SNRNP200 RNA-Seq in HepG2

General Information


RBP	SNRNP200
Cell_Line	HepG2
Method	shRNA
Exp_Name	SNRNP200-BGHLV26-HepG2
ENCODE_series_ID	ENCSR166KII
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR003LSA
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	SNRNP200_BGHLV26_57
Rep2	SNRNP200_BGHLV26_58
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	69.7
Rep2_qPCR	61.0
Rep1_WB	54.1
Rep2_WB	66.9
Antibody Cat#	A303-453A
Antibody Lot#	A303-453A
Antibody DCC ID	ENCAB770ROF
Status	Released
Project	ENCODE3
ID	637

Experiment Information (Status: Released)

	BGHLV26-57	BGHLV26-58
idx	613	614
TRCN#_or_BGC#	TRCN0000051832	TRCN0000051832
shRNA_or_gRNA_sequence	CCAATGATACAGTGCAGACTT	CCAATGATACAGTGCAGACTT
PAM
Name	SNRNP200	SNRNP200
Sample_ID	BGHLV26-57	BGHLV26-58
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	SNRNP200	SNRNP200
qPCR_result	69.7	61.0
Ave_qPCR	65.4
RT-qPCR_primer-F	agctgccacacttcacctct
RT-qPCR_primer-R	gttccgttcttcatcctcca
protein_conc	4765	4221
WB_result	54.1	66.9
Ave_WB	60.5
WB_DONE_date	7/6/2015
MW	244kDa
IP	1	1
antibody_Cat#	A303-453A	A303-453A
Antibody DCC ID	ENCAB770ROF	ENCAB770ROF
submitted_to_DCC_date	8/6/2015
Rep1_TPM	80.3	0
Rep2_TPM	67.5	0
Action
Library_start_date	9/8/2015	9/8/2015
repeat_library
Note	x	x
ID	2700	2701

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SNRNP200	Product_ID: A303-453A Lot_ID: 1 Source: Bethyl Labs Target Name: SNRNP200-human

Experiment Status

	BGHLV26-57	BGHLV26-58
Sample_ID	BGHLV26-57	BGHLV26-58
Sample Name	SNRNP200_BGHLV26_57	SNRNP200_BGHLV26_58
Sample Name	SNRNP200_BGHLV26_57	SNRNP200_BGHLV26_58
RBP	SNRNP200	SNRNP200
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	958	959

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-57	BGHLV26-58
Sample #
Sample Name	SNRNP200-BGHLV26-57	SNRNP200-BGHLV26-58
Sample_Name_Alias	SNRNP200_BGHLV26_57	SNRNP200_BGHLV26_58
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/C10.png	DNA_Library_LV24-25-26/set1/D10.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/E3.png	RNA_Library_LV26-27-28-29/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-57	BGHLV26-58
RBP	SNRNP200	SNRNP200
Batch_ID	BGHLV26	BGHLV26
WB_result	54.100	66.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2646	2647

Sequencing Information

	BGHLV26-57	BGHLV26-58
Sample_ID	BGHLV26-57	BGHLV26-58
Sample Name	SNRNP200_BGHLV26_57	SNRNP200_BGHLV26_58
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	84,709,790	54,209,770
total_aligned_reads	73,813,740	48,395,222
unique_aligned_reads	69,429,388	45,665,584
percent_uniqueAligned	0.81961	0.84239
correlation_replicates	0.997255	0.997255
spikein_reads	224,172	145,088
percent_spikeins	0.00265	0.00268
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1288	1289

Data Submission Information

	BGHLV26-57	BGHLV26-57
ENCODE_alias	brenton-graveley:SNRNP200_BGHLV26	brenton-graveley:SNRNP200-BGHLV26-HepG2
ENCODE_accession	ENCSR003LSA	ENCSR166KII
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-57	BGHLV26-57
Sample Name	SNRNP200_BGHLV26_57	SNRNP200_BGHLV26_57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3026	6958

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
SNRNP200_BGHLV26_57_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1288	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19832
SNRNP200_BGHLV26_57_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1288	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19854
SNRNP200_BGHLV26_57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1288					GRCh38	V40	SNRNP200_BGHLV26_57_1.fastq.gz,SNRNP200_BGHLV26_57_2.fastq.gz		ENCORE2	19876
SNRNP200_BGHLV26_57_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1288					GRCh38	V40	SNRNP200_BGHLV26_57/Aligned.sortedByCoord.out.bam		ENCORE2	19898
SNRNP200_BGHLV26_57_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1288					GRCh38	V40	SNRNP200_BGHLV26_57/Aligned.sortedByCoord.out.bam		ENCORE2	19920
SNRNP200_BGHLV26_57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1288					GRCh38	V40	SNRNP200_BGHLV26_57/Aligned.sortedByCoord.out.bam		ENCORE2	19942
SNRNP200_BGHLV26_57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1288					GRCh38	V40	SNRNP200_BGHLV26_57/Aligned.sortedByCoord.out.bam		ENCORE2	19964
SNRNP200_BGHLV26_57_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1288					GRCh38	V40	SNRNP200_BGHLV26_57_1.fastq.gz,SNRNP200_BGHLV26_57_2.fastq.gz		ENCORE2	20672
SNRNP200_BGHLV26_58_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1289	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19833
SNRNP200_BGHLV26_58_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1289	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19855
SNRNP200_BGHLV26_58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1289					GRCh38	V40	SNRNP200_BGHLV26_58_1.fastq.gz,SNRNP200_BGHLV26_58_2.fastq.gz		ENCORE2	19877
SNRNP200_BGHLV26_58_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1289					GRCh38	V40	SNRNP200_BGHLV26_58/Aligned.sortedByCoord.out.bam		ENCORE2	19899
SNRNP200_BGHLV26_58_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1289					GRCh38	V40	SNRNP200_BGHLV26_58/Aligned.sortedByCoord.out.bam		ENCORE2	19921
SNRNP200_BGHLV26_58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1289					GRCh38	V40	SNRNP200_BGHLV26_58/Aligned.sortedByCoord.out.bam		ENCORE2	19943
SNRNP200_BGHLV26_58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1289					GRCh38	V40	SNRNP200_BGHLV26_58/Aligned.sortedByCoord.out.bam		ENCORE2	19965
SNRNP200_BGHLV26_58_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1289					GRCh38	V40	SNRNP200_BGHLV26_58_1.fastq.gz,SNRNP200_BGHLV26_58_2.fastq.gz		ENCORE2	20673