NCL RNA-Seq in HepG2

General Information


RBP	NCL
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NCL-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR214EQY
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR013PBS
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	NCL-BGHcLV18-29
Rep2	NCL-BGHcLV18-30
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	76.6
Rep2_WB	78.8
Antibody Cat#	A300-710A
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB686POR
Status	Released
Project	ENCODE4
ID	111

Experiment Information (Status: Released)

	BGHcLV18-29	BGHcLV18-29	BGHcLV18-30	BGHcLV18-30
idx	522	522	523	523
TRCN#_or_BGC#	BGC#0000400	BGC#0000400	BGC#0000400	BGC#0000400
shRNA_or_gRNA_sequence	TTCACACTCCGCCGCCATCA	TTCACACTCCGCCGCCATCA	TTCACACTCCGCCGCCATCA	TTCACACTCCGCCGCCATCA
PAM	TGG	TGG	TGG	TGG
Name	NCL_94	NCL_94	NCL_94	NCL_94
Sample_ID	BGHcLV18-29	BGHcLV18-29	BGHcLV18-30	BGHcLV18-30
transduction_Date	8/13/19	8/13/19	8/13/19	8/13/19
days	D6	D6	D6	D6
RBP_name	NCL	NCL	NCL	NCL
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F	AGATGAAGAAGATGATAGCAGTGGA	AGATGAAGAAGATGATAGCAGTGGA
RT-qPCR_primer-R	GGGAAACGACCACCTTCTTT	GGGAAACGACCACCTTCTTT
protein_conc	4175	4175	3412	3412
WB_result	76.6	85.9	78.8	79.7
Ave_WB	77.7
WB_DONE_date	8/26/19	6/28/24	wes
MW	77KD	70KD
IP	Rabbit / I		Polyclonal
antibody_Cat#	A300-710A	14574S	lot #1	lot #1
Antibody DCC ID	ENCAB686POR
submitted_to_DCC_date
Rep1_TPM	1605	0	0	0
Rep2_TPM	1434	0	0	0
Action	Ready		Ready
Library_start_date	12/11/19		12/11/19
repeat_library
Note
ID	6675	6677	6676	6678

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
NCL	Product_ID: 14574S Lot_ID: 1 Source: Cell Signaling Technology Target Name: NCL-human

Experiment Status

	BGHcLV18-29	BGHcLV18-30
Sample_ID	BGHcLV18-29	BGHcLV18-30
Sample Name
Sample Name	NCL-BGHcLV18-29	NCL-BGHcLV18-30
RBP	NCL	NCL
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5639	5640

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-29	BGHcLV18-30
Sample #	145	146
Sample Name	NCL-BGHcLV18-29	NCL-BGHcLV18-30
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	4-E2	4-F2
Tecan	41.67	34.92
Tecan_date	2019-12-16	2019-12-16
Size_bp	267	273
Peak_Molarity	31.60	29.50
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G7.png	DNA_Library_set43-44/set2/H7.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/C9.png	RNA_Library_set43-44/set4/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-29	BGHcLV18-30
RBP	NCL	NCL
Batch_ID	BGHcLV18	BGHcLV18
WB_result	76.600	78.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	721	722

Sequencing Information

	BGHcLV18-29	BGHcLV18-30
Sample_ID	BGHcLV18-29	BGHcLV18-30
Sample Name	NCL-BGHcLV18-29	NCL-BGHcLV18-30
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	240,484,694	149,519,906
total_aligned_reads	232,178,328	142,724,070
unique_aligned_reads	217,233,452	133,757,884
percent_uniqueAligned	0.90332	0.89458
correlation_replicates	0.999325	0.999325
spikein_reads	376,374	211,716
percent_spikeins	0.00157	0.00142
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	227	228

Data Submission Information

	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-30	BGHcLV18-30	BGHcLV18-30	BGHcLV18-30
ENCODE_alias	brenton-graveley:NCL-BGHcLV18	brenton-graveley:NCL-BGHcLV18-29	brenton-graveley:L-NCL-BGHcLV18-29	brenton-graveley:NCL-BGHcLV18-29_S57_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCL-BGHcLV18-29_S57_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCL-BGHcLV18-HepG2	brenton-graveley:NCL-BGHcLV18-30	brenton-graveley:L-NCL-BGHcLV18-30	brenton-graveley:NCL-BGHcLV18-30_S58_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCL-BGHcLV18-30_S58_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR013PBS	ENCBS969RYG	ENCLB229UZX	ENCFF453FLY	ENCFF784SYJ	ENCSR214EQY	ENCBS841WPR	ENCLB881OAU	ENCFF692NAO	ENCFF649ODX
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	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-29	BGHcLV18-30	BGHcLV18-30	BGHcLV18-30	BGHcLV18-30
Sample Name	NCL-BGHcLV18-29	NCL-BGHcLV18-29	NCL-BGHcLV18-29	NCL-BGHcLV18-29	NCL-BGHcLV18-29	NCL-BGHcLV18-29	NCL-BGHcLV18-30	NCL-BGHcLV18-30	NCL-BGHcLV18-30	NCL-BGHcLV18-30
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		NCL-BGHcLV18-29.pdf	L-NCL-BGHcLV18-29.pdf				NCL-BGHcLV18-30.pdf	L-NCL-BGHcLV18-30.pdf
ID	58	196	362	612	664	7263	197	363	613	665

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-BGHcLV18-29_S57_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	227	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	195
NCL-BGHcLV18-29_S57_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	227	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	247
NCL-BGHcLV18-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	227					GRCh38	V40	NCL-BGHcLV18-29_S57_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGHcLV18-29_S57_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24915
NCL-BGHcLV18-29_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	227					GRCh38	V40	NCL-BGHcLV18-29/Aligned.sortedByCoord.out.bam		ENCORE2	24967
NCL-BGHcLV18-29_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	227					GRCh38	V40	NCL-BGHcLV18-29/Aligned.sortedByCoord.out.bam		ENCORE2	25019
NCL-BGHcLV18-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	227					GRCh38	V40	NCL-BGHcLV18-29/Aligned.sortedByCoord.out.bam		ENCORE2	25071
NCL-BGHcLV18-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	227					GRCh38	V40	NCL-BGHcLV18-29/Aligned.sortedByCoord.out.bam		ENCORE2	25123
NCL-BGHcLV18-29_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	227					GRCh38	V40	NCL-BGHcLV18-29_S57_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGHcLV18-29_S57_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25175
NCL-BGHcLV18-30_S58_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	228	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	196
NCL-BGHcLV18-30_S58_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	228	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	248
NCL-BGHcLV18-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	228					GRCh38	V40	NCL-BGHcLV18-30_S58_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGHcLV18-30_S58_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24916
NCL-BGHcLV18-30_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	228					GRCh38	V40	NCL-BGHcLV18-30/Aligned.sortedByCoord.out.bam		ENCORE2	24968
NCL-BGHcLV18-30_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	228					GRCh38	V40	NCL-BGHcLV18-30/Aligned.sortedByCoord.out.bam		ENCORE2	25020
NCL-BGHcLV18-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	228					GRCh38	V40	NCL-BGHcLV18-30/Aligned.sortedByCoord.out.bam		ENCORE2	25072
NCL-BGHcLV18-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	228					GRCh38	V40	NCL-BGHcLV18-30/Aligned.sortedByCoord.out.bam		ENCORE2	25124
NCL-BGHcLV18-30_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	228					GRCh38	V40	NCL-BGHcLV18-30_S58_R1_001.filtered.trimmed.paired.fastq.gz,NCL-BGHcLV18-30_S58_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25176