RPRD1B RNA-Seq in K562

General Information


RBP	RPRD1B
Cell_Line	K562
Method	CRISPR
Exp_Name	RPRD1B-BGKcLV30-K562
ENCODE_series_ID	ENCSR817CSO
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR737OPD
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RPRD1B-BGKcLV30-59
Rep2	RPRD1B-BGKcLV30-60
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	61.7
Rep2_qPCR	65.6
Rep1_WB	75.4
Rep2_WB	80.1
Antibody Cat#	A303-782A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB524ERY
Status	Submitted
Project	ENCODE4
ID	878

Experiment Information (Status: Released)

	BGKcLV30-59	BGKcLV30-60
idx	1088	1089
TRCN#_or_BGC#	BGC#0000806	BGC#0000806
shRNA_or_gRNA_sequence	CGGTGCCACACGGAGACGAT	CGGTGCCACACGGAGACGAT
PAM	GGG	GGG
Name	RPRD1B_97	RPRD1B_97
Sample_ID	BGKcLV30-59	BGKcLV30-60
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RPRD1B	RPRD1B
qPCR_result	61.7	65.6
Ave_qPCR	63.7
RT-qPCR_primer-F	tctggcaagaacgaagtgtg
RT-qPCR_primer-R	cctcctcctgaatttgctga
protein_conc	2478	2361
WB_result	75.4	80.1
Ave_WB	77.7
WB_DONE_date	10/4/21
MW	37KD
IP
antibody_Cat#	A303-782A	LOT #2
Antibody DCC ID	ENCAB524ERY
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/10/21	11/10/21
repeat_library
Note
ID	5228	5229

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

	BGKcLV30-59	BGKcLV30-60
Sample_ID	BGKcLV30-59	BGKcLV30-60
Sample Name
Sample Name	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-60
RBP	RPRD1B	RPRD1B
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10081	10082

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-59	BGKcLV30-60
Sample #	71	72
Sample Name	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-60
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101A	Lib-211101A
Tecan_Location
Tecan
Tecan_date
Size_bp	288	290
Peak_Molarity	51.50	57.20
libSampleQC_DNA_Well	DNA_Library_set50/set2/C12.png	DNA_Library_set50/set2/D12.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set50/set2/C12.png	RNA_Library_set50/set2/D12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-59	BGKcLV30-60
RBP	RPRD1B	RPRD1B
Batch_ID	BGKcLV30	BGKcLV30
WB_result	75.400	80.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3158	3159

Sequencing Information

	BGKcLV30-59	BGKcLV30-60
Sample_ID	BGKcLV30-59	BGKcLV30-60
Sample Name	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-60
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	102,858,582	137,616,936
total_aligned_reads	97,327,434	131,035,322
unique_aligned_reads	89,041,478	120,293,710
percent_uniqueAligned	0.86567	0.87412
correlation_replicates	0.996474	0.996474
spikein_reads	13,632	12,290
percent_spikeins	0.00013	0.00009
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1943	1944

Data Submission Information

	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-60	BGKcLV30-60	BGKcLV30-60	BGKcLV30-60
ENCODE_alias	brenton-graveley:RPRD1B-BGKcLV30	brenton-graveley:RPRD1B-BGKcLV30-59	brenton-graveley:L-RPRD1B-BGKcLV30-59	brenton-graveley:RPRD1B-BGKcLV30-59_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPRD1B-BGKcLV30-59_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPRD1B-BGKcLV30-K562	brenton-graveley:RPRD1B-BGKcLV30-60	brenton-graveley:L-RPRD1B-BGKcLV30-60	brenton-graveley:RPRD1B-BGKcLV30-60_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPRD1B-BGKcLV30-60_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR737OPD	ENCBS633IOB	ENCLB325FES	ENCFF337HRE	ENCFF921RYB	ENCSR817CSO	ENCBS174IZH	ENCLB715YSX	ENCFF379DXD	ENCFF762PJI
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	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-59	BGKcLV30-60	BGKcLV30-60	BGKcLV30-60	BGKcLV30-60
Sample Name	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-59	RPRD1B-BGKcLV30-60	RPRD1B-BGKcLV30-60	RPRD1B-BGKcLV30-60	RPRD1B-BGKcLV30-60
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50K_biosample_protocol	LV50K_library_protocol				LV50K_biosample_protocol	LV50K_library_protocol
protocol_URL		RPRD1B-BGKcLV30-59.pdf	L-RPRD1B-BGKcLV30-59.pdf				RPRD1B-BGKcLV30-60.pdf	L-RPRD1B-BGKcLV30-60.pdf
ID	5877	5947	6019	6091	6163	6199	5948	6020	6092	6164

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-BGKcLV30-59_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1943	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5871
RPRD1B-BGKcLV30-59_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1943	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5901
RPRD1B-BGKcLV30-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1943					GRCh38	V40	RPRD1B-BGKcLV30-59_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGKcLV30-59_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18772
RPRD1B-BGKcLV30-59_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1943					GRCh38	V40	RPRD1B-BGKcLV30-59/Aligned.sortedByCoord.out.bam		ENCORE2	18802
RPRD1B-BGKcLV30-59_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1943					GRCh38	V40	RPRD1B-BGKcLV30-59/Aligned.sortedByCoord.out.bam		ENCORE2	18832
RPRD1B-BGKcLV30-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1943					GRCh38	V40	RPRD1B-BGKcLV30-59/Aligned.sortedByCoord.out.bam		ENCORE2	18862
RPRD1B-BGKcLV30-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1943					GRCh38	V40	RPRD1B-BGKcLV30-59/Aligned.sortedByCoord.out.bam		ENCORE2	18892
RPRD1B-BGKcLV30-59_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1943					GRCh38	V40	RPRD1B-BGKcLV30-59_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGKcLV30-59_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18922
RPRD1B-BGKcLV30-60_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1944	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5872
RPRD1B-BGKcLV30-60_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1944	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5902
RPRD1B-BGKcLV30-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1944					GRCh38	V40	RPRD1B-BGKcLV30-60_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGKcLV30-60_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18773
RPRD1B-BGKcLV30-60_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1944					GRCh38	V40	RPRD1B-BGKcLV30-60/Aligned.sortedByCoord.out.bam		ENCORE2	18803
RPRD1B-BGKcLV30-60_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1944					GRCh38	V40	RPRD1B-BGKcLV30-60/Aligned.sortedByCoord.out.bam		ENCORE2	18833
RPRD1B-BGKcLV30-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1944					GRCh38	V40	RPRD1B-BGKcLV30-60/Aligned.sortedByCoord.out.bam		ENCORE2	18863
RPRD1B-BGKcLV30-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1944					GRCh38	V40	RPRD1B-BGKcLV30-60/Aligned.sortedByCoord.out.bam		ENCORE2	18893
RPRD1B-BGKcLV30-60_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1944					GRCh38	V40	RPRD1B-BGKcLV30-60_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPRD1B-BGKcLV30-60_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18923