NXF1 RNA-Seq in K562

General Information


RBP	NXF1
Cell_Line	K562
Method	CRISPR
Exp_Name	NXF1-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NXF1-BGKcLV46-49
Rep2	NXF1-BGKcLV46-50
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	68.2
Rep2_WB	68.8
Antibody Cat#	A303-915A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1644

Experiment Information (Status: Submitting)

	BGKcLV46-49	BGKcLV46-49	BGKcLV46-50	BGKcLV46-50
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0000196	BGC#0000196	BGC#0000196	BGC#0000196
shRNA_or_gRNA_sequence	GTAGGTGGACTGGTCTCGGA	GTAGGTGGACTGGTCTCGGA	GTAGGTGGACTGGTCTCGGA	GTAGGTGGACTGGTCTCGGA
PAM	AGG	AGG	AGG	AGG
Name	NXF1-90F	NXF1-90F	NXF1-90F	NXF1-90F
Sample_ID	BGKcLV46-49	BGKcLV46-49	BGKcLV46-50	BGKcLV46-50
transduction_Date	12/20/24	12/20/24	12/20/24	12/20/24
days	D6	D6	D6	D6
RBP_name	NXF1	NXF1	NXF1	NXF1
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	2342	2342	2268	2268
WB_result	68.2	74.4	68.8	69.4267
Ave_WB
WB_DONE_date	1/6/25	1/31/25
MW	70kd	70kd
IP
antibody_Cat#	A303-915A	A303-914A	lot# 1	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	6043	6045	6044	6046

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV46-49	BGKcLV46-49	BGKcLV46-50	BGKcLV46-50
Sample_ID	BGKcLV46-49	BGKcLV46-49	BGKcLV46-50	BGKcLV46-50
Sample Name
Sample Name	NXF1-BGKcLV46-49		NXF1-BGKcLV46-50
RBP	NXF1	NXF1	NXF1	NXF1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-04-21	2025-02-10	2025-04-21	2025-02-10
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14042	14102	14043	14103

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-49	BGKcLV46-50
Sample #	21	22
Sample Name	NXF1-BGKcLV46-49	NXF1-BGKcLV46-50
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	310	306
Peak_Molarity	88.80	86.50
libSampleQC_DNA_Well	DNA_Library_set77/set1/E9.png	DNA_Library_set77/set1/F9.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set77/set1/E3.png	RNA_Library_set77/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-49	BGKcLV46-50
RBP	NXF1	NXF1
Batch_ID	BGKcLV46	BGKcLV46
WB_result	68.200	68.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4680	4681

Sequencing Information

	BGKcLV46-49	BGKcLV46-50
Sample_ID	BGKcLV46-49	BGKcLV46-50
Sample Name	NXF1-BGKcLV46-49	NXF1-BGKcLV46-50
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	53,756,890	48,170,087
total_aligned_reads	49,181,141	43,925,506
unique_aligned_reads	45,339,889	40,503,157
percent_uniqueAligned	0.84342	0.84084
correlation_replicates	0.999323	0.999323
spikein_reads	91,844	109,474
percent_spikeins	0.00171	0.00227
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3385	3386

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
NXF1-BGKcLV46-49_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3385	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32170
NXF1-BGKcLV46-49_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3385	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32220
NXF1-BGKcLV46-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3385					GRCh38	V40	NXF1-BGKcLV46-49_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGKcLV46-49_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32270
NXF1-BGKcLV46-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3385					GRCh38	V40	NXF1-BGKcLV46-49_Aligned.sortedByCoord.out.bam		ENCORE2	32320
NXF1-BGKcLV46-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3385					GRCh38	V40	NXF1-BGKcLV46-49_Aligned.sortedByCoord.out.bam		ENCORE2	32370
NXF1-BGKcLV46-49_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3385					GRCh38	V40	NXF1-BGKcLV46-49_Aligned.sortedByCoord.out.bam		ENCORE2	32420
NXF1-BGKcLV46-49_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3385					GRCh38	V40	NXF1-BGKcLV46-49_Aligned.sortedByCoord.out.bam		ENCORE2	32470
NXF1-BGKcLV46-49_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3385					GRCh38	V40	NXF1-BGKcLV46-49_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGKcLV46-49_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32520
NXF1-BGKcLV46-50_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3386	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32171
NXF1-BGKcLV46-50_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3386	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32221
NXF1-BGKcLV46-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3386					GRCh38	V40	NXF1-BGKcLV46-50_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGKcLV46-50_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32271
NXF1-BGKcLV46-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3386					GRCh38	V40	NXF1-BGKcLV46-50_Aligned.sortedByCoord.out.bam		ENCORE2	32321
NXF1-BGKcLV46-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3386					GRCh38	V40	NXF1-BGKcLV46-50_Aligned.sortedByCoord.out.bam		ENCORE2	32371
NXF1-BGKcLV46-50_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3386					GRCh38	V40	NXF1-BGKcLV46-50_Aligned.sortedByCoord.out.bam		ENCORE2	32421
NXF1-BGKcLV46-50_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3386					GRCh38	V40	NXF1-BGKcLV46-50_Aligned.sortedByCoord.out.bam		ENCORE2	32471
NXF1-BGKcLV46-50_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3386					GRCh38	V40	NXF1-BGKcLV46-50_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGKcLV46-50_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32521