RTF1 RNA-Seq in HepG2

General Information


RBP	RTF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	RTF1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR331QUE
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR906WTM
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	RTF1_BGHLV14-45
Rep2	RTF1_BGHLV14-46
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	57.4
Rep2_qPCR	57.3
Rep1_WB	72.0
Rep2_WB	69.4
Antibody Cat#	A300-178A
Antibody Lot#	A300-178A
Antibody DCC ID	ENCAB664NPT
Status	Released
Project	ENCODE3
ID	403

Experiment Information (Status: Released)

	BGHLV14-45	BGHLV14-45	BGHLV14-45	BGHLV14-46	BGHLV14-46	BGHLV14-46
idx	141	141	0	142	142	0
TRCN#_or_BGC#	TRCN0000022360	TRCN0000022360	TRCN0000022360	TRCN0000022360	TRCN0000022360	TRCN0000022360
shRNA_or_gRNA_sequence	GCCAAACAAATCCAAGATCAA	GCCAAACAAATCCAAGATCAA	GCCAAACAAATCCAAGATCAA	GCCAAACAAATCCAAGATCAA	GCCAAACAAATCCAAGATCAA	GCCAAACAAATCCAAGATCAA
PAM
Name	RTF1	RTF1	RTF1	RTF1	RTF1	RTF1
Sample_ID	BGHLV14-45	BGHLV14-45	BGHLV14-45	BGHLV14-46	BGHLV14-46	BGHLV14-46
transduction_Date	7/4/2014	7/4/2014	7/4/2014	7/4/2014	7/4/2014	7/4/2014
days
RBP_name	RTF1	RTF1	RTF1	RTF1	RTF1	RTF1
qPCR_result	57.4	57.4	57.4	57.3	57.3	57.3
Ave_qPCR	57.4	57.4	57.4
RT-qPCR_primer-F	acgcgtgttccgtttagag	acgcgtgttccgtttagag	acgcgtgttccgtttagag
RT-qPCR_primer-R	gcatgccagcagagaacat	gcatgccagcagagaacat	gcatgccagcagagaacat
protein_conc	3225	3225	3225	3324	3324	3324
WB_result	72.0	62.4	62.6	69.4	55.6	70.5
Ave_WB	70.7	59.0
WB_DONE_date	3/16/2016	6/17/2022	3/24/2022
MW	80kDa	80kDa	80kDa	WES
IP	1			1
antibody_Cat#	A300-178A	A301-329A	A300-179A	A300-178A	lot # 1	lot # 1
Antibody DCC ID	ENCAB664NPT	ENCAB195QAY	ENCAB525EGK	ENCAB664NPT
submitted_to_DCC_date	3/18/2016	8/16/2023	6/25/2024
Rep1_TPM	11.5	0	0	0	0	0
Rep2_TPM	8.5	0	0	0	0	0
Action
Library_start_date	8/12/2014			8/12/2014
repeat_library
Note
ID	2200	2202	2204	2201	2203	2205

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RTF1	Product_ID: A300-178A Lot_ID: 1 Source: Bethyl Labs Target Name: RTF1-human
RTF1	Product_ID: A301-329A Lot_ID: 1 Source: Bethyl Labs Target Name: RTF1-human
RTF1	Product_ID: A300-179A Lot_ID: 1 Source: Bethyl Labs Target Name: RTF1-human

Experiment Status

	BGHLV14-45	BGHLV14-46
Sample_ID	BGHLV14-45	BGHLV14-46
Sample Name	RTF1_BGHLV14-45	RTF1_BGHLV14-46
Sample Name	RTF1_BGHLV14-45	RTF1_BGHLV14-46
RBP	RTF1	RTF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	530	531

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-45	BGHLV14-46
Sample #
Sample Name	RTF1-BGHLV14-45	RTF1-BGHLV14-46
Sample_Name_Alias	RTF1_BGHLV14-45	RTF1_BGHLV14-46
Index Well Position	S25	S27
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/set1/H12.png	DNA_Library_LV13-14/set2/B1.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A9.png	RNA_Library_LV13-14-16/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-45	BGHLV14-46
RBP	RTF1	RTF1
Batch_ID	BGHLV14	BGHLV14
WB_result	72.000	69.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2214	2215

Sequencing Information

	BGHLV14-45	BGHLV14-46
Sample_ID	BGHLV14-45	BGHLV14-46
Sample Name	RTF1_BGHLV14-45	RTF1_BGHLV14-46
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	59,760,000	51,530,000
total_aligned_reads	55,121,286	47,916,592
unique_aligned_reads	52,023,260	45,163,100
percent_uniqueAligned	0.87054	0.87644
correlation_replicates	0.997703	0.997703
spikein_reads	284,866	213,466
percent_spikeins	0.00477	0.00414
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	856	857

Data Submission Information

	BGHLV14-45	BGHLV14-45
ENCODE_alias	brenton-graveley:RTF1_BGHLV14	brenton-graveley:RTF1-BGHLV14-HepG2
ENCODE_accession	ENCSR906WTM	ENCSR331QUE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-45	BGHLV14-45
Sample Name	RTF1_BGHLV14-45	RTF1_BGHLV14-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2814	6925

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
RTF1_BGHLV14-45_ACTGAT_L005_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	856	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13822
RTF1_BGHLV14-45_ACTGAT_L005_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	856	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13884
RTF1_BGHLV14-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	856					GRCh38	V40	RTF1_BGHLV14-45_ACTGAT_L005_R1_001.fastq.gz,RTF1_BGHLV14-45_ACTGAT_L005_R2_001.fastq.gz		ENCORE2	13946
RTF1_BGHLV14-45_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	856					GRCh38	V40	RTF1_BGHLV14-45/Aligned.sortedByCoord.out.bam		ENCORE2	14008
RTF1_BGHLV14-45_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	856					GRCh38	V40	RTF1_BGHLV14-45/Aligned.sortedByCoord.out.bam		ENCORE2	14070
RTF1_BGHLV14-45_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	856					GRCh38	V40	RTF1_BGHLV14-45/Aligned.sortedByCoord.out.bam		ENCORE2	14132
RTF1_BGHLV14-45_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	856					GRCh38	V40	RTF1_BGHLV14-45/Aligned.sortedByCoord.out.bam		ENCORE2	14194
RTF1_BGHLV14-45_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	856					GRCh38	V40	RTF1_BGHLV14-45_ACTGAT_L005_R1_001.fastq.gz,RTF1_BGHLV14-45_ACTGAT_L005_R2_001.fastq.gz		ENCORE2	14256
RTF1_BGHLV14-46_ATTCCT_L006_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	857	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13823
RTF1_BGHLV14-46_ATTCCT_L006_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	857	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13885
RTF1_BGHLV14-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	857					GRCh38	V40	RTF1_BGHLV14-46_ATTCCT_L006_R1_001.fastq.gz,RTF1_BGHLV14-46_ATTCCT_L006_R2_001.fastq.gz		ENCORE2	13947
RTF1_BGHLV14-46_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	857					GRCh38	V40	RTF1_BGHLV14-46/Aligned.sortedByCoord.out.bam		ENCORE2	14009
RTF1_BGHLV14-46_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	857					GRCh38	V40	RTF1_BGHLV14-46/Aligned.sortedByCoord.out.bam		ENCORE2	14071
RTF1_BGHLV14-46_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	857					GRCh38	V40	RTF1_BGHLV14-46/Aligned.sortedByCoord.out.bam		ENCORE2	14133
RTF1_BGHLV14-46_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	857					GRCh38	V40	RTF1_BGHLV14-46/Aligned.sortedByCoord.out.bam		ENCORE2	14195
RTF1_BGHLV14-46_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	857					GRCh38	V40	RTF1_BGHLV14-46_ATTCCT_L006_R1_001.fastq.gz,RTF1_BGHLV14-46_ATTCCT_L006_R2_001.fastq.gz		ENCORE2	14257