NFX1 RNA-Seq in HepG2

General Information


RBP	NFX1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NFX1-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR884IHR
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR548ORV
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	NFX1-BGHcLV10-29
Rep2	NFX1-BGHcLV10-30
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	32.4
Rep2_qPCR	38.3
Rep1_WB	65.9
Rep2_WB	60.7
Antibody Cat#	A302-914A
Antibody Lot#
Antibody DCC ID	ENCAB841CSS
Status	Released
Project	ENCODE4
ID	225

Experiment Information (Status: Released)

	BGHcLV10-29	BGHcLV10-30
idx	226	227
TRCN#_or_BGC#	BGC#0000129	BGC#0000129
shRNA_or_gRNA_sequence	GTCCTGCGTTTGTATGTCGG	GTCCTGCGTTTGTATGTCGG
PAM	TGG	TGG
Name	NFX1-93	NFX1-93
Sample_ID	BGHcLV10-29	BGHcLV10-30
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	NFX1	NFX1
qPCR_result	32.4	38.3
Ave_qPCR	35.4
RT-qPCR_primer-F	agaatgtggaaacgcacaca
RT-qPCR_primer-R	cgtgacacgaaccaattcac
protein_conc	2200	2503
WB_result	65.9	60.7
Ave_WB	63.3
WB_DONE_date	6/4/18	WES
MW	124kDa	lots of bands
IP	1
antibody_Cat#	A302-914A
Antibody DCC ID	ENCAB841CSS
submitted_to_DCC_date	9/6/18
Rep1_TPM	20	0
Rep2_TPM	25	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6369	6370

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NFX1	Product_ID: A302-914A Lot_ID: 1 Source: Bethyl Labs Target Name: NFX1-human

Experiment Status

	BGHcLV10-29	BGHcLV10-30
Sample_ID	BGHcLV10-29	BGHcLV10-30
Sample Name
Sample Name	NFX1-BGHcLV10-29	NFX1-BGHcLV10-30
RBP	NFX1	NFX1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6301	6302

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-29	BGHcLV10-30
Sample #	61	62
Sample Name	NFX1-BGHcLV10-29	NFX1-BGHcLV10-30
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	267	281
Peak_Molarity	28.40	38.20
libSampleQC_DNA_Well	DNA_Library_set41/set5/A9.png	DNA_Library_set41/set5/B9.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set41/set1/E8.png	RNA_Library_set41/set1/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-29	BGHcLV10-30
RBP	NFX1	NFX1
Batch_ID	BGHcLV10	BGHcLV10
WB_result	65.900	60.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	911	912

Sequencing Information

	BGHcLV10-29	BGHcLV10-30
Sample_ID	BGHcLV10-29	BGHcLV10-30
Sample Name	NFX1-BGHcLV10-29	NFX1-BGHcLV10-30
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	214,668,782	95,122,098
total_aligned_reads	207,908,048	91,679,748
unique_aligned_reads	191,835,244	85,242,874
percent_uniqueAligned	0.89363	0.89614
correlation_replicates	0.993244	0.993244
spikein_reads	510,984	194,502
percent_spikeins	0.00238	0.00204
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	317	318

Data Submission Information

	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-30	BGHcLV10-30	BGHcLV10-30	BGHcLV10-30
ENCODE_alias	brenton-graveley:NFX1-BGHcLV10	brenton-graveley:NFX1-BGHcLV10-29	brenton-graveley:L-NFX1-BGHcLV10-29	brenton-graveley:NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NFX1-BGHcLV10-HepG2	brenton-graveley:NFX1-BGHcLV10-30	brenton-graveley:L-NFX1-BGHcLV10-30	brenton-graveley:NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR548ORV	ENCBS889EOR	ENCLB138QFF	ENCFF390ZQU	ENCFF975SBB	ENCSR884IHR	ENCBS075ZEK	ENCLB903XOL	ENCFF885HXP	ENCFF318KYJ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-29	BGHcLV10-30	BGHcLV10-30	BGHcLV10-30	BGHcLV10-30
Sample Name	NFX1-BGHcLV10-29	NFX1-BGHcLV10-29	NFX1-BGHcLV10-29	NFX1-BGHcLV10-29	NFX1-BGHcLV10-29	NFX1-BGHcLV10-29	NFX1-BGHcLV10-30	NFX1-BGHcLV10-30	NFX1-BGHcLV10-30	NFX1-BGHcLV10-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		NFX1-BGHcLV10-29.pdf	L-NFX1-BGHcLV10-29.pdf				NFX1-BGHcLV10-30.pdf	L-NFX1-BGHcLV10-30.pdf
ID	1130	1180	1250	1320	1421	7265	1181	1251	1321	1422

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	317				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	527
NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	317				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	597
NFX1-BGHcLV10-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	317	GRCh38	V40	NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26765
NFX1-BGHcLV10-29_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	317	GRCh38	V40	NFX1-BGHcLV10-29/Aligned.sortedByCoord.out.bam		ENCORE2	26835
NFX1-BGHcLV10-29_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	317	GRCh38	V40	NFX1-BGHcLV10-29/Aligned.sortedByCoord.out.bam		ENCORE2	26905
NFX1-BGHcLV10-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	317	GRCh38	V40	NFX1-BGHcLV10-29/Aligned.sortedByCoord.out.bam		ENCORE2	26975
NFX1-BGHcLV10-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	317	GRCh38	V40	NFX1-BGHcLV10-29/Aligned.sortedByCoord.out.bam		ENCORE2	27045
NFX1-BGHcLV10-29_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	317	GRCh38	V40	NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGHcLV10-29_ACACTAAG+ATCCATAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27115
NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	318				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	528
NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	318				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	598
NFX1-BGHcLV10-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	318	GRCh38	V40	NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26766
NFX1-BGHcLV10-30_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	318	GRCh38	V40	NFX1-BGHcLV10-30/Aligned.sortedByCoord.out.bam		ENCORE2	26836
NFX1-BGHcLV10-30_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	318	GRCh38	V40	NFX1-BGHcLV10-30/Aligned.sortedByCoord.out.bam		ENCORE2	26906
NFX1-BGHcLV10-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	318	GRCh38	V40	NFX1-BGHcLV10-30/Aligned.sortedByCoord.out.bam		ENCORE2	26976
NFX1-BGHcLV10-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	318	GRCh38	V40	NFX1-BGHcLV10-30/Aligned.sortedByCoord.out.bam		ENCORE2	27046
NFX1-BGHcLV10-30_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	318	GRCh38	V40	NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGHcLV10-30_GTGTCGGA+GCTTGCGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27116