SEPT7 RNA-Seq in HepG2

General Information


RBP	SEPT7
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SEPT7-BGHcLV34-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV34
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SEPT7-BGHcLV34-45
Rep2	SEPT7-BGHcLV34-46
CN1	NT-BGHcLV34-1
CN2	NT-BGHcLV34-2
Rep1_qPCR	12.0
Rep2_qPCR	35.0
Rep1_WB	77.9
Rep2_WB	78.1
Antibody Cat#	A304-212A
Antibody Lot#	LOT #1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	946

Experiment Information (Status: Submitting)

	BGHcLV34-45	BGHcLV34-45	BGHcLV34-46	BGHcLV34-46
idx	1115	1115	1116	1116
TRCN#_or_BGC#	BGC#0000860	BGC#0000860	BGC#0000860	BGC#0000860
shRNA_or_gRNA_sequence	AGGTTTTGAATTCACGCTTA	AGGTTTTGAATTCACGCTTA	AGGTTTTGAATTCACGCTTA	AGGTTTTGAATTCACGCTTA
PAM	TGG	TGG	TGG	TGG
Name	SEPTIN7_87	SEPTIN7_87	SEPTIN7_87	SEPTIN7_87
Sample_ID	BGHcLV34-45	BGHcLV34-45	BGHcLV34-46	BGHcLV34-46
transduction_Date	3/24/22	3/24/22	3/24/22	3/24/22
days	D6	D6	D6	D6
RBP_name	SEPT7	SEPT7	SEPT7	SEPT7
qPCR_result	12.0	12.0	35.0	35.0
Ave_qPCR	23.5	23.5
RT-qPCR_primer-F	aggatttggagatgcagtgg
RT-qPCR_primer-R	aggcatctgacgtctgttca
protein_conc	2454	2454	3198	3198
WB_result	77.9	62.8	78.1	60.2
Ave_WB	78.0	61.5
WB_DONE_date	4/12/22	7/6/22
MW	51kd	51kd
IP
antibody_Cat#	A304-212A	A304-213A	LOT #1	LOT #1
Antibody DCC ID	NO ID	NO ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	06/17/22		06/17/22
repeat_library
Note
ID	7294	7296	7295	7297

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SEPT7	Product_ID: A304-213A Lot_ID: 1 Source: Bethyl Labs Target Name: SEPT7-human
SEPT7	Product_ID: A304-212A Lot_ID: 1 Source: Bethyl Labs Target Name: SEPT7-human

Experiment Status

	BGHcLV34-45	BGHcLV34-46
Sample_ID	BGHcLV34-45	BGHcLV34-46
Sample Name
Sample Name	SEPT7-BGHcLV34-45	SEPT7-BGHcLV34-46
RBP	SEPT7	SEPT7
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10813	10814

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-45	BGHcLV34-46
Sample #	17	18
Sample Name	SEPT7-BGHcLV34-45	SEPT7-BGHcLV34-46
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	281	283
Peak_Molarity	50.30	43.40
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/A7.png	DNA_Library_set54-56/set3/B7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/A3.png	RNA_Library_set54-56/set2/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-45	BGHcLV34-46
RBP	SEPT7	SEPT7
Batch_ID	BGHcLV34	BGHcLV34
WB_result	77.900	78.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3334	3335

Sequencing Information

	BGHcLV34-45	BGHcLV34-46
Sample_ID	BGHcLV34-45	BGHcLV34-46
Sample Name	SEPT7-BGHcLV34-45	SEPT7-BGHcLV34-46
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	60,683,580	82,373,784
total_aligned_reads	53,481,628	70,009,946
unique_aligned_reads	50,510,496	66,170,684
percent_uniqueAligned	0.83236	0.80330
correlation_replicates	0.993397	0.993397
spikein_reads	7,308	4,288
percent_spikeins	0.00012	0.00005
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2207	2208

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
SEPT7-BGHcLV34-45_S13_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2207	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8522
SEPT7-BGHcLV34-45_S13_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2207	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8572
SEPT7-BGHcLV34-45_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2207					GRCh38	V40	SEPT7-BGHcLV34-45/Aligned.sortedByCoord.out.bam		ENCORE2	17768
SEPT7-BGHcLV34-45_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2207					GRCh38	V40	SEPT7-BGHcLV34-45/Aligned.sortedByCoord.out.bam		ENCORE2	17818
SEPT7-BGHcLV34-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2207					GRCh38	V40	SEPT7-BGHcLV34-45/Aligned.sortedByCoord.out.bam		ENCORE2	17868
SEPT7-BGHcLV34-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2207					GRCh38	V40	SEPT7-BGHcLV34-45/Aligned.sortedByCoord.out.bam		ENCORE2	17918
SEPT7-BGHcLV34-45_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2207					GRCh38	V40	SEPT7-BGHcLV34-45_S13_R1_001.filtered.trimmed.paired.fastq.gz,SEPT7-BGHcLV34-45_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17968
SEPT7-BGHcLV34-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2207					GRCh38	V40	SEPT7-BGHcLV34-45_S13_R1_001.filtered.trimmed.paired.fastq.gz,SEPT7-BGHcLV34-45_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29309
SEPT7-BGHcLV34-46_S14_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2208	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8523
SEPT7-BGHcLV34-46_S14_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2208	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8573
SEPT7-BGHcLV34-46_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2208					GRCh38	V40	SEPT7-BGHcLV34-46/Aligned.sortedByCoord.out.bam		ENCORE2	17769
SEPT7-BGHcLV34-46_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2208					GRCh38	V40	SEPT7-BGHcLV34-46/Aligned.sortedByCoord.out.bam		ENCORE2	17819
SEPT7-BGHcLV34-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2208					GRCh38	V40	SEPT7-BGHcLV34-46/Aligned.sortedByCoord.out.bam		ENCORE2	17869
SEPT7-BGHcLV34-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2208					GRCh38	V40	SEPT7-BGHcLV34-46/Aligned.sortedByCoord.out.bam		ENCORE2	17919
SEPT7-BGHcLV34-46_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2208					GRCh38	V40	SEPT7-BGHcLV34-46_S14_R1_001.filtered.trimmed.paired.fastq.gz,SEPT7-BGHcLV34-46_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17969
SEPT7-BGHcLV34-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2208					GRCh38	V40	SEPT7-BGHcLV34-46_S14_R1_001.filtered.trimmed.paired.fastq.gz,SEPT7-BGHcLV34-46_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29310