CLASP2 RNA-Seq in K562

General Information


RBP	CLASP2
Cell_Line	K562
Method	CRISPR
Exp_Name	CLASP2-BGKcLV28-K562
ENCODE_series_ID	ENCSR218HPV
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR331MLG
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CLASP2-BGKcLV28-19
Rep2	CLASP2-BGKcLV28-20
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	40.8
Rep2_qPCR	28.8
Rep1_WB	57.9
Rep2_WB	55.0
Antibody Cat#	A302-155A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB751CST
Status	Released
Project	ENCODE4
ID	826

Experiment Information (Status: Released)

	BGKcLV28-19	BGKcLV28-20
idx	953	954
TRCN#_or_BGC#	BGC#0000696	BGC#0000696
shRNA_or_gRNA_sequence	GATGAGGACCTGTCTGATTG	GATGAGGACCTGTCTGATTG
PAM	TGG	TGG
Name	CLASP2_81	CLASP2_81
Sample_ID	BGKcLV28-19	BGKcLV28-20
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CLASP2	CLASP2
qPCR_result	40.8	28.8
Ave_qPCR	34.8
RT-qPCR_primer-F	tacgattgttggatggagca
RT-qPCR_primer-R	tgcactattggggacgagat
protein_conc	1908	1810
WB_result	57.9	55.0
Ave_WB	56.5
WB_DONE_date	6/25/21B	JESS
MW	141kd
IP
antibody_Cat#	A302-155A	LOT #2
Antibody DCC ID	ENCAB751CST	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	5087	5088

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CLASP2	Product_ID: A302-155A Lot_ID: 2 Source: Bethyl Labs Target Name: CLASP2-human

Experiment Status

	BGKcLV28-19	BGKcLV28-20
Sample_ID	BGKcLV28-19	BGKcLV28-20
Sample Name
Sample Name	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-20
RBP	CLASP2	CLASP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9911	9912

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-19	BGKcLV28-20
Sample #	19	20
Sample Name	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-20
Sample_Name_Alias
Index Well Position	C07	D07
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	326	328
Peak_Molarity	108.00	101.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/C3.png	DNA_Library_set48-49/set3/D3.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set48-49/set2/C3.png	RNA_Library_set48-49/set2/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-19	BGKcLV28-20
RBP	CLASP2	CLASP2
Batch_ID	BGKcLV28	BGKcLV28
WB_result	57.900	55.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2080	2081

Sequencing Information

	BGKcLV28-19	BGKcLV28-20
Sample_ID	BGKcLV28-19	BGKcLV28-20
Sample Name	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-20
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	142,258,648	80,713,686
total_aligned_reads	126,602,186	72,861,386
unique_aligned_reads	116,521,036	66,969,110
percent_uniqueAligned	0.81908	0.82971
correlation_replicates	0.998074	0.998074
spikein_reads	32,152	10,530
percent_spikeins	0.00023	0.00013
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1831	1832

Data Submission Information

	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-20	BGKcLV28-20	BGKcLV28-20	BGKcLV28-20
ENCODE_alias	brenton-graveley:CLASP2-BGKcLV28	brenton-graveley:CLASP2-BGKcLV28-19	brenton-graveley:L-CLASP2-BGKcLV28-19	brenton-graveley:CLASP2-BGKcLV28-19_S101_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLASP2-BGKcLV28-19_S101_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLASP2-BGKcLV28-K562	brenton-graveley:CLASP2-BGKcLV28-20	brenton-graveley:L-CLASP2-BGKcLV28-20	brenton-graveley:CLASP2-BGKcLV28-20_S102_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLASP2-BGKcLV28-20_S102_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR331MLG	ENCBS725YIG	ENCLB094LSK	ENCFF882BGF	ENCFF523LUY	ENCSR218HPV	ENCBS686VHT	ENCLB778RCO	ENCFF600WLI	ENCFF312KDW
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	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-19	BGKcLV28-20	BGKcLV28-20	BGKcLV28-20	BGKcLV28-20
Sample Name	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-19	CLASP2-BGKcLV28-20	CLASP2-BGKcLV28-20	CLASP2-BGKcLV28-20	CLASP2-BGKcLV28-20
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		CLASP2-BGKcLV28-19.pdf	L-CLASP2-BGKcLV28-19.pdf				CLASP2-BGKcLV28-20.pdf	L-CLASP2-BGKcLV28-20.pdf
ID	3480	3594	3728	3862	3996	7142	3595	3729	3863	3997

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
CLASP2-BGKcLV28-19_S101_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1831	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	3948
CLASP2-BGKcLV28-19_S101_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1831	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	4006
CLASP2-BGKcLV28-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1831					GRCh38	V40	CLASP2-BGKcLV28-19_S101_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLASP2-BGKcLV28-19_S101_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19230
CLASP2-BGKcLV28-19_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	1831					GRCh38	V40	CLASP2-BGKcLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	19288
CLASP2-BGKcLV28-19_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	1831					GRCh38	V40	CLASP2-BGKcLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	19346
CLASP2-BGKcLV28-19_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	1831					GRCh38	V40	CLASP2-BGKcLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	19404
CLASP2-BGKcLV28-19_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	1831					GRCh38	V40	CLASP2-BGKcLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	19462
CLASP2-BGKcLV28-19_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1831					GRCh38	V40	CLASP2-BGKcLV28-19_S101_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLASP2-BGKcLV28-19_S101_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19520
CLASP2-BGKcLV28-20_S102_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1832	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	3949
CLASP2-BGKcLV28-20_S102_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1832	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	4007
CLASP2-BGKcLV28-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1832					GRCh38	V40	CLASP2-BGKcLV28-20_S102_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLASP2-BGKcLV28-20_S102_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19231
CLASP2-BGKcLV28-20_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	1832					GRCh38	V40	CLASP2-BGKcLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	19289
CLASP2-BGKcLV28-20_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	1832					GRCh38	V40	CLASP2-BGKcLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	19347
CLASP2-BGKcLV28-20_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	1832					GRCh38	V40	CLASP2-BGKcLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	19405
CLASP2-BGKcLV28-20_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	1832					GRCh38	V40	CLASP2-BGKcLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	19463
CLASP2-BGKcLV28-20_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1832					GRCh38	V40	CLASP2-BGKcLV28-20_S102_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLASP2-BGKcLV28-20_S102_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19521