RNPC3 RNA-Seq in K562

General Information


RBP	RNPC3
Cell_Line	K562
Method	CRISPR
Exp_Name	RNPC3-BGKcLV30-K562
ENCODE_series_ID	ENCSR603LHS
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR631NIZ
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RNPC3-BGKcLV30-41
Rep2	RNPC3-BGKcLV30-42
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	11.7
Rep2_qPCR	2.1
Rep1_WB	72.2
Rep2_WB	62.7
Antibody Cat#	A305-145A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB974GCV
Status	Submitted
Project	ENCODE4
ID	876

Experiment Information (Status: Released)

	BGKcLV30-41	BGKcLV30-42
idx	1070	1071
TRCN#_or_BGC#	BGC#0000788	BGC#0000788
shRNA_or_gRNA_sequence	CATCCCCTTGATATCGCAAG	CATCCCCTTGATATCGCAAG
PAM	CGG	CGG
Name	RNPC3_95	RNPC3_95
Sample_ID	BGKcLV30-41	BGKcLV30-42
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RNPC3	RNPC3
qPCR_result	11.7	2.1
Ave_qPCR	6.9
RT-qPCR_primer-F	ccttccagcacaatcctagc
RT-qPCR_primer-R	aattggtccaaaaggtgtgg
protein_conc	2337	2560
WB_result	72.2	62.7
Ave_WB	67.4
WB_DONE_date	10/1/21
MW	59KD
IP
antibody_Cat#	A305-145A	LOT #1
Antibody DCC ID	ENCAB974GCV
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	5210	5211

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RNPC3	Product_ID: A305-145A Lot_ID: 1 Source: Bethyl Labs Target Name: RNPC3-human

Experiment Status

	BGKcLV30-41	BGKcLV30-42
Sample_ID	BGKcLV30-41	BGKcLV30-42
Sample Name
Sample Name	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-42
RBP	RNPC3	RNPC3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10077	10078

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-41	BGKcLV30-42
Sample #	67	68
Sample Name	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-42
Sample_Name_Alias
Index Well Position	G09	H09
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	285	277
Peak_Molarity	61.80	48.40
libSampleQC_DNA_Well	DNA_Library_set50/set2/G11.png	DNA_Library_set50/set2/H11.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set50/set2/G11.png	RNA_Library_set50/set2/H11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-41	BGKcLV30-42
RBP	RNPC3	RNPC3
Batch_ID	BGKcLV30	BGKcLV30
WB_result	72.200	62.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3154	3155

Sequencing Information

	BGKcLV30-41	BGKcLV30-42
Sample_ID	BGKcLV30-41	BGKcLV30-42
Sample Name	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-42
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	95,341,692	81,773,002
total_aligned_reads	90,452,712	72,045,198
unique_aligned_reads	82,412,180	65,492,744
percent_uniqueAligned	0.86439	0.80091
correlation_replicates	0.979668	0.979668
spikein_reads	9,352	7,556
percent_spikeins	0.00010	0.00009
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1939	1940

Data Submission Information

	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-42	BGKcLV30-42	BGKcLV30-42	BGKcLV30-42
ENCODE_alias	brenton-graveley:RNPC3-BGKcLV30	brenton-graveley:RNPC3-BGKcLV30-41	brenton-graveley:L-RNPC3-BGKcLV30-41	brenton-graveley:RNPC3-BGKcLV30-41_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNPC3-BGKcLV30-41_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNPC3-BGKcLV30-K562	brenton-graveley:RNPC3-BGKcLV30-42	brenton-graveley:L-RNPC3-BGKcLV30-42	brenton-graveley:RNPC3-BGKcLV30-42_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNPC3-BGKcLV30-42_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR631NIZ	ENCBS692XVD	ENCLB840RVK	ENCFF281HEC	ENCFF691OZL	ENCSR603LHS	ENCBS813IWN	ENCLB972SDZ	ENCFF186PDD	ENCFF573EON
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	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-41	BGKcLV30-42	BGKcLV30-42	BGKcLV30-42	BGKcLV30-42
Sample Name	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-41	RNPC3-BGKcLV30-42	RNPC3-BGKcLV30-42	RNPC3-BGKcLV30-42	RNPC3-BGKcLV30-42
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		RNPC3-BGKcLV30-41.pdf	L-RNPC3-BGKcLV30-41.pdf				RNPC3-BGKcLV30-42.pdf	L-RNPC3-BGKcLV30-42.pdf
ID	5875	5943	6015	6087	6159	6197	5944	6016	6088	6160

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
RNPC3-BGKcLV30-41_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1939	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	5867
RNPC3-BGKcLV30-41_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1939	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	5897
RNPC3-BGKcLV30-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1939					GRCh38	V40	RNPC3-BGKcLV30-41_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNPC3-BGKcLV30-41_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18768
RNPC3-BGKcLV30-41_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	1939					GRCh38	V40	RNPC3-BGKcLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	18798
RNPC3-BGKcLV30-41_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	1939					GRCh38	V40	RNPC3-BGKcLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	18828
RNPC3-BGKcLV30-41_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	1939					GRCh38	V40	RNPC3-BGKcLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	18858
RNPC3-BGKcLV30-41_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	1939					GRCh38	V40	RNPC3-BGKcLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	18888
RNPC3-BGKcLV30-41_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1939					GRCh38	V40	RNPC3-BGKcLV30-41_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNPC3-BGKcLV30-41_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18918
RNPC3-BGKcLV30-42_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1940	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	5868
RNPC3-BGKcLV30-42_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1940	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	5898
RNPC3-BGKcLV30-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1940					GRCh38	V40	RNPC3-BGKcLV30-42_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNPC3-BGKcLV30-42_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18769
RNPC3-BGKcLV30-42_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	1940					GRCh38	V40	RNPC3-BGKcLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	18799
RNPC3-BGKcLV30-42_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	1940					GRCh38	V40	RNPC3-BGKcLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	18829
RNPC3-BGKcLV30-42_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	1940					GRCh38	V40	RNPC3-BGKcLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	18859
RNPC3-BGKcLV30-42_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	1940					GRCh38	V40	RNPC3-BGKcLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	18889
RNPC3-BGKcLV30-42_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1940					GRCh38	V40	RNPC3-BGKcLV30-42_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNPC3-BGKcLV30-42_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18919