FTSJ3 RNA-Seq in K562

General Information


RBP	FTSJ3
Cell_Line	K562
Method	CRISPR
Exp_Name	FTSJ3-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	FTSJ3-BGKcLV40-61
Rep2	FTSJ3-BGKcLV40-62
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	need discussion
Rep2_WB
Antibody Cat#	A304-198A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1376

Experiment Information (Status: Submitting)

	BGKcLV40-61	BGKcLV40-61	BGKcLV40-62	BGKcLV40-62
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001027	BGC#0001027	BGC#0001027	BGC#0001027
shRNA_or_gRNA_sequence	AGTGTTACGAACCATCCCCC	AGTGTTACGAACCATCCCCC	AGTGTTACGAACCATCCCCC	AGTGTTACGAACCATCCCCC
PAM	TGG	TGG	TGG	TGG
Name	FTSJ3_93	FTSJ3_93	FTSJ3_93	FTSJ3_93
Sample_ID	BGKcLV40-61	BGKcLV40-61	BGKcLV40-62	BGKcLV40-62
transduction_Date	10/31/23	10/31/23	10/31/23	10/31/23
days	D6	D6	D6	D6
RBP_name	FTSJ3	FTSJ3	FTSJ3	FTSJ3
qPCR_result		45.6		46.5
Ave_qPCR		46.1
RT-qPCR_primer-F		ccctgttgacttcctctcca
RT-qPCR_primer-R		tcagtggtagctggatgctg
protein_conc	3615	3615	3902	3902
WB_result	need discussion	90.5		82.2
Ave_WB		86.4
WB_DONE_date		11/27/23,12/12/23
MW	97kd	97kd
IP
antibody_Cat#	A304-198A	A304-199A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date		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	5742	5744	5743	5745

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FTSJ3	Product_ID: A304-199A Lot_ID: 1 Source: Bethyl Labs Target Name: FTSJ3-human

Experiment Status

	BGKcLV40-61	BGKcLV40-61	BGKcLV40-62	BGKcLV40-62
Sample_ID	BGKcLV40-61	BGKcLV40-61	BGKcLV40-62	BGKcLV40-62
Sample Name
Sample Name	FTSJ3-BGKcLV40-61		FTSJ3-BGKcLV40-62
RBP	FTSJ3	FTSJ3	FTSJ3	FTSJ3
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	12796	12828	12797	12829

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-61	BGKcLV40-62
Sample #	43	44
Sample Name	FTSJ3-BGKcLV40-61	FTSJ3-BGKcLV40-62
Sample_Name_Alias
Index Well Position	C06	D06
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	278	274
Peak_Molarity	80.80	68.70
libSampleQC_DNA_Well	DNA_Library_set67/set1/C12.png	DNA_Library_set67/set1/D12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/C6.png	RNA_Library_set67/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-61	BGKcLV40-62
RBP	FTSJ3	FTSJ3
Batch_ID	BGKcLV40	BGKcLV40
WB_result	90.500	82.220
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4180	4181

Sequencing Information

	BGKcLV40-61	BGKcLV40-62
Sample_ID	BGKcLV40-61	BGKcLV40-62
Sample Name	FTSJ3-BGKcLV40-61	FTSJ3-BGKcLV40-62
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	26,726,478	25,077,224
total_aligned_reads	23,755,567	22,205,511
unique_aligned_reads	21,924,036	20,469,330
percent_uniqueAligned	0.82031	0.81625
correlation_replicates	0.997730	0.997730
spikein_reads	3,012	830
percent_spikeins	0.00011	0.00003
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2835	2836

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
FTSJ3-BGKcLV40-61_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2835	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	28181
FTSJ3-BGKcLV40-61_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2835	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	28225
FTSJ3-BGKcLV40-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2835					GRCh38	V40	FTSJ3-BGKcLV40-61_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,FTSJ3-BGKcLV40-61_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28269
FTSJ3-BGKcLV40-61_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	2835					GRCh38	V40	FTSJ3-BGKcLV40-61/Aligned.sortedByCoord.out.bam		ENCORE2	28313
FTSJ3-BGKcLV40-61_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	2835					GRCh38	V40	FTSJ3-BGKcLV40-61/Aligned.sortedByCoord.out.bam		ENCORE2	28357
FTSJ3-BGKcLV40-61_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	2835					GRCh38	V40	FTSJ3-BGKcLV40-61/Aligned.sortedByCoord.out.bam		ENCORE2	28401
FTSJ3-BGKcLV40-61_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	2835					GRCh38	V40	FTSJ3-BGKcLV40-61/Aligned.sortedByCoord.out.bam		ENCORE2	28445
FTSJ3-BGKcLV40-61_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2835					GRCh38	V40	FTSJ3-BGKcLV40-61_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,FTSJ3-BGKcLV40-61_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28489
FTSJ3-BGKcLV40-62_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2836	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	28182
FTSJ3-BGKcLV40-62_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2836	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	28226
FTSJ3-BGKcLV40-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2836					GRCh38	V40	FTSJ3-BGKcLV40-62_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,FTSJ3-BGKcLV40-62_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28270
FTSJ3-BGKcLV40-62_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	2836					GRCh38	V40	FTSJ3-BGKcLV40-62/Aligned.sortedByCoord.out.bam		ENCORE2	28314
FTSJ3-BGKcLV40-62_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	2836					GRCh38	V40	FTSJ3-BGKcLV40-62/Aligned.sortedByCoord.out.bam		ENCORE2	28358
FTSJ3-BGKcLV40-62_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	2836					GRCh38	V40	FTSJ3-BGKcLV40-62/Aligned.sortedByCoord.out.bam		ENCORE2	28402
FTSJ3-BGKcLV40-62_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	2836					GRCh38	V40	FTSJ3-BGKcLV40-62/Aligned.sortedByCoord.out.bam		ENCORE2	28446
FTSJ3-BGKcLV40-62_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2836					GRCh38	V40	FTSJ3-BGKcLV40-62_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,FTSJ3-BGKcLV40-62_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28490