300-957A
Antibody DCC ID	ENCAB787OVJ
Status	Released
Project	ENCODE3
ID	416

Experiment Information (Status: Released)

	BGHLV16-21	BGHLV16-22
idx	189	190
TRCN#_or_BGC#	TRCN0000074654	TRCN0000074654
shRNA_or_gRNA_sequence	CCCATTATTAAGCCAGTGAAA	CCCATTATTAAGCCAGTGAAA
PAM
Name	EFTUD2	EFTUD2
Sample_ID	BGHLV16-21	BGHLV16-22
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	EFTUD2	EFTUD2
qPCR_result	65.4	69.6
Ave_qPCR	67.5
RT-qPCR_primer-F	ttattacaagctgcgccaca
RT-qPCR_primer-R	gaagcagacgttacccagga
protein_conc	2745	3166
WB_result	46.2	34.6
Ave_WB	40.4
WB_DONE_date	12/22/2014
MW	109kDa
IP	1	1
antibody_Cat#	A300-957A	A300-957A
Antibody DCC ID	ENCAB787OVJ	ENCAB787OVJ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	38.8	0
Rep2_TPM	35.2	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2256	2257

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EFTUD2	Product_ID: A300-957A Lot_ID: 1 Source: Bethyl Labs Target Name: EFTUD2-human

Experiment Status

	BGHLV16-21	BGHLV16-22
Sample_ID	BGHLV16-21	BGHLV16-22
Sample Name	EFTUD2_BGHLV16_21	EFTUD2_BGHLV16_22
Sample Name	EFTUD2_BGHLV16_21	EFTUD2_BGHLV16_22
RBP	EFTUD2	EFTUD2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	556	557

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-21	BGHLV16-22
Sample #
Sample Name	EFTUD2-BGHLV16-21	EFTUD2-BGHLV16-22
Sample_Name_Alias	EFTUD2_BGHLV16_21	EFTUD2_BGHLV16_22
Index Well Position	S07	S08
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/G6.png	DNA_Library_LV16-17/set1/H6.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E12.png	RNA_Library_LV13-14-16/set1/F12.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-21	BGHLV16-22
RBP	EFTUD2	EFTUD2
Batch_ID	BGHLV16	BGHLV16
WB_result	46.200	34.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2240	2241

Sequencing Information

	BGHLV16-21	BGHLV16-22
Sample_ID	BGHLV16-21	BGHLV16-22
Sample Name	EFTUD2_BGHLV16_21	EFTUD2_BGHLV16_22
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	51,630,000	51,110,000
total_aligned_reads	46,327,742	46,278,038
unique_aligned_reads	43,673,874	43,721,124
percent_uniqueAligned	0.84590	0.85543
correlation_replicates	0.997649	0.997649
spikein_reads	70,914	85,728
percent_spikeins	0.00137	0.00168
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	882	883

Data Submission Information

	BGHLV16-21	BGHLV16-21
ENCODE_alias	brenton-graveley:EFTUD2_BGHLV16	brenton-graveley:EFTUD2-BGHLV16-HepG2
ENCODE_accession	ENCSR620OKS	ENCSR669NXJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-21	BGHLV16-21
Sample Name	EFTUD2_BGHLV16_21	EFTUD2_BGHLV16_21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2846	6676

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
EFTUD2_BGHLV16_21_CAGATC_L006_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	882	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14282
EFTUD2_BGHLV16_21_CAGATC_L006_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	882	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14308
EFTUD2_BGHLV16_21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	882					GRCh38	V40	EFTUD2_BGHLV16_21_CAGATC_L006_R1_001.fastq.gz,EFTUD2_BGHLV16_21_CAGATC_L006_R2_001.fastq.gz		ENCORE2	14334
EFTUD2_BGHLV16_21_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	882					GRCh38	V40	EFTUD2_BGHLV16_21/Aligned.sortedByCoord.out.bam		ENCORE2	14360
EFTUD2_BGHLV16_21_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	882					GRCh38	V40	EFTUD2_BGHLV16_21/Aligned.sortedByCoord.out.bam		ENCORE2	14386
EFTUD2_BGHLV16_21_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	882					GRCh38	V40	EFTUD2_BGHLV16_21/Aligned.sortedByCoord.out.bam		ENCORE2	14412
EFTUD2_BGHLV16_21_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	882					GRCh38	V40	EFTUD2_BGHLV16_21/Aligned.sortedByCoord.out.bam		ENCORE2	14438
EFTUD2_BGHLV16_21_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	882					GRCh38	V40	EFTUD2_BGHLV16_21_CAGATC_L006_R1_001.fastq.gz,EFTUD2_BGHLV16_21_CAGATC_L006_R2_001.fastq.gz		ENCORE2	14464
EFTUD2_BGHLV16_22_ACTTGA_L006_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	883	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14283
EFTUD2_BGHLV16_22_ACTTGA_L006_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	883	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14309
EFTUD2_BGHLV16_22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	883					GRCh38	V40	EFTUD2_BGHLV16_22_ACTTGA_L006_R1_001.fastq.gz,EFTUD2_BGHLV16_22_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	14335
EFTUD2_BGHLV16_22_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	883					GRCh38	V40	EFTUD2_BGHLV16_22/Aligned.sortedByCoord.out.bam		ENCORE2	14361
EFTUD2_BGHLV16_22_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	883					GRCh38	V40	EFTUD2_BGHLV16_22/Aligned.sortedByCoord.out.bam		ENCORE2	14387
EFTUD2_BGHLV16_22_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	883					GRCh38	V40	EFTUD2_BGHLV16_22/Aligned.sortedByCoord.out.bam		ENCORE2	14413
EFTUD2_BGHLV16_22_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	883					GRCh38	V40	EFTUD2_BGHLV16_22/Aligned.sortedByCoord.out.bam		ENCORE2	14439
EFTUD2_BGHLV16_22_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	883					GRCh38	V40	EFTUD2_BGHLV16_22_ACTTGA_L006_R1_001.fastq.gz,EFTUD2_BGHLV16_22_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	14465