PRPF39 RNA-Seq in HepG2

General Information


RBP	PRPF39
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PRPF39-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR004UEZ
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR511QFJ
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	PRPF39-BGHcLV18-37
Rep2	PRPF39-BGHcLV18-38
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	29.7
Rep2_qPCR	3.3
Rep1_WB	79.0
Rep2_WB	76.8
Antibody Cat#	PA5-21627
Antibody Lot#	UC2743613B
Antibody DCC ID	ENCAB901VHL
Status	Released
Project	ENCODE4
ID	114

Experiment Information (Status: Released)

	BGHcLV18-37	BGHcLV18-38
idx	530	531
TRCN#_or_BGC#	BGC#0000451	BGC#0000451
shRNA_or_gRNA_sequence	GCCCAAAGCATATGCACCAT	GCCCAAAGCATATGCACCAT
PAM	GGG	GGG
Name	PRPF39_80	PRPF39_80
Sample_ID	BGHcLV18-37	BGHcLV18-38
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	PRPF39	PRPF39
qPCR_result	29.7	3.3
Ave_qPCR	16.5
RT-qPCR_primer-F	cttgaagattttggttccgatgt
RT-qPCR_primer-R	tgtgctttcttttcctctggt
protein_conc	3851	4221
WB_result	79.0	76.8
Ave_WB	77.9
WB_DONE_date	8/22/19	wes
MW	78KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-21627	UC2743613B
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	30	0
Rep2_TPM	28	0
Action	Question	Question
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6685	6686

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV18-37	BGHcLV18-38
Sample_ID	BGHcLV18-37	BGHcLV18-38
Sample Name
Sample Name	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-38
RBP	PRPF39	PRPF39
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5645	5646

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-37	BGHcLV18-38
Sample #	151	152
Sample Name	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-38
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	5-C1	5-D1
Tecan	36.32	35.39
Tecan_date	2019-12-16	2019-12-16
Size_bp	273	275
Peak_Molarity	25.70	29.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E8.png	DNA_Library_set43-44/set2/F8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/A10.png	RNA_Library_set43-44/set4/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-37	BGHcLV18-38
RBP	PRPF39	PRPF39
Batch_ID	BGHcLV18	BGHcLV18
WB_result	79.000	76.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	727	728

Sequencing Information

	BGHcLV18-37	BGHcLV18-38
Sample_ID	BGHcLV18-37	BGHcLV18-38
Sample Name	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-38
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	169,642,382	159,646,092
total_aligned_reads	163,210,688	152,714,210
unique_aligned_reads	152,833,286	142,778,626
percent_uniqueAligned	0.90091	0.89434
correlation_replicates	0.996560	0.996560
spikein_reads	259,448	277,040
percent_spikeins	0.00153	0.00174
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	233	234

Data Submission Information

	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-38	BGHcLV18-38	BGHcLV18-38	BGHcLV18-38
ENCODE_alias	brenton-graveley:PRPF39-BGHcLV18	brenton-graveley:PRPF39-BGHcLV18-37	brenton-graveley:L-PRPF39-BGHcLV18-37	brenton-graveley:PRPF39-BGHcLV18-37_S63_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF39-BGHcLV18-37_S63_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF39-BGHcLV18-HepG2	brenton-graveley:PRPF39-BGHcLV18-38	brenton-graveley:L-PRPF39-BGHcLV18-38	brenton-graveley:PRPF39-BGHcLV18-38_S64_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF39-BGHcLV18-38_S64_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR511QFJ	ENCBS699GAM	ENCLB685RNC	ENCFF589AEL	ENCFF662GDS	ENCSR004UEZ	ENCBS467XOJ	ENCLB148GNM	ENCFF197SMX	ENCFF060QXE
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	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-37	BGHcLV18-38	BGHcLV18-38	BGHcLV18-38	BGHcLV18-38
Sample Name	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-37	PRPF39-BGHcLV18-38	PRPF39-BGHcLV18-38	PRPF39-BGHcLV18-38	PRPF39-BGHcLV18-38
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV44H_library_protocol					LV44H_library_protocol
protocol_URL			L-PRPF39-BGHcLV18-37.pdf					L-PRPF39-BGHcLV18-38.pdf
ID	61	202	368	618	670	7289	203	369	619	671

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
PRPF39-BGHcLV18-37_S63_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	233	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	205
PRPF39-BGHcLV18-37_S63_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	233	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	257
PRPF39-BGHcLV18-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	233					GRCh38	V40	PRPF39-BGHcLV18-37_S63_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGHcLV18-37_S63_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24925
PRPF39-BGHcLV18-37_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	233					GRCh38	V40	PRPF39-BGHcLV18-37/Aligned.sortedByCoord.out.bam		ENCORE2	24977
PRPF39-BGHcLV18-37_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	233					GRCh38	V40	PRPF39-BGHcLV18-37/Aligned.sortedByCoord.out.bam		ENCORE2	25029
PRPF39-BGHcLV18-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	233					GRCh38	V40	PRPF39-BGHcLV18-37/Aligned.sortedByCoord.out.bam		ENCORE2	25081
PRPF39-BGHcLV18-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	233					GRCh38	V40	PRPF39-BGHcLV18-37/Aligned.sortedByCoord.out.bam		ENCORE2	25133
PRPF39-BGHcLV18-37_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	233					GRCh38	V40	PRPF39-BGHcLV18-37_S63_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGHcLV18-37_S63_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25185
PRPF39-BGHcLV18-38_S64_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	234	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	206
PRPF39-BGHcLV18-38_S64_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	234	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	258
PRPF39-BGHcLV18-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	234					GRCh38	V40	PRPF39-BGHcLV18-38_S64_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGHcLV18-38_S64_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24926
PRPF39-BGHcLV18-38_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	234					GRCh38	V40	PRPF39-BGHcLV18-38/Aligned.sortedByCoord.out.bam		ENCORE2	24978
PRPF39-BGHcLV18-38_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	234					GRCh38	V40	PRPF39-BGHcLV18-38/Aligned.sortedByCoord.out.bam		ENCORE2	25030
PRPF39-BGHcLV18-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	234					GRCh38	V40	PRPF39-BGHcLV18-38/Aligned.sortedByCoord.out.bam		ENCORE2	25082
PRPF39-BGHcLV18-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	234					GRCh38	V40	PRPF39-BGHcLV18-38/Aligned.sortedByCoord.out.bam		ENCORE2	25134
PRPF39-BGHcLV18-38_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	234					GRCh38	V40	PRPF39-BGHcLV18-38_S64_R1_001.filtered.trimmed.paired.fastq.gz,PRPF39-BGHcLV18-38_S64_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25186