EFTUD2 RNA-Seq in K562

General Information


RBP	EFTUD2
Cell_Line	K562
Method	shRNA
Exp_Name	EFTUD2-BGKLV19-K562
ENCODE_series_ID	ENCSR136YDL
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR117WLY
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	EFTUD2_BGKLV19_23B
Rep2	EFTUD2_BGKLV19_24B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	66.8
Rep2_qPCR	77.0
Rep1_WB	80.2
Rep2_WB	77.2
Antibody Cat#	A300-957A
Antibody Lot#	A300-957A
Antibody DCC ID	ENCAB787OVJ
Status	Released
Project	ENCODE3
ID	471

Experiment Information (Status: Released)

	BGKLV19-23	BGKLV19-24
idx	230	231
TRCN#_or_BGC#	TRCN0000074654	TRCN0000074654
shRNA_or_gRNA_sequence	CCCATTATTAAGCCAGTGAAA	CCCATTATTAAGCCAGTGAAA
PAM
Name	EFTUD2	EFTUD2
Sample_ID	BGKLV19-23	BGKLV19-24
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	EFTUD2	EFTUD2
qPCR_result	66.8	77.0
Ave_qPCR	71.9
RT-qPCR_primer-F	ttattacaagctgcgccaca
RT-qPCR_primer-R	gaagcagacgttacccagga
protein_conc	2910	2863
WB_result	80.2	77.2
Ave_WB	78.7
WB_DONE_date	12/5/2014
MW
IP	1	1
antibody_Cat#	A300-957A	A300-957A
Antibody DCC ID	ENCAB787OVJ	ENCAB787OVJ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	80.3868614	0
Rep2_TPM	57.5111699	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	257	258

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

	BGKLV19-23	BGKLV19-24
Sample_ID	BGKLV19-23	BGKLV19-24
Sample Name	EFTUD2_BGKLV19_23B	EFTUD2_BGKLV19_24B
Sample Name	EFTUD2_BGKLV19_23B	EFTUD2_BGKLV19_24B
RBP	EFTUD2	EFTUD2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	672	673

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-23	BGKLV19-24
Sample #
Sample Name	EFTUD2-BGKLV19-23B	EFTUD2-BGKLV19-24B
Sample_Name_Alias	EFTUD2_BGKLV19_23B	EFTUD2_BGKLV19_24B
Index Well Position	S13	S14
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/E8.png	DNA_Library_LV18-19/set1/F8.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/A3.png	RNA_Library_LV19-21-24/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-23	BGKLV19-24
RBP	EFTUD2	EFTUD2
Batch_ID	BGKLV19	BGKLV19
WB_result	80.200	77.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2358	2359

Sequencing Information

	BGKLV19-23	BGKLV19-24
Sample_ID	BGKLV19-23	BGKLV19-24
Sample Name	EFTUD2_BGKLV19_23B	EFTUD2_BGKLV19_24B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	56,880,000	41,630,000
total_aligned_reads	51,694,278	38,498,736
unique_aligned_reads	47,384,232	35,287,306
percent_uniqueAligned	0.83306	0.84764
correlation_replicates	0.998900	0.998900
spikein_reads	251,620	165,800
percent_spikeins	0.00442	0.00398
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1000	1001

Data Submission Information

	BGKLV19-23	BGKLV19-23
ENCODE_alias	brenton-graveley:EFTUD2_BGKLV19	brenton-graveley:EFTUD2-BGKLV19-K562
ENCODE_accession	ENCSR117WLY	ENCSR136YDL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-23	BGKLV19-23
Sample Name	EFTUD2_BGKLV19_23B	EFTUD2_BGKLV19_23B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2885	6677

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_BGKLV19_23B_AGTCAA_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1000	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15112
EFTUD2_BGKLV19_23B_AGTCAA_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1000	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15170
EFTUD2_BGKLV19_23B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1000					GRCh38	V40	EFTUD2_BGKLV19_23B_AGTCAA_L003_R1_001.fastq.gz,EFTUD2_BGKLV19_23B_AGTCAA_L003_R2_001.fastq.gz		ENCORE2	15228
EFTUD2_BGKLV19_23B_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	1000					GRCh38	V40	EFTUD2_BGKLV19_23B/Aligned.sortedByCoord.out.bam		ENCORE2	15299
EFTUD2_BGKLV19_23B_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	1000					GRCh38	V40	EFTUD2_BGKLV19_23B/Aligned.sortedByCoord.out.bam		ENCORE2	15357
EFTUD2_BGKLV19_23B_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	1000					GRCh38	V40	EFTUD2_BGKLV19_23B/Aligned.sortedByCoord.out.bam		ENCORE2	15415
EFTUD2_BGKLV19_23B_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	1000					GRCh38	V40	EFTUD2_BGKLV19_23B/Aligned.sortedByCoord.out.bam		ENCORE2	15473
EFTUD2_BGKLV19_23B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1000					GRCh38	V40	EFTUD2_BGKLV19_23B_AGTCAA_L003_R1_001.fastq.gz,EFTUD2_BGKLV19_23B_AGTCAA_L003_R2_001.fastq.gz		ENCORE2	16370
EFTUD2_BGKLV19_24B_AGTTCC_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1001	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15113
EFTUD2_BGKLV19_24B_AGTTCC_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1001	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15171
EFTUD2_BGKLV19_24B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1001					GRCh38	V40	EFTUD2_BGKLV19_24B_AGTTCC_L003_R1_001.fastq.gz,EFTUD2_BGKLV19_24B_AGTTCC_L003_R2_001.fastq.gz		ENCORE2	15229
EFTUD2_BGKLV19_24B_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	1001					GRCh38	V40	EFTUD2_BGKLV19_24B/Aligned.sortedByCoord.out.bam		ENCORE2	15300
EFTUD2_BGKLV19_24B_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	1001					GRCh38	V40	EFTUD2_BGKLV19_24B/Aligned.sortedByCoord.out.bam		ENCORE2	15358
EFTUD2_BGKLV19_24B_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	1001					GRCh38	V40	EFTUD2_BGKLV19_24B/Aligned.sortedByCoord.out.bam		ENCORE2	15416
EFTUD2_BGKLV19_24B_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	1001					GRCh38	V40	EFTUD2_BGKLV19_24B/Aligned.sortedByCoord.out.bam		ENCORE2	15474
EFTUD2_BGKLV19_24B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1001					GRCh38	V40	EFTUD2_BGKLV19_24B_AGTTCC_L003_R1_001.fastq.gz,EFTUD2_BGKLV19_24B_AGTTCC_L003_R2_001.fastq.gz		ENCORE2	16371