NFX1 RNA-Seq in K562

General Information


RBP	NFX1
Cell_Line	K562
Method	CRISPR
Exp_Name	NFX1-BGKcLV02-K562
ENCODE_series_ID
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NFX1_BGKcLV02-13
Rep2	NFX1_BGKcLV02-14
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	67.3
Rep2_qPCR	52.7
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A302-914A
Antibody Lot#	A302-914A
Antibody DCC ID
Status	NotSatisfied
Project	ENCODE3
ID	587

Experiment Information (Status: NotSatisfied)

	BGKcLV02-13	BGKcLV02-14
idx	15	16
TRCN#_or_BGC#	BGC#0000011	BGC#0000011
shRNA_or_gRNA_sequence	CTGTGAATTGGTTCGTGTCA	CTGTGAATTGGTTCGTGTCA
PAM
Name	NFX1-Z1-A	NFX1-Z1-A
Sample_ID	BGKcLV02-13	BGKcLV02-14
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	NFX1	NFX1
qPCR_result	67.3	52.7
Ave_qPCR	60.0
RT-qPCR_primer-F	agaatgtggaaacgcacaca
RT-qPCR_primer-R	cgtgacacgaaccaattcac
protein_conc	2656	3490
WB_result	0.0	0.0
Ave_WB	0.0
WB_DONE_date	1/4/2016
MW	124kDa
IP	1
antibody_Cat#	A302-914A	A302-914A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	14.6	0
Rep2_TPM	10.6	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4109	4110

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV02-13	BGKcLV02-14
Sample_ID	BGKcLV02-13	BGKcLV02-14
Sample Name	NFX1_BGKcLV02-13	NFX1_BGKcLV02-14
Sample Name	NFX1_BGKcLV02-13	NFX1_BGKcLV02-14
RBP	NFX1	NFX1
Cell_Line	K562	K562
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2016-03-16	2016-03-16
Project	ENCODE3	ENCODE3
Note
ID	32	33

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-13	BGKcLV02-14
Sample #
Sample Name	NFX1-BGKcLV02-13	NFX1-BGKcLV02-14
Sample_Name_Alias	NFX1_BGKcLV02-13	NFX1_BGKcLV02-14
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/G4.png	DNA_Library_cLV02/set1/H4.png
RIN	9.0	9.8
libSample_RNA_Well	RNA_Library_cLV02/set1/A6.png	RNA_Library_cLV02/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-13	BGKcLV02-14
RBP	NFX1	NFX1
Batch_ID	BGKcLV02	BGKcLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2780	2781

Sequencing Information

	BGKcLV02-13	BGKcLV02-14
Sample_ID	BGKcLV02-13	BGKcLV02-14
Sample Name	NFX1_BGKcLV02-13	NFX1_BGKcLV02-14
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	58,807,902	57,415,614
total_aligned_reads	54,265,136	53,130,370
unique_aligned_reads	49,431,426	48,490,628
percent_uniqueAligned	0.84056	0.84455
correlation_replicates	0.986746	0.986746
spikein_reads	209,334	117,516
percent_spikeins	0.00356	0.00205
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1429	1430

Data Submission Information DCC submission information was not avaliable

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
NFX1_BGKcLV02-13_ACTGAT_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1429	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22762
NFX1_BGKcLV02-13_ACTGAT_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1429	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22782
NFX1_BGKcLV02-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1429					GRCh38	V40	NFX1_BGKcLV02-13_ACTGAT_L008_001.R1.fastq.gz,NFX1_BGKcLV02-13_ACTGAT_L008_001.R2.fastq.gz		ENCORE2	22802
NFX1_BGKcLV02-13_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1429					GRCh38	V40	NFX1_BGKcLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	22822
NFX1_BGKcLV02-13_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1429					GRCh38	V40	NFX1_BGKcLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	22842
NFX1_BGKcLV02-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1429					GRCh38	V40	NFX1_BGKcLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	22862
NFX1_BGKcLV02-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1429					GRCh38	V40	NFX1_BGKcLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	22882
NFX1_BGKcLV02-13_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1429					GRCh38	V40	NFX1_BGKcLV02-13_ACTGAT_L008_001.R1.fastq.gz,NFX1_BGKcLV02-13_ACTGAT_L008_001.R2.fastq.gz		ENCORE2	22902
NFX1_BGKcLV02-14_ATTCCT_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1430	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22763
NFX1_BGKcLV02-14_ATTCCT_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1430	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22783
NFX1_BGKcLV02-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1430					GRCh38	V40	NFX1_BGKcLV02-14_ATTCCT_L008_001.R1.fastq.gz,NFX1_BGKcLV02-14_ATTCCT_L008_001.R2.fastq.gz		ENCORE2	22803
NFX1_BGKcLV02-14_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1430					GRCh38	V40	NFX1_BGKcLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	22823
NFX1_BGKcLV02-14_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1430					GRCh38	V40	NFX1_BGKcLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	22843
NFX1_BGKcLV02-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1430					GRCh38	V40	NFX1_BGKcLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	22863
NFX1_BGKcLV02-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1430					GRCh38	V40	NFX1_BGKcLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	22883
NFX1_BGKcLV02-14_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1430					GRCh38	V40	NFX1_BGKcLV02-14_ATTCCT_L008_001.R1.fastq.gz,NFX1_BGKcLV02-14_ATTCCT_L008_001.R2.fastq.gz		ENCORE2	22903