CDC40 RNA-Seq in K562

General Information


RBP	CDC40
Cell_Line	K562
Method	CRISPR
Exp_Name	CDC40-BGKcLV08-K562
ENCODE_series_ID	ENCSR455YLP
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR354DVY
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	CDC40-BGKcLV08-3
Rep2	CDC40-BGKcLV08-4
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	27.9
Rep2_qPCR	30.8
Rep1_WB	57.0
Rep2_WB	56.0
Antibody Cat#	A303-699A
Antibody Lot#	A303-699A
Antibody DCC ID	ENCAB127ICL
Status	Released
Project	ENCODE4
ID	198

Experiment Information (Status: Released)

	BGKcLV08-3	BGKcLV08-3	BGKcLV08-4	BGKcLV08-4
idx	228	228	229	229
TRCN#_or_BGC#	BGC#0000026	BGC#0000026	BGC#0000026	BGC#0000026
shRNA_or_gRNA_sequence	GGCTCCGGAGGTGGCAGTTA	GGCTCCGGAGGTGGCAGTTA	GGCTCCGGAGGTGGCAGTTA	GGCTCCGGAGGTGGCAGTTA
PAM
Name	CDC40_71-F	CDC40_71-F	CDC40_71-F	CDC40_71-F
Sample_ID	BGKcLV08-3	BGKcLV08-3	BGKcLV08-4	BGKcLV08-4
transduction_Date	3/8/18	3/8/18	3/8/18	3/8/18
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CDC40	CDC40	CDC40	CDC40
qPCR_result	27.9	27.9	30.8	30.8
Ave_qPCR	27.9	29.4
RT-qPCR_primer-F	GAAACCTGGGGAGGAGAAGA	GAAACCTGGGGAGGAGAAGA
RT-qPCR_primer-R	TGAAGATAGGACCTGCCTTGA	TGAAGATAGGACCTGCCTTGA
protein_conc	2810	2810	2664	2664
WB_result	57.0	no band	56.0
Ave_WB	56.5
WB_DONE_date	3/9/18	6/28/23	wes
MW	66 kDa	66 kDa
IP	1
antibody_Cat#	A303-699A	99086S	A303-699A	lot# 1
Antibody DCC ID	ENCAB127ICL
submitted_to_DCC_date	9/6/18
Rep1_TPM	6.5	0	0	0
Rep2_TPM	5.2	0	0	0
Action	Ready		Ready
Library_start_date	7/26/18		7/26/18
repeat_library
Note
ID	4326	4328	4327	4329

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CDC40	Product_ID: A303-699A Lot_ID: 1 Source: Bethyl Labs Target Name: CDC40-human

Experiment Status

	BGKcLV08-3	BGKcLV08-4
Sample_ID	BGKcLV08-3	BGKcLV08-4
Sample Name
Sample Name	CDC40-BGKcLV08-3	CDC40-BGKcLV08-4
RBP	CDC40	CDC40
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6167	6168

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-3	BGKcLV08-4
Sample #	3	4
Sample Name	CDC40-BGKcLV08-3	CDC40-BGKcLV08-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	281	274
Peak_Molarity	51.00	58.90
libSampleQC_DNA_Well	DNA_Library_set41/set2/C1.png	DNA_Library_set41/set2/D1.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set41/set1/C1.png	RNA_Library_set41/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-3	BGKcLV08-4
RBP	CDC40	CDC40
Batch_ID	BGKcLV08	BGKcLV08
WB_result	57.000	56.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	853	854

Sequencing Information

	BGKcLV08-3	BGKcLV08-4
Sample_ID	BGKcLV08-3	BGKcLV08-4
Sample Name	CDC40-BGKcLV08-3	CDC40-BGKcLV08-4
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	156,216,600	131,764,264
total_aligned_reads	146,917,866	124,822,466
unique_aligned_reads	132,354,842	112,382,370
percent_uniqueAligned	0.84725	0.85290
correlation_replicates	0.995882	0.995882
spikein_reads	373,926	294,894
percent_spikeins	0.00239	0.00224
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	259	260

Data Submission Information

	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-4	BGKcLV08-4	BGKcLV08-4	BGKcLV08-4
ENCODE_alias	brenton-graveley:CDC40-BGKcLV08	brenton-graveley:CDC40-BGKcLV08-3	brenton-graveley:L-CDC40-BGKcLV08-3	brenton-graveley:CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC40-BGKcLV08-K562	brenton-graveley:CDC40-BGKcLV08-4	brenton-graveley:L-CDC40-BGKcLV08-4	brenton-graveley:CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR354DVY	ENCBS050VON	ENCLB384SYD	ENCFF514QRX	ENCFF999GWJ	ENCSR455YLP	ENCBS194YRU	ENCLB798YHX	ENCFF673ZNM	ENCFF278HMM
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	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-3	BGKcLV08-4	BGKcLV08-4	BGKcLV08-4	BGKcLV08-4
Sample Name	CDC40-BGKcLV08-3	CDC40-BGKcLV08-3	CDC40-BGKcLV08-3	CDC40-BGKcLV08-3	CDC40-BGKcLV08-3	CDC40-BGKcLV08-3	CDC40-BGKcLV08-4	CDC40-BGKcLV08-4	CDC40-BGKcLV08-4	CDC40-BGKcLV08-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		CDC40-BGKcLV08-3.pdf	L-CDC40-BGKcLV08-3.pdf				CDC40-BGKcLV08-4.pdf	L-CDC40-BGKcLV08-4.pdf
ID	1115	1150	1220	1290	1360	7128	1151	1221	1291	1361

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	259				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	497
CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	259				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	567
CDC40-BGKcLV08-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	259	GRCh38	V40	CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26735
CDC40-BGKcLV08-3_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	259	GRCh38	V40	CDC40-BGKcLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	26805
CDC40-BGKcLV08-3_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	259	GRCh38	V40	CDC40-BGKcLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	26875
CDC40-BGKcLV08-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	259	GRCh38	V40	CDC40-BGKcLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	26945
CDC40-BGKcLV08-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	259	GRCh38	V40	CDC40-BGKcLV08-3/Aligned.sortedByCoord.out.bam		ENCORE2	27015
CDC40-BGKcLV08-3_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	259	GRCh38	V40	CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BGKcLV08-3_GGACTTGG+CGCAGACG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27085
CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	260				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	498
CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	260				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	568
CDC40-BGKcLV08-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	260	GRCh38	V40	CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26736
CDC40-BGKcLV08-4_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	260	GRCh38	V40	CDC40-BGKcLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	26806
CDC40-BGKcLV08-4_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	260	GRCh38	V40	CDC40-BGKcLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	26876
CDC40-BGKcLV08-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	260	GRCh38	V40	CDC40-BGKcLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	26946
CDC40-BGKcLV08-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	260	GRCh38	V40	CDC40-BGKcLV08-4/Aligned.sortedByCoord.out.bam		ENCORE2	27016
CDC40-BGKcLV08-4_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	260	GRCh38	V40	CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDC40-BGKcLV08-4_AAGTCCAA+TATGAGTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27086