ERO1A RNA-Seq in K562

General Information


RBP	ERO1L
Cell_Line	K562
Method	CRISPR
Exp_Name	ERO1L-BGKcLV15-K562
ENCODE_series_ID	ENCSR940ASR
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR353OQP
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	ERO1L-BGKcLV15-47
Rep2	ERO1L-BGKcLV15-48
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	51.1
Rep2_qPCR	67.9
Rep1_WB	64.2
Rep2_WB	71.3
Antibody Cat#	702709
Antibody Lot#	LOT# 2000403
Antibody DCC ID	ENCAB894YPF
Status	Released
Project	ENCODE4
ID	132

Experiment Information (Status: Released)

	BGKcLV15-47	BGKcLV15-48
idx	585	586
TRCN#_or_BGC#	BGC#0000361	BGC#0000361
shRNA_or_gRNA_sequence	CAAACAAGAATCCCCAGCCG	CAAACAAGAATCCCCAGCCG
PAM	CGG	CGG
Name	ERO1L-81	ERO1L-81
Sample_ID	BGKcLV15-47	BGKcLV15-48
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	ERO1L	ERO1L
qPCR_result	51.1	67.9
Ave_qPCR	59.5
RT-qPCR_primer-F	AGCGGCACAGAGGTGCTT
RT-qPCR_primer-R	TCAATGGTTTCAACATCACAGG
protein_conc	6177	5422
WB_result	64.2	71.3
Ave_WB	67.7
WB_DONE_date	4/9/19
MW	54KD
IP	Rabbit / I
antibody_Cat#	702709	LOT# 2000403
Antibody DCC ID	ENCAB894YPF	11/29/20
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4697	4698

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

	BGKcLV15-47	BGKcLV15-48
Sample_ID	BGKcLV15-47	BGKcLV15-48
Sample Name	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-48
Sample Name	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-48
RBP	ERO1L	ERO1L
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5353	5354

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-47	BGKcLV15-48
Sample #	23	24
Sample Name	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-48
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	2-G1	2-H1
Tecan	38.91	32.82
Tecan_date	2019-12-10	2019-12-10
Size_bp	266	266
Peak_Molarity	17.60	17.00
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G3.png	DNA_Library_set43-44/set1/H3.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set43-44/set1/G3.png	RNA_Library_set43-44/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-47	BGKcLV15-48
RBP	ERO1L	ERO1L
Batch_ID	BGKcLV15	BGKcLV15
WB_result	64.200	71.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	599	600

Sequencing Information

	BGKcLV15-47	BGKcLV15-48
Sample_ID	BGKcLV15-47	BGKcLV15-48
Sample Name	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-48
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	124,525,038	106,760,470
total_aligned_reads	121,979,232	99,739,646
unique_aligned_reads	111,483,862	91,213,738
percent_uniqueAligned	0.89527	0.85438
correlation_replicates	0.999449	0.999449
spikein_reads	57,668	57,076
percent_spikeins	0.00046	0.00053
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	105	106

Data Submission Information

	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-48	BGKcLV15-48	BGKcLV15-48	BGKcLV15-48
ENCODE_alias	brenton-graveley:ERO1L-BGKcLV15	brenton-graveley:ERO1L-BGKcLV15-47	brenton-graveley:L-ERO1L-BGKcLV15-47	brenton-graveley:ERO1L-BGKcLV15-47_S23_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERO1L-BGKcLV15-47_S23_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERO1L-BGKcLV15-K562	brenton-graveley:ERO1L-BGKcLV15-48	brenton-graveley:L-ERO1L-BGKcLV15-48	brenton-graveley:ERO1L-BGKcLV15-48_S24_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERO1L-BGKcLV15-48_S24_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR353OQP	ENCBS499VIT	ENCLB870EKW	ENCFF100SJH	ENCFF735CTP	ENCSR940ASR	ENCBS590BHJ	ENCLB471AIY	ENCFF885MSV	ENCFF305ONX
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	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-47	BGKcLV15-48	BGKcLV15-48	BGKcLV15-48	BGKcLV15-48
Sample Name	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-47	ERO1L-BGKcLV15-48	ERO1L-BGKcLV15-48	ERO1L-BGKcLV15-48	ERO1L-BGKcLV15-48
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		ERO1L-BGKcLV15-47.pdf	L-NSUN4-BGKcLV15-43.pdf				ERO1L-BGKcLV15-48.pdf	L-NSUN4-BGKcLV15-44.pdf
ID	28	138	302	500	552	7214	139	303	501	553

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-BGKcLV15-47_S23_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	105	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	89
ERO1L-BGKcLV15-47_S23_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	105	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	141
ERO1L-BGKcLV15-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	105					GRCh38	V40	ERO1L-BGKcLV15-47_S23_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGKcLV15-47_S23_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24380
ERO1L-BGKcLV15-47_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	105					GRCh38	V40	ERO1L-BGKcLV15-47/Aligned.sortedByCoord.out.bam		ENCORE2	24432
ERO1L-BGKcLV15-47_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	105					GRCh38	V40	ERO1L-BGKcLV15-47/Aligned.sortedByCoord.out.bam		ENCORE2	24484
ERO1L-BGKcLV15-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	105					GRCh38	V40	ERO1L-BGKcLV15-47/Aligned.sortedByCoord.out.bam		ENCORE2	24536
ERO1L-BGKcLV15-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	105					GRCh38	V40	ERO1L-BGKcLV15-47/Aligned.sortedByCoord.out.bam		ENCORE2	24588
ERO1L-BGKcLV15-47_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	105					GRCh38	V40	ERO1L-BGKcLV15-47_S23_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGKcLV15-47_S23_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24640
ERO1L-BGKcLV15-48_S24_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	106	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	90
ERO1L-BGKcLV15-48_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	106	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	142
ERO1L-BGKcLV15-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	106					GRCh38	V40	ERO1L-BGKcLV15-48_S24_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGKcLV15-48_S24_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24381
ERO1L-BGKcLV15-48_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	106					GRCh38	V40	ERO1L-BGKcLV15-48/Aligned.sortedByCoord.out.bam		ENCORE2	24433
ERO1L-BGKcLV15-48_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	106					GRCh38	V40	ERO1L-BGKcLV15-48/Aligned.sortedByCoord.out.bam		ENCORE2	24485
ERO1L-BGKcLV15-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	106					GRCh38	V40	ERO1L-BGKcLV15-48/Aligned.sortedByCoord.out.bam		ENCORE2	24537
ERO1L-BGKcLV15-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	106					GRCh38	V40	ERO1L-BGKcLV15-48/Aligned.sortedByCoord.out.bam		ENCORE2	24589
ERO1L-BGKcLV15-48_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	106					GRCh38	V40	ERO1L-BGKcLV15-48_S24_R1_001.filtered.trimmed.paired.fastq.gz,ERO1L-BGKcLV15-48_S24_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24641