SEPT11 RNA-Seq in HepG2

General Information


RBP	SEPT11
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SEPT11-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR037RRC
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR036HUB
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SEPT11-BGHcLV31-41
Rep2	SEPT11-BGHcLV31-42
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	78.6
Rep2_qPCR	74.7
Rep1_WB	81.6
Rep2_WB	81.6
Antibody Cat#	A304-176A
Antibody Lot#	LOT #1
Antibody DCC ID	no ID
Status	Submitted
Project	ENCODE4
ID	930

Experiment Information (Status: Released)

	BGHcLV31-41	BGHcLV31-42
idx	961	962
TRCN#_or_BGC#	BGC#0000857	BGC#0000857
shRNA_or_gRNA_sequence	TTAACCATTGTTGACACCGT	TTAACCATTGTTGACACCGT
PAM	GGG	GGG
Name	SEPTIN11_91	SEPTIN11_91
Sample_ID	BGHcLV31-41	BGHcLV31-42
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SEPT11	SEPT11
qPCR_result	78.6	74.7
Ave_qPCR	76.7
RT-qPCR_primer-F	actgaccctgacagcaaacc
RT-qPCR_primer-R	tctgcagttctcccaggaat
protein_conc	3766	3352
WB_result	81.6	81.6
Ave_WB	81.6
WB_DONE_date	11/8/21
MW	49kd
IP
antibody_Cat#	A304-176A	LOT #1
Antibody DCC ID	no ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7140	7141

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV31-41	BGHcLV31-42
Sample_ID	BGHcLV31-41	BGHcLV31-42
Sample Name
Sample Name	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-42
RBP	SEPT11	SEPT11
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10315	10316

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-41	BGHcLV31-42
Sample #	29	30
Sample Name	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-42
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	295	285
Peak_Molarity	62.90	74.80
libSampleQC_DNA_Well	DNA_Library_set52/set1/E11.png	DNA_Library_set52/set1/F11.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set52/set1/E4.png	RNA_Library_set52/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-41	BGHcLV31-42
RBP	SEPT11	SEPT11
Batch_ID	BGHcLV31	BGHcLV31
WB_result	81.600	81.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3206	3207

Sequencing Information

	BGHcLV31-41	BGHcLV31-42
Sample_ID	BGHcLV31-41	BGHcLV31-42
Sample Name	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-42
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	104,981,668	84,819,982
total_aligned_reads	94,592,884	76,297,558
unique_aligned_reads	89,221,912	71,917,856
percent_uniqueAligned	0.84988	0.84789
correlation_replicates	0.996991	0.996991
spikein_reads	3,466	3,180
percent_spikeins	0.00003	0.00004
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2003	2004

Data Submission Information

	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-42	BGHcLV31-42	BGHcLV31-42	BGHcLV31-42
ENCODE_alias	brenton-graveley:SEPT11-BGHcLV31	brenton-graveley:SEPT11-BGHcLV31-41	brenton-graveley:L-SEPT11-BGHcLV31-41	brenton-graveley:SEPT11-BGHcLV31-41_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEPT11-BGHcLV31-41_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEPT11-BGHcLV31-HepG2	brenton-graveley:SEPT11-BGHcLV31-42	brenton-graveley:L-SEPT11-BGHcLV31-42	brenton-graveley:SEPT11-BGHcLV31-42_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEPT11-BGHcLV31-42_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR036HUB	ENCBS024CFI	ENCLB656ZWO	ENCFF108GSR	ENCFF559IYP	ENCSR037RRC	ENCBS236PDD	ENCLB401CQK	ENCFF157CFY	ENCFF737YBD
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	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-41	BGHcLV31-42	BGHcLV31-42	BGHcLV31-42	BGHcLV31-42
Sample Name	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-41	SEPT11-BGHcLV31-42	SEPT11-BGHcLV31-42	SEPT11-BGHcLV31-42	SEPT11-BGHcLV31-42
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV52_library_protocol					LV52_library_protocol
protocol_URL			L-SEPT11-BGHcLV31-41.pdf					L-SEPT11-BGHcLV31-42.pdf
ID	7458	7527	7635	7745	7855	7950	7528	7636	7746	7856

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
SEPT11-BGHcLV31-41_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2003	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6549
SEPT11-BGHcLV31-41_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2003	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6603
SEPT11-BGHcLV31-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2003					GRCh38	V40	SEPT11-BGHcLV31-41_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGHcLV31-41_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18470
SEPT11-BGHcLV31-41_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2003					GRCh38	V40	SEPT11-BGHcLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	18524
SEPT11-BGHcLV31-41_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2003					GRCh38	V40	SEPT11-BGHcLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	18578
SEPT11-BGHcLV31-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2003					GRCh38	V40	SEPT11-BGHcLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	18632
SEPT11-BGHcLV31-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2003					GRCh38	V40	SEPT11-BGHcLV31-41/Aligned.sortedByCoord.out.bam		ENCORE2	18686
SEPT11-BGHcLV31-41_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2003					GRCh38	V40	SEPT11-BGHcLV31-41_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGHcLV31-41_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18740
SEPT11-BGHcLV31-42_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2004	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6550
SEPT11-BGHcLV31-42_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2004	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6604
SEPT11-BGHcLV31-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2004					GRCh38	V40	SEPT11-BGHcLV31-42_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGHcLV31-42_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18471
SEPT11-BGHcLV31-42_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2004					GRCh38	V40	SEPT11-BGHcLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	18525
SEPT11-BGHcLV31-42_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2004					GRCh38	V40	SEPT11-BGHcLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	18579
SEPT11-BGHcLV31-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2004					GRCh38	V40	SEPT11-BGHcLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	18633
SEPT11-BGHcLV31-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2004					GRCh38	V40	SEPT11-BGHcLV31-42/Aligned.sortedByCoord.out.bam		ENCORE2	18687
SEPT11-BGHcLV31-42_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2004					GRCh38	V40	SEPT11-BGHcLV31-42_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGHcLV31-42_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18741