HLTF RNA-Seq in HepG2

General Information


RBP	HLTF
Cell_Line	HepG2
Method	shRNA
Exp_Name	HLTF-BGHLV14-HepG2
ENCODE_series_ID	ENCSR575OUX
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR010ZMZ
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	HLTF_BGHLV14-25
Rep2	HLTF_BGHLV14-26
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	77.9
Rep2_qPCR	74.4
Rep1_WB	91.8
Rep2_WB	92.9
Antibody Cat#	A300-230A
Antibody Lot#	A300-230A
Antibody DCC ID	ENCAB902OZZ
Status	Released
Project	ENCODE3
ID	395

Experiment Information (Status: Released)

	BGHLV14-25	BGHLV14-26
idx	121	122
TRCN#_or_BGC#	TRCN0000010836	TRCN0000010836
shRNA_or_gRNA_sequence	GCAGGTGGAGTTGGTTTGAAT	GCAGGTGGAGTTGGTTTGAAT
PAM
Name	HLTF	HLTF
Sample_ID	BGHLV14-25	BGHLV14-26
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	HLTF	HLTF
qPCR_result	77.9	74.4
Ave_qPCR	76.2
RT-qPCR_primer-F	tgtcctccagaagaattagca
RT-qPCR_primer-R	cgtgcattagcgcattaatct
protein_conc	4402	4260
WB_result	91.8	92.9
Ave_WB	92.4
WB_DONE_date	7/30/2014
MW	114kDa
IP	1	1
antibody_Cat#	A300-230A	A300-230A
Antibody DCC ID	ENCAB902OZZ	ENCAB902OZZ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	14.2	0
Rep2_TPM	11.3	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2180	2181

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HLTF	Product_ID: A300-230A Lot_ID: 2 Source: Bethyl Labs Target Name: HLTF-human

Experiment Status

	BGHLV14-25	BGHLV14-26
Sample_ID	BGHLV14-25	BGHLV14-26
Sample Name	HLTF_BGHLV14-25	HLTF_BGHLV14-26
Sample Name	HLTF_BGHLV14-25	HLTF_BGHLV14-26
RBP	HLTF	HLTF
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	512	513

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-25	BGHLV14-26
Sample #
Sample Name	HLTF-BGHLV14-25	HLTF-BGHLV14-26
Sample_Name_Alias	HLTF_BGHLV14-25	HLTF_BGHLV14-26
Index Well Position	S07	S08
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/H10.png	DNA_Library_LV13-14/set1/A11.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A7.png	RNA_Library_LV13-14-16/set1/B7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-25	BGHLV14-26
RBP	HLTF	HLTF
Batch_ID	BGHLV14	BGHLV14
WB_result	91.800	92.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2198	2199

Sequencing Information

	BGHLV14-25	BGHLV14-26
Sample_ID	BGHLV14-25	BGHLV14-26
Sample Name	HLTF_BGHLV14-25	HLTF_BGHLV14-26
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	56,110,000	51,810,000
total_aligned_reads	51,383,506	47,548,984
unique_aligned_reads	48,452,180	44,885,740
percent_uniqueAligned	0.86352	0.86635
correlation_replicates	0.998061	0.998061
spikein_reads	293,344	218,734
percent_spikeins	0.00523	0.00422
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	840	841

Data Submission Information

	BGHLV14-25	BGHLV14-25
ENCODE_alias	brenton-graveley:HLTF_BGHLV14	brenton-graveley:HLTF-BGHLV14-HepG2
ENCODE_accession	ENCSR010ZMZ	ENCSR575OUX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-25	BGHLV14-25
Sample Name	HLTF_BGHLV14-25	HLTF_BGHLV14-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2806	6744

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
HLTF_BGHLV14-25_CAGATC_L003_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	840	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13804
HLTF_BGHLV14-25_CAGATC_L003_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	840	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13866
HLTF_BGHLV14-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	840					GRCh38	V40	HLTF_BGHLV14-25_CAGATC_L003_R1_001.fastq.gz,HLTF_BGHLV14-25_CAGATC_L003_R2_001.fastq.gz		ENCORE2	13928
HLTF_BGHLV14-25_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	840					GRCh38	V40	HLTF_BGHLV14-25/Aligned.sortedByCoord.out.bam		ENCORE2	13990
HLTF_BGHLV14-25_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	840					GRCh38	V40	HLTF_BGHLV14-25/Aligned.sortedByCoord.out.bam		ENCORE2	14052
HLTF_BGHLV14-25_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	840					GRCh38	V40	HLTF_BGHLV14-25/Aligned.sortedByCoord.out.bam		ENCORE2	14114
HLTF_BGHLV14-25_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	840					GRCh38	V40	HLTF_BGHLV14-25/Aligned.sortedByCoord.out.bam		ENCORE2	14176
HLTF_BGHLV14-25_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	840					GRCh38	V40	HLTF_BGHLV14-25_CAGATC_L003_R1_001.fastq.gz,HLTF_BGHLV14-25_CAGATC_L003_R2_001.fastq.gz		ENCORE2	14238
HLTF_BGHLV14-26_ACTTGA_L003_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	841	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13805
HLTF_BGHLV14-26_ACTTGA_L003_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	841	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13867
HLTF_BGHLV14-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	841					GRCh38	V40	HLTF_BGHLV14-26_ACTTGA_L003_R1_001.fastq.gz,HLTF_BGHLV14-26_ACTTGA_L003_R2_001.fastq.gz		ENCORE2	13929
HLTF_BGHLV14-26_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	841					GRCh38	V40	HLTF_BGHLV14-26/Aligned.sortedByCoord.out.bam		ENCORE2	13991
HLTF_BGHLV14-26_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	841					GRCh38	V40	HLTF_BGHLV14-26/Aligned.sortedByCoord.out.bam		ENCORE2	14053
HLTF_BGHLV14-26_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	841					GRCh38	V40	HLTF_BGHLV14-26/Aligned.sortedByCoord.out.bam		ENCORE2	14115
HLTF_BGHLV14-26_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	841					GRCh38	V40	HLTF_BGHLV14-26/Aligned.sortedByCoord.out.bam		ENCORE2	14177
HLTF_BGHLV14-26_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	841					GRCh38	V40	HLTF_BGHLV14-26_ACTTGA_L003_R1_001.fastq.gz,HLTF_BGHLV14-26_ACTTGA_L003_R2_001.fastq.gz		ENCORE2	14239