SNRPC RNA-Seq in HepG2

General Information


RBP	SNRPC
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SNRPC-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR424ALD
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR005RUR
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	SNRPC-BGHcLV22-53
Rep2	SNRPC-BGHcLV22-54
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	75.6
Rep2_WB	73.9
Antibody Cat#	A303-947A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB311PIH
Status	Released
Project	ENCODE4
ID	49

Experiment Information (Status: Released)

	BGHcLV22-53	BGHcLV22-54
idx	646	647
TRCN#_or_BGC#	BGC#0000548	BGC#0000548
shRNA_or_gRNA_sequence	TCAAACTTACCAGGTCCCAC	TCAAACTTACCAGGTCCCAC
PAM	TGG	TGG
Name	SNRPC_84	SNRPC_84
Sample_ID	BGHcLV22-53	BGHcLV22-54
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	SNRPC	SNRPC
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GATGATGCCAGTGGGACCT
RT-qPCR_primer-R	GGGCAGGAGGTCTCATCATT
protein_conc	2724	2425
WB_result	75.6	73.9
Ave_WB	74.7
WB_DONE_date	9/9/20
MW	17.4kDa
IP	Rabbit / I
antibody_Cat#	A303-947A	LOT# 1
Antibody DCC ID	ENCAB311PIH
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6801	6802

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SNRPC	Product_ID: A303-947A Lot_ID: 1 Source: Bethyl Labs Target Name: SNRPC-human

Experiment Status

	BGHcLV22-53	BGHcLV22-54
Sample_ID	BGHcLV22-53	BGHcLV22-54
Sample Name
Sample Name	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-54
RBP	SNRPC	SNRPC
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7391	7392

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-53	BGHcLV22-54
Sample #	27	28
Sample Name	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-54
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	301	296
Peak_Molarity	125.00	149.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/C4.png	DNA_Library_set46/set1/D4.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set46/set1/C12.png	RNA_Library_set46/set1/D12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-53	BGHcLV22-54
RBP	SNRPC	SNRPC
Batch_ID	BGHcLV22	BGHcLV22
WB_result	75.600	73.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1402	1403

Sequencing Information

	BGHcLV22-53	BGHcLV22-54
Sample_ID	BGHcLV22-53	BGHcLV22-54
Sample Name	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-54
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	156,108,648	226,316,618
total_aligned_reads	137,415,262	198,923,248
unique_aligned_reads	128,809,754	186,384,204
percent_uniqueAligned	0.82513	0.82356
correlation_replicates	0.999111	0.999111
spikein_reads	66,550	57,134
percent_spikeins	0.00043	0.00025
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	508	509

Data Submission Information

	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-54	BGHcLV22-54	BGHcLV22-54	BGHcLV22-54
ENCODE_alias	brenton-graveley:SNRPC-BGHcLV22	brenton-graveley:SNRPC-BGHcLV22-53	brenton-graveley:L-SNRPC-BGHcLV22-53	brenton-graveley:SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNRPC-BGHcLV22-HepG2	brenton-graveley:SNRPC-BGHcLV22-54	brenton-graveley:L-SNRPC-BGHcLV22-54	brenton-graveley:SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR005RUR	ENCBS909DXM	ENCLB450TMT	ENCFF184XJG	ENCFF050LCF	ENCSR424ALD	ENCBS360XRD	ENCLB874EUT	ENCFF919AVX	ENCFF225XYU
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	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-53	BGHcLV22-54	BGHcLV22-54	BGHcLV22-54	BGHcLV22-54
Sample Name	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-53	SNRPC-BGHcLV22-54	SNRPC-BGHcLV22-54	SNRPC-BGHcLV22-54	SNRPC-BGHcLV22-54
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		SNRPC-BGHcLV22-53.pdf	L-SNRPC-BGHcLV22-53.pdf				SNRPC-BGHcLV22-54.pdf	L-SNRPC-BGHcLV22-54.pdf
ID	2408	2453	2517	2581	2611	7333	2454	2518	2582	2612

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
SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	508	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1374
SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	508	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1438
SNRPC-BGHcLV22-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	508					GRCh38	V40	SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25277
SNRPC-BGHcLV22-53_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	508					GRCh38	V40	SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGHcLV22-53_CTTGGTAT+GGACTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25375
SNRPC-BGHcLV22-53_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	508					GRCh38	V40	SNRPC-BGHcLV22-53/Aligned.sortedByCoord.out.bam		ENCORE2	26025
SNRPC-BGHcLV22-53_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	508					GRCh38	V40	SNRPC-BGHcLV22-53/Aligned.sortedByCoord.out.bam		ENCORE2	26055
SNRPC-BGHcLV22-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	508					GRCh38	V40	SNRPC-BGHcLV22-53/Aligned.sortedByCoord.out.bam		ENCORE2	26085
SNRPC-BGHcLV22-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	508					GRCh38	V40	SNRPC-BGHcLV22-53/Aligned.sortedByCoord.out.bam		ENCORE2	26115
SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	509	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1375
SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	509	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1439
SNRPC-BGHcLV22-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	509					GRCh38	V40	SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25278
SNRPC-BGHcLV22-54_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	509					GRCh38	V40	SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGHcLV22-54_TCCAACGC+AAGTCCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25376
SNRPC-BGHcLV22-54_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	509					GRCh38	V40	SNRPC-BGHcLV22-54/Aligned.sortedByCoord.out.bam		ENCORE2	26026
SNRPC-BGHcLV22-54_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	509					GRCh38	V40	SNRPC-BGHcLV22-54/Aligned.sortedByCoord.out.bam		ENCORE2	26056
SNRPC-BGHcLV22-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	509					GRCh38	V40	SNRPC-BGHcLV22-54/Aligned.sortedByCoord.out.bam		ENCORE2	26086
SNRPC-BGHcLV22-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	509					GRCh38	V40	SNRPC-BGHcLV22-54/Aligned.sortedByCoord.out.bam		ENCORE2	26116