NELFE RNA-Seq in K562

General Information


RBP	NELFE
Cell_Line	K562
Method	shRNA
Exp_Name	NELFE-BGKLV11-K562
ENCODE_series_ID	ENCSR017RVL
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR201WFU
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	RDBP-LV11-45
Rep2	RDBP-LV11-46
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	82.3
Rep2_qPCR	79.0
Rep1_WB	89.6
Rep2_WB	91.9
Antibody Cat#	A301-913A
Antibody Lot#	A301-913A
Antibody DCC ID	ENCAB361TEG
Status	Released
Project	ENCODE3
ID	321

Experiment Information (Status: Released)

	BGKLV11-45	BGKLV11-46
idx	114	115
TRCN#_or_BGC#	TRCN0000074958	TRCN0000074958
shRNA_or_gRNA_sequence	CTGGATTCCTTGTGCCTCATA	CTGGATTCCTTGTGCCTCATA
PAM
Name	RDBP	RDBP
Sample_ID	BGKLV11-45	BGKLV11-46
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	NELFE	NELFE
qPCR_result	82.3	79.0
Ave_qPCR	80.6
RT-qPCR_primer-F	AGCAAAGTAGCAGCAGCACA
RT-qPCR_primer-R	GTCTCAGCCTTGATGGCACT
protein_conc	1912	1838
WB_result	89.6	91.9
Ave_WB	90.8
WB_DONE_date
MW	43kDa
IP	1	1
antibody_Cat#	A301-913A	A301-913A
Antibody DCC ID	ENCAB361TEG	ENCAB361TEG
submitted_to_DCC_date	4/2/2015
Rep1_TPM	53.996654	0
Rep2_TPM	60.9482139	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	127	128

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NELFE	Product_ID: A301-913A Lot_ID: 1 Source: Bethyl Labs Target Name: NELFE-human

Experiment Status

	BGKLV11-45	BGKLV11-46
Sample_ID	BGKLV11-45	BGKLV11-46
Sample Name	RDBP-LV11-45	RDBP-LV11-46
Sample Name	RDBP-LV11-45	RDBP-LV11-46
RBP	NELFE	NELFE
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	356	357

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-45	BGKLV11-46
Sample #
Sample Name	NELFE-BGKLV11-45	NELFE-BGKLV11-46
Sample_Name_Alias	RDBP-LV11-45	RDBP-LV11-46
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set3/D1.png	DNA_Library_LV11/set3/E1.png
RIN	8.6	9.0
libSample_RNA_Well	RNA_Library_LV11/set1/A5.png	RNA_Library_LV11/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-45	BGKLV11-46
RBP	NELFE	NELFE
Batch_ID	BGKLV11	BGKLV11
WB_result	89.600	91.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1978	1979

Sequencing Information

	BGKLV11-45	BGKLV11-46
Sample_ID	BGKLV11-45	BGKLV11-46
Sample Name	RDBP-LV11-45	RDBP-LV11-46
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	56,030,000	61,780,000
total_aligned_reads	45,262,878	48,607,216
unique_aligned_reads	41,666,828	44,695,402
percent_uniqueAligned	0.74365	0.72346
correlation_replicates	0.996602	0.996602
spikein_reads	364,788	287,966
percent_spikeins	0.00651	0.00466
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	678	679

Data Submission Information

	BGKLV11-45	BGKLV11-45
ENCODE_alias	brenton-graveley:RDBP-LV11	brenton-graveley:NELFE-BGKLV11-K562
ENCODE_accession	ENCSR201WFU	ENCSR017RVL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-45	BGKLV11-45
Sample Name	RDBP-LV11-45	RDBP-LV11-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2727	6821

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
RDBP-LV11-45_GATCAG_L006_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	678	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12399
RDBP-LV11-45_GATCAG_L006_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	678	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12447
RDBP-LV11-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	678					GRCh38	V40	RDBP-LV11-45_GATCAG_L006_R1_001.fastq.gz,RDBP-LV11-45_GATCAG_L006_R2_001.fastq.gz		ENCORE2	12495
RDBP-LV11-45_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	678					GRCh38	V40	RDBP-LV11-45/Aligned.sortedByCoord.out.bam		ENCORE2	12543
RDBP-LV11-45_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	678					GRCh38	V40	RDBP-LV11-45/Aligned.sortedByCoord.out.bam		ENCORE2	12591
RDBP-LV11-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	678					GRCh38	V40	RDBP-LV11-45/Aligned.sortedByCoord.out.bam		ENCORE2	12639
RDBP-LV11-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	678					GRCh38	V40	RDBP-LV11-45/Aligned.sortedByCoord.out.bam		ENCORE2	12687
RDBP-LV11-45_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	678					GRCh38	V40	RDBP-LV11-45_GATCAG_L006_R1_001.fastq.gz,RDBP-LV11-45_GATCAG_L006_R2_001.fastq.gz		ENCORE2	12735
RDBP-LV11-46_TAGCTT_L006_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	679	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12400
RDBP-LV11-46_TAGCTT_L006_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	679	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12448
RDBP-LV11-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	679					GRCh38	V40	RDBP-LV11-46_TAGCTT_L006_R1_001.fastq.gz,RDBP-LV11-46_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	12496
RDBP-LV11-46_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	679					GRCh38	V40	RDBP-LV11-46/Aligned.sortedByCoord.out.bam		ENCORE2	12544
RDBP-LV11-46_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	679					GRCh38	V40	RDBP-LV11-46/Aligned.sortedByCoord.out.bam		ENCORE2	12592
RDBP-LV11-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	679					GRCh38	V40	RDBP-LV11-46/Aligned.sortedByCoord.out.bam		ENCORE2	12640
RDBP-LV11-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	679					GRCh38	V40	RDBP-LV11-46/Aligned.sortedByCoord.out.bam		ENCORE2	12688
RDBP-LV11-46_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	679					GRCh38	V40	RDBP-LV11-46_TAGCTT_L006_R1_001.fastq.gz,RDBP-LV11-46_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	12736