FAM98B RNA-Seq in K562

General Information


RBP	FAM98B
Cell_Line	K562
Method	CRISPR
Exp_Name	FAM98B-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	FAM98B-BGKcLV40-47
Rep2	FAM98B-BGKcLV40-48
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	43.4
Rep2_qPCR	41.9
Rep1_WB	87.3
Rep2_WB	84.7
Antibody Cat#	A305-818A-M
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1371

Experiment Information (Status: Submitting)

	BGKcLV40-47	BGKcLV40-48
idx	0	0
TRCN#_or_BGC#	BGC#0001013	BGC#0001013
shRNA_or_gRNA_sequence	GGGTCCCCAACCGACGATGG	GGGTCCCCAACCGACGATGG
PAM	AGG	AGG
Name	FAM98B_95	FAM98B_95
Sample_ID	BGKcLV40-47	BGKcLV40-48
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	FAM98B	FAM98B
qPCR_result	43.4	41.9
Ave_qPCR	42.7
RT-qPCR_primer-F	gggaaaaccactgctgaaaa
RT-qPCR_primer-R	cggcactcatattcacagga
protein_conc	3524	3545
WB_result	87.3	84.7
Ave_WB	86.0
WB_DONE_date	11/15/23
MW	46kd
IP
antibody_Cat#	A305-818A-M	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	5726	5727

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FAM98B	Product_ID: A305-818A-M Lot_ID: 1 Source: Bethyl Labs Target Name: FAM98B-human

Experiment Status

	BGKcLV40-47	BGKcLV40-48
Sample_ID	BGKcLV40-47	BGKcLV40-48
Sample Name
Sample Name	FAM98B-BGKcLV40-47	FAM98B-BGKcLV40-48
RBP	FAM98B	FAM98B
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12786	12787

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-47	BGKcLV40-48
Sample #	33	34
Sample Name	FAM98B-BGKcLV40-47	FAM98B-BGKcLV40-48
Sample_Name_Alias
Index Well Position	A05	B05
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	281
Peak_Molarity	57.30	64.90
libSampleQC_DNA_Well	DNA_Library_set67/set1/A11.png	DNA_Library_set67/set1/B11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/A5.png	RNA_Library_set67/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-47	BGKcLV40-48
RBP	FAM98B	FAM98B
Batch_ID	BGKcLV40	BGKcLV40
WB_result	87.300	84.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4170	4171

Sequencing Information

	BGKcLV40-47	BGKcLV40-48
Sample_ID	BGKcLV40-47	BGKcLV40-48
Sample Name	FAM98B-BGKcLV40-47	FAM98B-BGKcLV40-48
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	35,482,065	30,305,043
total_aligned_reads	29,908,575	25,534,580
unique_aligned_reads	27,502,099	23,475,989
percent_uniqueAligned	0.77510	0.77466
correlation_replicates	0.992573	0.992573
spikein_reads	6,936	2,210
percent_spikeins	0.00020	0.00007
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2825	2826

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
FAM98B-BGKcLV40-47_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2825	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	28171
FAM98B-BGKcLV40-47_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2825	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	28215
FAM98B-BGKcLV40-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2825					GRCh38	V40	FAM98B-BGKcLV40-47_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98B-BGKcLV40-47_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28259
FAM98B-BGKcLV40-47_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	2825					GRCh38	V40	FAM98B-BGKcLV40-47/Aligned.sortedByCoord.out.bam		ENCORE2	28303
FAM98B-BGKcLV40-47_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	2825					GRCh38	V40	FAM98B-BGKcLV40-47/Aligned.sortedByCoord.out.bam		ENCORE2	28347
FAM98B-BGKcLV40-47_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	2825					GRCh38	V40	FAM98B-BGKcLV40-47/Aligned.sortedByCoord.out.bam		ENCORE2	28391
FAM98B-BGKcLV40-47_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	2825					GRCh38	V40	FAM98B-BGKcLV40-47/Aligned.sortedByCoord.out.bam		ENCORE2	28435
FAM98B-BGKcLV40-47_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2825					GRCh38	V40	FAM98B-BGKcLV40-47_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98B-BGKcLV40-47_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28479
FAM98B-BGKcLV40-48_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2826	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	28172
FAM98B-BGKcLV40-48_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2826	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	28216
FAM98B-BGKcLV40-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2826					GRCh38	V40	FAM98B-BGKcLV40-48_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98B-BGKcLV40-48_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28260
FAM98B-BGKcLV40-48_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	2826					GRCh38	V40	FAM98B-BGKcLV40-48/Aligned.sortedByCoord.out.bam		ENCORE2	28304
FAM98B-BGKcLV40-48_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	2826					GRCh38	V40	FAM98B-BGKcLV40-48/Aligned.sortedByCoord.out.bam		ENCORE2	28348
FAM98B-BGKcLV40-48_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	2826					GRCh38	V40	FAM98B-BGKcLV40-48/Aligned.sortedByCoord.out.bam		ENCORE2	28392
FAM98B-BGKcLV40-48_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	2826					GRCh38	V40	FAM98B-BGKcLV40-48/Aligned.sortedByCoord.out.bam		ENCORE2	28436
FAM98B-BGKcLV40-48_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2826					GRCh38	V40	FAM98B-BGKcLV40-48_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98B-BGKcLV40-48_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28480