NCL RNA-Seq in K562

General Information


RBP	NCL
Cell_Line	K562
Method	CRISPR
Exp_Name	NCL-BGKcLV19-K562
ENCODE_series_ID	ENCSR970EBI
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR665CVU
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	NCL-BGKcLV19-25
Rep2	NCL-BGKcLV19-26
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	81.1
Rep2_qPCR	85.2
Rep1_WB	66.3
Rep2_WB	64.2
Antibody Cat#	A300-710A
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB686POR
Status	Released
Project	ENCODE4
ID	54

Experiment Information (Status: Released)

	BGKcLV19-25	BGKcLV19-26
idx	697	698
TRCN#_or_BGC#	BGC#0000401	BGC#0000401
shRNA_or_gRNA_sequence	TCCTGTGAAAGCCAAGAACG	TCCTGTGAAAGCCAAGAACG
PAM	TGG	TGG
Name	NCL_80	NCL_80
Sample_ID	BGKcLV19-25	BGKcLV19-26
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	NCL	NCL
qPCR_result	81.1	85.2
Ave_qPCR
RT-qPCR_primer-F	TCTTGCTGTTGTGGATGTCAG
RT-qPCR_primer-R	ACGCTTTCTCCAGGTCTTCA
protein_conc	3725	3845
WB_result	66.3	64.2
Ave_WB	65.2
WB_DONE_date	11/14/19	jess
MW	77KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	A300-710A	lot #1
Antibody DCC ID	ENCAB686POR
submitted_to_DCC_date	11/16/20
Rep1_TPM	438.4	0
Rep2_TPM	491.7	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4817	4818

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NCL	Product_ID: A300-710A Lot_ID: 1 Source: Bethyl Labs Target Name: NCL-human

Experiment Status

	BGKcLV19-25	BGKcLV19-26
Sample_ID	BGKcLV19-25	BGKcLV19-26
Sample Name
Sample Name	NCL-BGKcLV19-25	NCL-BGKcLV19-26
RBP	NCL	NCL
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5701	5702

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-25	BGKcLV19-26
Sample #	15	16
Sample Name	NCL-BGKcLV19-25	NCL-BGKcLV19-26
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	305	309
Peak_Molarity	113.00	104.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/A2.png	DNA_Library_set45/set1/B2.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set45/set1/A2.png	RNA_Library_set45/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-25	BGKcLV19-26
RBP	NCL	NCL
Batch_ID	BGKcLV19	BGKcLV19
WB_result	66.300	64.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	789	790

Sequencing Information

	BGKcLV19-25	BGKcLV19-26
Sample_ID	BGKcLV19-25	BGKcLV19-26
Sample Name	NCL-BGKcLV19-25	NCL-BGKcLV19-26
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	90,547,266	93,586,902
total_aligned_reads	87,140,460	88,015,580
unique_aligned_reads	79,893,200	80,640,056
percent_uniqueAligned	0.88234	0.86166
correlation_replicates	0.988680	0.988680
spikein_reads	90,266	72,208
percent_spikeins	0.00100	0.00077
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	420	421

Data Submission Information

	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-26	BGKcLV19-26	BGKcLV19-26	BGKcLV19-26
ENCODE_alias	brenton-graveley:NCL-BGKcLV19	brenton-graveley:NCL-BGKcLV19-25	brenton-graveley:L-NCL-BGKcLV19-25	brenton-graveley:NCL-BGKcLV19-25_S9_R1_001.fastq.gz	brenton-graveley:NCL-BGKcLV19-25_S9_R2_001.fastq.gz	brenton-graveley:NCL-BGKcLV19-K562	brenton-graveley:NCL-BGKcLV19-26	brenton-graveley:L-NCL-BGKcLV19-26	brenton-graveley:NCL-BGKcLV19-26_S10_R1_001.fastq.gz	brenton-graveley:NCL-BGKcLV19-26_S10_R2_001.fastq.gz
ENCODE_accession	ENCSR665CVU	ENCBS383YWT	ENCLB754LHH	ENCFF361LRD	ENCFF786KPC	ENCSR970EBI	ENCBS298ZDQ	ENCLB140EDP	ENCFF917JQX	ENCFF381MBJ
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	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-25	BGKcLV19-26	BGKcLV19-26	BGKcLV19-26	BGKcLV19-26
Sample Name	NCL-BGKcLV19-25	NCL-BGKcLV19-25	NCL-BGKcLV19-25	NCL-BGKcLV19-25	NCL-BGKcLV19-25	NCL-BGKcLV19-25	NCL-BGKcLV19-26	NCL-BGKcLV19-26	NCL-BGKcLV19-26	NCL-BGKcLV19-26
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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		NCL-BGKcLV19-25.pdf	L-NCL-BGKcLV19-25.pdf				NCL-BGKcLV19-26.pdf	L-NCL-BGKcLV19-26.pdf
ID	2094	2143	2213	2283	2353	7264	2144	2214	2284	2354

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
NCL-BGKcLV19-25_S9_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	420	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1232
NCL-BGKcLV19-25_S9_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	420	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1282
NCL-BGKcLV19-25_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	420					GRCh38	V40	NCL-BGKcLV19-25_S9_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGKcLV19-25_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25225
NCL-BGKcLV19-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	420					GRCh38	V40	NCL-BGKcLV19-25_S9_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGKcLV19-25_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27179
NCL-BGKcLV19-25_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	420					GRCh38	V40	NCL-BGKcLV19-25/Aligned.sortedByCoord.out.bam		ENCORE2	27229
NCL-BGKcLV19-25_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	420					GRCh38	V40	NCL-BGKcLV19-25/Aligned.sortedByCoord.out.bam		ENCORE2	27279
NCL-BGKcLV19-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	420					GRCh38	V40	NCL-BGKcLV19-25/Aligned.sortedByCoord.out.bam		ENCORE2	27329
NCL-BGKcLV19-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	420					GRCh38	V40	NCL-BGKcLV19-25/Aligned.sortedByCoord.out.bam		ENCORE2	27379
NCL-BGKcLV19-26_S10_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	421	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1233
NCL-BGKcLV19-26_S10_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	421	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1283
NCL-BGKcLV19-26_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	421					GRCh38	V40	NCL-BGKcLV19-26_S10_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGKcLV19-26_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25226
NCL-BGKcLV19-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	421					GRCh38	V40	NCL-BGKcLV19-26_S10_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGKcLV19-26_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27180
NCL-BGKcLV19-26_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	421					GRCh38	V40	NCL-BGKcLV19-26/Aligned.sortedByCoord.out.bam		ENCORE2	27230
NCL-BGKcLV19-26_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	421					GRCh38	V40	NCL-BGKcLV19-26/Aligned.sortedByCoord.out.bam		ENCORE2	27280
NCL-BGKcLV19-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	421					GRCh38	V40	NCL-BGKcLV19-26/Aligned.sortedByCoord.out.bam		ENCORE2	27330
NCL-BGKcLV19-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	421					GRCh38	V40	NCL-BGKcLV19-26/Aligned.sortedByCoord.out.bam		ENCORE2	27380