ERN1 RNA-Seq in K562

General Information


RBP	ERN1
Cell_Line	K562
Method	CRISPR
Exp_Name	ERN1-BGKcLV17-K562
ENCODE_series_ID	ENCSR620VTT
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR026FEM
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	ERN1-BGKcLV17-17
Rep2	ERN1-BGKcLV17-18
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	96.2
Rep2_qPCR	93.5
Rep1_WB	92.9
Rep2_WB	96.8
Antibody Cat#	MA5-14991
Antibody Lot#	lot# TL2693035
Antibody DCC ID	ENCAB311UNO
Status	Released
Project	ENCODE4
ID	84

Experiment Information (Status: Released)

	BGKcLV17-17	BGKcLV17-18
idx	624	625
TRCN#_or_BGC#	BGC#0000428	BGC#0000428
shRNA_or_gRNA_sequence	CTTGTTGTTTGTGTCAACGC	CTTGTTGTTTGTGTCAACGC
PAM	TGG	TGG
Name	ERN1_92	ERN1_92
Sample_ID	BGKcLV17-17	BGKcLV17-18
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	ERN1	ERN1
qPCR_result	96.2	93.5
Ave_qPCR	94.9
RT-qPCR_primer-F	GTTGTTTGTGTCAACGCTGG
RT-qPCR_primer-R	CTTCCACATGTGTTGGGACC
protein_conc	4836	4542
WB_result	92.9	96.8
Ave_WB	94.9
WB_DONE_date	7/10/19	WES
MW	110KD
IP	Rabbit / I	Monoclonal
antibody_Cat#	MA5-14991	lot# TL2693035
Antibody DCC ID	ENCAB311UNO
submitted_to_DCC_date
Rep1_TPM	6	0
Rep2_TPM	4.5	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4740	4741

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

	BGKcLV17-17	BGKcLV17-18
Sample_ID	BGKcLV17-17	BGKcLV17-18
Sample Name
Sample Name	ERN1-BGKcLV17-17	ERN1-BGKcLV17-18
RBP	ERN1	ERN1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5501	5502

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-17	BGKcLV17-18
Sample #	91	92
Sample Name	ERN1-BGKcLV17-17	ERN1-BGKcLV17-18
Sample_Name_Alias
Index Well Position	A12	B12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-G1	1-H1
Tecan	19.74	31.81
Tecan_date	2019-12-16	2019-12-16
Size_bp	274	275
Peak_Molarity	27.80	28.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A8.png	DNA_Library_set43-44/set1/B8.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/A3.png	RNA_Library_set43-44/set4/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-17	BGKcLV17-18
RBP	ERN1	ERN1
Batch_ID	BGKcLV17	BGKcLV17
WB_result	92.900	96.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	667	668

Sequencing Information

	BGKcLV17-17	BGKcLV17-18
Sample_ID	BGKcLV17-17	BGKcLV17-18
Sample Name	ERN1-BGKcLV17-17	ERN1-BGKcLV17-18
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	249,532,242	231,004,068
total_aligned_reads	240,214,340	218,076,852
unique_aligned_reads	217,683,238	197,505,566
percent_uniqueAligned	0.87237	0.85499
correlation_replicates	0.997110	0.997110
spikein_reads	89,308	37,614
percent_spikeins	0.00036	0.00016
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	173	174

Data Submission Information

	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-18	BGKcLV17-18	BGKcLV17-18	BGKcLV17-18
ENCODE_alias	brenton-graveley:ERN1-BGKcLV17	brenton-graveley:ERN1-BGKcLV17-17	brenton-graveley:L-ERN1-BGKcLV17-17	brenton-graveley:ERN1-BGKcLV17-17_S3_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERN1-BGKcLV17-17_S3_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERN1-BGKcLV17-K562	brenton-graveley:ERN1-BGKcLV17-18	brenton-graveley:L-ERN1-BGKcLV17-18	brenton-graveley:ERN1-BGKcLV17-18_S4_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ERN1-BGKcLV17-18_S4_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR026FEM	ENCBS635PSX	ENCLB581ZUO	ENCFF676ELJ	ENCFF748KXB	ENCSR620VTT	ENCBS765QWV	ENCLB279OZG	ENCFF598RHC	ENCFF290BZR
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	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-17	BGKcLV17-18	BGKcLV17-18	BGKcLV17-18	BGKcLV17-18
Sample Name	ERN1-BGKcLV17-17	ERN1-BGKcLV17-17	ERN1-BGKcLV17-17	ERN1-BGKcLV17-17	ERN1-BGKcLV17-17	ERN1-BGKcLV17-17	ERN1-BGKcLV17-18	ERN1-BGKcLV17-18	ERN1-BGKcLV17-18	ERN1-BGKcLV17-18
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
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		ERN1-BGKcLV17-17.pdf	L-ERN1-BGKcLV17-17.pdf				ERN1-BGKcLV17-18.pdf	L-ERN1-BGKcLV17-18.pdf
ID	70	220	386	688	718	7212	221	387	689	719

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-BGKcLV17-17_S3_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	173	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	275
ERN1-BGKcLV17-17_S3_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	173	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	305
ERN1-BGKcLV17-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	173					GRCh38	V40	ERN1-BGKcLV17-17_S3_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGKcLV17-17_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24671
ERN1-BGKcLV17-17_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	173					GRCh38	V40	ERN1-BGKcLV17-17/Aligned.sortedByCoord.out.bam		ENCORE2	24701
ERN1-BGKcLV17-17_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	173					GRCh38	V40	ERN1-BGKcLV17-17/Aligned.sortedByCoord.out.bam		ENCORE2	24731
ERN1-BGKcLV17-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	173					GRCh38	V40	ERN1-BGKcLV17-17/Aligned.sortedByCoord.out.bam		ENCORE2	24761
ERN1-BGKcLV17-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	173					GRCh38	V40	ERN1-BGKcLV17-17/Aligned.sortedByCoord.out.bam		ENCORE2	24791
ERN1-BGKcLV17-17_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	173					GRCh38	V40	ERN1-BGKcLV17-17_S3_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGKcLV17-17_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24821
ERN1-BGKcLV17-18_S4_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	174	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	276
ERN1-BGKcLV17-18_S4_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	174	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	306
ERN1-BGKcLV17-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	174					GRCh38	V40	ERN1-BGKcLV17-18_S4_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGKcLV17-18_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24672
ERN1-BGKcLV17-18_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	174					GRCh38	V40	ERN1-BGKcLV17-18/Aligned.sortedByCoord.out.bam		ENCORE2	24702
ERN1-BGKcLV17-18_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	174					GRCh38	V40	ERN1-BGKcLV17-18/Aligned.sortedByCoord.out.bam		ENCORE2	24732
ERN1-BGKcLV17-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	174					GRCh38	V40	ERN1-BGKcLV17-18/Aligned.sortedByCoord.out.bam		ENCORE2	24762
ERN1-BGKcLV17-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	174					GRCh38	V40	ERN1-BGKcLV17-18/Aligned.sortedByCoord.out.bam		ENCORE2	24792
ERN1-BGKcLV17-18_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	174					GRCh38	V40	ERN1-BGKcLV17-18_S4_R1_001.filtered.trimmed.paired.fastq.gz,ERN1-BGKcLV17-18_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24822