CENPI RNA-Seq in HepG2

General Information


RBP	CENPI
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CENPI-BGHcLV09-HepG2
ENCODE_series_ID	ENCSR562NZE
Batch_ID	BGHcLV09
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR603TOC
ENCODE_CN_Exp_ID	ENCSR300EBW
Rep1	CENPI-BGHcLV09-3
Rep2	CENPI-BGHcLV09-4
CN1	NT-BGHcLV09-1
CN2	NT-BGHcLV09-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	77.3
Rep2_WB	75.0
Antibody Cat#	A303-374A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB545QJU
Status	Released
Project	ENCODE4
ID	215

Experiment Information (Status: Released)

	BGHcLV09-3	BGHcLV09-4
idx	165	166
TRCN#_or_BGC#	BGC#0000106	BGC#0000106
shRNA_or_gRNA_sequence	AAAGAGAGTTAAGAACGTCC	AAAGAGAGTTAAGAACGTCC
PAM	AGG	AGG
Name	CENPI-82F	CENPI-82F
Sample_ID	BGHcLV09-3	BGHcLV09-4
transduction_Date	4/20/18	4/20/18
days	D6	D6
RBP_name	CENPI	CENPI
qPCR_result	0.0	0.0
Ave_qPCR	0
RT-qPCR_primer-F	gcaaatggcagtgggatatt
RT-qPCR_primer-R	tcttccaagccacattttcc
protein_conc	4309	3633
WB_result	77.3	75.0
Ave_WB	76.2
WB_DONE_date	6/4/18	WES
MW	87kd
IP
antibody_Cat#	A303-374A
Antibody DCC ID	NO ID
submitted_to_DCC_date
Rep1_TPM	8	0
Rep2_TPM	12	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6308	6309

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CENPI	Product_ID: A303-374A Lot_ID: 1 Source: Bethyl Labs Target Name: CENPI-human

Experiment Status

	BGHcLV09-3	BGHcLV09-4
Sample_ID	BGHcLV09-3	BGHcLV09-4
Sample Name
Sample Name	CENPI-BGHcLV09-3	CENPI-BGHcLV09-4
RBP	CENPI	CENPI
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6257	6258

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV09-3	BGHcLV09-4
Sample #	39	40
Sample Name	CENPI-BGHcLV09-3	CENPI-BGHcLV09-4
Sample_Name_Alias
Index Well Position	C06	D06
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	267	263
Peak_Molarity	65.90	43.50
libSampleQC_DNA_Well	DNA_Library_set41/set5/C6.png	DNA_Library_set41/set4/G10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set41/set1/G5.png	RNA_Library_set41/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV09-3	BGHcLV09-4
RBP	CENPI	CENPI
Batch_ID	BGHcLV09	BGHcLV09
WB_result	77.300	75.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	889	890

Sequencing Information

	BGHcLV09-3	BGHcLV09-4
Sample_ID	BGHcLV09-3	BGHcLV09-4
Sample Name	CENPI-BGHcLV09-3	CENPI-BGHcLV09-4
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	102,025,302	164,793,072
total_aligned_reads	98,703,824	163,039,402
unique_aligned_reads	91,141,072	150,169,916
percent_uniqueAligned	0.89332	0.91126
correlation_replicates	0.990645	0.990645
spikein_reads	68,432	119,678
percent_spikeins	0.00067	0.00073
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	295	296

Data Submission Information

	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-4	BGHcLV09-4	BGHcLV09-4	BGHcLV09-4
ENCODE_alias	brenton-graveley:CENPI-BGHcLV09	brenton-graveley:CENPI-BGHcLV09-3	brenton-graveley:L-CENPI-BGHcLV09-3	brenton-graveley:CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CENPI-BGHcLV09-HepG2	brenton-graveley:CENPI-BGHcLV09-4	brenton-graveley:L-CENPI-BGHcLV09-4	brenton-graveley:CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR603TOC	ENCBS056BIT	ENCLB428CDP	ENCFF603SFC	ENCFF215VTC	ENCSR562NZE	ENCBS926GVT	ENCLB276DVN	ENCFF981MEW	ENCFF889LQI
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	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-3	BGHcLV09-4	BGHcLV09-4	BGHcLV09-4	BGHcLV09-4
Sample Name	CENPI-BGHcLV09-3	CENPI-BGHcLV09-3	CENPI-BGHcLV09-3	CENPI-BGHcLV09-3	CENPI-BGHcLV09-3	CENPI-BGHcLV09-3	CENPI-BGHcLV09-4	CENPI-BGHcLV09-4	CENPI-BGHcLV09-4	CENPI-BGHcLV09-4
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		CENPI-BGHcLV09-3.pdf	L-CENPI-BGHcLV09-3.pdf				CENPI-BGHcLV09-4.pdf	L-CENPI-BGHcLV09-4.pdf
ID	1116	1152	1222	1292	1362	7132	1153	1223	1293	1363

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
CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	295				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	499
CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	295				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	569
CENPI-BGHcLV09-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	295	GRCh38	V40	CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26737
CENPI-BGHcLV09-3_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	295	GRCh38	V40	CENPI-BGHcLV09-3/Aligned.sortedByCoord.out.bam		ENCORE2	26807
CENPI-BGHcLV09-3_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	295	GRCh38	V40	CENPI-BGHcLV09-3/Aligned.sortedByCoord.out.bam		ENCORE2	26877
CENPI-BGHcLV09-3_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	295	GRCh38	V40	CENPI-BGHcLV09-3/Aligned.sortedByCoord.out.bam		ENCORE2	26947
CENPI-BGHcLV09-3_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	295	GRCh38	V40	CENPI-BGHcLV09-3/Aligned.sortedByCoord.out.bam		ENCORE2	27017
CENPI-BGHcLV09-3_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	295	GRCh38	V40	CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGHcLV09-3_AAGATACT+ACTTACAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27087
CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	296				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	500
CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	296				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	570
CENPI-BGHcLV09-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	296	GRCh38	V40	CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26738
CENPI-BGHcLV09-4_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	296	GRCh38	V40	CENPI-BGHcLV09-4/Aligned.sortedByCoord.out.bam		ENCORE2	26808
CENPI-BGHcLV09-4_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	296	GRCh38	V40	CENPI-BGHcLV09-4/Aligned.sortedByCoord.out.bam		ENCORE2	26878
CENPI-BGHcLV09-4_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	296	GRCh38	V40	CENPI-BGHcLV09-4/Aligned.sortedByCoord.out.bam		ENCORE2	26948
CENPI-BGHcLV09-4_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	296	GRCh38	V40	CENPI-BGHcLV09-4/Aligned.sortedByCoord.out.bam		ENCORE2	27018
CENPI-BGHcLV09-4_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	296	GRCh38	V40	CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGHcLV09-4_GGAGCGTC+GTCCGTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27088