NOLC1 RNA-Seq in K562

General Information


RBP	NOLC1
Cell_Line	K562
Method	CRISPR
Exp_Name	NOLC1-BGKcLV08-K562
ENCODE_series_ID	ENCSR180AST
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR410USU
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	NOLC1-BGKcLV08-47
Rep2	NOLC1-BGKcLV08-48
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	78.4
Rep2_qPCR	88.0
Rep1_WB	84.0
Rep2_WB	86.2
Antibody Cat#	A302-185A
Antibody Lot#	A302-185A
Antibody DCC ID	ENCAB398VAP
Status	Released
Project	ENCODE4
ID	207

Experiment Information (Status: Released)

	BGKcLV08-47	BGKcLV08-48
idx	272	273
TRCN#_or_BGC#	BGC#0000133	BGC#0000133
shRNA_or_gRNA_sequence	GCGCGATAACCAACTCTCAG	GCGCGATAACCAACTCTCAG
PAM	AGG	AGG
Name	NOLC1-89F	NOLC1-89F
Sample_ID	BGKcLV08-47	BGKcLV08-48
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	NOLC1	NOLC1
qPCR_result	78.4	88.0
Ave_qPCR	83.2
RT-qPCR_primer-F	ccaatgcctcttccctctta
RT-qPCR_primer-R	gcctgtaactttcgctctgg
protein_conc	3603	3523
WB_result	84.0	86.2
Ave_WB	85.1
WB_DONE_date	3/12/18	wes
MW	74kDa
IP	1MW	1MW
antibody_Cat#	A302-185A	A302-185A
Antibody DCC ID	ENCAB398VAP
submitted_to_DCC_date	9/6/18
Rep1_TPM	84.4	0
Rep2_TPM	41.2	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4372	4373

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NOLC1	Product_ID: A302-185A Lot_ID: 1 Source: Bethyl Labs Target Name: NOLC1-human

Experiment Status

	BGKcLV08-47	BGKcLV08-48
Sample_ID	BGKcLV08-47	BGKcLV08-48
Sample Name
Sample Name	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-48
RBP	NOLC1	NOLC1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6185	6186

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-47	BGKcLV08-48
Sample #	21	22
Sample Name	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-48
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	285	279
Peak_Molarity	39.50	53.30
libSampleQC_DNA_Well	DNA_Library_set41/set2/E3.png	DNA_Library_set41/set2/F3.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set41/set1/E3.png	RNA_Library_set41/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-47	BGKcLV08-48
RBP	NOLC1	NOLC1
Batch_ID	BGKcLV08	BGKcLV08
WB_result	84.000	86.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	871	872

Sequencing Information

	BGKcLV08-47	BGKcLV08-48
Sample_ID	BGKcLV08-47	BGKcLV08-48
Sample Name	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-48
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	97,965,960	67,405,414
total_aligned_reads	91,983,350	64,434,666
unique_aligned_reads	82,749,142	57,856,620
percent_uniqueAligned	0.84467	0.85834
correlation_replicates	0.998998	0.998998
spikein_reads	148,908	96,096
percent_spikeins	0.00152	0.00143
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	277	278

Data Submission Information

	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-48	BGKcLV08-48	BGKcLV08-48	BGKcLV08-48
ENCODE_alias	brenton-graveley:NOLC1-BGKcLV08	brenton-graveley:NOLC1-BGKcLV08-47	brenton-graveley:L-NOLC1-BGKcLV08-47	brenton-graveley:NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NOLC1-BGKcLV08-K562	brenton-graveley:NOLC1-BGKcLV08-48	brenton-graveley:L-NOLC1-BGKcLV08-48	brenton-graveley:NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR410USU	ENCBS087YBZ	ENCLB700QMR	ENCFF244QJS	ENCFF736GSG	ENCSR180AST	ENCBS147HGT	ENCLB878KZJ	ENCFF135UPG	ENCFF101AHA
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	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-47	BGKcLV08-48	BGKcLV08-48	BGKcLV08-48	BGKcLV08-48
Sample Name	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-47	NOLC1-BGKcLV08-48	NOLC1-BGKcLV08-48	NOLC1-BGKcLV08-48	NOLC1-BGKcLV08-48
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		NOLC1-BGKcLV08-47.pdf	L-NOLC1-BGKcLV08-47.pdf				NOLC1-BGKcLV08-48.pdf	L-NOLC1-BGKcLV08-48.pdf
ID	1133	1186	1256	1326	1390	7270	1187	1257	1327	1391

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	277				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	533
NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	277				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	603
NOLC1-BGKcLV08-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	277	GRCh38	V40	NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26771
NOLC1-BGKcLV08-47_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	277	GRCh38	V40	NOLC1-BGKcLV08-47/Aligned.sortedByCoord.out.bam		ENCORE2	26841
NOLC1-BGKcLV08-47_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	277	GRCh38	V40	NOLC1-BGKcLV08-47/Aligned.sortedByCoord.out.bam		ENCORE2	26911
NOLC1-BGKcLV08-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	277	GRCh38	V40	NOLC1-BGKcLV08-47/Aligned.sortedByCoord.out.bam		ENCORE2	26981
NOLC1-BGKcLV08-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	277	GRCh38	V40	NOLC1-BGKcLV08-47/Aligned.sortedByCoord.out.bam		ENCORE2	27051
NOLC1-BGKcLV08-47_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	277	GRCh38	V40	NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOLC1-BGKcLV08-47_GGTACCTT+AAGACGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27121
NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	278				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	534
NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	278				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	604
NOLC1-BGKcLV08-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	278	GRCh38	V40	NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26772
NOLC1-BGKcLV08-48_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	278	GRCh38	V40	NOLC1-BGKcLV08-48/Aligned.sortedByCoord.out.bam		ENCORE2	26842
NOLC1-BGKcLV08-48_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	278	GRCh38	V40	NOLC1-BGKcLV08-48/Aligned.sortedByCoord.out.bam		ENCORE2	26912
NOLC1-BGKcLV08-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	278	GRCh38	V40	NOLC1-BGKcLV08-48/Aligned.sortedByCoord.out.bam		ENCORE2	26982
NOLC1-BGKcLV08-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	278	GRCh38	V40	NOLC1-BGKcLV08-48/Aligned.sortedByCoord.out.bam		ENCORE2	27052
NOLC1-BGKcLV08-48_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	278	GRCh38	V40	NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NOLC1-BGKcLV08-48_AACGTTCC+GGAGTACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27122