SNRNP70 RNA-Seq in HepG2

General Information


RBP	SNRNP70
Cell_Line	HepG2
Method	shRNA
Exp_Name	SNRNP70-BGHLV35-HepG2
ENCODE_series_ID	ENCSR019AYN
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR635BOO
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	SNRNP70_BGHLV35-45
Rep2	SNRNP70_BGHLV35-46
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	68.5
Rep2_qPCR	65.0
Rep1_WB	81.2
Rep2_WB	78.8
Antibody Cat#	sc-9571
Antibody Lot#	sc-9571
Antibody DCC ID	ENCAB649NDD
Status	Released
Project	ENCODE3
ID	739

Experiment Information (Status: Released)

	BGHLV35-45	BGHLV35-46
idx	901	902
TRCN#_or_BGC#	TRCN0000000012	TRCN0000000012
shRNA_or_gRNA_sequence	TCCGCTTACAAACACGCAGAT	TCCGCTTACAAACACGCAGAT
PAM
Name	SNRNP70	SNRNP70
Sample_ID	BGHLV35-45	BGHLV35-46
transduction_Date	4/29/16	4/29/16
days
RBP_name	SNRNP70	SNRNP70
qPCR_result	68.5	65.0
Ave_qPCR	66.7
RT-qPCR_primer-F	AAGATTGATGGCAGGAGGGT
RT-qPCR_primer-R	ACATCAGCCCCTCCTCTTCT
protein_conc	4010	3424
WB_result	81.2	78.8
Ave_WB	80.0
WB_DONE_date	5/23/16
MW	63kDa	Goat antibody
IP		FU'S
antibody_Cat#	sc-9571	sc-9571
Antibody DCC ID	ENCAB649NDD
submitted_to_DCC_date	10/26/16
Rep1_TPM	38.6	38.6
Rep2_TPM	47.6	47.6
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2990	2991

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SNRNP70	Product_ID: sc-9571 Lot_ID: B2409 Source: Santa Cruz Biotech Target Name: SNRNP70-human

Experiment Status

	BGHLV35-45	BGHLV35-46
Sample_ID	BGHLV35-45	BGHLV35-46
Sample Name	SNRNP70_BGHLV35-45	SNRNP70_BGHLV35-46
Sample Name	SNRNP70_BGHLV35-45	SNRNP70_BGHLV35-46
RBP	SNRNP70	SNRNP70
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1269	1270

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-45	BGHLV35-46
Sample #
Sample Name	SNRNP70-BGHLV35-45	SNRNP70-BGHLV35-46
Sample_Name_Alias	SNRNP70_BGHLV35-45	SNRNP70_BGHLV35-46
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set1/E3.png	DNA_Library_LV35/set1/F3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/E3.png	RNA_Library_LV35_LV36/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-45	BGHLV35-46
RBP	SNRNP70	SNRNP70
Batch_ID	BGHLV35	BGHLV35
WB_result	81.200	78.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2954	2955

Sequencing Information

	BGHLV35-45	BGHLV35-46
Sample_ID	BGHLV35-45	BGHLV35-46
Sample Name	SNRNP70_BGHLV35-45	SNRNP70_BGHLV35-46
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	79,541,538	92,000,202
total_aligned_reads	62,229,908	71,196,844
unique_aligned_reads	58,548,644	66,807,930
percent_uniqueAligned	0.73608	0.72617
correlation_replicates	0.997757	0.997757
spikein_reads	117,420	130,166
percent_spikeins	0.00148	0.00141
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1603	1604

Data Submission Information

	BGHLV35-45	BGHLV35-45
ENCODE_alias	brenton-graveley:SNRNP70_BGHLV35	brenton-graveley:SNRNP70-BGHLV35-HepG2
ENCODE_accession	ENCSR635BOO	ENCSR019AYN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-45	BGHLV35-45
Sample Name	SNRNP70_BGHLV35-45	SNRNP70_BGHLV35-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3174	6960

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
SNRNP70_BGHLV35-45_CGTACG_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1603	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21702
SNRNP70_BGHLV35-45_CGTACG_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1603	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21728
SNRNP70_BGHLV35-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1603					GRCh38	V40	SNRNP70_BGHLV35-45_CGTACG_L007_001.R1.fastq.gz,SNRNP70_BGHLV35-45_CGTACG_L007_001.R2.fastq.gz		ENCORE2	21754
SNRNP70_BGHLV35-45_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1603					GRCh38	V40	SNRNP70_BGHLV35-45/Aligned.sortedByCoord.out.bam		ENCORE2	21780
SNRNP70_BGHLV35-45_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1603					GRCh38	V40	SNRNP70_BGHLV35-45/Aligned.sortedByCoord.out.bam		ENCORE2	21806
SNRNP70_BGHLV35-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1603					GRCh38	V40	SNRNP70_BGHLV35-45/Aligned.sortedByCoord.out.bam		ENCORE2	21832
SNRNP70_BGHLV35-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1603					GRCh38	V40	SNRNP70_BGHLV35-45/Aligned.sortedByCoord.out.bam		ENCORE2	21858
SNRNP70_BGHLV35-45_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1603					GRCh38	V40	SNRNP70_BGHLV35-45_CGTACG_L007_001.R1.fastq.gz,SNRNP70_BGHLV35-45_CGTACG_L007_001.R2.fastq.gz		ENCORE2	21884
SNRNP70_BGHLV35-46_GAGTGG_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1604	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21703
SNRNP70_BGHLV35-46_GAGTGG_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1604	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21729
SNRNP70_BGHLV35-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1604					GRCh38	V40	SNRNP70_BGHLV35-46_GAGTGG_L007_001.R1.fastq.gz,SNRNP70_BGHLV35-46_GAGTGG_L007_001.R2.fastq.gz		ENCORE2	21755
SNRNP70_BGHLV35-46_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1604					GRCh38	V40	SNRNP70_BGHLV35-46/Aligned.sortedByCoord.out.bam		ENCORE2	21781
SNRNP70_BGHLV35-46_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1604					GRCh38	V40	SNRNP70_BGHLV35-46/Aligned.sortedByCoord.out.bam		ENCORE2	21807
SNRNP70_BGHLV35-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1604					GRCh38	V40	SNRNP70_BGHLV35-46/Aligned.sortedByCoord.out.bam		ENCORE2	21833
SNRNP70_BGHLV35-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1604					GRCh38	V40	SNRNP70_BGHLV35-46/Aligned.sortedByCoord.out.bam		ENCORE2	21859
SNRNP70_BGHLV35-46_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1604					GRCh38	V40	SNRNP70_BGHLV35-46_GAGTGG_L007_001.R1.fastq.gz,SNRNP70_BGHLV35-46_GAGTGG_L007_001.R2.fastq.gz		ENCORE2	21885