SND1 RNA-Seq in HepG2

General Information


RBP	SND1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SND1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR332BHS
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR398LZW
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	SND1_BGHLV14-51
Rep2	SND1_BGHLV14-52
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	88.1
Rep2_qPCR	94.1
Rep1_WB	80.4
Rep2_WB	81.4
Antibody Cat#	A302-883A
Antibody Lot#	A302-883A
Antibody DCC ID	ENCAB162GME
Status	Released
Project	ENCODE3
ID	406

Experiment Information (Status: Released)

	BGHLV14-51	BGHLV14-52
idx	147	148
TRCN#_or_BGC#	TRCN0000049653	TRCN0000049653
shRNA_or_gRNA_sequence	CCCACAGCTAATTTGGACCAA	CCCACAGCTAATTTGGACCAA
PAM
Name	SND1	SND1
Sample_ID	BGHLV14-51	BGHLV14-52
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	SND1	SND1
qPCR_result	88.1	94.1
Ave_qPCR	91.1
RT-qPCR_primer-F	GTGAAGGAAGGGCTGGTCAT
RT-qPCR_primer-R	CGCTCTTGGCTGACTCTTG
protein_conc	3403	3200
WB_result	80.4	81.4
Ave_WB	80.9
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A302-883A	A302-883A
Antibody DCC ID	ENCAB162GME	ENCAB162GME
submitted_to_DCC_date	5/6/2015
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2210	2211

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SND1	Product_ID: A302-883A Lot_ID: 1 Source: Bethyl Labs Target Name: SND1-human

Experiment Status

	BGHLV14-51	BGHLV14-52
Sample_ID	BGHLV14-51	BGHLV14-52
Sample Name	SND1_BGHLV14-51	SND1_BGHLV14-52
Sample Name	SND1_BGHLV14-51	SND1_BGHLV14-52
RBP	SND1	SND1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	536	537

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-51	BGHLV14-52
Sample #
Sample Name	SND1-BGHLV14-51	SND1-BGHLV14-52
Sample_Name_Alias	SND1_BGHLV14-51	SND1_BGHLV14-52
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set2/G1.png	DNA_Library_LV13-14/set2/H1.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G9.png	RNA_Library_LV13-14-16/set1/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-51	BGHLV14-52
RBP	SND1	SND1
Batch_ID	BGHLV14	BGHLV14
WB_result	80.400	81.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2220	2221

Sequencing Information

	BGHLV14-51	BGHLV14-52
Sample_ID	BGHLV14-51	BGHLV14-52
Sample Name	SND1_BGHLV14-51	SND1_BGHLV14-52
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	47,750,000	48,020,000
total_aligned_reads	43,733,364	44,134,502
unique_aligned_reads	41,337,752	41,686,816
percent_uniqueAligned	0.86571	0.86811
correlation_replicates	0.998882	0.998882
spikein_reads	278,830	218,634
percent_spikeins	0.00584	0.00455
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	862	863

Data Submission Information

	BGHLV14-51	BGHLV14-51
ENCODE_alias	brenton-graveley:SND1_BGHLV14	brenton-graveley:SND1-BGHLV14-HepG2
ENCODE_accession	ENCSR398LZW	ENCSR332BHS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-51	BGHLV14-51
Sample Name	SND1_BGHLV14-51	SND1_BGHLV14-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2817	6956

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
SND1_BGHLV14-51_ACAGTG_L006_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	862	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13828
SND1_BGHLV14-51_ACAGTG_L006_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	862	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13890
SND1_BGHLV14-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	862					GRCh38	V40	SND1_BGHLV14-51_ACAGTG_L006_R1_001.fastq.gz,SND1_BGHLV14-51_ACAGTG_L006_R2_001.fastq.gz		ENCORE2	13952
SND1_BGHLV14-51_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	862					GRCh38	V40	SND1_BGHLV14-51/Aligned.sortedByCoord.out.bam		ENCORE2	14014
SND1_BGHLV14-51_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	862					GRCh38	V40	SND1_BGHLV14-51/Aligned.sortedByCoord.out.bam		ENCORE2	14076
SND1_BGHLV14-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	862					GRCh38	V40	SND1_BGHLV14-51/Aligned.sortedByCoord.out.bam		ENCORE2	14138
SND1_BGHLV14-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	862					GRCh38	V40	SND1_BGHLV14-51/Aligned.sortedByCoord.out.bam		ENCORE2	14200
SND1_BGHLV14-51_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	862					GRCh38	V40	SND1_BGHLV14-51_ACAGTG_L006_R1_001.fastq.gz,SND1_BGHLV14-51_ACAGTG_L006_R2_001.fastq.gz		ENCORE2	14262
SND1_BGHLV14-52_GCCAAT_L006_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	863	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13829
SND1_BGHLV14-52_GCCAAT_L006_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	863	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13891
SND1_BGHLV14-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	863					GRCh38	V40	SND1_BGHLV14-52_GCCAAT_L006_R1_001.fastq.gz,SND1_BGHLV14-52_GCCAAT_L006_R2_001.fastq.gz		ENCORE2	13953
SND1_BGHLV14-52_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	863					GRCh38	V40	SND1_BGHLV14-52/Aligned.sortedByCoord.out.bam		ENCORE2	14015
SND1_BGHLV14-52_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	863					GRCh38	V40	SND1_BGHLV14-52/Aligned.sortedByCoord.out.bam		ENCORE2	14077
SND1_BGHLV14-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	863					GRCh38	V40	SND1_BGHLV14-52/Aligned.sortedByCoord.out.bam		ENCORE2	14139
SND1_BGHLV14-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	863					GRCh38	V40	SND1_BGHLV14-52/Aligned.sortedByCoord.out.bam		ENCORE2	14201
SND1_BGHLV14-52_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	863					GRCh38	V40	SND1_BGHLV14-52_GCCAAT_L006_R1_001.fastq.gz,SND1_BGHLV14-52_GCCAAT_L006_R2_001.fastq.gz		ENCORE2	14263