FAM98A RNA-Seq in K562

General Information


RBP	FAM98A
Cell_Line	K562
Method	CRISPR
Exp_Name	FAM98A-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	FAM98A-BGKcLV40-45
Rep2	FAM98A-BGKcLV40-46
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	65.1
Rep2_qPCR	59.4
Rep1_WB	93.808
Rep2_WB	93.2015
Antibody Cat#	A305-817A-M
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1370

Experiment Information (Status: Submitting)

	BGKcLV40-45	BGKcLV40-46
idx	0	0
TRCN#_or_BGC#	BGC#0001011	BGC#0001011
shRNA_or_gRNA_sequence	ATGATTACTACTCACCCAGT	ATGATTACTACTCACCCAGT
PAM	GGG	GGG
Name	FAM98A_81	FAM98A_81
Sample_ID	BGKcLV40-45	BGKcLV40-46
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	FAM98A	FAM98A
qPCR_result	65.1	59.4
Ave_qPCR	62.3
RT-qPCR_primer-F	ccaagccatagccaatgaat
RT-qPCR_primer-R	gaacgtttcggctggtaaac
protein_conc	3879	3905
WB_result	93.808	93.2015
Ave_WB	93.50475
WB_DONE_date	11/15/23
MW	55kd
IP
antibody_Cat#	A305-817A-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	5724	5725

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FAM98A	Product_ID: A305-817A-M Lot_ID: 1 Source: Bethyl Labs Target Name: FAM98A-human

Experiment Status

	BGKcLV40-45	BGKcLV40-46
Sample_ID	BGKcLV40-45	BGKcLV40-46
Sample Name
Sample Name	FAM98A-BGKcLV40-45	FAM98A-BGKcLV40-46
RBP	FAM98A	FAM98A
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12784	12785

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-45	BGKcLV40-46
Sample #	31	32
Sample Name	FAM98A-BGKcLV40-45	FAM98A-BGKcLV40-46
Sample_Name_Alias
Index Well Position	G04	H04
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	280
Peak_Molarity	75.20	71.80
libSampleQC_DNA_Well	DNA_Library_set67/set1/G10.png	DNA_Library_set67/set1/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/G4.png	RNA_Library_set67/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-45	BGKcLV40-46
RBP	FAM98A	FAM98A
Batch_ID	BGKcLV40	BGKcLV40
WB_result	93.808	93.202
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4168	4169

Sequencing Information

	BGKcLV40-45	BGKcLV40-46
Sample_ID	BGKcLV40-45	BGKcLV40-46
Sample Name	FAM98A-BGKcLV40-45	FAM98A-BGKcLV40-46
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	42,884,139	29,723,321
total_aligned_reads	38,851,675	26,776,002
unique_aligned_reads	35,716,818	24,597,288
percent_uniqueAligned	0.83287	0.82754
correlation_replicates	0.998728	0.998728
spikein_reads	7,080	9,598
percent_spikeins	0.00017	0.00032
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2823	2824

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
FAM98A-BGKcLV40-45_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2823	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	28169
FAM98A-BGKcLV40-45_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2823	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	28213
FAM98A-BGKcLV40-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2823					GRCh38	V40	FAM98A-BGKcLV40-45_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98A-BGKcLV40-45_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28257
FAM98A-BGKcLV40-45_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	2823					GRCh38	V40	FAM98A-BGKcLV40-45/Aligned.sortedByCoord.out.bam		ENCORE2	28301
FAM98A-BGKcLV40-45_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	2823					GRCh38	V40	FAM98A-BGKcLV40-45/Aligned.sortedByCoord.out.bam		ENCORE2	28345
FAM98A-BGKcLV40-45_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	2823					GRCh38	V40	FAM98A-BGKcLV40-45/Aligned.sortedByCoord.out.bam		ENCORE2	28389
FAM98A-BGKcLV40-45_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	2823					GRCh38	V40	FAM98A-BGKcLV40-45/Aligned.sortedByCoord.out.bam		ENCORE2	28433
FAM98A-BGKcLV40-45_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2823					GRCh38	V40	FAM98A-BGKcLV40-45_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98A-BGKcLV40-45_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28477
FAM98A-BGKcLV40-46_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2824	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	28170
FAM98A-BGKcLV40-46_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2824	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	28214
FAM98A-BGKcLV40-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2824					GRCh38	V40	FAM98A-BGKcLV40-46_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98A-BGKcLV40-46_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28258
FAM98A-BGKcLV40-46_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	2824					GRCh38	V40	FAM98A-BGKcLV40-46/Aligned.sortedByCoord.out.bam		ENCORE2	28302
FAM98A-BGKcLV40-46_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	2824					GRCh38	V40	FAM98A-BGKcLV40-46/Aligned.sortedByCoord.out.bam		ENCORE2	28346
FAM98A-BGKcLV40-46_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	2824					GRCh38	V40	FAM98A-BGKcLV40-46/Aligned.sortedByCoord.out.bam		ENCORE2	28390
FAM98A-BGKcLV40-46_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	2824					GRCh38	V40	FAM98A-BGKcLV40-46/Aligned.sortedByCoord.out.bam		ENCORE2	28434
FAM98A-BGKcLV40-46_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2824					GRCh38	V40	FAM98A-BGKcLV40-46_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,FAM98A-BGKcLV40-46_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28478