NFX1 RNA-Seq in HepG2

General Information


RBP	NFX1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NFX1-BGHcLV03-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NFX1_BGHcLV03-11
Rep2	NFX1_BGHcLV03-12
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	34.6
Rep2_qPCR	49.3
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A302-914A
Antibody Lot#	A302-914A
Antibody DCC ID
Status	NotSatisfied
Project	ENCODE3
ID	575

Experiment Information (Status: NotSatisfied)

	BGHcLV03-11	BGHcLV03-12
idx	11	12
TRCN#_or_BGC#	BGC#0000012	BGC#0000012
shRNA_or_gRNA_sequence	AATAAATCGCCCAAGAGCCA	AATAAATCGCCCAAGAGCCA
PAM
Name	NFX1-C1-A	NFX1-C1-A
Sample_ID	BGHcLV03-11	BGHcLV03-12
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	NFX1	NFX1
qPCR_result	34.6	49.3
Ave_qPCR	42.0
RT-qPCR_primer-F	ctgcccacattcctgtaacc
RT-qPCR_primer-R	tggttcgtccacattcacat
protein_conc	2354	2079
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	8	0
Rep2_TPM	8	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6152	6153

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV03-11	BGHcLV03-12
Sample_ID	BGHcLV03-11	BGHcLV03-12
Sample Name	NFX1_BGHcLV03-11	NFX1_BGHcLV03-12
Sample Name	NFX1_BGHcLV03-11	NFX1_BGHcLV03-12
RBP	NFX1	NFX1
Cell_Line	HepG2	HepG2
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	38	39

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-11	BGHcLV03-12
Sample #
Sample Name	NFX1-BGHcLV03-11	NFX1-BGHcLV03-12
Sample_Name_Alias	NFX1_BGHcLV03-11	NFX1_BGHcLV03-12
Index Well Position	S03	S04
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/C2.png	DNA_Library_cLV02/set1/D2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/E3.png	RNA_Library_cLV02/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-11	BGHcLV03-12
RBP	NFX1	NFX1
Batch_ID	BGHcLV03	BGHcLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2798	2799

Sequencing Information

	BGHcLV03-11	BGHcLV03-12
Sample_ID	BGHcLV03-11	BGHcLV03-12
Sample Name	NFX1_BGHcLV03-11	NFX1_BGHcLV03-12
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	56,323,276	66,996,886
total_aligned_reads	48,825,976	58,343,452
unique_aligned_reads	45,830,222	54,763,468
percent_uniqueAligned	0.81370	0.81740
correlation_replicates	0.993477	0.993477
spikein_reads	113,538	117,064
percent_spikeins	0.00202	0.00175
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1447	1448

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_BGHcLV03-11_TTAGGC_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1447	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22920
NFX1_BGHcLV03-11_TTAGGC_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1447	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22938
NFX1_BGHcLV03-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1447					GRCh38	V40	NFX1_BGHcLV03-11_TTAGGC_L006_001.R1.fastq.gz,NFX1_BGHcLV03-11_TTAGGC_L006_001.R2.fastq.gz		ENCORE2	22956
NFX1_BGHcLV03-11_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1447					GRCh38	V40	NFX1_BGHcLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	22974
NFX1_BGHcLV03-11_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1447					GRCh38	V40	NFX1_BGHcLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	22992
NFX1_BGHcLV03-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1447					GRCh38	V40	NFX1_BGHcLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	23010
NFX1_BGHcLV03-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1447					GRCh38	V40	NFX1_BGHcLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	23028
NFX1_BGHcLV03-11_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1447					GRCh38	V40	NFX1_BGHcLV03-11_TTAGGC_L006_001.R1.fastq.gz,NFX1_BGHcLV03-11_TTAGGC_L006_001.R2.fastq.gz		ENCORE2	23046
NFX1_BGHcLV03-12_TGACCA_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1448	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22921
NFX1_BGHcLV03-12_TGACCA_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1448	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22939
NFX1_BGHcLV03-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1448					GRCh38	V40	NFX1_BGHcLV03-12_TGACCA_L006_001.R1.fastq.gz,NFX1_BGHcLV03-12_TGACCA_L006_001.R2.fastq.gz		ENCORE2	22957
NFX1_BGHcLV03-12_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1448					GRCh38	V40	NFX1_BGHcLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	22975
NFX1_BGHcLV03-12_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1448					GRCh38	V40	NFX1_BGHcLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	22993
NFX1_BGHcLV03-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1448					GRCh38	V40	NFX1_BGHcLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	23011
NFX1_BGHcLV03-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1448					GRCh38	V40	NFX1_BGHcLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	23029
NFX1_BGHcLV03-12_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1448					GRCh38	V40	NFX1_BGHcLV03-12_TGACCA_L006_001.R1.fastq.gz,NFX1_BGHcLV03-12_TGACCA_L006_001.R2.fastq.gz		ENCORE2	23047