CSNK1E RNA-Seq in K562

General Information


RBP	CSNK1E
Cell_Line	K562
Method	CRISPR
Exp_Name	CSNK1E-BGKcLV28-K562
ENCODE_series_ID	ENCSR169PVW
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR251LKQ
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CSNK1E-BGKcLV28-45
Rep2	CSNK1E-BGKcLV28-46
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	33.6
Rep2_qPCR	29.7
Rep1_WB	84.7
Rep2_WB	85.2
Antibody Cat#	A302-135A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB344UBI
Status	Released
Project	ENCODE4
ID	835

Experiment Information (Status: Released)

	BGKcLV28-45	BGKcLV28-46
idx	987	988
TRCN#_or_BGC#	BGC#0000721	BGC#0000721
shRNA_or_gRNA_sequence	GTGGGGAACAAGTACCGCCT	GTGGGGAACAAGTACCGCCT
PAM	GGG	GGG
Name	CSNK1E_94	CSNK1E_94
Sample_ID	BGKcLV28-45	BGKcLV28-46
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CSNK1E	CSNK1E
qPCR_result	33.6	29.7
Ave_qPCR	31.7
RT-qPCR_primer-F	tgcacatcgagagcaagttc
RT-qPCR_primer-R	gttgtagtcgccctcagctc
protein_conc	2107	2644
WB_result	84.7	85.2
Ave_WB	85.0
WB_DONE_date	6/30/21	JESS
MW	47KD
IP
antibody_Cat#	A302-135A	LOT #1
Antibody DCC ID	ENCAB344UBI	1/19/22
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	5121	5122

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSNK1E	Product_ID: A302-135A Lot_ID: 1 Source: Bethyl Labs Target Name: CSNK1E-human

Experiment Status

	BGKcLV28-45	BGKcLV28-46
Sample_ID	BGKcLV28-45	BGKcLV28-46
Sample Name
Sample Name	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-46
RBP	CSNK1E	CSNK1E
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9929	9930

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-45	BGKcLV28-46
Sample #	37	38
Sample Name	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-46
Sample_Name_Alias
Index Well Position	E09	F09
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	321
Peak_Molarity	102.00	113.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/E5.png	DNA_Library_set48-49/set3/F5.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/E5.png	RNA_Library_set48-49/set2/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-45	BGKcLV28-46
RBP	CSNK1E	CSNK1E
Batch_ID	BGKcLV28	BGKcLV28
WB_result	84.700	85.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2098	2099

Sequencing Information

	BGKcLV28-45	BGKcLV28-46
Sample_ID	BGKcLV28-45	BGKcLV28-46
Sample Name	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-46
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	116,927,436	93,725,526
total_aligned_reads	111,578,300	79,886,658
unique_aligned_reads	102,679,914	73,410,618
percent_uniqueAligned	0.87815	0.78325
correlation_replicates	0.951506	0.951506
spikein_reads	25,814	17,946
percent_spikeins	0.00022	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1849	1850

Data Submission Information

	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-46	BGKcLV28-46	BGKcLV28-46	BGKcLV28-46
ENCODE_alias	brenton-graveley:CSNK1E-BGKcLV28	brenton-graveley:CSNK1E-BGKcLV28-45	brenton-graveley:L-CSNK1E-BGKcLV28-45	brenton-graveley:CSNK1E-BGKcLV28-45_S119_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSNK1E-BGKcLV28-45_S119_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSNK1E-BGKcLV28-K562	brenton-graveley:CSNK1E-BGKcLV28-46	brenton-graveley:L-CSNK1E-BGKcLV28-46	brenton-graveley:CSNK1E-BGKcLV28-46_S120_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSNK1E-BGKcLV28-46_S120_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR251LKQ	ENCBS140SWH	ENCLB668VDO	ENCFF384GPZ	ENCFF850FNR	ENCSR169PVW	ENCBS394PBH	ENCLB656CKD	ENCFF551KBO	ENCFF705CAH
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	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-45	BGKcLV28-46	BGKcLV28-46	BGKcLV28-46	BGKcLV28-46
Sample Name	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-45	CSNK1E-BGKcLV28-46	CSNK1E-BGKcLV28-46	CSNK1E-BGKcLV28-46	CSNK1E-BGKcLV28-46
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		CSNK1E-BGKcLV28-45.pdf	L-CSNK1E-BGKcLV28-45.pdf				CSNK1E-BGKcLV28-46.pdf	L-CSNK1E-BGKcLV28-46.pdf
ID	3489	3612	3746	3880	4014	7158	3613	3747	3881	4015

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
CSNK1E-BGKcLV28-45_S119_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1849	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	3966
CSNK1E-BGKcLV28-45_S119_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1849	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	4024
CSNK1E-BGKcLV28-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1849					GRCh38	V40	CSNK1E-BGKcLV28-45_S119_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSNK1E-BGKcLV28-45_S119_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19248
CSNK1E-BGKcLV28-45_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	1849					GRCh38	V40	CSNK1E-BGKcLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	19306
CSNK1E-BGKcLV28-45_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	1849					GRCh38	V40	CSNK1E-BGKcLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	19364
CSNK1E-BGKcLV28-45_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	1849					GRCh38	V40	CSNK1E-BGKcLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	19422
CSNK1E-BGKcLV28-45_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	1849					GRCh38	V40	CSNK1E-BGKcLV28-45/Aligned.sortedByCoord.out.bam		ENCORE2	19480
CSNK1E-BGKcLV28-45_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1849					GRCh38	V40	CSNK1E-BGKcLV28-45_S119_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSNK1E-BGKcLV28-45_S119_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19538
CSNK1E-BGKcLV28-46_S120_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1850	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	3967
CSNK1E-BGKcLV28-46_S120_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1850	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	4025
CSNK1E-BGKcLV28-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1850					GRCh38	V40	CSNK1E-BGKcLV28-46_S120_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSNK1E-BGKcLV28-46_S120_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19249
CSNK1E-BGKcLV28-46_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	1850					GRCh38	V40	CSNK1E-BGKcLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	19307
CSNK1E-BGKcLV28-46_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	1850					GRCh38	V40	CSNK1E-BGKcLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	19365
CSNK1E-BGKcLV28-46_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	1850					GRCh38	V40	CSNK1E-BGKcLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	19423
CSNK1E-BGKcLV28-46_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	1850					GRCh38	V40	CSNK1E-BGKcLV28-46/Aligned.sortedByCoord.out.bam		ENCORE2	19481
CSNK1E-BGKcLV28-46_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1850					GRCh38	V40	CSNK1E-BGKcLV28-46_S120_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSNK1E-BGKcLV28-46_S120_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19539