RPS21 RNA-Seq in K562

General Information


RBP	RPS21
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS21-BGKcLV33-K562
ENCODE_series_ID	ENCSR816GWS
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR925SFP
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	RPS21-BGKcLV33-11
Rep2	RPS21-BGKcLV33-12
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	79.3
Rep2_WB	83.0
Antibody Cat#	A304-202A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	894

Experiment Information (Status: Released)

	BGKcLV33-3	BGKcLV33-3	BGKcLV33-4	BGKcLV33-4
idx	1105	1178	1106	1179
TRCN#_or_BGC#	BGC#0000821	BGC#0000647	BGC#0000821	BGC#0000647
shRNA_or_gRNA_sequence	GGGGGCGCTTACCATTTCCG	TCACCGATACCTGAAAAACG	GGGGGCGCTTACCATTTCCG	TCACCGATACCTGAAAAACG
PAM	CGG	TGG	CGG	TGG
Name	RPS21_72	BMS1_87	RPS21_72	BMS1_87
Sample_ID	BGKcLV33-3	BGKcLV33-3	BGKcLV33-4	BGKcLV33-4
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	RPS21	BMS1	RPS21	BMS1
qPCR_result		1.0		0.0
Ave_qPCR		0.5
RT-qPCR_primer-F		tttgaaggtgctgtgattcg
RT-qPCR_primer-R		ccaagttcgcatgaagacaa
protein_conc	315	1459	443	1883
WB_result	26.0	52.0	0.0	62.9
Ave_WB	18.2	57.5
WB_DONE_date	1/13/22	3/25/22		JESS
MW	9.1kd	146kd
IP
antibody_Cat#	A305-070A	A305-109A	LOT #1	LOT #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action		Ready		Ready
Library_start_date		04/13/22		04/13/22
repeat_library
Note
ID	5245	5318	5246	5319

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BMS1	Product_ID: A305-109A Lot_ID: 1 Source: Bethyl Labs Target Name: BMS1-human

Experiment Status

	BGKcLV33-3	BGKcLV33-3	BGKcLV33-4	BGKcLV33-4
Sample_ID	BGKcLV33-3	BGKcLV33-3	BGKcLV33-4	BGKcLV33-4
Sample Name
Sample Name	BMS1-BGKcLV33-3		BMS1-BGKcLV33-4
RBP	BMS1	RPS21	BMS1	RPS21
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-10-28	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10633	10689	10634	10690

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-3	BGKcLV33-4
Sample #	3	4
Sample Name	BMS1-BGKcLV33-3	BMS1-BGKcLV33-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	306	299
Peak_Molarity	51.10	64.20
libSampleQC_DNA_Well	DNA_Library_set53/set1/C5.png	DNA_Library_set53/set1/D5.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set53/set1/C1.png	RNA_Library_set53/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-3	BGKcLV33-4
RBP	BMS1	BMS1
Batch_ID	BGKcLV33	BGKcLV33
WB_result	52.000	62.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3264	3265

Sequencing Information

	BGKcLV33-3	BGKcLV33-4
Sample_ID	BGKcLV33-3	BGKcLV33-4
Sample Name	BMS1-BGKcLV33-3	BMS1-BGKcLV33-4
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	66,153,404	84,313,350
total_aligned_reads	59,349,622	75,670,736
unique_aligned_reads	54,246,206	69,121,844
percent_uniqueAligned	0.82001	0.81982
correlation_replicates	0.997940	0.997940
spikein_reads	21,132	29,218
percent_spikeins	0.00032	0.00035
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2031	2032

Data Submission Information

	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-4	BGKcLV33-4	BGKcLV33-4	BGKcLV33-4
ENCODE_alias	brenton-graveley:BMS1-BGKcLV33	brenton-graveley:BMS1-BGKcLV33-3	brenton-graveley:L-BMS1-BGKcLV33-3	brenton-graveley:BMS1-BGKcLV33-3_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BMS1-BGKcLV33-3_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BMS1-BGKcLV33-K562	brenton-graveley:BMS1-BGKcLV33-4	brenton-graveley:L-BMS1-BGKcLV33-4	brenton-graveley:BMS1-BGKcLV33-4_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BMS1-BGKcLV33-4_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR778XFE	ENCBS045QZE	ENCLB570OVB	ENCFF123MJU	ENCFF767HDX	ENCSR872LJT	ENCBS786TTZ	ENCLB522WZE	ENCFF002PSQ	ENCFF716CXY
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-3	BGKcLV33-4	BGKcLV33-4	BGKcLV33-4	BGKcLV33-4
Sample Name	BMS1-BGKcLV33-3	BMS1-BGKcLV33-3	BMS1-BGKcLV33-3	BMS1-BGKcLV33-3	BMS1-BGKcLV33-3	BMS1-BGKcLV33-3	BMS1-BGKcLV33-4	BMS1-BGKcLV33-4	BMS1-BGKcLV33-4	BMS1-BGKcLV33-4
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV53_library_protocol					LV53_library_protocol
protocol_URL			L-BMS1-BGKcLV33-3.pdf					L-BMS1-BGKcLV33-4.pdf
ID	7472	7553	7663	7773	7883	7961	7554	7664	7774	7884

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
BMS1-BGKcLV33-3_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2031	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6609
BMS1-BGKcLV33-3_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2031	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6665
BMS1-BGKcLV33-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2031					GRCh38	V40	BMS1-BGKcLV33-3_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,BMS1-BGKcLV33-3_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18086
BMS1-BGKcLV33-3_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2031					GRCh38	V40	BMS1-BGKcLV33-3/Aligned.sortedByCoord.out.bam		ENCORE2	18142
BMS1-BGKcLV33-3_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2031					GRCh38	V40	BMS1-BGKcLV33-3/Aligned.sortedByCoord.out.bam		ENCORE2	18198
BMS1-BGKcLV33-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2031					GRCh38	V40	BMS1-BGKcLV33-3/Aligned.sortedByCoord.out.bam		ENCORE2	18254
BMS1-BGKcLV33-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2031					GRCh38	V40	BMS1-BGKcLV33-3/Aligned.sortedByCoord.out.bam		ENCORE2	18310
BMS1-BGKcLV33-3_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2031					GRCh38	V40	BMS1-BGKcLV33-3_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,BMS1-BGKcLV33-3_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18366
BMS1-BGKcLV33-4_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2032	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6610
BMS1-BGKcLV33-4_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2032	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6666
BMS1-BGKcLV33-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2032					GRCh38	V40	BMS1-BGKcLV33-4_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,BMS1-BGKcLV33-4_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18087
BMS1-BGKcLV33-4_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2032					GRCh38	V40	BMS1-BGKcLV33-4/Aligned.sortedByCoord.out.bam		ENCORE2	18143
BMS1-BGKcLV33-4_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2032					GRCh38	V40	BMS1-BGKcLV33-4/Aligned.sortedByCoord.out.bam		ENCORE2	18199
BMS1-BGKcLV33-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2032					GRCh38	V40	BMS1-BGKcLV33-4/Aligned.sortedByCoord.out.bam		ENCORE2	18255
BMS1-BGKcLV33-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2032					GRCh38	V40	BMS1-BGKcLV33-4/Aligned.sortedByCoord.out.bam		ENCORE2	18311
BMS1-BGKcLV33-4_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2032					GRCh38	V40	BMS1-BGKcLV33-4_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,BMS1-BGKcLV33-4_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18367