FSCN1 RNA-Seq in K562

General Information


RBP	FSCN1
Cell_Line	K562
Method	CRISPR
Exp_Name	FSCN1-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	FSCN1-BGKcLV40-59
Rep2	FSCN1-BGKcLV40-60
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	58.5
Rep2_qPCR	60.2
Rep1_WB	61.9
Rep2_WB	67.6444
Antibody Cat#	A305-240A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1375

Experiment Information (Status: Submitting)

	BGKcLV40-59	BGKcLV40-60
idx	0	0
TRCN#_or_BGC#	BGC#0001024	BGC#0001024
shRNA_or_gRNA_sequence	GCGCCACCAGGCGCCCGTCG	GCGCCACCAGGCGCCCGTCG
PAM	TGG	TGG
Name	FSCN1_90	FSCN1_90
Sample_ID	BGKcLV40-59	BGKcLV40-60
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	FSCN1	FSCN1
qPCR_result	58.5	60.2
Ave_qPCR	59.4
RT-qPCR_primer-F	caccaaaaagtgtgccttcc
RT-qPCR_primer-R	cgccactcgatgtcaaagta
protein_conc	3513	3311
WB_result	61.9	67.6444
Ave_WB	64.8
WB_DONE_date	12/7/23,12/12/23
MW	55kd
IP
antibody_Cat#	A305-240A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5740	5741

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FSCN1	Product_ID: A305-240A Lot_ID: 1 Source: Bethyl Labs Target Name: FSCN1-human

Experiment Status

	BGKcLV40-59	BGKcLV40-60
Sample_ID	BGKcLV40-59	BGKcLV40-60
Sample Name
Sample Name	FSCN1-BGKcLV40-59	FSCN1-BGKcLV40-60
RBP	FSCN1	FSCN1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12794	12795

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-59	BGKcLV40-60
Sample #	41	42
Sample Name	FSCN1-BGKcLV40-59	FSCN1-BGKcLV40-60
Sample_Name_Alias
Index Well Position	A06	B06
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	274	277
Peak_Molarity	71.00	53.20
libSampleQC_DNA_Well	DNA_Library_set67/set1/A12.png	DNA_Library_set67/set1/B12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/A6.png	RNA_Library_set67/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-59	BGKcLV40-60
RBP	FSCN1	FSCN1
Batch_ID	BGKcLV40	BGKcLV40
WB_result	61.900	67.644
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4178	4179

Sequencing Information

	BGKcLV40-59	BGKcLV40-60
Sample_ID	BGKcLV40-59	BGKcLV40-60
Sample Name	FSCN1-BGKcLV40-59	FSCN1-BGKcLV40-60
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	19,565,978	19,804,150
total_aligned_reads	15,829,063	16,840,633
unique_aligned_reads	14,574,451	15,536,817
percent_uniqueAligned	0.74489	0.78452
correlation_replicates	0.994177	0.994177
spikein_reads	2,004	436
percent_spikeins	0.00010	0.00002
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2833	2834

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
FSCN1-BGKcLV40-59_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2833	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	28179
FSCN1-BGKcLV40-59_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2833	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	28223
FSCN1-BGKcLV40-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2833					GRCh38	V40	FSCN1-BGKcLV40-59_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,FSCN1-BGKcLV40-59_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28267
FSCN1-BGKcLV40-59_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	2833					GRCh38	V40	FSCN1-BGKcLV40-59/Aligned.sortedByCoord.out.bam		ENCORE2	28311
FSCN1-BGKcLV40-59_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	2833					GRCh38	V40	FSCN1-BGKcLV40-59/Aligned.sortedByCoord.out.bam		ENCORE2	28355
FSCN1-BGKcLV40-59_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	2833					GRCh38	V40	FSCN1-BGKcLV40-59/Aligned.sortedByCoord.out.bam		ENCORE2	28399
FSCN1-BGKcLV40-59_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	2833					GRCh38	V40	FSCN1-BGKcLV40-59/Aligned.sortedByCoord.out.bam		ENCORE2	28443
FSCN1-BGKcLV40-59_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2833					GRCh38	V40	FSCN1-BGKcLV40-59_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,FSCN1-BGKcLV40-59_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28487
FSCN1-BGKcLV40-60_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2834	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	28180
FSCN1-BGKcLV40-60_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2834	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	28224
FSCN1-BGKcLV40-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2834					GRCh38	V40	FSCN1-BGKcLV40-60_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,FSCN1-BGKcLV40-60_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28268
FSCN1-BGKcLV40-60_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	2834					GRCh38	V40	FSCN1-BGKcLV40-60/Aligned.sortedByCoord.out.bam		ENCORE2	28312
FSCN1-BGKcLV40-60_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	2834					GRCh38	V40	FSCN1-BGKcLV40-60/Aligned.sortedByCoord.out.bam		ENCORE2	28356
FSCN1-BGKcLV40-60_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	2834					GRCh38	V40	FSCN1-BGKcLV40-60/Aligned.sortedByCoord.out.bam		ENCORE2	28400
FSCN1-BGKcLV40-60_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	2834					GRCh38	V40	FSCN1-BGKcLV40-60/Aligned.sortedByCoord.out.bam		ENCORE2	28444
FSCN1-BGKcLV40-60_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2834					GRCh38	V40	FSCN1-BGKcLV40-60_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,FSCN1-BGKcLV40-60_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28488