SNRPC RNA-Seq in K562

General Information


RBP	SNRPC
Cell_Line	K562
Method	CRISPR
Exp_Name	SNRPC-BGKcLV23-K562
ENCODE_series_ID	ENCSR027HBT
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR840JRU
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	SNRPC-BGKcLV23-61
Rep2	SNRPC-BGKcLV23-62
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	18.0
Rep2_qPCR	5.0
Rep1_WB	68.1
Rep2_WB	68.7613052
Antibody Cat#	A303-947A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB311PIH
Status	Released
Project	ENCODE4
ID	35

Experiment Information (Status: Released)

	BGKcLV23-61	BGKcLV23-62
idx	847	848
TRCN#_or_BGC#	BGC#0000548	BGC#0000548
shRNA_or_gRNA_sequence	TCAAACTTACCAGGTCCCAC	TCAAACTTACCAGGTCCCAC
PAM	TGG	TGG
Name	SNRPC_84	SNRPC_84
Sample_ID	BGKcLV23-61	BGKcLV23-62
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	SNRPC	SNRPC
qPCR_result	18.0	5.0
Ave_qPCR	11.5
RT-qPCR_primer-F	GATGATGCCAGTGGGACCT
RT-qPCR_primer-R	GGGCAGGAGGTCTCATCATT
protein_conc	2546	2919
WB_result	68.1	68.7613052
Ave_WB	68.5
WB_DONE_date	12/14/20	LICOR
MW	17.4KD
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	4979	4980

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

	BGKcLV23-61	BGKcLV23-62
Sample_ID	BGKcLV23-61	BGKcLV23-62
Sample Name
Sample Name	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-62
RBP	SNRPC	SNRPC
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7459	7460

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-61	BGKcLV23-62
Sample #	61	62
Sample Name	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-62
Sample_Name_Alias
Index Well Position	E08	F08
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	292	291
Peak_Molarity	118.00	144.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/E8.png	DNA_Library_set46/set1/F8.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set46/set2/E12.png	RNA_Library_set46/set2/F12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-61	BGKcLV23-62
RBP	SNRPC	SNRPC
Batch_ID	BGKcLV23	BGKcLV23
WB_result	52.600	54.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1436	1437

Sequencing Information

	BGKcLV23-61	BGKcLV23-62
Sample_ID	BGKcLV23-61	BGKcLV23-62
Sample Name	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-62
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	149,973,248	147,628,826
total_aligned_reads	139,009,974	140,666,160
unique_aligned_reads	126,326,274	128,112,650
percent_uniqueAligned	0.84233	0.86780
correlation_replicates	0.998249	0.998249
spikein_reads	46,796	50,952
percent_spikeins	0.00031	0.00035
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	542	543

Data Submission Information

	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-62	BGKcLV23-62	BGKcLV23-62	BGKcLV23-62
ENCODE_alias	brenton-graveley:SNRPC-BGKcLV23	brenton-graveley:SNRPC-BGKcLV23-61	brenton-graveley:L-SNRPC-BGKcLV23-61	brenton-graveley:SNRPC-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNRPC-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNRPC-BGKcLV23-K562	brenton-graveley:SNRPC-BGKcLV23-62	brenton-graveley:L-SNRPC-BGKcLV23-62	brenton-graveley:SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR840JRU	ENCBS368CQY	ENCLB619QEM	ENCFF525VQG	ENCFF013GFT	ENCSR027HBT	ENCBS883NPJ	ENCLB965UGR	ENCFF985LPX	ENCFF895OPR
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	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-61	BGKcLV23-62	BGKcLV23-62	BGKcLV23-62	BGKcLV23-62
Sample Name	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-61	SNRPC-BGKcLV23-62	SNRPC-BGKcLV23-62	SNRPC-BGKcLV23-62	SNRPC-BGKcLV23-62
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
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		SNRPC-BGKcLV23-61.pdf	L-SNRPC-BGKcLV23-61.pdf				SNRPC-BGKcLV23-62.pdf	L-SNRPC-BGKcLV23-62.pdf
ID	2425	2487	2551	2645	2679	7334	2488	2552	2646	2680

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-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	542	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1408
SNRPC-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	542	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1472
SNRPC-BGKcLV23-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	542					GRCh38	V40	SNRPC-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25311
SNRPC-BGKcLV23-61_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	542					GRCh38	V40	SNRPC-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGKcLV23-61_CGGAACTG+TCGTAGTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25345
SNRPC-BGKcLV23-61_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	542					GRCh38	V40	SNRPC-BGKcLV23-61/Aligned.sortedByCoord.out.bam		ENCORE2	26149
SNRPC-BGKcLV23-61_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	542					GRCh38	V40	SNRPC-BGKcLV23-61/Aligned.sortedByCoord.out.bam		ENCORE2	26183
SNRPC-BGKcLV23-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	542					GRCh38	V40	SNRPC-BGKcLV23-61/Aligned.sortedByCoord.out.bam		ENCORE2	26217
SNRPC-BGKcLV23-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	542					GRCh38	V40	SNRPC-BGKcLV23-61/Aligned.sortedByCoord.out.bam		ENCORE2	26251
SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	543	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1409
SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	543	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1473
SNRPC-BGKcLV23-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	543					GRCh38	V40	SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25312
SNRPC-BGKcLV23-62_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	543					GRCh38	V40	SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,SNRPC-BGKcLV23-62_TAAGGTCA+CTACGACA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25346
SNRPC-BGKcLV23-62_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	543					GRCh38	V40	SNRPC-BGKcLV23-62/Aligned.sortedByCoord.out.bam		ENCORE2	26150
SNRPC-BGKcLV23-62_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	543					GRCh38	V40	SNRPC-BGKcLV23-62/Aligned.sortedByCoord.out.bam		ENCORE2	26184
SNRPC-BGKcLV23-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	543					GRCh38	V40	SNRPC-BGKcLV23-62/Aligned.sortedByCoord.out.bam		ENCORE2	26218
SNRPC-BGKcLV23-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	543					GRCh38	V40	SNRPC-BGKcLV23-62/Aligned.sortedByCoord.out.bam		ENCORE2	26252