NUFIP2 RNA-Seq in K562

General Information


RBP	NUFIP2
Cell_Line	K562
Method	shRNA
Exp_Name	NUFIP2-BGKLV34-K562
ENCODE_series_ID	ENCSR789PSL
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR754RJA
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	NUFIP2_BGKLV34-27
Rep2	NUFIP2_BGKLV34-28
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	77.6
Rep2_WB	77.8
Antibody Cat#	A301-599A
Antibody Lot#	A301-599A
Antibody DCC ID	ENCAB072KYE
Status	Released
Project	ENCODE3
ID	724

Experiment Information (Status: Released)

	BGKLV34-27	BGKLV34-28
idx	690	691
TRCN#_or_BGC#	TRCN0000166959	TRCN0000166959
shRNA_or_gRNA_sequence	GAACAAATTAAGACTAGCCTT	GAACAAATTAAGACTAGCCTT
PAM
Name	NUFIP2	NUFIP2
Sample_ID	BGKLV34-27	BGKLV34-28
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	NUFIP2	NUFIP2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ttgacctgagggctgctatt
RT-qPCR_primer-R	ggcagtctggtccttcattg
protein_conc	2718	2772
WB_result	77.6	77.8
Ave_WB	77.7
WB_DONE_date	1/4/2016
MW	76kDa
IP	1	1
antibody_Cat#	A301-599A	A301-599A
Antibody DCC ID	ENCAB072KYE	ENCAB072KYE
submitted_to_DCC_date	10/26/16
Rep1_TPM	7.46996274	0
Rep2_TPM	5.77721515	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	777	778

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NUFIP2	Product_ID: A301-599A Lot_ID: 1 Source: Bethyl Labs Target Name: NUFIP2-human

Experiment Status

	BGKLV34-27	BGKLV34-28
Sample_ID	BGKLV34-27	BGKLV34-28
Sample Name	NUFIP2_BGKLV34-27	NUFIP2_BGKLV34-28
Sample Name	NUFIP2_BGKLV34-27	NUFIP2_BGKLV34-28
RBP	NUFIP2	NUFIP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1237	1238

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-27	BGKLV34-28
Sample #
Sample Name	NUFIP2-BGKLV34-27	NUFIP2-BGKLV34-28
Sample_Name_Alias	NUFIP2_BGKLV34-27	NUFIP2_BGKLV34-28
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/E3.png	DNA_Library_LV34_2-28/set2/B1.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/C5.png	RNA_Library_LV32-33-34/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-27	BGKLV34-28
RBP	NUFIP2	NUFIP2
Batch_ID	BGKLV34	BGKLV34
WB_result	77.600	77.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2922	2923

Sequencing Information

	BGKLV34-27	BGKLV34-28
Sample_ID	BGKLV34-27	BGKLV34-28
Sample Name	NUFIP2_BGKLV34-27	NUFIP2_BGKLV34-28
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	66,127,784	72,465,380
total_aligned_reads	57,639,514	63,579,800
unique_aligned_reads	52,652,086	58,333,462
percent_uniqueAligned	0.79622	0.80498
correlation_replicates	0.997542	0.997542
spikein_reads	208,346	256,236
percent_spikeins	0.00315	0.00354
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1571	1572

Data Submission Information

	BGKLV34-27	BGKLV34-27
ENCODE_alias	brenton-graveley:NUFIP2_BGKLV34	brenton-graveley:NUFIP2-BGKLV34-K562
ENCODE_accession	ENCSR754RJA	ENCSR789PSL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-27	BGKLV34-27
Sample Name	NUFIP2_BGKLV34-27	NUFIP2_BGKLV34-27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3158	6835

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
NUFIP2_BGKLV34-27_ACAGTG_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1571	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21530
NUFIP2_BGKLV34-27_ACAGTG_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1571	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21550
NUFIP2_BGKLV34-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1571					GRCh38	V40	NUFIP2_BGKLV34-27_ACAGTG_L003_001.R1.fastq.gz,NUFIP2_BGKLV34-27_ACAGTG_L003_001.R2.fastq.gz		ENCORE2	21570
NUFIP2_BGKLV34-27_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1571					GRCh38	V40	NUFIP2_BGKLV34-27/Aligned.sortedByCoord.out.bam		ENCORE2	21590
NUFIP2_BGKLV34-27_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1571					GRCh38	V40	NUFIP2_BGKLV34-27/Aligned.sortedByCoord.out.bam		ENCORE2	21610
NUFIP2_BGKLV34-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1571					GRCh38	V40	NUFIP2_BGKLV34-27/Aligned.sortedByCoord.out.bam		ENCORE2	21630
NUFIP2_BGKLV34-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1571					GRCh38	V40	NUFIP2_BGKLV34-27/Aligned.sortedByCoord.out.bam		ENCORE2	21650
NUFIP2_BGKLV34-27_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1571					GRCh38	V40	NUFIP2_BGKLV34-27_ACAGTG_L003_001.R1.fastq.gz,NUFIP2_BGKLV34-27_ACAGTG_L003_001.R2.fastq.gz		ENCORE2	21670
NUFIP2_BGKLV34-28_GCCAAT_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1572	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21531
NUFIP2_BGKLV34-28_GCCAAT_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1572	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21551
NUFIP2_BGKLV34-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1572					GRCh38	V40	NUFIP2_BGKLV34-28_GCCAAT_L003_001.R1.fastq.gz,NUFIP2_BGKLV34-28_GCCAAT_L003_001.R2.fastq.gz		ENCORE2	21571
NUFIP2_BGKLV34-28_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1572					GRCh38	V40	NUFIP2_BGKLV34-28/Aligned.sortedByCoord.out.bam		ENCORE2	21591
NUFIP2_BGKLV34-28_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1572					GRCh38	V40	NUFIP2_BGKLV34-28/Aligned.sortedByCoord.out.bam		ENCORE2	21611
NUFIP2_BGKLV34-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1572					GRCh38	V40	NUFIP2_BGKLV34-28/Aligned.sortedByCoord.out.bam		ENCORE2	21631
NUFIP2_BGKLV34-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1572					GRCh38	V40	NUFIP2_BGKLV34-28/Aligned.sortedByCoord.out.bam		ENCORE2	21651
NUFIP2_BGKLV34-28_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1572					GRCh38	V40	NUFIP2_BGKLV34-28_GCCAAT_L003_001.R1.fastq.gz,NUFIP2_BGKLV34-28_GCCAAT_L003_001.R2.fastq.gz		ENCORE2	21671