CWF19L2 RNA-Seq in K562

General Information


RBP	CWF19L2
Cell_Line	K562
Method	CRISPR
Exp_Name	CWF19L2-BGKcLV28-K562
ENCODE_series_ID	ENCSR665JUV
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR582AOQ
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CWF19L2-BGKcLV28-55
Rep2	CWF19L2-BGKcLV28-56
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	74.2
Rep2_WB	79.9
Antibody Cat#	A303-322A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB287TFY
Status	Released
Project	ENCODE4
ID	838

Experiment Information (Status: Released)

	BGKcLV28-55	BGKcLV28-56
idx	1001	1002
TRCN#_or_BGC#	BGC#0000731	BGC#0000731
shRNA_or_gRNA_sequence	GTGCGAAGAGTATCGAAGAG	GTGCGAAGAGTATCGAAGAG
PAM	CGG	CGG
Name	CWF19L2_94	CWF19L2_94
Sample_ID	BGKcLV28-55	BGKcLV28-56
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CWF19L2	CWF19L2
qPCR_result	16.0	0.0
Ave_qPCR	8.0
RT-qPCR_primer-F	ggtggattaagctggctaagg
RT-qPCR_primer-R	ggatgcagctttttcagcat
protein_conc	2930	2339
WB_result	74.2	79.9
Ave_WB	77.0
WB_DONE_date	6/30/21	JESS
MW	104KD
IP
antibody_Cat#	A303-322A	LOT #1
Antibody DCC ID	ENCAB287TFY
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5135	5136

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CWF19L2	Product_ID: A303-322A Lot_ID: 1 Source: Bethyl Labs Target Name: CWF19L2-human

Experiment Status

	BGKcLV28-55	BGKcLV28-56
Sample_ID	BGKcLV28-55	BGKcLV28-56
Sample Name
Sample Name	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-56
RBP	CWF19L2	CWF19L2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9935	9936

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-55	BGKcLV28-56
Sample #	43	44
Sample Name	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-56
Sample_Name_Alias
Index Well Position	C10	D10
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	327	334
Peak_Molarity	90.80	116.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/C6.png	DNA_Library_set48-49/set3/D6.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set48-49/set2/C6.png	RNA_Library_set48-49/set2/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-55	BGKcLV28-56
RBP	CWF19L2	CWF19L2
Batch_ID	BGKcLV28	BGKcLV28
WB_result	74.200	79.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2104	2105

Sequencing Information

	BGKcLV28-55	BGKcLV28-56
Sample_ID	BGKcLV28-55	BGKcLV28-56
Sample Name	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-56
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	110,294,174	133,143,792
total_aligned_reads	103,612,664	130,158,586
unique_aligned_reads	95,583,682	120,179,616
percent_uniqueAligned	0.86662	0.90263
correlation_replicates	0.993681	0.993681
spikein_reads	23,536	11,650
percent_spikeins	0.00021	0.00009
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1855	1856

Data Submission Information

	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-56	BGKcLV28-56	BGKcLV28-56	BGKcLV28-56
ENCODE_alias	brenton-graveley:CWF19L2-BGKcLV28	brenton-graveley:CWF19L2-BGKcLV28-55	brenton-graveley:L-CWF19L2-BGKcLV28-55	brenton-graveley:CWF19L2-BGKcLV28-55_S125_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CWF19L2-BGKcLV28-55_S125_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CWF19L2-BGKcLV28-K562	brenton-graveley:CWF19L2-BGKcLV28-56	brenton-graveley:L-CWF19L2-BGKcLV28-56	brenton-graveley:CWF19L2-BGKcLV28-56_S126_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CWF19L2-BGKcLV28-56_S126_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR582AOQ	ENCBS639LVM	ENCLB811YBR	ENCFF348HNZ	ENCFF146HKG	ENCSR665JUV	ENCBS488OTG	ENCLB234HYF	ENCFF870AJW	ENCFF731AFQ
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	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-55	BGKcLV28-56	BGKcLV28-56	BGKcLV28-56	BGKcLV28-56
Sample Name	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-55	CWF19L2-BGKcLV28-56	CWF19L2-BGKcLV28-56	CWF19L2-BGKcLV28-56	CWF19L2-BGKcLV28-56
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		CWF19L2-BGKcLV28-55.pdf	L-CWF19L2-BGKcLV28-55.pdf				CWF19L2-BGKcLV28-56.pdf	L-CWF19L2-BGKcLV28-56.pdf
ID	3492	3618	3752	3886	4020	7165	3619	3753	3887	4021

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
CWF19L2-BGKcLV28-55_S125_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1855	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	3972
CWF19L2-BGKcLV28-55_S125_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1855	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	4030
CWF19L2-BGKcLV28-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1855					GRCh38	V40	CWF19L2-BGKcLV28-55_S125_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWF19L2-BGKcLV28-55_S125_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19254
CWF19L2-BGKcLV28-55_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	1855					GRCh38	V40	CWF19L2-BGKcLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	19312
CWF19L2-BGKcLV28-55_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	1855					GRCh38	V40	CWF19L2-BGKcLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	19370
CWF19L2-BGKcLV28-55_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	1855					GRCh38	V40	CWF19L2-BGKcLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	19428
CWF19L2-BGKcLV28-55_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	1855					GRCh38	V40	CWF19L2-BGKcLV28-55/Aligned.sortedByCoord.out.bam		ENCORE2	19486
CWF19L2-BGKcLV28-55_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1855					GRCh38	V40	CWF19L2-BGKcLV28-55_S125_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWF19L2-BGKcLV28-55_S125_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19544
CWF19L2-BGKcLV28-56_S126_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1856	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	3973
CWF19L2-BGKcLV28-56_S126_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1856	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	4031
CWF19L2-BGKcLV28-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1856					GRCh38	V40	CWF19L2-BGKcLV28-56_S126_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWF19L2-BGKcLV28-56_S126_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19255
CWF19L2-BGKcLV28-56_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	1856					GRCh38	V40	CWF19L2-BGKcLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	19313
CWF19L2-BGKcLV28-56_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	1856					GRCh38	V40	CWF19L2-BGKcLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	19371
CWF19L2-BGKcLV28-56_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	1856					GRCh38	V40	CWF19L2-BGKcLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	19429
CWF19L2-BGKcLV28-56_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	1856					GRCh38	V40	CWF19L2-BGKcLV28-56/Aligned.sortedByCoord.out.bam		ENCORE2	19487
CWF19L2-BGKcLV28-56_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1856					GRCh38	V40	CWF19L2-BGKcLV28-56_S126_L004_R1_001.filtered.trimmed.paired.fastq.gz,CWF19L2-BGKcLV28-56_S126_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19545