NIPBL RNA-Seq in K562

General Information


RBP	NIPBL
Cell_Line	K562
Method	CRISPR
Exp_Name	NIPBL-BGKcLV08-K562
ENCODE_series_ID	ENCSR890SYA
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR999DVK
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	NIPBL-BGKcLV08-43
Rep2	NIPBL-BGKcLV08-44
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	5.8
Rep2_qPCR	19.0
Rep1_WB	64.5
Rep2_WB	64.4
Antibody Cat#
Antibody Lot#
Antibody DCC ID
Status	Released
Project	ENCODE4
ID	206

Experiment Information (Status: Released)

	BGKcLV08-43	BGKcLV08-44
idx	268	269
TRCN#_or_BGC#	BGC#0000131	BGC#0000131
shRNA_or_gRNA_sequence	GCTTGTCCATAGCCTCAACC	GCTTGTCCATAGCCTCAACC
PAM	AGG	AGG
Name	NIPBL-82F	NIPBL-82F
Sample_ID	BGKcLV08-43	BGKcLV08-44
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	NIPBL	NIPBL
qPCR_result	5.8	19.0
Ave_qPCR	12.4
RT-qPCR_primer-F	tactcttgcggggattgcta
RT-qPCR_primer-R	ggcagttcacctcttctgct
protein_conc	3446	3794
WB_result	64.5	64.4
Ave_WB	64.5
WB_DONE_date	4/13/18
MW	320kDa
IP
antibody_Cat#
Antibody DCC ID	no ID
submitted_to_DCC_date
Rep1_TPM	23	0
Rep2_TPM	25.7	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4368	4369

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NIPBL	Product_ID: KY_SCC2C_01 Lot_ID: 93015 Source: Kyoko Yokomori Target Name: NIPBL-human

Experiment Status

	BGKcLV08-43	BGKcLV08-44
Sample_ID	BGKcLV08-43	BGKcLV08-44
Sample Name
Sample Name	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-44
RBP	NIPBL	NIPBL
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6183	6184

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-43	BGKcLV08-44
Sample #	19	20
Sample Name	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-44
Sample_Name_Alias
Index Well Position	C03	D03
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	274	280
Peak_Molarity	67.60	59.30
libSampleQC_DNA_Well	DNA_Library_set41/set2/C3.png	DNA_Library_set41/set2/D3.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set41/set1/C3.png	RNA_Library_set41/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-43	BGKcLV08-44
RBP	NIPBL	NIPBL
Batch_ID	BGKcLV08	BGKcLV08
WB_result	64.500	64.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	869	870

Sequencing Information

	BGKcLV08-43	BGKcLV08-44
Sample_ID	BGKcLV08-43	BGKcLV08-44
Sample Name	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-44
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	212,935,028	97,725,182
total_aligned_reads	202,092,424	93,599,024
unique_aligned_reads	181,448,758	83,727,722
percent_uniqueAligned	0.85213	0.85677
correlation_replicates	0.997995	0.997995
spikein_reads	361,824	188,372
percent_spikeins	0.00170	0.00193
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	275	276

Data Submission Information

	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-44	BGKcLV08-44	BGKcLV08-44	BGKcLV08-44
ENCODE_alias	brenton-graveley:NIPBL-BGKcLV08	brenton-graveley:NIPBL-BGKcLV08-43	brenton-graveley:L-NIPBL-BGKcLV08-43	brenton-graveley:NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIPBL-BGKcLV08-K562	brenton-graveley:NIPBL-BGKcLV08-44	brenton-graveley:L-NIPBL-BGKcLV08-44	brenton-graveley:NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR999DVK	ENCBS217NYK	ENCLB514FXP	ENCFF863RMG	ENCFF808JYV	ENCSR890SYA	ENCBS316QHL	ENCLB863BTV	ENCFF442UYN	ENCFF313JCA
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	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-43	BGKcLV08-44	BGKcLV08-44	BGKcLV08-44	BGKcLV08-44
Sample Name	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-43	NIPBL-BGKcLV08-44	NIPBL-BGKcLV08-44	NIPBL-BGKcLV08-44	NIPBL-BGKcLV08-44
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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_library_protocol					LV41_library_protocol
protocol_URL			L-NIPBL-BGKcLV08-43.pdf					L-NIPBL-BGKcLV08-44.pdf
ID	1132	1184	1254	1324	1425	7268	1185	1255	1325	1426

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
NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	275				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	531
NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	275				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	601
NIPBL-BGKcLV08-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	275	GRCh38	V40	NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26769
NIPBL-BGKcLV08-43_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	275	GRCh38	V40	NIPBL-BGKcLV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	26839
NIPBL-BGKcLV08-43_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	275	GRCh38	V40	NIPBL-BGKcLV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	26909
NIPBL-BGKcLV08-43_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	275	GRCh38	V40	NIPBL-BGKcLV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	26979
NIPBL-BGKcLV08-43_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	275	GRCh38	V40	NIPBL-BGKcLV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	27049
NIPBL-BGKcLV08-43_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	275	GRCh38	V40	NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIPBL-BGKcLV08-43_ATGTAAGT+ACTCTATG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27119
NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	276				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	532
NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	276				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	602
NIPBL-BGKcLV08-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	276	GRCh38	V40	NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26770
NIPBL-BGKcLV08-44_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	276	GRCh38	V40	NIPBL-BGKcLV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	26840
NIPBL-BGKcLV08-44_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	276	GRCh38	V40	NIPBL-BGKcLV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	26910
NIPBL-BGKcLV08-44_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	276	GRCh38	V40	NIPBL-BGKcLV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	26980
NIPBL-BGKcLV08-44_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	276	GRCh38	V40	NIPBL-BGKcLV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	27050
NIPBL-BGKcLV08-44_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	276	GRCh38	V40	NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIPBL-BGKcLV08-44_GCACGGAC+GTCTCGCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27120