ERN1 RNA-Seq in HepG2

General Information


RBP	ERN1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ERN1-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR234PSZ
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR005UDT
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	ERN1-BGHcLV18-17
Rep2	ERN1-BGHcLV18-18
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	92.3
Rep2_qPCR	90.3
Rep1_WB	95.2
Rep2_WB	98.4
Antibody Cat#	MA5-14991
Antibody Lot#	lot# TL2693035
Antibody DCC ID	ENCAB311UNO
Status	Released
Project	ENCODE4
ID	106

Experiment Information (Status: Released)

	BGHcLV18-17	BGHcLV18-18
idx	510	511
TRCN#_or_BGC#	BGC#0000428	BGC#0000428
shRNA_or_gRNA_sequence	CTTGTTGTTTGTGTCAACGC	CTTGTTGTTTGTGTCAACGC
PAM	TGG	TGG
Name	ERN1_92	ERN1_92
Sample_ID	BGHcLV18-17	BGHcLV18-18
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	ERN1	ERN1
qPCR_result	92.3	90.3
Ave_qPCR	91.3
RT-qPCR_primer-F	GTTGTTTGTGTCAACGCTGG
RT-qPCR_primer-R	CTTCCACATGTGTTGGGACC
protein_conc	4518	3879
WB_result	95.2	98.4
Ave_WB	96.8
WB_DONE_date	8/20/19	wes
MW	110KD
IP	Rabbit / I	Monoclonal
antibody_Cat#	MA5-14991	lot# TL2693035
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	4	0
Rep2_TPM	5	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6663	6664

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ERN1	Product_ID: MA5-14991 Lot_ID: TL2693035 Source: Thermo Fisher Target Name: ERN1-human

Experiment Status

	BGHcLV18-17	BGHcLV18-18
Sample_ID	BGHcLV18-17	BGHcLV18-18
Sample Name
Sample Name	ERN1-BGHcLV18-17	ERN1-BGHcLV18-18
RBP	ERN1	ERN1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5629	5630

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-17	BGHcLV18-18
Sample #	135	136
Sample Name	ERN1-BGHcLV18-17	ERN1-BGHcLV18-18
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	4-C1	4-D1
Tecan	27.10	36.98
Tecan_date	2019-12-16	2019-12-16
Size_bp	285	275
Peak_Molarity	27.60	24.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A7.png	DNA_Library_set43-44/set2/B7.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/E8.png	RNA_Library_set43-44/set4/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-17	BGHcLV18-18
RBP	ERN1	ERN1
Batch_ID	BGHcLV18	BGHcLV18
WB_result	95.200	98.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	711	712

Sequencing Information

	BGHcLV18-17	BGHcLV18-18
Sample_ID	BGHcLV18-17	BGHcLV18-18
Sample Name	ERN1-BGHcLV18-17	ERN1-BGHcLV18-18
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	183,471,136	167,870,946
total_aligned_reads	179,755,408	163,301,326
unique_aligned_reads	168,195,900	152,901,898
percent_uniqueAligned	0.91674	0.91083
correlation_replicates	0.999621	0.999621
spikein_reads	365,808	317,346
percent_spikeins	0.00199	0.00189
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	217	218

Data Submission Information

	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-18	BGHcLV18-18	BGHcLV18-18	BGHcLV18-18
ENCODE_alias	brenton-graveley:ERN1-BGHcLV18	brenton-graveley:ERN1-BGHcLV18-17	brenton-graveley:L-ERN1-BGHcLV18-17	brenton-graveley:ERN1-BGHcLV18-17_S51_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERN1-BGHcLV18-17_S51_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERN1-BGHcLV18-HepG2	brenton-graveley:ERN1-BGHcLV18-18	brenton-graveley:L-ERN1-BGHcLV18-18	brenton-graveley:ERN1-BGHcLV18-18_S52_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERN1-BGHcLV18-18_S52_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR005UDT	ENCBS617GJQ	ENCLB589LLZ	ENCFF256SMC	ENCFF296MAO	ENCSR234PSZ	ENCBS948BPV	ENCLB081HVQ	ENCFF600MSK	ENCFF899ECA
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-17	BGHcLV18-18	BGHcLV18-18	BGHcLV18-18	BGHcLV18-18
Sample Name	ERN1-BGHcLV18-17	ERN1-BGHcLV18-17	ERN1-BGHcLV18-17	ERN1-BGHcLV18-17	ERN1-BGHcLV18-17	ERN1-BGHcLV18-17	ERN1-BGHcLV18-18	ERN1-BGHcLV18-18	ERN1-BGHcLV18-18	ERN1-BGHcLV18-18
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		ERN1-BGHcLV18-17.pdf	L-ERN1-BGHcLV18-17.pdf				ERN1-BGHcLV18-18.pdf	L-ERN1-BGHcLV18-18.pdf
ID	53	186	352	602	654	7211	187	353	603	655

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
ERN1-BGHcLV18-17_S51_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	217	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	183
ERN1-BGHcLV18-17_S51_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	217	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	235
ERN1-BGHcLV18-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	217					GRCh38	V40	ERN1-BGHcLV18-17_S51_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGHcLV18-17_S51_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24903
ERN1-BGHcLV18-17_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	217					GRCh38	V40	ERN1-BGHcLV18-17/Aligned.sortedByCoord.out.bam		ENCORE2	24955
ERN1-BGHcLV18-17_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	217					GRCh38	V40	ERN1-BGHcLV18-17/Aligned.sortedByCoord.out.bam		ENCORE2	25007
ERN1-BGHcLV18-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	217					GRCh38	V40	ERN1-BGHcLV18-17/Aligned.sortedByCoord.out.bam		ENCORE2	25059
ERN1-BGHcLV18-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	217					GRCh38	V40	ERN1-BGHcLV18-17/Aligned.sortedByCoord.out.bam		ENCORE2	25111
ERN1-BGHcLV18-17_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	217					GRCh38	V40	ERN1-BGHcLV18-17_S51_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGHcLV18-17_S51_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25163
ERN1-BGHcLV18-18_S52_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	218	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	184
ERN1-BGHcLV18-18_S52_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	218	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	236
ERN1-BGHcLV18-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	218					GRCh38	V40	ERN1-BGHcLV18-18_S52_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGHcLV18-18_S52_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24904
ERN1-BGHcLV18-18_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	218					GRCh38	V40	ERN1-BGHcLV18-18/Aligned.sortedByCoord.out.bam		ENCORE2	24956
ERN1-BGHcLV18-18_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	218					GRCh38	V40	ERN1-BGHcLV18-18/Aligned.sortedByCoord.out.bam		ENCORE2	25008
ERN1-BGHcLV18-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	218					GRCh38	V40	ERN1-BGHcLV18-18/Aligned.sortedByCoord.out.bam		ENCORE2	25060
ERN1-BGHcLV18-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	218					GRCh38	V40	ERN1-BGHcLV18-18/Aligned.sortedByCoord.out.bam		ENCORE2	25112
ERN1-BGHcLV18-18_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	218					GRCh38	V40	ERN1-BGHcLV18-18_S52_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGHcLV18-18_S52_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25164