SNW1 RNA-Seq in K562

General Information


RBP	SNW1
Cell_Line	K562
Method	CRISPR
Exp_Name	SNW1-BGKcLV33-K562
ENCODE_series_ID	ENCSR019QSE
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR458FLK
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SNW1-BGKcLV33-65
Rep2	SNW1-BGKcLV33-66
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	no band on the position
Rep2_WB
Antibody Cat#	A304-970A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	913

Experiment Information (Status: Released)

	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-62	BGKcLV33-62	BGKcLV33-62
idx	1163	1252	1254	1164	1253	1255
TRCN#_or_BGC#	BGC#0000880	BGC#0000876	BGC#0000876	BGC#0000880	BGC#0000876	BGC#0000876
shRNA_or_gRNA_sequence	CCACAGCTTCACGAGCCTGT	ATGGGATAGAGCGGCGGCGA	ATGGGATAGAGCGGCGGCGA	CCACAGCTTCACGAGCCTGT	ATGGGATAGAGCGGCGGCGA	ATGGGATAGAGCGGCGGCGA
PAM	TGG	CGG	CGG	TGG	CGG	CGG
Name	SNW1_83	SMG9_91	SMG9_91	SNW1_83	SMG9_91	SMG9_91
Sample_ID	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-62	BGKcLV33-62	BGKcLV33-62
transduction_Date	12/7/21	2/22/22	2/22/22	12/7/21	2/22/22	2/22/22
days	D6	D6	D6	D6	D6	D6
RBP_name	SNW1	SMG9	SMG9	SNW1	SMG9	SMG9
qPCR_result		25.7	25.7		31.9	31.9
Ave_qPCR		28.8	28.8
RT-qPCR_primer-F		cagcctgtgtaccagatcca	cagcctgtgtaccagatcca
RT-qPCR_primer-R		caccaacttgatgctgtgct	caccaacttgatgctgtgct
protein_conc	475	2699	2699	450	2516	2516
WB_result	band isn't on the position	65.8	not as good as A302-210A		61.6
Ave_WB		63.7
WB_DONE_date	2/1/22	3/10/22
MW	61kd	58kd	58kd
IP
antibody_Cat#	A300-784A	A302-210A	A302-211A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB220KQW			8/4/22
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action		Ready			Ready
Library_start_date		04/13/22			04/13/22
repeat_library
Note
ID	5303	5394	5396	5304	5395	5397

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMG9	Product_ID: A302-210A Lot_ID: 1 Source: Bethyl Labs Target Name: SMG9-human

Experiment Status

	BGKcLV33-61	BGKcLV33-61	BGKcLV33-62	BGKcLV33-62
Sample_ID	BGKcLV33-61	BGKcLV33-61	BGKcLV33-62	BGKcLV33-62
Sample Name
Sample Name	SMG9-BGKcLV33-61		SMG9-BGKcLV33-62
RBP	SMG9	SNW1	SMG9	SNW1
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	10677	10747	10678	10748

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-61	BGKcLV33-62
Sample #	47	48
Sample Name	SMG9-BGKcLV33-61	SMG9-BGKcLV33-62
Sample_Name_Alias
Index Well Position	G06	H06
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	307	318
Peak_Molarity	56.00	65.70
libSampleQC_DNA_Well	DNA_Library_set53/set1/G10.png	DNA_Library_set53/set1/H10.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set53/set1/G6.png	RNA_Library_set53/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-61	BGKcLV33-62
RBP	SMG9	SMG9
Batch_ID	BGKcLV33	BGKcLV33
WB_result	65.800	61.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3308	3309

Sequencing Information

	BGKcLV33-61	BGKcLV33-62
Sample_ID	BGKcLV33-61	BGKcLV33-62
Sample Name	SMG9-BGKcLV33-61	SMG9-BGKcLV33-62
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	100,845,922	130,528,254
total_aligned_reads	94,035,454	120,930,696
unique_aligned_reads	86,154,662	110,781,738
percent_uniqueAligned	0.85432	0.84872
correlation_replicates	0.999080	0.999080
spikein_reads	4,932	9,872
percent_spikeins	0.00005	0.00008
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2075	2076

Data Submission Information

	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-62	BGKcLV33-62	BGKcLV33-62	BGKcLV33-62
ENCODE_alias	brenton-graveley:SMG9-BGKcLV33	brenton-graveley:SMG9-BGKcLV33-61	brenton-graveley:L-SMG9-BGKcLV33-61	brenton-graveley:SMG9-BGKcLV33-61_S101_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG9-BGKcLV33-61_S101_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG9-BGKcLV33-K562	brenton-graveley:SMG9-BGKcLV33-62	brenton-graveley:L-SMG9-BGKcLV33-62	brenton-graveley:SMG9-BGKcLV33-62_S102_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG9-BGKcLV33-62_S102_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR971FJU	ENCBS924AYQ	ENCLB663TZM	ENCFF769DYT	ENCFF693ZRY	ENCSR648SPD	ENCBS518YBV	ENCLB907TJM	ENCFF124QXP	ENCFF254YOA
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	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-61	BGKcLV33-62	BGKcLV33-62	BGKcLV33-62	BGKcLV33-62
Sample Name	SMG9-BGKcLV33-61	SMG9-BGKcLV33-61	SMG9-BGKcLV33-61	SMG9-BGKcLV33-61	SMG9-BGKcLV33-61	SMG9-BGKcLV33-61	SMG9-BGKcLV33-62	SMG9-BGKcLV33-62	SMG9-BGKcLV33-62	SMG9-BGKcLV33-62
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	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_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		SMG9-BGKcLV33-61.pdf	L-SMG9-BGKcLV33-61.pdf				SMG9-BGKcLV33-62.pdf	L-SMG9-BGKcLV33-62.pdf
ID	7493	7595	7705	7817	7927	7983	7596	7706	7818	7928

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
SMG9-BGKcLV33-61_S101_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2075	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	6655
SMG9-BGKcLV33-61_S101_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2075	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	6711
SMG9-BGKcLV33-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2075					GRCh38	V40	SMG9-BGKcLV33-61_S101_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGKcLV33-61_S101_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18132
SMG9-BGKcLV33-61_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	2075					GRCh38	V40	SMG9-BGKcLV33-61/Aligned.sortedByCoord.out.bam		ENCORE2	18188
SMG9-BGKcLV33-61_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	2075					GRCh38	V40	SMG9-BGKcLV33-61/Aligned.sortedByCoord.out.bam		ENCORE2	18244
SMG9-BGKcLV33-61_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	2075					GRCh38	V40	SMG9-BGKcLV33-61/Aligned.sortedByCoord.out.bam		ENCORE2	18300
SMG9-BGKcLV33-61_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	2075					GRCh38	V40	SMG9-BGKcLV33-61/Aligned.sortedByCoord.out.bam		ENCORE2	18356
SMG9-BGKcLV33-61_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2075					GRCh38	V40	SMG9-BGKcLV33-61_S101_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGKcLV33-61_S101_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18412
SMG9-BGKcLV33-62_S102_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2076	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	6656
SMG9-BGKcLV33-62_S102_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2076	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	6712
SMG9-BGKcLV33-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2076					GRCh38	V40	SMG9-BGKcLV33-62_S102_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGKcLV33-62_S102_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18133
SMG9-BGKcLV33-62_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	2076					GRCh38	V40	SMG9-BGKcLV33-62/Aligned.sortedByCoord.out.bam		ENCORE2	18189
SMG9-BGKcLV33-62_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	2076					GRCh38	V40	SMG9-BGKcLV33-62/Aligned.sortedByCoord.out.bam		ENCORE2	18245
SMG9-BGKcLV33-62_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	2076					GRCh38	V40	SMG9-BGKcLV33-62/Aligned.sortedByCoord.out.bam		ENCORE2	18301
SMG9-BGKcLV33-62_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	2076					GRCh38	V40	SMG9-BGKcLV33-62/Aligned.sortedByCoord.out.bam		ENCORE2	18357
SMG9-BGKcLV33-62_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2076					GRCh38	V40	SMG9-BGKcLV33-62_S102_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGKcLV33-62_S102_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18413