RPS9 RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-7	BGKcLV33-7	BGKcLV33-8	BGKcLV33-8
idx	1109	1182	1110	1183
TRCN#_or_BGC#	BGC#0000828	BGC#0000686	BGC#0000828	BGC#0000686
shRNA_or_gRNA_sequence	GCACCTTCGAACAGACGCCG	GTGGCGGAAGTCGCCCAGCG	GCACCTTCGAACAGACGCCG	GTGGCGGAAGTCGCCCAGCG
PAM	TGG	GGG	TGG	GGG
Name	RPS9_90	CDC42EP4_91	RPS9_90	CDC42EP4_91
Sample_ID	BGKcLV33-7	BGKcLV33-7	BGKcLV33-8	BGKcLV33-8
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	RPS9	CDC42EP4	RPS9	CDC42EP4
qPCR_result		34.0		0.0
Ave_qPCR		17.0
RT-qPCR_primer-F		acgaacagccctcttcttca
RT-qPCR_primer-R		agggacatggcattcttgac
protein_conc	506	2181	512	2176
WB_result	19.4	70.4	2.5	67.0
Ave_WB	10.9	68.7
WB_DONE_date	1/13/21	3/16/22
MW	23kd	38kd
IP
antibody_Cat#	A303-946A	A302-380A	LOT #1	LOT #1
Antibody DCC ID		ENCAB379GNR		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	5249	5322	5250	5323

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CDC42EP4	Product_ID: A302-380A Lot_ID: 1 Source: Bethyl Labs Target Name: CDC42EP4-human

Experiment Status

	BGKcLV33-7	BGKcLV33-7	BGKcLV33-8	BGKcLV33-8
Sample_ID	BGKcLV33-7	BGKcLV33-7	BGKcLV33-8	BGKcLV33-8
Sample Name
Sample Name	CDC42EP4-BGKcLV33-7		CDC42EP4-BGKcLV33-8
RBP	CDC42EP4	RPS9	CDC42EP4	RPS9
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	10637	10693	10638	10694

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-7	BGKcLV33-8
Sample #	7	8
Sample Name	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-8
Sample_Name_Alias
Index Well Position	G01	H01
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	305	310
Peak_Molarity	49.30	47.60
libSampleQC_DNA_Well	DNA_Library_set53/set1/G5.png	DNA_Library_set53/set1/H5.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set53/set1/G1.png	RNA_Library_set53/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-7	BGKcLV33-8
RBP	CDC42EP4	CDC42EP4
Batch_ID	BGKcLV33	BGKcLV33
WB_result	70.400	67.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3268	3269

Sequencing Information

	BGKcLV33-7	BGKcLV33-8
Sample_ID	BGKcLV33-7	BGKcLV33-8
Sample Name	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-8
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	131,494,076	103,952,934
total_aligned_reads	115,212,728	89,837,168
unique_aligned_reads	105,401,494	82,279,532
percent_uniqueAligned	0.80157	0.79151
correlation_replicates	0.997580	0.997580
spikein_reads	23,568	25,484
percent_spikeins	0.00018	0.00025
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2035	2036

Data Submission Information

	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-8	BGKcLV33-8	BGKcLV33-8	BGKcLV33-8
ENCODE_alias	brenton-graveley:CDC42EP4-BGKcLV33	brenton-graveley:CDC42EP4-BGKcLV33-7	brenton-graveley:L-CDC42EP4-BGKcLV33-7	brenton-graveley:CDC42EP4-BGKcLV33-7_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC42EP4-BGKcLV33-7_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC42EP4-BGKcLV33-K562	brenton-graveley:CDC42EP4-BGKcLV33-8	brenton-graveley:L-CDC42EP4-BGKcLV33-8	brenton-graveley:CDC42EP4-BGKcLV33-8_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC42EP4-BGKcLV33-8_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR323RFB	ENCBS665FPO	ENCLB625HZR	ENCFF248PIZ	ENCFF662SQF	ENCSR422RMW	ENCBS098OWP	ENCLB102QFO	ENCFF156UAZ	ENCFF294KJO
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	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-7	BGKcLV33-8	BGKcLV33-8	BGKcLV33-8	BGKcLV33-8
Sample Name	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-7	CDC42EP4-BGKcLV33-8	CDC42EP4-BGKcLV33-8	CDC42EP4-BGKcLV33-8	CDC42EP4-BGKcLV33-8
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-CDC42EP4-BGKcLV33-7.pdf					L-CDC42EP4-BGKcLV33-8.pdf
ID	7474	7557	7667	7777	7887	7963	7558	7668	7778	7888

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
CDC42EP4-BGKcLV33-7_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2035	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	6613
CDC42EP4-BGKcLV33-7_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2035	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	6669
CDC42EP4-BGKcLV33-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2035					GRCh38	V40	CDC42EP4-BGKcLV33-7_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,CDC42EP4-BGKcLV33-7_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18090
CDC42EP4-BGKcLV33-7_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	2035					GRCh38	V40	CDC42EP4-BGKcLV33-7/Aligned.sortedByCoord.out.bam		ENCORE2	18146
CDC42EP4-BGKcLV33-7_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	2035					GRCh38	V40	CDC42EP4-BGKcLV33-7/Aligned.sortedByCoord.out.bam		ENCORE2	18202
CDC42EP4-BGKcLV33-7_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	2035					GRCh38	V40	CDC42EP4-BGKcLV33-7/Aligned.sortedByCoord.out.bam		ENCORE2	18258
CDC42EP4-BGKcLV33-7_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	2035					GRCh38	V40	CDC42EP4-BGKcLV33-7/Aligned.sortedByCoord.out.bam		ENCORE2	18314
CDC42EP4-BGKcLV33-7_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2035					GRCh38	V40	CDC42EP4-BGKcLV33-7_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,CDC42EP4-BGKcLV33-7_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18370
CDC42EP4-BGKcLV33-8_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2036	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	6614
CDC42EP4-BGKcLV33-8_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2036	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	6670
CDC42EP4-BGKcLV33-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2036					GRCh38	V40	CDC42EP4-BGKcLV33-8_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,CDC42EP4-BGKcLV33-8_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18091
CDC42EP4-BGKcLV33-8_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	2036					GRCh38	V40	CDC42EP4-BGKcLV33-8/Aligned.sortedByCoord.out.bam		ENCORE2	18147
CDC42EP4-BGKcLV33-8_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	2036					GRCh38	V40	CDC42EP4-BGKcLV33-8/Aligned.sortedByCoord.out.bam		ENCORE2	18203
CDC42EP4-BGKcLV33-8_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	2036					GRCh38	V40	CDC42EP4-BGKcLV33-8/Aligned.sortedByCoord.out.bam		ENCORE2	18259
CDC42EP4-BGKcLV33-8_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	2036					GRCh38	V40	CDC42EP4-BGKcLV33-8/Aligned.sortedByCoord.out.bam		ENCORE2	18315
CDC42EP4-BGKcLV33-8_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2036					GRCh38	V40	CDC42EP4-BGKcLV33-8_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,CDC42EP4-BGKcLV33-8_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18371