FKBP3 RNA-Seq in K562

General Information


RBP	FKBP3
Cell_Line	K562
Method	CRISPR
Exp_Name	FKBP3-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	FKBP3-BGKcLV40-55
Rep2	FKBP3-BGKcLV40-56
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	44.8
Rep2_qPCR	61.7
Rep1_WB	59.2
Rep2_WB	67.7
Antibody Cat#	A302-600A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1374

Experiment Information (Status: Submitting)

	BGKcLV40-55	BGKcLV40-56
idx	0	0
TRCN#_or_BGC#	BGC#0001021	BGC#0001021
shRNA_or_gRNA_sequence	TCCACGGTCCACGCCCGCTG	TCCACGGTCCACGCCCGCTG
PAM	TGG	TGG
Name	FKBP3_90	FKBP3_90
Sample_ID	BGKcLV40-55	BGKcLV40-56
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	FKBP3	FKBP3
qPCR_result	44.8	61.7
Ave_qPCR	53.3
RT-qPCR_primer-F	aaggctcgactggagattga
RT-qPCR_primer-R	tgagttttgcatttggtgga
protein_conc	3523	3381
WB_result	59.2	67.7
Ave_WB	63.4
WB_DONE_date	11/8/23
MW	25kd
IP
antibody_Cat#	A302-600A	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	5736	5737

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FKBP3	Product_ID: A302-600A Lot_ID: 1 Source: Bethyl Labs Target Name: FKBP3-human

Experiment Status

	BGKcLV40-55	BGKcLV40-56
Sample_ID	BGKcLV40-55	BGKcLV40-56
Sample Name
Sample Name	FKBP3-BGKcLV40-55	FKBP3-BGKcLV40-56
RBP	FKBP3	FKBP3
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12792	12793

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-55	BGKcLV40-56
Sample #	39	40
Sample Name	FKBP3-BGKcLV40-55	FKBP3-BGKcLV40-56
Sample_Name_Alias
Index Well Position	G05	H05
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	281	285
Peak_Molarity	81.40	74.30
libSampleQC_DNA_Well	DNA_Library_set67/set1/G11.png	DNA_Library_set67/set1/H11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/G5.png	RNA_Library_set67/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-55	BGKcLV40-56
RBP	FKBP3	FKBP3
Batch_ID	BGKcLV40	BGKcLV40
WB_result	59.200	67.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4176	4177

Sequencing Information

	BGKcLV40-55	BGKcLV40-56
Sample_ID	BGKcLV40-55	BGKcLV40-56
Sample Name	FKBP3-BGKcLV40-55	FKBP3-BGKcLV40-56
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	23,190,841	22,956,546
total_aligned_reads	20,380,688	19,597,996
unique_aligned_reads	18,767,672	18,001,447
percent_uniqueAligned	0.80927	0.78415
correlation_replicates	0.999521	0.999521
spikein_reads	3,816	6,766
percent_spikeins	0.00016	0.00029
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2831	2832

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
FKBP3-BGKcLV40-55_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2831	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	28177
FKBP3-BGKcLV40-55_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2831	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	28221
FKBP3-BGKcLV40-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2831					GRCh38	V40	FKBP3-BGKcLV40-55_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,FKBP3-BGKcLV40-55_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28265
FKBP3-BGKcLV40-55_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	2831					GRCh38	V40	FKBP3-BGKcLV40-55/Aligned.sortedByCoord.out.bam		ENCORE2	28309
FKBP3-BGKcLV40-55_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	2831					GRCh38	V40	FKBP3-BGKcLV40-55/Aligned.sortedByCoord.out.bam		ENCORE2	28353
FKBP3-BGKcLV40-55_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	2831					GRCh38	V40	FKBP3-BGKcLV40-55/Aligned.sortedByCoord.out.bam		ENCORE2	28397
FKBP3-BGKcLV40-55_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	2831					GRCh38	V40	FKBP3-BGKcLV40-55/Aligned.sortedByCoord.out.bam		ENCORE2	28441
FKBP3-BGKcLV40-55_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2831					GRCh38	V40	FKBP3-BGKcLV40-55_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,FKBP3-BGKcLV40-55_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28485
FKBP3-BGKcLV40-56_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2832	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	28178
FKBP3-BGKcLV40-56_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2832	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	28222
FKBP3-BGKcLV40-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2832					GRCh38	V40	FKBP3-BGKcLV40-56_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,FKBP3-BGKcLV40-56_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28266
FKBP3-BGKcLV40-56_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	2832					GRCh38	V40	FKBP3-BGKcLV40-56/Aligned.sortedByCoord.out.bam		ENCORE2	28310
FKBP3-BGKcLV40-56_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	2832					GRCh38	V40	FKBP3-BGKcLV40-56/Aligned.sortedByCoord.out.bam		ENCORE2	28354
FKBP3-BGKcLV40-56_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	2832					GRCh38	V40	FKBP3-BGKcLV40-56/Aligned.sortedByCoord.out.bam		ENCORE2	28398
FKBP3-BGKcLV40-56_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	2832					GRCh38	V40	FKBP3-BGKcLV40-56/Aligned.sortedByCoord.out.bam		ENCORE2	28442
FKBP3-BGKcLV40-56_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2832					GRCh38	V40	FKBP3-BGKcLV40-56_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,FKBP3-BGKcLV40-56_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28486