CWC15 RNA-Seq in K562

General Information


RBP	CWC15
Cell_Line	K562
Method	CRISPR
Exp_Name	CWC15-BGKcLV28-K562
ENCODE_series_ID	ENCSR082GWT
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR825RYR
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CWC15-BGKcLV28-53
Rep2	CWC15-BGKcLV28-54
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	70.2
Rep2_qPCR	57.2
Rep1_WB	51.7
Rep2_WB	53.4
Antibody Cat#	A304-900A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB616CRG
Status	Released
Project	ENCODE4
ID	837

Experiment Information (Status: Released)

	BGKcLV28-53	BGKcLV28-53	BGKcLV28-54	BGKcLV28-54
idx	997	999	998	1000
TRCN#_or_BGC#	BGC#0000730	BGC#0000730	BGC#0000730	BGC#0000730
shRNA_or_gRNA_sequence	GCAGGAATCTGGTCTAACCG	GCAGGAATCTGGTCTAACCG	GCAGGAATCTGGTCTAACCG	GCAGGAATCTGGTCTAACCG
PAM	TGG	TGG	TGG	TGG
Name	CWC15_97	CWC15_97	CWC15_97	CWC15_97
Sample_ID	BGKcLV28-53	BGKcLV28-53	BGKcLV28-54	BGKcLV28-54
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CWC15	CWC15	CWC15	CWC15
qPCR_result	70.2	70.2	57.2	57.2
Ave_qPCR	63.7	63.7
RT-qPCR_primer-F	cgtccaacccgagaacatac	cgtccaacccgagaacatac
RT-qPCR_primer-R	gggtcatctgcatcaaggtt	gggtcatctgcatcaaggtt
protein_conc	2814	2814	2783	2783
WB_result	51.7	64.9	53.4	62.0249845
Ave_WB	52.6	63.5
WB_DONE_date	7/13/21	2/22/22
MW	27KD	27KD
IP
antibody_Cat#	A304-900A	A304-901A	LOT #1	LOT #1
Antibody DCC ID	ENCAB616CRG
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5131	5133	5132	5134

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CWC15	Product_ID: A304-900A Lot_ID: 1 Source: Bethyl Labs Target Name: CWC15-human

Experiment Status

	BGKcLV28-53	BGKcLV28-54
Sample_ID	BGKcLV28-53	BGKcLV28-54
Sample Name
Sample Name	CWC15-BGKcLV28-53	CWC15-BGKcLV28-54
RBP	CWC15	CWC15
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9933	9934

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-53	BGKcLV28-54
Sample #	41	42
Sample Name	CWC15-BGKcLV28-53	CWC15-BGKcLV28-54
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	324	325
Peak_Molarity	91.00	84.50
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/A6.png	DNA_Library_set48-49/set3/B6.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set48-49/set2/A6.png	RNA_Library_set48-49/set2/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-53	BGKcLV28-54
RBP	CWC15	CWC15
Batch_ID	BGKcLV28	BGKcLV28
WB_result	51.700	53.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2102	2103

Sequencing Information

	BGKcLV28-53	BGKcLV28-54
Sample_ID	BGKcLV28-53	BGKcLV28-54
Sample Name	CWC15-BGKcLV28-53	CWC15-BGKcLV28-54
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	61,879,816	82,269,570
total_aligned_reads	60,555,544	77,169,270
unique_aligned_reads	55,903,848	71,112,848
percent_uniqueAligned	0.90343	0.86439
correlation_replicates	0.992928	0.992928
spikein_reads	20,668	18,758
percent_spikeins	0.00033	0.00023
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1853	1854

Data Submission Information

	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-54	BGKcLV28-54	BGKcLV28-54	BGKcLV28-54
ENCODE_alias	brenton-graveley:CWC15-BGKcLV28	brenton-graveley:CWC15-BGKcLV28-53	brenton-graveley:L-CWC15-BGKcLV28-53	brenton-graveley:CWC15-BGKcLV28-53_S123_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CWC15-BGKcLV28-53_S123_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CWC15-BGKcLV28-K562	brenton-graveley:CWC15-BGKcLV28-54	brenton-graveley:L-CWC15-BGKcLV28-54	brenton-graveley:CWC15-BGKcLV28-54_S124_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CWC15-BGKcLV28-54_S124_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR825RYR	ENCBS757ZRT	ENCLB377VVP	ENCFF555ZOR	ENCFF929AWN	ENCSR082GWT	ENCBS922IOX	ENCLB130FIV	ENCFF716HII	ENCFF688SGV
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	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-53	BGKcLV28-54	BGKcLV28-54	BGKcLV28-54	BGKcLV28-54
Sample Name	CWC15-BGKcLV28-53	CWC15-BGKcLV28-53	CWC15-BGKcLV28-53	CWC15-BGKcLV28-53	CWC15-BGKcLV28-53	CWC15-BGKcLV28-53	CWC15-BGKcLV28-54	CWC15-BGKcLV28-54	CWC15-BGKcLV28-54	CWC15-BGKcLV28-54
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		CWC15-BGKcLV28-53.pdf	L-CWC15-BGKcLV28-53.pdf				CWC15-BGKcLV28-54.pdf	L-CWC15-BGKcLV28-54.pdf
ID	3491	3616	3750	3884	4018	7164	3617	3751	3885	4019

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
CWC15-BGKcLV28-53_S123_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1853	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3970
CWC15-BGKcLV28-53_S123_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1853	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4028
CWC15-BGKcLV28-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1853					GRCh38	V40	CWC15-BGKcLV28-53_S123_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWC15-BGKcLV28-53_S123_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19252
CWC15-BGKcLV28-53_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1853					GRCh38	V40	CWC15-BGKcLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	19310
CWC15-BGKcLV28-53_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1853					GRCh38	V40	CWC15-BGKcLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	19368
CWC15-BGKcLV28-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1853					GRCh38	V40	CWC15-BGKcLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	19426
CWC15-BGKcLV28-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1853					GRCh38	V40	CWC15-BGKcLV28-53/Aligned.sortedByCoord.out.bam		ENCORE2	19484
CWC15-BGKcLV28-53_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1853					GRCh38	V40	CWC15-BGKcLV28-53_S123_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWC15-BGKcLV28-53_S123_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19542
CWC15-BGKcLV28-54_S124_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1854	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3971
CWC15-BGKcLV28-54_S124_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1854	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4029
CWC15-BGKcLV28-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1854					GRCh38	V40	CWC15-BGKcLV28-54_S124_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWC15-BGKcLV28-54_S124_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19253
CWC15-BGKcLV28-54_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1854					GRCh38	V40	CWC15-BGKcLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	19311
CWC15-BGKcLV28-54_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1854					GRCh38	V40	CWC15-BGKcLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	19369
CWC15-BGKcLV28-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1854					GRCh38	V40	CWC15-BGKcLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	19427
CWC15-BGKcLV28-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1854					GRCh38	V40	CWC15-BGKcLV28-54/Aligned.sortedByCoord.out.bam		ENCORE2	19485
CWC15-BGKcLV28-54_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1854					GRCh38	V40	CWC15-BGKcLV28-54_S124_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWC15-BGKcLV28-54_S124_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19543