EIF4B RNA-Seq in K562

General Information


RBP	EIF4B
Cell_Line	K562
Method	shRNA
Exp_Name	EIF4B-BGKLV08-K562
ENCODE_series_ID	ENCSR172VUX
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR774BXV
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	EIF4B-LV08-23
Rep2	EIF4B-LV08-24
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	71.9
Rep2_qPCR	62.2
Rep1_WB	31.6
Rep2_WB	43.9
Antibody Cat#	A301-767A
Antibody Lot#	A301-767A
Antibody DCC ID	ENCAB697PTS
Status	Released
Project	ENCODE3
ID	288

Experiment Information (Status: Released)

	BGKLV08-23	BGKLV08-24
idx	24	25
TRCN#_or_BGC#	TRCN0000062598	TRCN0000062598
shRNA_or_gRNA_sequence	GCGGAGAAACACCTTGATCTT	GCGGAGAAACACCTTGATCTT
PAM
Name	EIF4B	EIF4B
Sample_ID	BGKLV08-23	BGKLV08-24
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	EIF4B	EIF4B
qPCR_result	71.9	62.2
Ave_qPCR	67.1
RT-qPCR_primer-F	AGCTCCAGCTCAACCATCTG
RT-qPCR_primer-R	AGAGTTCCCAGTTTGGCCTT
protein_conc	2910	2792
WB_result	31.6	43.9
Ave_WB	37.7
WB_DONE_date	7/22/2015	not passing
MW	65kDa
IP	1	1
antibody_Cat#	A301-767A	A301-767A
Antibody DCC ID	ENCAB697PTS	ENCAB697PTS
submitted_to_DCC_date	10/26/2016
Rep1_TPM	123.857233	0
Rep2_TPM	178.604388	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	23	24

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4B	Product_ID: A301-767A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF4B-human

Experiment Status

	BGKLV08-23	BGKLV08-24
Sample_ID	BGKLV08-23	BGKLV08-24
Sample Name	EIF4B-LV08-23	EIF4B-LV08-24
Sample Name	EIF4B-LV08-23	EIF4B-LV08-24
RBP	EIF4B	EIF4B
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	284	285

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-23	BGKLV08-24
Sample #
Sample Name	EIF4B-BGKLV08-23	EIF4B-BGKLV08-24
Sample_Name_Alias	EIF4B-LV08-23	EIF4B-LV08-24
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set2/E1.png	DNA_Library_LV08/set2/F1.png
RIN	9.2	9.4
libSample_RNA_Well	RNA_Library_LV08/set2/G1.png	RNA_Library_LV08/set2/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-23	BGKLV08-24
RBP	EIF4B	EIF4B
Batch_ID	BGKLV08	BGKLV08
WB_result	31.600	43.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1906	1907

Sequencing Information

	BGKLV08-23	BGKLV08-24
Sample_ID	BGKLV08-23	BGKLV08-24
Sample Name	EIF4B-LV08-23	EIF4B-LV08-24
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	41,000,000	45,250,000
total_aligned_reads	36,021,202	39,836,800
unique_aligned_reads	32,715,490	36,244,810
percent_uniqueAligned	0.79794	0.80099
correlation_replicates	0.993425	0.993425
spikein_reads	358,994	342,988
percent_spikeins	0.00876	0.00758
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	606	607

Data Submission Information

	BGKLV08-23	BGKLV08-23
ENCODE_alias	brenton-graveley:EIF4B-LV08	brenton-graveley:EIF4B-BGKLV08-K562
ENCODE_accession	ENCSR774BXV	ENCSR172VUX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-23	BGKLV08-23
Sample Name	EIF4B-LV08-23	EIF4B-LV08-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2691	6692

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
EIF4B-LV08-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	606					GRCh38	V40	EIF4B-LV08-23_GTGGCC_L003_R1_001.fastq.gz,EIF4B-LV08-23_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	11991
EIF4B-LV08-23_GTGGCC_L003_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	606	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12047
EIF4B-LV08-23_GTGGCC_L003_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	606	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12103
EIF4B-LV08-23_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	606					GRCh38	V40	EIF4B-LV08-23/Aligned.sortedByCoord.out.bam		ENCORE2	12159
EIF4B-LV08-23_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	606					GRCh38	V40	EIF4B-LV08-23/Aligned.sortedByCoord.out.bam		ENCORE2	12215
EIF4B-LV08-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	606					GRCh38	V40	EIF4B-LV08-23/Aligned.sortedByCoord.out.bam		ENCORE2	12271
EIF4B-LV08-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	606					GRCh38	V40	EIF4B-LV08-23/Aligned.sortedByCoord.out.bam		ENCORE2	12327
EIF4B-LV08-23_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	606					GRCh38	V40	EIF4B-LV08-23_GTGGCC_L003_R1_001.fastq.gz,EIF4B-LV08-23_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	13326
EIF4B-LV08-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	607					GRCh38	V40	EIF4B-LV08-24_GTTTCG_L003_R1_001.fastq.gz,EIF4B-LV08-24_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	11992
EIF4B-LV08-24_GTTTCG_L003_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	607	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12048
EIF4B-LV08-24_GTTTCG_L003_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	607	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12104
EIF4B-LV08-24_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	607					GRCh38	V40	EIF4B-LV08-24/Aligned.sortedByCoord.out.bam		ENCORE2	12160
EIF4B-LV08-24_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	607					GRCh38	V40	EIF4B-LV08-24/Aligned.sortedByCoord.out.bam		ENCORE2	12216
EIF4B-LV08-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	607					GRCh38	V40	EIF4B-LV08-24/Aligned.sortedByCoord.out.bam		ENCORE2	12272
EIF4B-LV08-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	607					GRCh38	V40	EIF4B-LV08-24/Aligned.sortedByCoord.out.bam		ENCORE2	12328
EIF4B-LV08-24_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	607					GRCh38	V40	EIF4B-LV08-24_GTTTCG_L003_R1_001.fastq.gz,EIF4B-LV08-24_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	13327