PRPF8 RNA-Seq in K562

General Information


RBP	PRPF8
Cell_Line	K562
Method	shRNA
Exp_Name	PRPF8-BGKLV19-K562
ENCODE_series_ID	ENCSR177TPO
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR137HKS
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	PRPF8_BGKLV19_43B
Rep2	PRPF8_BGKLV19_44B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	65.7
Rep2_qPCR	66.4
Rep1_WB
Rep2_WB
Antibody Cat#	A303-921A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB207WIC
Status	Archived
Project	ENCODE3
ID	478

Experiment Information (Status: Released)

	BGKLV19-43	BGKLV19-44
idx	250	251
TRCN#_or_BGC#	TRCN0000075112	TRCN0000075112
shRNA_or_gRNA_sequence	CGCCTCATGAAACATGATGTT	CGCCTCATGAAACATGATGTT
PAM
Name	PRPF8	PRPF8
Sample_ID	BGKLV19-43	BGKLV19-44
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	PRPF8	PRPF8
qPCR_result	65.7	66.4
Ave_qPCR	66.1
RT-qPCR_primer-F	ttttctgggagaaggccagt
RT-qPCR_primer-R	ttgggaatctggttcagtcc
protein_conc	1218	1315
WB_result
Ave_WB	bad imgen
WB_DONE_date	1/14/2015
MW	274kDa
IP	1	1
antibody_Cat#	A303-921A	A303-921A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	119.6148	0
Rep2_TPM	92.4165454	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	275	276

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV19-43	BGKLV19-44
Sample_ID	BGKLV19-43	BGKLV19-44
Sample Name	PRPF8_BGKLV19_43B	PRPF8_BGKLV19_44B
Sample Name	PRPF8_BGKLV19_43B	PRPF8_BGKLV19_44B
RBP	PRPF8	PRPF8
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	690	691

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-43	BGKLV19-44
Sample #
Sample Name	PRPF8-BGKLV19-43B	PRPF8-BGKLV19-44B
Sample_Name_Alias	PRPF8_BGKLV19_43B	PRPF8_BGKLV19_44B
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C10.png	DNA_Library_LV18-19/set1/D10.png
RIN	9.7	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G4.png	RNA_Library_LV19-21-24/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-43	BGKLV19-44
RBP	PRPF8	PRPF8
Batch_ID	BGKLV19	BGKLV19
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2374	2375

Sequencing Information

	BGKLV19-43	BGKLV19-44
Sample_ID	BGKLV19-43	BGKLV19-44
Sample Name	PRPF8_BGKLV19_43B	PRPF8_BGKLV19_44B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	45,460,000	47,920,000
total_aligned_reads	41,358,692	43,898,836
unique_aligned_reads	38,059,422	40,404,658
percent_uniqueAligned	0.83721	0.84317
correlation_replicates	0.998232	0.998232
spikein_reads	762,136	546,744
percent_spikeins	0.01676	0.01141
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1016	1017

Data Submission Information

	BGKLV19-43	BGKLV19-43
ENCODE_alias	brenton-graveley:PRPF8_BGKLV19	brenton-graveley:PRPF8-BGKLV19-K562
ENCODE_accession	ENCSR137HKS	ENCSR177TPO
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-43	BGKLV19-43
Sample Name	PRPF8_BGKLV19_43B	PRPF8_BGKLV19_43B
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2893	6871

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
PRPF8_BGKLV19_43B_TTAGGC_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1016	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15132
PRPF8_BGKLV19_43B_TTAGGC_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1016	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15190
PRPF8_BGKLV19_43B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1016					GRCh38	V40	PRPF8_BGKLV19_43B_TTAGGC_L005_R1_001.fastq.gz,PRPF8_BGKLV19_43B_TTAGGC_L005_R2_001.fastq.gz		ENCORE2	15248
PRPF8_BGKLV19_43B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1016					GRCh38	V40	PRPF8_BGKLV19_43B/Aligned.sortedByCoord.out.bam		ENCORE2	15319
PRPF8_BGKLV19_43B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1016					GRCh38	V40	PRPF8_BGKLV19_43B/Aligned.sortedByCoord.out.bam		ENCORE2	15377
PRPF8_BGKLV19_43B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1016					GRCh38	V40	PRPF8_BGKLV19_43B/Aligned.sortedByCoord.out.bam		ENCORE2	15435
PRPF8_BGKLV19_43B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1016					GRCh38	V40	PRPF8_BGKLV19_43B/Aligned.sortedByCoord.out.bam		ENCORE2	15493
PRPF8_BGKLV19_43B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1016					GRCh38	V40	PRPF8_BGKLV19_43B_TTAGGC_L005_R1_001.fastq.gz,PRPF8_BGKLV19_43B_TTAGGC_L005_R2_001.fastq.gz		ENCORE2	16390
PRPF8_BGKLV19_44B_TGACCA_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1017	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15133
PRPF8_BGKLV19_44B_TGACCA_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1017	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15191
PRPF8_BGKLV19_44B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1017					GRCh38	V40	PRPF8_BGKLV19_44B_TGACCA_L005_R1_001.fastq.gz,PRPF8_BGKLV19_44B_TGACCA_L005_R2_001.fastq.gz		ENCORE2	15249
PRPF8_BGKLV19_44B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1017					GRCh38	V40	PRPF8_BGKLV19_44B/Aligned.sortedByCoord.out.bam		ENCORE2	15320
PRPF8_BGKLV19_44B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1017					GRCh38	V40	PRPF8_BGKLV19_44B/Aligned.sortedByCoord.out.bam		ENCORE2	15378
PRPF8_BGKLV19_44B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1017					GRCh38	V40	PRPF8_BGKLV19_44B/Aligned.sortedByCoord.out.bam		ENCORE2	15436
PRPF8_BGKLV19_44B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1017					GRCh38	V40	PRPF8_BGKLV19_44B/Aligned.sortedByCoord.out.bam		ENCORE2	15494
PRPF8_BGKLV19_44B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1017					GRCh38	V40	PRPF8_BGKLV19_44B_TGACCA_L005_R1_001.fastq.gz,PRPF8_BGKLV19_44B_TGACCA_L005_R2_001.fastq.gz		ENCORE2	16391