CDC40 RNA-Seq in HepG2

General Information


RBP	CDC40
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CDC40-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR135ZOJ
Batch_ID	BGHcLV05
Pool ID	Pool-161129
Local_Set_Name	BGHcLV05
ENCODE_KD_Exp_ID	ENCSR278NFF
ENCODE_CN_Exp_ID	ENCSR481WJH
Rep1	CDC40_BGHcLV05_7
Rep2	CDC40_BGHcLV05_8
CN1	NT_BGHcLV05-1
CN2	NT_BGHcLV05-2
Rep1_qPCR	27.4
Rep2_qPCR	30.9
Rep1_WB	70.8
Rep2_WB	65.7
Antibody Cat#	A303-699A
Antibody Lot#	A303-699A
Antibody DCC ID	ENCAB127ICL
Status	Released
Project	ENCODE3
ID	578

Experiment Information (Status: Released)

	BGHcLV05-7	BGHcLV05-7	BGHcLV05-8	BGHcLV05-8
idx	43	80	44	81
TRCN#_or_BGC#	BGC#0000026	BGC#0000026	BGC#0000026	BGC#0000026
shRNA_or_gRNA_sequence	GGCTCCGGAGGTGGCAGTTA	GGCTCCGGAGGTGGCAGTTA	GGCTCCGGAGGTGGCAGTTA	GGCTCCGGAGGTGGCAGTTA
PAM
Name	CDC40_71	CDC40_71	CDC40_71	CDC40_71
Sample_ID	BGHcLV05-7	BGHcLV05-7	BGHcLV05-8	BGHcLV05-8
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	CDC40	CDC40	CDC40	CDC40
qPCR_result	27.4		30.9
Ave_qPCR	29.1
RT-qPCR_primer-F	GAAACCTGGGGAGGAGAAGA
RT-qPCR_primer-R	TGAAGATAGGACCTGCCTTGA
protein_conc	3833	0	3729	0
WB_result	70.8		65.7
Ave_WB	68.2
WB_DONE_date	7/22/16		WES
MW	66 kDa
IP	1
antibody_Cat#	A303-699A		A303-699A
Antibody DCC ID	ENCAB127ICL		ENCAB127ICL
submitted_to_DCC_date	10/26/16
Rep1_TPM	7	0	0	0
Rep2_TPM	12	0	0	0
Action	Ready		Ready
Library_start_date	08/15/16		08/15/16
repeat_library
Note
ID	6184	6223	6185	6224

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

	BGHcLV05-7	BGHcLV05-8
Sample_ID	BGHcLV05-7	BGHcLV05-8
Sample Name	CDC40_BGHcLV05_7	CDC40_BGHcLV05_8
Sample Name	CDC40_BGHcLV05_7	CDC40_BGHcLV05_8
RBP	CDC40	CDC40
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1323	1324

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-7	BGHcLV05-8
Sample #
Sample Name	CDC40-BGHcLV05-7	CDC40-BGHcLV05-8
Sample_Name_Alias	CDC40_BGHcLV05_7	CDC40_BGHcLV05_8
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-08-15	2016-08-15
Lib_ID	Lib-160815	Lib-160815
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/D1.png	DNA_Library_LV37-38/set1/E1.png
RIN	9.2	9.1
libSample_RNA_Well	RNA_Library_cLV04-05/set1/E7.png	RNA_Library_cLV04-05/set1/F7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV05-7	BGHcLV05-8
RBP	CDC40	CDC40
Batch_ID	BGHcLV05	BGHcLV05
WB_result	70.800	65.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3014	3015

Sequencing Information

	BGHcLV05-7	BGHcLV05-8
Sample_ID	BGHcLV05-7	BGHcLV05-8
Sample Name	CDC40_BGHcLV05_7	CDC40_BGHcLV05_8
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	BGHcLV05	BGHcLV05
total_reads	72,269,290	86,186,238
total_aligned_reads	55,308,598	68,089,868
unique_aligned_reads	51,666,482	63,434,862
percent_uniqueAligned	0.71492	0.73602
correlation_replicates	0.998723	0.998723
spikein_reads	77,272	107,446
percent_spikeins	0.00107	0.00125
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1667	1668

Data Submission Information

	BGHcLV05-7	BGHcLV05-7
ENCODE_alias	brenton-graveley:CDC40_BGHcLV05	brenton-graveley:CDC40-BGHcLV05-HepG2
ENCODE_accession	ENCSR278NFF	ENCSR135ZOJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV05-7	BGHcLV05-7
Sample Name	CDC40_BGHcLV05_7	CDC40_BGHcLV05_7
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-12	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3201	6614

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
CDC40_BGHcLV05_7_AGTCAA_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1667	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23136
CDC40_BGHcLV05_7_AGTCAA_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1667	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23148
CDC40_BGHcLV05_7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1667					GRCh38	V40	CDC40_BGHcLV05_7_AGTCAA_L003_001.R1.fastq.gz,CDC40_BGHcLV05_7_AGTCAA_L003_001.R2.fastq.gz		ENCORE2	23160
CDC40_BGHcLV05_7_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1667					GRCh38	V40	CDC40_BGHcLV05_7/Aligned.sortedByCoord.out.bam		ENCORE2	23172
CDC40_BGHcLV05_7_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1667					GRCh38	V40	CDC40_BGHcLV05_7/Aligned.sortedByCoord.out.bam		ENCORE2	23184
CDC40_BGHcLV05_7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1667					GRCh38	V40	CDC40_BGHcLV05_7/Aligned.sortedByCoord.out.bam		ENCORE2	23196
CDC40_BGHcLV05_7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1667					GRCh38	V40	CDC40_BGHcLV05_7/Aligned.sortedByCoord.out.bam		ENCORE2	23208
CDC40_BGHcLV05_7_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1667					GRCh38	V40	CDC40_BGHcLV05_7_AGTCAA_L003_001.R1.fastq.gz,CDC40_BGHcLV05_7_AGTCAA_L003_001.R2.fastq.gz		ENCORE2	23220
CDC40_BGHcLV05_8_AGTTCC_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1668	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23137
CDC40_BGHcLV05_8_AGTTCC_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1668	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23149
CDC40_BGHcLV05_8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1668					GRCh38	V40	CDC40_BGHcLV05_8_AGTTCC_L003_001.R1.fastq.gz,CDC40_BGHcLV05_8_AGTTCC_L003_001.R2.fastq.gz		ENCORE2	23161
CDC40_BGHcLV05_8_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1668					GRCh38	V40	CDC40_BGHcLV05_8/Aligned.sortedByCoord.out.bam		ENCORE2	23173
CDC40_BGHcLV05_8_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1668					GRCh38	V40	CDC40_BGHcLV05_8/Aligned.sortedByCoord.out.bam		ENCORE2	23185
CDC40_BGHcLV05_8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1668					GRCh38	V40	CDC40_BGHcLV05_8/Aligned.sortedByCoord.out.bam		ENCORE2	23197
CDC40_BGHcLV05_8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1668					GRCh38	V40	CDC40_BGHcLV05_8/Aligned.sortedByCoord.out.bam		ENCORE2	23209
CDC40_BGHcLV05_8_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1668					GRCh38	V40	CDC40_BGHcLV05_8_AGTTCC_L003_001.R1.fastq.gz,CDC40_BGHcLV05_8_AGTTCC_L003_001.R2.fastq.gz		ENCORE2	23221