ERO1A RNA-Seq in HepG2

General Information


RBP	ERO1L
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ERO1L-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR570IMD
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR561IMV
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	ERO1L-BGHcLV16-43
Rep2	ERO1L-BGHcLV16-44
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	17.4
Rep2_qPCR	30.0
Rep1_WB	60.6
Rep2_WB	58.5
Antibody Cat#	702709
Antibody Lot#	LOT# 2000403
Antibody DCC ID	ENCAB894YPF
Status	Released
Project	ENCODE4
ID	154

Experiment Information (Status: Released)

	BGHcLV16-43	BGHcLV16-44
idx	473	474
TRCN#_or_BGC#	BGC#0000361	BGC#0000361
shRNA_or_gRNA_sequence	CAAACAAGAATCCCCAGCCG	CAAACAAGAATCCCCAGCCG
PAM	CGG	CGG
Name	ERO1L-81	ERO1L-81
Sample_ID	BGHcLV16-43	BGHcLV16-44
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	ERO1L	ERO1L
qPCR_result	17.4	30.0
Ave_qPCR	23.7
RT-qPCR_primer-F	AGCGGCACAGAGGTGCTT
RT-qPCR_primer-R	TCAATGGTTTCAACATCACAGG
protein_conc	3964	3384
WB_result	60.6	58.5
Ave_WB	59.5
WB_DONE_date	4/24/19
MW	54KD
IP	Rabbit / I
antibody_Cat#	702709	LOT# 2000403
Antibody DCC ID	ENCAB894YPF	11/29/20
submitted_to_DCC_date
Rep1_TPM	25	0
Rep2_TPM	55	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6622	6623

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ERO1A	Product_ID: 702709 Lot_ID: 2000403 Source: Thermo Fisher Target Name: ERO1A-human

Experiment Status

	BGHcLV16-43	BGHcLV16-44
Sample_ID	BGHcLV16-43	BGHcLV16-44
Sample Name	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-44
Sample Name	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-44
RBP	ERO1L	ERO1L
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5427	5428

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-43	BGHcLV16-44
Sample #	61	62
Sample Name	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-44
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-C1	2-D1
Tecan	37.87	37.23
Tecan_date	2019-12-10	2019-12-10
Size_bp	273	284
Peak_Molarity	32.50	35.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C3.png	DNA_Library_set43-44/set2/D3.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/C8.png	RNA_Library_set43-44/set1/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-43	BGHcLV16-44
RBP	ERO1L	ERO1L
Batch_ID	BGHcLV16	BGHcLV16
WB_result	60.600	58.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	637	638

Sequencing Information

	BGHcLV16-43	BGHcLV16-44
Sample_ID	BGHcLV16-43	BGHcLV16-44
Sample Name	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-44
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	152,226,204	119,366,342
total_aligned_reads	143,417,530	109,325,980
unique_aligned_reads	134,303,226	102,545,990
percent_uniqueAligned	0.88226	0.85909
correlation_replicates	0.999879	0.999879
spikein_reads	204,138	151,634
percent_spikeins	0.00134	0.00127
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	139	140

Data Submission Information

	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-44	BGHcLV16-44	BGHcLV16-44	BGHcLV16-44
ENCODE_alias	brenton-graveley:ERO1L-BGHcLV16	brenton-graveley:ERO1L-BGHcLV16-43	brenton-graveley:L-ERO1L-BGHcLV16-43	brenton-graveley:ERO1L-BGHcLV16-43_S57_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERO1L-BGHcLV16-43_S57_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERO1L-BGHcLV16-HepG2	brenton-graveley:ERO1L-BGHcLV16-44	brenton-graveley:L-ERO1L-BGHcLV16-44	brenton-graveley:ERO1L-BGHcLV16-44_S58_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERO1L-BGHcLV16-44_S58_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR561IMV	ENCBS626UNQ	ENCLB324PXG	ENCFF821FFX	ENCFF544PQM	ENCSR570IMD	ENCBS526OCD	ENCLB032OUE	ENCFF507ZIL	ENCFF042ECU
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	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-43	BGHcLV16-44	BGHcLV16-44	BGHcLV16-44	BGHcLV16-44
Sample Name	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-43	ERO1L-BGHcLV16-44	ERO1L-BGHcLV16-44	ERO1L-BGHcLV16-44	ERO1L-BGHcLV16-44
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
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		ERO1L-BGHcLV16-43.pdf	L-ERO1L-BGHcLV16-43.pdf				ERO1L-BGHcLV16-44.pdf	L-ERO1L-BGHcLV16-44.pdf
ID	10	102	266	432	464	7213	103	267	433	465

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
ERO1L-BGHcLV16-43_S57_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	139	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	11
ERO1L-BGHcLV16-43_S57_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	139	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	43
ERO1L-BGHcLV16-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	139					GRCh38	V40	ERO1L-BGHcLV16-43_S57_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGHcLV16-43_S57_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24174
ERO1L-BGHcLV16-43_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	139					GRCh38	V40	ERO1L-BGHcLV16-43/Aligned.sortedByCoord.out.bam		ENCORE2	24206
ERO1L-BGHcLV16-43_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	139					GRCh38	V40	ERO1L-BGHcLV16-43/Aligned.sortedByCoord.out.bam		ENCORE2	24238
ERO1L-BGHcLV16-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	139					GRCh38	V40	ERO1L-BGHcLV16-43/Aligned.sortedByCoord.out.bam		ENCORE2	24270
ERO1L-BGHcLV16-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	139					GRCh38	V40	ERO1L-BGHcLV16-43/Aligned.sortedByCoord.out.bam		ENCORE2	24302
ERO1L-BGHcLV16-43_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	139					GRCh38	V40	ERO1L-BGHcLV16-43_S57_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGHcLV16-43_S57_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24334
ERO1L-BGHcLV16-44_S58_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	140	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	12
ERO1L-BGHcLV16-44_S58_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	140	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	44
ERO1L-BGHcLV16-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	140					GRCh38	V40	ERO1L-BGHcLV16-44_S58_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGHcLV16-44_S58_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24175
ERO1L-BGHcLV16-44_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	140					GRCh38	V40	ERO1L-BGHcLV16-44/Aligned.sortedByCoord.out.bam		ENCORE2	24207
ERO1L-BGHcLV16-44_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	140					GRCh38	V40	ERO1L-BGHcLV16-44/Aligned.sortedByCoord.out.bam		ENCORE2	24239
ERO1L-BGHcLV16-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	140					GRCh38	V40	ERO1L-BGHcLV16-44/Aligned.sortedByCoord.out.bam		ENCORE2	24271
ERO1L-BGHcLV16-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	140					GRCh38	V40	ERO1L-BGHcLV16-44/Aligned.sortedByCoord.out.bam		ENCORE2	24303
ERO1L-BGHcLV16-44_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	140					GRCh38	V40	ERO1L-BGHcLV16-44_S58_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGHcLV16-44_S58_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24335