FEN1 RNA-Seq in K562

General Information


RBP	FEN1
Cell_Line	K562
Method	CRISPR
Exp_Name	FEN1-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	FEN1-BGKcLV40-51
Rep2	FEN1-BGKcLV40-52
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	57.3
Rep2_qPCR	57.8
Rep1_WB	81.5
Rep2_WB	82.9
Antibody Cat#	A300-255A
Antibody Lot#	lot # 3
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1373

Experiment Information (Status: Submitting)

	BGKcLV40-51	BGKcLV40-51	BGKcLV40-52	BGKcLV40-52
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001017	BGC#0001017	BGC#0001017	BGC#0001017
shRNA_or_gRNA_sequence	GACTACTGTGAGAGTATCCG	GACTACTGTGAGAGTATCCG	GACTACTGTGAGAGTATCCG	GACTACTGTGAGAGTATCCG
PAM	GGG	GGG	GGG	GGG
Name	FEN1_93	FEN1_93	FEN1_93	FEN1_93
Sample_ID	BGKcLV40-51	BGKcLV40-51	BGKcLV40-52	BGKcLV40-52
transduction_Date	10/31/23	10/31/23	10/31/23	10/31/23
days	D6	D6	D6	D6
RBP_name	FEN1	FEN1	FEN1	FEN1
qPCR_result	57.3		57.8
Ave_qPCR	57.6
RT-qPCR_primer-F	ACTAAGCGGCTGGTGAAGGTCA
RT-qPCR_primer-R	GCAGCATAGACTTTGCCAGCCT
protein_conc	3490	3490	3468	3468
WB_result	81.5	70.3	82.9	69.4
Ave_WB	82.2	69.9
WB_DONE_date	11/17/23	12/12/23
MW	43kd	43kd
IP
antibody_Cat#	A300-255A	A300-256A	lot # 3	lot # 2
Antibody DCC ID
submitted_to_DCC_date	1/4/24	1/4/24
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5730	5732	5731	5733

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FEN1	Product_ID: A300-255A Lot_ID: 3 Source: Bethyl Labs Target Name: FEN1-human
FEN1	Product_ID: A300-256A Lot_ID: 2 Source: Bethyl Labs Target Name: FEN1-human

Experiment Status

	BGKcLV40-51	BGKcLV40-51	BGKcLV40-52	BGKcLV40-52
Sample_ID	BGKcLV40-51	BGKcLV40-51	BGKcLV40-52	BGKcLV40-52
Sample Name
Sample Name	FEN1-BGKcLV40-51		FEN1-BGKcLV40-52
RBP	FEN1	FEN1	FEN1	FEN1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2024-02-16	2023-12-15	2024-02-16	2023-12-15
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	12790	12822	12791	12823

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-51	BGKcLV40-52
Sample #	37	38
Sample Name	FEN1-BGKcLV40-51	FEN1-BGKcLV40-52
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	289	290
Peak_Molarity	86.80	94.50
libSampleQC_DNA_Well	DNA_Library_set67/set1/E11.png	DNA_Library_set67/set1/F11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/E5.png	RNA_Library_set67/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-51	BGKcLV40-52
RBP	FEN1	FEN1
Batch_ID	BGKcLV40	BGKcLV40
WB_result	81.500	82.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4174	4175

Sequencing Information

	BGKcLV40-51	BGKcLV40-52
Sample_ID	BGKcLV40-51	BGKcLV40-52
Sample Name	FEN1-BGKcLV40-51	FEN1-BGKcLV40-52
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	42,477,914	21,701,491
total_aligned_reads	37,527,787	19,538,670
unique_aligned_reads	34,490,643	17,974,549
percent_uniqueAligned	0.81197	0.82826
correlation_replicates	0.993950	0.993950
spikein_reads	3,828	3,318
percent_spikeins	0.00009	0.00015
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2829	2830

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
FEN1-BGKcLV40-51_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2829	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28175
FEN1-BGKcLV40-51_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2829	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28219
FEN1-BGKcLV40-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2829					GRCh38	V40	FEN1-BGKcLV40-51_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,FEN1-BGKcLV40-51_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28263
FEN1-BGKcLV40-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2829					GRCh38	V40	FEN1-BGKcLV40-51/Aligned.sortedByCoord.out.bam		ENCORE2	28307
FEN1-BGKcLV40-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2829					GRCh38	V40	FEN1-BGKcLV40-51/Aligned.sortedByCoord.out.bam		ENCORE2	28351
FEN1-BGKcLV40-51_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2829					GRCh38	V40	FEN1-BGKcLV40-51/Aligned.sortedByCoord.out.bam		ENCORE2	28395
FEN1-BGKcLV40-51_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2829					GRCh38	V40	FEN1-BGKcLV40-51/Aligned.sortedByCoord.out.bam		ENCORE2	28439
FEN1-BGKcLV40-51_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2829					GRCh38	V40	FEN1-BGKcLV40-51_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,FEN1-BGKcLV40-51_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28483
FEN1-BGKcLV40-52_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2830	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28176
FEN1-BGKcLV40-52_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2830	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28220
FEN1-BGKcLV40-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2830					GRCh38	V40	FEN1-BGKcLV40-52_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,FEN1-BGKcLV40-52_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28264
FEN1-BGKcLV40-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2830					GRCh38	V40	FEN1-BGKcLV40-52/Aligned.sortedByCoord.out.bam		ENCORE2	28308
FEN1-BGKcLV40-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2830					GRCh38	V40	FEN1-BGKcLV40-52/Aligned.sortedByCoord.out.bam		ENCORE2	28352
FEN1-BGKcLV40-52_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2830					GRCh38	V40	FEN1-BGKcLV40-52/Aligned.sortedByCoord.out.bam		ENCORE2	28396
FEN1-BGKcLV40-52_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2830					GRCh38	V40	FEN1-BGKcLV40-52/Aligned.sortedByCoord.out.bam		ENCORE2	28440
FEN1-BGKcLV40-52_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2830					GRCh38	V40	FEN1-BGKcLV40-52_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,FEN1-BGKcLV40-52_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28484