CENPI RNA-Seq in K562

General Information


RBP	CENPI
Cell_Line	K562
Method	CRISPR
Exp_Name	CENPI-BGKcLV08-K562
ENCODE_series_ID	ENCSR283HNL
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR242VKR
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	CENPI-BGKcLV08-7
Rep2	CENPI-BGKcLV08-8
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	94.6
Rep2_WB	80.7
Antibody Cat#	A303-374A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB545QJU
Status	Released
Project	ENCODE4
ID	199

Experiment Information (Status: Released)

	BGKcLV08-7	BGKcLV08-8
idx	232	233
TRCN#_or_BGC#	BGC#0000107	BGC#0000107
shRNA_or_gRNA_sequence	TACTTTCCAGGCTGAAAGCG	TACTTTCCAGGCTGAAAGCG
PAM	TGG	TGG
Name	CENPI-73F	CENPI-73F
Sample_ID	BGKcLV08-7	BGKcLV08-8
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	CENPI	CENPI
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gcaaatggcagtgggatatt
RT-qPCR_primer-R	tcttccaagccacattttcc
protein_conc	3448	3057
WB_result	94.6	80.7
Ave_WB	87.6
WB_DONE_date	6/4/18	WES
MW	87kd
IP
antibody_Cat#	A303-374A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	9.2	0
Rep2_TPM	10	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4332	4333

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV08-7	BGKcLV08-8
Sample_ID	BGKcLV08-7	BGKcLV08-8
Sample Name
Sample Name	CENPI-BGKcLV08-7	CENPI-BGKcLV08-8
RBP	CENPI	CENPI
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6169	6170

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-7	BGKcLV08-8
Sample #	5	6
Sample Name	CENPI-BGKcLV08-7	CENPI-BGKcLV08-8
Sample_Name_Alias
Index Well Position	E01	F01
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	280
Peak_Molarity	46.40	51.00
libSampleQC_DNA_Well	DNA_Library_set41/set2/E1.png	DNA_Library_set41/set2/F1.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_set41/set1/E1.png	RNA_Library_set41/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-7	BGKcLV08-8
RBP	CENPI	CENPI
Batch_ID	BGKcLV08	BGKcLV08
WB_result	94.600	80.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	855	856

Sequencing Information

	BGKcLV08-7	BGKcLV08-8
Sample_ID	BGKcLV08-7	BGKcLV08-8
Sample Name	CENPI-BGKcLV08-7	CENPI-BGKcLV08-8
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	141,998,142	87,805,050
total_aligned_reads	136,643,510	83,672,638
unique_aligned_reads	122,477,620	74,942,090
percent_uniqueAligned	0.86253	0.85351
correlation_replicates	0.995064	0.995064
spikein_reads	244,226	144,802
percent_spikeins	0.00172	0.00165
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	261	262

Data Submission Information

	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-8	BGKcLV08-8	BGKcLV08-8	BGKcLV08-8
ENCODE_alias	brenton-graveley:CENPI-BGKcLV08	brenton-graveley:CENPI-BGKcLV08-7	brenton-graveley:L-CENPI-BGKcLV08-7	brenton-graveley:CENPI-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CENPI-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CENPI-BGKcLV08-K562	brenton-graveley:CENPI-BGKcLV08-8	brenton-graveley:L-CENPI-BGKcLV08-8	brenton-graveley:CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR242VKR	ENCBS833MOI	ENCLB723ZEQ	ENCFF957WSL	ENCFF906CMI	ENCSR283HNL	ENCBS105PBU	ENCLB184VXE	ENCFF946GCH	ENCFF025QCJ
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	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-7	BGKcLV08-8	BGKcLV08-8	BGKcLV08-8	BGKcLV08-8
Sample Name	CENPI-BGKcLV08-7	CENPI-BGKcLV08-7	CENPI-BGKcLV08-7	CENPI-BGKcLV08-7	CENPI-BGKcLV08-7	CENPI-BGKcLV08-7	CENPI-BGKcLV08-8	CENPI-BGKcLV08-8	CENPI-BGKcLV08-8	CENPI-BGKcLV08-8
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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_library_protocol					LV41_library_protocol
protocol_URL			L-CENPI-BGKcLV08-7.pdf					L-CENPI-BGKcLV08-8.pdf
ID	1117	1154	1224	1294	1364	7133	1155	1225	1295	1365

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-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	261				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	501
CENPI-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	261				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	571
CENPI-BGKcLV08-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	261	GRCh38	V40	CENPI-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26739
CENPI-BGKcLV08-7_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	261	GRCh38	V40	CENPI-BGKcLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	26809
CENPI-BGKcLV08-7_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	261	GRCh38	V40	CENPI-BGKcLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	26879
CENPI-BGKcLV08-7_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	261	GRCh38	V40	CENPI-BGKcLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	26949
CENPI-BGKcLV08-7_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	261	GRCh38	V40	CENPI-BGKcLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	27019
CENPI-BGKcLV08-7_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	261	GRCh38	V40	CENPI-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGKcLV08-7_ATCCACTG+AGGTGCGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27089
CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	262				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	502
CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	262				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	572
CENPI-BGKcLV08-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	262	GRCh38	V40	CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26740
CENPI-BGKcLV08-8_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	262	GRCh38	V40	CENPI-BGKcLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	26810
CENPI-BGKcLV08-8_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	262	GRCh38	V40	CENPI-BGKcLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	26880
CENPI-BGKcLV08-8_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	262	GRCh38	V40	CENPI-BGKcLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	26950
CENPI-BGKcLV08-8_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	262	GRCh38	V40	CENPI-BGKcLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	27020
CENPI-BGKcLV08-8_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	262	GRCh38	V40	CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,CENPI-BGKcLV08-8_GCTTGTCA+GAACATAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27090