RPS28 RNA-Seq in K562

General Information


RBP	RPS28
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS28-BGKcLV33-K562
ENCODE_series_ID	ENCSR355OJK
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR928XFZ
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	RPS28-BGKcLV33-13
Rep2	RPS28-BGKcLV33-14
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A304-202A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	895

Experiment Information (Status: Released)

	BGKcLV33-5	BGKcLV33-5	BGKcLV33-6	BGKcLV33-6
idx	1107	1180	1108	1181
TRCN#_or_BGC#	BGC#0000823	BGC#0000681	BGC#0000823	BGC#0000681
shRNA_or_gRNA_sequence	TTCGGGCCCCCACCTCACCC	TTTGCCCCGTCATGCCAAAG	TTCGGGCCCCCACCTCACCC	TTTGCCCCGTCATGCCAAAG
PAM	TGG	AGG	TGG	AGG
Name	RPS28_55	CD2BP2_89	RPS28_55	CD2BP2_89
Sample_ID	BGKcLV33-5	BGKcLV33-5	BGKcLV33-6	BGKcLV33-6
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	RPS28	CD2BP2	RPS28	CD2BP2
qPCR_result		16.5		9.3
Ave_qPCR		12.9
RT-qPCR_primer-F		ggacatgttcgctgaggagt
RT-qPCR_primer-R		acatcacatccaccagacca
protein_conc	429	2210	473	2153
WB_result	12.2	77.4	18.2	78.1001402
Ave_WB	18.2	77.8
WB_DONE_date	1/13/22	3/14/22
MW	7.8kd	38kd
IP
antibody_Cat#	A305-095A	A304-826A	LOT #1	LOT #1
Antibody DCC ID		ENCAB273AEY		12/4/24
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	5247	5320	5248	5321

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CD2BP2	Product_ID: A304-826A Lot_ID: 1 Source: Bethyl Labs Target Name: CD2BP2-human

Experiment Status

	BGKcLV33-5	BGKcLV33-5	BGKcLV33-6	BGKcLV33-6
Sample_ID	BGKcLV33-5	BGKcLV33-5	BGKcLV33-6	BGKcLV33-6
Sample Name
Sample Name	CD2BP2-BGKcLV33-5		CD2BP2-BGKcLV33-6
RBP	CD2BP2	RPS28	CD2BP2	RPS28
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	10635	10691	10636	10692

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-5	BGKcLV33-6
Sample #	5	6
Sample Name	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-6
Sample_Name_Alias
Index Well Position	E01	F01
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	296	318
Peak_Molarity	59.50	57.20
libSampleQC_DNA_Well	DNA_Library_set53/set1/E5.png	DNA_Library_set53/set1/F5.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set53/set1/E1.png	RNA_Library_set53/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-5	BGKcLV33-6
RBP	CD2BP2	CD2BP2
Batch_ID	BGKcLV33	BGKcLV33
WB_result	77.400	78.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3266	3267

Sequencing Information

	BGKcLV33-5	BGKcLV33-6
Sample_ID	BGKcLV33-5	BGKcLV33-6
Sample Name	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-6
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	93,287,234	87,942,348
total_aligned_reads	82,052,752	79,333,188
unique_aligned_reads	75,144,606	72,667,312
percent_uniqueAligned	0.80552	0.82631
correlation_replicates	0.991561	0.991561
spikein_reads	25,568	9,196
percent_spikeins	0.00027	0.00010
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2033	2034

Data Submission Information

	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-6	BGKcLV33-6	BGKcLV33-6	BGKcLV33-6
ENCODE_alias	brenton-graveley:CD2BP2-BGKcLV33	brenton-graveley:CD2BP2-BGKcLV33-5	brenton-graveley:L-CD2BP2-BGKcLV33-5	brenton-graveley:CD2BP2-BGKcLV33-5_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD2BP2-BGKcLV33-5_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD2BP2-BGKcLV33-K562	brenton-graveley:CD2BP2-BGKcLV33-6	brenton-graveley:L-CD2BP2-BGKcLV33-6	brenton-graveley:CD2BP2-BGKcLV33-6_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD2BP2-BGKcLV33-6_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR383FCI	ENCBS934KIY	ENCLB212ZTZ	ENCFF565PLM	ENCFF310WAN	ENCSR124IOF	ENCBS321ZFD	ENCLB200FHT	ENCFF398KDM	ENCFF514FHX
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	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-5	BGKcLV33-6	BGKcLV33-6	BGKcLV33-6	BGKcLV33-6
Sample Name	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-5	CD2BP2-BGKcLV33-6	CD2BP2-BGKcLV33-6	CD2BP2-BGKcLV33-6	CD2BP2-BGKcLV33-6
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-CD2BP2-BGKcLV33-5.pdf					L-CD2BP2-BGKcLV33-6.pdf
ID	7473	7555	7665	7775	7885	7962	7556	7666	7776	7886

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
CD2BP2-BGKcLV33-5_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2033	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	6611
CD2BP2-BGKcLV33-5_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2033	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	6667
CD2BP2-BGKcLV33-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2033					GRCh38	V40	CD2BP2-BGKcLV33-5_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,CD2BP2-BGKcLV33-5_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18088
CD2BP2-BGKcLV33-5_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	2033					GRCh38	V40	CD2BP2-BGKcLV33-5/Aligned.sortedByCoord.out.bam		ENCORE2	18144
CD2BP2-BGKcLV33-5_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	2033					GRCh38	V40	CD2BP2-BGKcLV33-5/Aligned.sortedByCoord.out.bam		ENCORE2	18200
CD2BP2-BGKcLV33-5_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	2033					GRCh38	V40	CD2BP2-BGKcLV33-5/Aligned.sortedByCoord.out.bam		ENCORE2	18256
CD2BP2-BGKcLV33-5_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	2033					GRCh38	V40	CD2BP2-BGKcLV33-5/Aligned.sortedByCoord.out.bam		ENCORE2	18312
CD2BP2-BGKcLV33-5_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2033					GRCh38	V40	CD2BP2-BGKcLV33-5_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,CD2BP2-BGKcLV33-5_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18368
CD2BP2-BGKcLV33-6_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2034	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	6612
CD2BP2-BGKcLV33-6_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2034	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	6668
CD2BP2-BGKcLV33-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2034					GRCh38	V40	CD2BP2-BGKcLV33-6_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,CD2BP2-BGKcLV33-6_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18089
CD2BP2-BGKcLV33-6_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	2034					GRCh38	V40	CD2BP2-BGKcLV33-6/Aligned.sortedByCoord.out.bam		ENCORE2	18145
CD2BP2-BGKcLV33-6_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	2034					GRCh38	V40	CD2BP2-BGKcLV33-6/Aligned.sortedByCoord.out.bam		ENCORE2	18201
CD2BP2-BGKcLV33-6_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	2034					GRCh38	V40	CD2BP2-BGKcLV33-6/Aligned.sortedByCoord.out.bam		ENCORE2	18257
CD2BP2-BGKcLV33-6_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	2034					GRCh38	V40	CD2BP2-BGKcLV33-6/Aligned.sortedByCoord.out.bam		ENCORE2	18313
CD2BP2-BGKcLV33-6_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2034					GRCh38	V40	CD2BP2-BGKcLV33-6_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,CD2BP2-BGKcLV33-6_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18369