NFX1 RNA-Seq in K562

General Information


RBP	NFX1
Cell_Line	K562
Method	CRISPR
Exp_Name	NFX1-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NFX1-BGKcLV44-35
Rep2	NFX1-BGKcLV44-36
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	66.8
Rep2_qPCR	66.4
Rep1_WB	61.6
Rep2_WB	61.9
Antibody Cat#	A302-916A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1601

Experiment Information (Status: Submitting)

	BGKcLV44-35	BGKcLV44-36
idx	0	0
TRCN#_or_BGC#	BGC#0001221	BGC#0001221
shRNA_or_gRNA_sequence	TTCGTGTCACGGCCCCAGTG	TTCGTGTCACGGCCCCAGTG
PAM	TGG	TGG
Name	NFX1_81	NFX1_81
Sample_ID	BGKcLV44-35	BGKcLV44-36
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	NFX1	NFX1
qPCR_result	66.8	66.4
Ave_qPCR	66.6
RT-qPCR_primer-F	agaatgtggaaacgcacaca
RT-qPCR_primer-R	cgtgacacgaaccaattcac
protein_conc	3146	2946
WB_result	61.6	61.9
Ave_WB	61.7
WB_DONE_date	8/12/24
MW	124kd
IP
antibody_Cat#	A302-916A	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5914	5915

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NFX1	Product_ID: A302-916A Lot_ID: 1 Source: Bethyl Labs Target Name: NFX1-human

Experiment Status

	BGKcLV44-35	BGKcLV44-36
Sample_ID	BGKcLV44-35	BGKcLV44-36
Sample Name
Sample Name	NFX1-BGKcLV44-35	NFX1-BGKcLV44-36
RBP	NFX1	NFX1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13594	13595

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-35	BGKcLV44-36
Sample #	23	24
Sample Name	NFX1-BGKcLV44-35	NFX1-BGKcLV44-36
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	291	286
Peak_Molarity	67.80	51.90
libSampleQC_DNA_Well	DNA_Library_set75/set1/G8.png	DNA_Library_set75/set1/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/G2.png	RNA_Library_set75/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-35	BGKcLV44-36
RBP	NFX1	NFX1
Batch_ID	BGKcLV44	BGKcLV44
WB_result	61.600	61.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4582	4583

Sequencing Information

	BGKcLV44-35	BGKcLV44-36
Sample_ID	BGKcLV44-35	BGKcLV44-36
Sample Name	NFX1-BGKcLV44-35	NFX1-BGKcLV44-36
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	50,530,092	56,370,464
total_aligned_reads	48,711,312	53,929,379
unique_aligned_reads	45,069,668	49,925,734
percent_uniqueAligned	0.89194	0.88567
correlation_replicates	0.997904	0.997904
spikein_reads	70,214	116,490
percent_spikeins	0.00139	0.00207
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3293	3294

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-BGKcLV44-35_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3293	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30948
NFX1-BGKcLV44-35_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3293	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30990
NFX1-BGKcLV44-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3293					GRCh38	V40	NFX1-BGKcLV44-35_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGKcLV44-35_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31032
NFX1-BGKcLV44-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3293					GRCh38	V40	NFX1-BGKcLV44-35_Aligned.sortedByCoord.out.bam		ENCORE2	31074
NFX1-BGKcLV44-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3293					GRCh38	V40	NFX1-BGKcLV44-35_Aligned.sortedByCoord.out.bam		ENCORE2	31116
NFX1-BGKcLV44-35_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3293					GRCh38	V40	NFX1-BGKcLV44-35_Aligned.sortedByCoord.out.bam		ENCORE2	31158
NFX1-BGKcLV44-35_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3293					GRCh38	V40	NFX1-BGKcLV44-35_Aligned.sortedByCoord.out.bam		ENCORE2	31200
NFX1-BGKcLV44-35_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3293					GRCh38	V40	NFX1-BGKcLV44-35_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGKcLV44-35_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31242
NFX1-BGKcLV44-36_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3294	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30949
NFX1-BGKcLV44-36_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3294	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30991
NFX1-BGKcLV44-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3294					GRCh38	V40	NFX1-BGKcLV44-36_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGKcLV44-36_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31033
NFX1-BGKcLV44-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3294					GRCh38	V40	NFX1-BGKcLV44-36_Aligned.sortedByCoord.out.bam		ENCORE2	31075
NFX1-BGKcLV44-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3294					GRCh38	V40	NFX1-BGKcLV44-36_Aligned.sortedByCoord.out.bam		ENCORE2	31117
NFX1-BGKcLV44-36_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3294					GRCh38	V40	NFX1-BGKcLV44-36_Aligned.sortedByCoord.out.bam		ENCORE2	31159
NFX1-BGKcLV44-36_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3294					GRCh38	V40	NFX1-BGKcLV44-36_Aligned.sortedByCoord.out.bam		ENCORE2	31201
NFX1-BGKcLV44-36_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3294					GRCh38	V40	NFX1-BGKcLV44-36_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,NFX1-BGKcLV44-36_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31243