RPRD1B RNA-Seq in HepG2

General Information


RBP	RPRD1B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPRD1B-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR987QQV
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR747MHD
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	RPRD1B-BGHcLV32-57
Rep2	RPRD1B-BGHcLV32-58
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	46.9
Rep2_qPCR	47.4
Rep1_WB	78.6
Rep2_WB	77.3
Antibody Cat#	A303-782A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB524ERY
Status	Submitted
Project	ENCODE4
ID	938

Experiment Information (Status: Released)

	BGHcLV32-57	BGHcLV32-58
idx	1058	1059
TRCN#_or_BGC#	BGC#0000806	BGC#0000806
shRNA_or_gRNA_sequence	CGGTGCCACACGGAGACGAT	CGGTGCCACACGGAGACGAT
PAM	GGG	GGG
Name	RPRD1B_97	RPRD1B_97
Sample_ID	BGHcLV32-57	BGHcLV32-58
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	RPRD1B	RPRD1B
qPCR_result	46.9	47.4
Ave_qPCR	47.2
RT-qPCR_primer-F	tctggcaagaacgaagtgtg
RT-qPCR_primer-R	cctcctcctgaatttgctga
protein_conc	4072	4415
WB_result	78.6	77.3
Ave_WB	77.9
WB_DONE_date	12/15/21
MW	37KD
IP
antibody_Cat#	A303-782A	LOT #2
Antibody DCC ID	ENCAB524ERY	8/4/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library
Note
ID	7237	7238

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPRD1B	Product_ID: A303-782A Lot_ID: 2 Source: Bethyl Labs Target Name: RPRD1B-human

Experiment Status

	BGHcLV32-57	BGHcLV32-58
Sample_ID	BGHcLV32-57	BGHcLV32-58
Sample Name
Sample Name	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-58
RBP	RPRD1B	RPRD1B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10375	10376

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-57	BGHcLV32-58
Sample #	49	50
Sample Name	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-58
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-01
Lib_ID	Lib-220201	Lib-220201
Tecan_Location
Tecan
Tecan_date
Size_bp	293	292
Peak_Molarity	63.60	55.30
libSampleQC_DNA_Well	DNA_Library_set52/set2/A7.png	DNA_Library_set52/set2/B7.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set52/set2/E9.png	RNA_Library_set52/set2/F9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-57	BGHcLV32-58
RBP	RPRD1B	RPRD1B
Batch_ID	BGHcLV32	BGHcLV32
WB_result	78.600	77.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3226	3227

Sequencing Information

	BGHcLV32-57	BGHcLV32-58
Sample_ID	BGHcLV32-57	BGHcLV32-58
Sample Name	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-58
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	96,547,056	79,521,060
total_aligned_reads	80,766,426	67,620,758
unique_aligned_reads	75,901,826	63,601,412
percent_uniqueAligned	0.78616	0.79981
correlation_replicates	0.998334	0.998334
spikein_reads	11,488	4,542
percent_spikeins	0.00012	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2021	2022

Data Submission Information

	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-58	BGHcLV32-58	BGHcLV32-58	BGHcLV32-58
ENCODE_alias	brenton-graveley:RPRD1B-BGHcLV32	brenton-graveley:RPRD1B-BGHcLV32-57	brenton-graveley:L-RPRD1B-BGHcLV32-57	brenton-graveley:RPRD1B-BGHcLV32-57_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPRD1B-BGHcLV32-57_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPRD1B-BGHcLV32-HepG2	brenton-graveley:RPRD1B-BGHcLV32-58	brenton-graveley:L-RPRD1B-BGHcLV32-58	brenton-graveley:RPRD1B-BGHcLV32-58_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPRD1B-BGHcLV32-58_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR747MHD	ENCBS060LCH	ENCLB192ZWS	ENCFF511GUH	ENCFF170XHB	ENCSR987QQV	ENCBS634TDN	ENCLB718SSA	ENCFF644MSH	ENCFF569QTZ
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	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-57	BGHcLV32-58	BGHcLV32-58	BGHcLV32-58	BGHcLV32-58
Sample Name	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-57	RPRD1B-BGHcLV32-58	RPRD1B-BGHcLV32-58	RPRD1B-BGHcLV32-58	RPRD1B-BGHcLV32-58
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		RPRD1B-BGHcLV32-57.pdf	L-RPRD1B-BGHcLV32-57.pdf				RPRD1B-BGHcLV32-58.pdf	L-RPRD1B-BGHcLV32-58.pdf
ID	7467	7541	7653	7763	7873	7958	7542	7654	7764	7874

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
RPRD1B-BGHcLV32-57_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2021	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6521
RPRD1B-BGHcLV32-57_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2021	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6575
RPRD1B-BGHcLV32-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2021					GRCh38	V40	RPRD1B-BGHcLV32-57_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGHcLV32-57_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18442
RPRD1B-BGHcLV32-57_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2021					GRCh38	V40	RPRD1B-BGHcLV32-57/Aligned.sortedByCoord.out.bam		ENCORE2	18496
RPRD1B-BGHcLV32-57_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2021					GRCh38	V40	RPRD1B-BGHcLV32-57/Aligned.sortedByCoord.out.bam		ENCORE2	18550
RPRD1B-BGHcLV32-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2021					GRCh38	V40	RPRD1B-BGHcLV32-57/Aligned.sortedByCoord.out.bam		ENCORE2	18604
RPRD1B-BGHcLV32-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2021					GRCh38	V40	RPRD1B-BGHcLV32-57/Aligned.sortedByCoord.out.bam		ENCORE2	18658
RPRD1B-BGHcLV32-57_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2021					GRCh38	V40	RPRD1B-BGHcLV32-57_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGHcLV32-57_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18712
RPRD1B-BGHcLV32-58_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2022	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6522
RPRD1B-BGHcLV32-58_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2022	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6576
RPRD1B-BGHcLV32-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2022					GRCh38	V40	RPRD1B-BGHcLV32-58_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGHcLV32-58_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18443
RPRD1B-BGHcLV32-58_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2022					GRCh38	V40	RPRD1B-BGHcLV32-58/Aligned.sortedByCoord.out.bam		ENCORE2	18497
RPRD1B-BGHcLV32-58_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2022					GRCh38	V40	RPRD1B-BGHcLV32-58/Aligned.sortedByCoord.out.bam		ENCORE2	18551
RPRD1B-BGHcLV32-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2022					GRCh38	V40	RPRD1B-BGHcLV32-58/Aligned.sortedByCoord.out.bam		ENCORE2	18605
RPRD1B-BGHcLV32-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2022					GRCh38	V40	RPRD1B-BGHcLV32-58/Aligned.sortedByCoord.out.bam		ENCORE2	18659
RPRD1B-BGHcLV32-58_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2022					GRCh38	V40	RPRD1B-BGHcLV32-58_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGHcLV32-58_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18713