PRPF8 RNA-Seq in K562

General Information


RBP	PRPF8
Cell_Line	K562
Method	CRISPR
Exp_Name	PRPF8-BGKcLV08-K562
ENCODE_series_ID	ENCSR217BVW
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR320IEK
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	PRPF8-BGKcLV08-51
Rep2	PRPF8-BGKcLV08-52
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	13.3
Rep2_qPCR	26.1
Rep1_WB	62.4
Rep2_WB	66.2
Antibody Cat#	A303-921A
Antibody Lot#
Antibody DCC ID	ENCAB207WIC
Status	Released
Project	ENCODE4
ID	208

Experiment Information (Status: Released)

	BGKcLV08-51	BGKcLV08-52
idx	276	277
TRCN#_or_BGC#	BGC#0000137	BGC#0000137
shRNA_or_gRNA_sequence	AGTCCGGTAGCGGGGCTAGA	AGTCCGGTAGCGGGGCTAGA
PAM	GGG	GGG
Name	PRPF8-88F	PRPF8-88F
Sample_ID	BGKcLV08-51	BGKcLV08-52
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	PRPF8	PRPF8
qPCR_result	13.3	26.1
Ave_qPCR	19.7
RT-qPCR_primer-F	ttttctgggagaaggccagt
RT-qPCR_primer-R	ttgggaatctggttcagtcc
protein_conc	3789	3533
WB_result	62.4	66.2
Ave_WB	64.3
WB_DONE_date	4/13/18
MW	274kDa
IP	1
antibody_Cat#	A303-921A
Antibody DCC ID	ENCAB207WIC
submitted_to_DCC_date	9/6/2018
Rep1_TPM	119.6	0
Rep2_TPM	92.4	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4376	4377

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRPF8	Product_ID: A303-921A Lot_ID: 1 Source: Bethyl Labs Target Name: PRPF8-human

Experiment Status

	BGKcLV08-51	BGKcLV08-52
Sample_ID	BGKcLV08-51	BGKcLV08-52
Sample Name
Sample Name	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-52
RBP	PRPF8	PRPF8
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6187	6188

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-51	BGKcLV08-52
Sample #	23	24
Sample Name	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-52
Sample_Name_Alias
Index Well Position	G03	H03
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	278	276
Peak_Molarity	50.40	58.80
libSampleQC_DNA_Well	DNA_Library_set41/set2/G3.png	DNA_Library_set41/set2/H3.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set41/set1/G3.png	RNA_Library_set41/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-51	BGKcLV08-52
RBP	PRPF8	PRPF8
Batch_ID	BGKcLV08	BGKcLV08
WB_result	62.400	66.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	873	874

Sequencing Information

	BGKcLV08-51	BGKcLV08-52
Sample_ID	BGKcLV08-51	BGKcLV08-52
Sample Name	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-52
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	71,248,702	62,917,748
total_aligned_reads	67,330,330	59,738,310
unique_aligned_reads	60,608,606	53,823,146
percent_uniqueAligned	0.85066	0.85545
correlation_replicates	0.991474	0.991474
spikein_reads	129,902	101,326
percent_spikeins	0.00182	0.00161
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	279	280

Data Submission Information

	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-52	BGKcLV08-52	BGKcLV08-52	BGKcLV08-52
ENCODE_alias	brenton-graveley:PRPF8-BGKcLV08	brenton-graveley:PRPF8-BGKcLV08-51	brenton-graveley:L-PRPF8-BGKcLV08-51	brenton-graveley:PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF8-BGKcLV08-K562	brenton-graveley:PRPF8-BGKcLV08-52	brenton-graveley:L-PRPF8-BGKcLV08-52	brenton-graveley:PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR320IEK	ENCBS820MRK	ENCLB066CFQ	ENCFF568PEP	ENCFF908JTP	ENCSR217BVW	ENCBS235VRF	ENCLB464IQH	ENCFF538SEK	ENCFF392OOZ
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	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-51	BGKcLV08-52	BGKcLV08-52	BGKcLV08-52	BGKcLV08-52
Sample Name	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-51	PRPF8-BGKcLV08-52	PRPF8-BGKcLV08-52	PRPF8-BGKcLV08-52	PRPF8-BGKcLV08-52
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		PRPF8-BGKcLV08-51.pdf	L-PRPF8-BGKcLV08-51.pdf				PRPF8-BGKcLV08-52.pdf	L-PRPF8-BGKcLV08-52.pdf
ID	1137	1194	1264	1334	1398	7291	1195	1265	1335	1399

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
PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	279				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	541
PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	279				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	611
PRPF8-BGKcLV08-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	279	GRCh38	V40	PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26779
PRPF8-BGKcLV08-51_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	279	GRCh38	V40	PRPF8-BGKcLV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	26849
PRPF8-BGKcLV08-51_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	279	GRCh38	V40	PRPF8-BGKcLV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	26919
PRPF8-BGKcLV08-51_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	279	GRCh38	V40	PRPF8-BGKcLV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	26989
PRPF8-BGKcLV08-51_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	279	GRCh38	V40	PRPF8-BGKcLV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	27059
PRPF8-BGKcLV08-51_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	279	GRCh38	V40	PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF8-BGKcLV08-51_GCAGAATT+ACCGGCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27129
PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	280				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	542
PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	280				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	612
PRPF8-BGKcLV08-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	280	GRCh38	V40	PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26780
PRPF8-BGKcLV08-52_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	280	GRCh38	V40	PRPF8-BGKcLV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	26850
PRPF8-BGKcLV08-52_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	280	GRCh38	V40	PRPF8-BGKcLV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	26920
PRPF8-BGKcLV08-52_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	280	GRCh38	V40	PRPF8-BGKcLV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	26990
PRPF8-BGKcLV08-52_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	280	GRCh38	V40	PRPF8-BGKcLV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	27060
PRPF8-BGKcLV08-52_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	280	GRCh38	V40	PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF8-BGKcLV08-52_ATGAGGCC+GTTAATTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27130