NIPBL RNA-Seq in HepG2

Experiment Information (Status: NotSatisfied)

	BGHcLV07-17	BGHcLV07-18
idx	129	130
TRCN#_or_BGC#	BGC#0000061	BGC#0000061
shRNA_or_gRNA_sequence	GGCTTGTAGGGATGACAATT	GGCTTGTAGGGATGACAATT
PAM
Name	NIPBL_81	NIPBL_81
Sample_ID	BGHcLV07-17	BGHcLV07-18
transduction_Date	6/13/17	6/13/17
days	D6	D6
RBP_name	NIPBL	NIPBL
qPCR_result	0.0	0.0
Ave_qPCR	0
RT-qPCR_primer-F	tactcttgcggggattgcta
RT-qPCR_primer-R	ggcagttcacctcttctgct
protein_conc	3671	3373
WB_result
Ave_WB
WB_DONE_date	7/25/17
MW	316kd
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	15	0
Rep2_TPM	17	0
Action	Ready	Ready
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	6272	6273

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV07-17	BGHcLV07-18
Sample_ID	BGHcLV07-17	BGHcLV07-18
Sample Name	NIPBL-BGHcLV07-17B	NIPBL-BGHcLV07-18B
Sample Name
RBP	NIPBL	NIPBL
Cell_Line	HepG2	HepG2
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2020-11-04	2020-11-04
Project	ENCODE4	ENCODE4
Note	bad KD%	bad KD%
ID	6427	6428

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV07-17	BGHcLV07-18
Sample #	11	12
Sample Name	NIPBL-BGHcLV07-17B	NIPBL-BGHcLV07-18B
Sample_Name_Alias
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	291	297
Peak_Molarity	14.30	16.30
libSampleQC_DNA_Well	DNA_Library_set40/set1/E8.png	DNA_Library_set40/set1/F8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set40/set1/G3.png	RNA_Library_set40/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHcLV07-17	BGHcLV07-18
RBP	NIPBL	NIPBL
Batch_ID	BGHcLV07	BGHcLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	934	935

Sequencing Information

	BGHcLV07-17	BGHcLV07-18	BGHcLV07-18
Sample_ID	BGHcLV07-17	BGHcLV07-18	BGHcLV07-18
Sample Name	NIPBL-BGHcLV07-17B	NIPBL-BGHcLV07-18B	NIPBL-BGHcLV07-18B
Pool ID	Pool-180109	Pool-180109	Pool-180316
LocalServer_folder	set40_H	set40_H	set40_H
total_reads	35,036,162	21,450,590	25,378,156
total_aligned_reads	28,981,030	17,218,132	19,778,148
unique_aligned_reads	27,332,422	16,265,750	18,681,632
percent_uniqueAligned	0.78012	0.75829	0.73613
correlation_replicates	0.994170	0.994170
spikein_reads	4,422	3,204	3,644
percent_spikeins	0.00013	0.00015	0.00014
original_ReadLength	100	100	100
QC_Status	OtherReasonsNotToSubmit	OtherReasonsNotToSubmit	OtherReasonsNotToSubmit
ID	337	338	397

Data Submission Information DCC submission information was not avaliable

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
NIPBL-BGHcLV07-17B_ACAGTG_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	337	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	653
NIPBL-BGHcLV07-17B_ACAGTG_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	337	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	695
NIPBL-BGHcLV07-17B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	337					GRCh38	V40	NIPBL-BGHcLV07-17B_ACAGTG_ACBYWVANXX_L004_001.R1.fastq.gz,NIPBL-BGHcLV07-17B_ACAGTG_ACBYWVANXX_L004_001.R2.fastq.gz		ENCORE2	23258
NIPBL-BGHcLV07-17B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	337					GRCh38	V40	NIPBL-BGHcLV07-17B/Aligned.sortedByCoord.out.bam		ENCORE2	23292
NIPBL-BGHcLV07-17B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	337					GRCh38	V40	NIPBL-BGHcLV07-17B/Aligned.sortedByCoord.out.bam		ENCORE2	23326
NIPBL-BGHcLV07-17B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	337					GRCh38	V40	NIPBL-BGHcLV07-17B/Aligned.sortedByCoord.out.bam		ENCORE2	23360
NIPBL-BGHcLV07-17B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	337					GRCh38	V40	NIPBL-BGHcLV07-17B/Aligned.sortedByCoord.out.bam		ENCORE2	23394
NIPBL-BGHcLV07-17B_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	337					GRCh38	V40	NIPBL-BGHcLV07-17B_ACAGTG_ACBYWVANXX_L004_001.R1.fastq.gz,NIPBL-BGHcLV07-17B_ACAGTG_ACBYWVANXX_L004_001.R2.fastq.gz		ENCORE2	23428
NIPBL-BGHcLV07-18B_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	338	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	23234
NIPBL-BGHcLV07-18B_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	338	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	23242
NIPBL-BGHcLV07-18B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	338					GRCh38	V40	NIPBL-BGHcLV07-18B_L001_001.R1.fastq.gz,NIPBL-BGHcLV07-18B_L001_001.R2.fastq.gz		ENCORE2	23259
NIPBL-BGHcLV07-18B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	338					GRCh38	V40	NIPBL-BGHcLV07-18B/Aligned.sortedByCoord.out.bam		ENCORE2	23293
NIPBL-BGHcLV07-18B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	338					GRCh38	V40	NIPBL-BGHcLV07-18B/Aligned.sortedByCoord.out.bam		ENCORE2	23327
NIPBL-BGHcLV07-18B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	338					GRCh38	V40	NIPBL-BGHcLV07-18B/Aligned.sortedByCoord.out.bam		ENCORE2	23361
NIPBL-BGHcLV07-18B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	338					GRCh38	V40	NIPBL-BGHcLV07-18B/Aligned.sortedByCoord.out.bam		ENCORE2	23395
NIPBL-BGHcLV07-18B_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	338					GRCh38	V40	NIPBL-BGHcLV07-18B_L001_001.R1.fastq.gz,NIPBL-BGHcLV07-18B_L001_001.R2.fastq.gz		ENCORE2	23429