FDPS RNA-Seq in K562

General Information


RBP	FDPS
Cell_Line	K562
Method	CRISPR
Exp_Name	FDPS-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	FDPS-BGKcLV40-49
Rep2	FDPS-BGKcLV40-50
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	59.9
Rep2_qPCR	66.0
Rep1_WB	59.8
Rep2_WB	60.9
Antibody Cat#	A305-045A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1372

Experiment Information (Status: Submitting)

	BGKcLV40-49	BGKcLV40-50
idx	0	0
TRCN#_or_BGC#	BGC#0001015	BGC#0001015
shRNA_or_gRNA_sequence	GATTCATCCCTTACCCGCCG	GATTCATCCCTTACCCGCCG
PAM	GGG	GGG
Name	FDPS_95	FDPS_95
Sample_ID	BGKcLV40-49	BGKcLV40-50
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	FDPS	FDPS
qPCR_result	59.9	66.0
Ave_qPCR	63.0
RT-qPCR_primer-F	CTTTCTTCCTGGTGGCAGATGAC
RT-qPCR_primer-R	AGAGCTTCAGCAGGCGGTAGAT
protein_conc	3635	3825
WB_result	59.8	60.9
Ave_WB	60.4
WB_DONE_date	11/15/23
MW	48kd
IP
antibody_Cat#	A305-045A	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	5728	5729

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FDPS	Product_ID: A305-045A Lot_ID: 1 Source: Bethyl Labs Target Name: FDPS-human

Experiment Status

	BGKcLV40-49	BGKcLV40-50
Sample_ID	BGKcLV40-49	BGKcLV40-50
Sample Name
Sample Name	FDPS-BGKcLV40-49	FDPS-BGKcLV40-50
RBP	FDPS	FDPS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12788	12789

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-49	BGKcLV40-50
Sample #	35	36
Sample Name	FDPS-BGKcLV40-49	FDPS-BGKcLV40-50
Sample_Name_Alias
Index Well Position	C05	D05
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	284	281
Peak_Molarity	88.00	87.70
libSampleQC_DNA_Well	DNA_Library_set67/set1/C11.png	DNA_Library_set67/set1/D11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/C5.png	RNA_Library_set67/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-49	BGKcLV40-50
RBP	FDPS	FDPS
Batch_ID	BGKcLV40	BGKcLV40
WB_result	59.800	60.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4172	4173

Sequencing Information

	BGKcLV40-49	BGKcLV40-50
Sample_ID	BGKcLV40-49	BGKcLV40-50
Sample Name	FDPS-BGKcLV40-49	FDPS-BGKcLV40-50
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	43,489,542	31,465,692
total_aligned_reads	39,111,394	27,869,925
unique_aligned_reads	35,981,430	25,667,197
percent_uniqueAligned	0.82736	0.81572
correlation_replicates	0.996085	0.996085
spikein_reads	5,636	220
percent_spikeins	0.00013	0.00001
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2827	2828

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
FDPS-BGKcLV40-49_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2827	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	28173
FDPS-BGKcLV40-49_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2827	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	28217
FDPS-BGKcLV40-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2827					GRCh38	V40	FDPS-BGKcLV40-49_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,FDPS-BGKcLV40-49_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28261
FDPS-BGKcLV40-49_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	2827					GRCh38	V40	FDPS-BGKcLV40-49/Aligned.sortedByCoord.out.bam		ENCORE2	28305
FDPS-BGKcLV40-49_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	2827					GRCh38	V40	FDPS-BGKcLV40-49/Aligned.sortedByCoord.out.bam		ENCORE2	28349
FDPS-BGKcLV40-49_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	2827					GRCh38	V40	FDPS-BGKcLV40-49/Aligned.sortedByCoord.out.bam		ENCORE2	28393
FDPS-BGKcLV40-49_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	2827					GRCh38	V40	FDPS-BGKcLV40-49/Aligned.sortedByCoord.out.bam		ENCORE2	28437
FDPS-BGKcLV40-49_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2827					GRCh38	V40	FDPS-BGKcLV40-49_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,FDPS-BGKcLV40-49_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28481
FDPS-BGKcLV40-50_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2828	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	28174
FDPS-BGKcLV40-50_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2828	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	28218
FDPS-BGKcLV40-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2828					GRCh38	V40	FDPS-BGKcLV40-50_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,FDPS-BGKcLV40-50_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28262
FDPS-BGKcLV40-50_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	2828					GRCh38	V40	FDPS-BGKcLV40-50/Aligned.sortedByCoord.out.bam		ENCORE2	28306
FDPS-BGKcLV40-50_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	2828					GRCh38	V40	FDPS-BGKcLV40-50/Aligned.sortedByCoord.out.bam		ENCORE2	28350
FDPS-BGKcLV40-50_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	2828					GRCh38	V40	FDPS-BGKcLV40-50/Aligned.sortedByCoord.out.bam		ENCORE2	28394
FDPS-BGKcLV40-50_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	2828					GRCh38	V40	FDPS-BGKcLV40-50/Aligned.sortedByCoord.out.bam		ENCORE2	28438
FDPS-BGKcLV40-50_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2828					GRCh38	V40	FDPS-BGKcLV40-50_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,FDPS-BGKcLV40-50_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28482