SLTM RNA-Seq in HepG2

General Information


RBP	SLTM
Cell_Line	HepG2
Method	shRNA
Exp_Name	SLTM-BGHLV14-HepG2
ENCODE_series_ID	ENCSR284QBD
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR185JGT
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	SLTM_BGHLV14-47
Rep2	SLTM_BGHLV14-48
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	80.9
Rep2_qPCR	84.4
Rep1_WB	86.3
Rep2_WB	69.3
Antibody Cat#	A302-834A
Antibody Lot#	A302-834A
Antibody DCC ID	ENCAB526HXQ
Status	Released
Project	ENCODE3
ID	404

Experiment Information (Status: Released)

	BGHLV14-47	BGHLV14-48
idx	143	144
TRCN#_or_BGC#	TRCN0000135106	TRCN0000135106
shRNA_or_gRNA_sequence	CCCAACATTCAAGTAACGCAT	CCCAACATTCAAGTAACGCAT
PAM
Name	SLTM	SLTM
Sample_ID	BGHLV14-47	BGHLV14-48
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	SLTM	SLTM
qPCR_result	80.9	84.4
Ave_qPCR	82.7
RT-qPCR_primer-F	AGAGGAGTCATCACAGACCGA
RT-qPCR_primer-R	CTTTCCTTGGTCCGCTTGT
protein_conc	3382	3433
WB_result	86.3	69.3
Ave_WB	77.8
WB_DONE_date	5/27/2015
MW	115kDa
IP	1	1
antibody_Cat#	A302-834A	A302-834A
Antibody DCC ID	ENCAB526HXQ	ENCAB526HXQ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	60.3	0
Rep2_TPM	51.1	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2206	2207

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SLTM	Product_ID: A302-834A Lot_ID: 1 Source: Bethyl Labs Target Name: SLTM-human

Experiment Status

	BGHLV14-47	BGHLV14-48
Sample_ID	BGHLV14-47	BGHLV14-48
Sample Name	SLTM_BGHLV14-47	SLTM_BGHLV14-48
Sample Name	SLTM_BGHLV14-47	SLTM_BGHLV14-48
RBP	SLTM	SLTM
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	532	533

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-47	BGHLV14-48
Sample #
Sample Name	SLTM-BGHLV14-47	SLTM-BGHLV14-48
Sample_Name_Alias	SLTM_BGHLV14-47	SLTM_BGHLV14-48
Index Well Position	S01	S02
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/C1.png	DNA_Library_LV13-14/set2/D1.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C9.png	RNA_Library_LV13-14-16/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-47	BGHLV14-48
RBP	SLTM	SLTM
Batch_ID	BGHLV14	BGHLV14
WB_result	86.300	69.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2216	2217

Sequencing Information

	BGHLV14-47	BGHLV14-48
Sample_ID	BGHLV14-47	BGHLV14-48
Sample Name	SLTM_BGHLV14-47	SLTM_BGHLV14-48
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	53,870,000	47,240,000
total_aligned_reads	49,868,794	43,002,006
unique_aligned_reads	47,104,278	40,636,550
percent_uniqueAligned	0.87441	0.86021
correlation_replicates	0.988135	0.988135
spikein_reads	371,016	305,056
percent_spikeins	0.00689	0.00646
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	858	859

Data Submission Information

	BGHLV14-47	BGHLV14-47
ENCODE_alias	brenton-graveley:SLTM_BGHLV14	brenton-graveley:SLTM-BGHLV14-HepG2
ENCODE_accession	ENCSR185JGT	ENCSR284QBD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-47	BGHLV14-47
Sample Name	SLTM_BGHLV14-47	SLTM_BGHLV14-47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2815	6950

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
SLTM_BGHLV14-47_ATCACG_L006_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	858	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13824
SLTM_BGHLV14-47_ATCACG_L006_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	858	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13886
SLTM_BGHLV14-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	858					GRCh38	V40	SLTM_BGHLV14-47_ATCACG_L006_R1_001.fastq.gz,SLTM_BGHLV14-47_ATCACG_L006_R2_001.fastq.gz		ENCORE2	13948
SLTM_BGHLV14-47_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	858					GRCh38	V40	SLTM_BGHLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	14010
SLTM_BGHLV14-47_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	858					GRCh38	V40	SLTM_BGHLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	14072
SLTM_BGHLV14-47_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	858					GRCh38	V40	SLTM_BGHLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	14134
SLTM_BGHLV14-47_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	858					GRCh38	V40	SLTM_BGHLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	14196
SLTM_BGHLV14-47_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	858					GRCh38	V40	SLTM_BGHLV14-47_ATCACG_L006_R1_001.fastq.gz,SLTM_BGHLV14-47_ATCACG_L006_R2_001.fastq.gz		ENCORE2	14258
SLTM_BGHLV14-48_CGATGT_L006_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	859	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13825
SLTM_BGHLV14-48_CGATGT_L006_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	859	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13887
SLTM_BGHLV14-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	859					GRCh38	V40	SLTM_BGHLV14-48_CGATGT_L006_R1_001.fastq.gz,SLTM_BGHLV14-48_CGATGT_L006_R2_001.fastq.gz		ENCORE2	13949
SLTM_BGHLV14-48_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	859					GRCh38	V40	SLTM_BGHLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	14011
SLTM_BGHLV14-48_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	859					GRCh38	V40	SLTM_BGHLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	14073
SLTM_BGHLV14-48_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	859					GRCh38	V40	SLTM_BGHLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	14135
SLTM_BGHLV14-48_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	859					GRCh38	V40	SLTM_BGHLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	14197
SLTM_BGHLV14-48_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	859					GRCh38	V40	SLTM_BGHLV14-48_CGATGT_L006_R1_001.fastq.gz,SLTM_BGHLV14-48_CGATGT_L006_R2_001.fastq.gz		ENCORE2	14259