TAF9 RNA-Seq in HepG2

General Information


RBP	TAF9
Cell_Line	HepG2
Method	CRISPR
Exp_Name	TAF9-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR884YQK
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR861BRA
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	TAF9-BGHcLV20-37
Rep2	TAF9-BGHcLV20-38
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	97.7
Rep2_qPCR	98.6
Rep1_WB	69.8
Rep2_WB	73.4
Antibody Cat#	PA5-40919
Antibody Lot#	lot# TL2693011
Antibody DCC ID	ENCAB320JFK
Status	Released
Project	ENCODE4
ID	82

Experiment Information (Status: Released)

	BGHcLV20-37	BGHcLV20-38
idx	587	588
TRCN#_or_BGC#	BGC#0000491	BGC#0000491
shRNA_or_gRNA_sequence	TTGTCTTACAGGTACACCAG	TTGTCTTACAGGTACACCAG
PAM	GGG	GGG
Name	TAF9_70	TAF9_70
Sample_ID	BGHcLV20-37	BGHcLV20-38
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	TAF9	TAF9
qPCR_result	97.7	98.6
Ave_qPCR	98.2
RT-qPCR_primer-F	CGAAGTACCGACCCGAGTTA
RT-qPCR_primer-R	TTTTTCCAACCCCTGGTGTA
protein_conc	6681	6349
WB_result	69.8	73.4
Ave_WB	71.6
WB_DONE_date	2/6/20
MW	29KD
IP	Rabbit / I
antibody_Cat#	PA5-40919	lot# TL2693011
Antibody DCC ID	ENCAB320JFK
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	6742	6743

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV20-37	BGHcLV20-38
Sample_ID	BGHcLV20-37	BGHcLV20-38
Sample Name
Sample Name	TAF9-BGHcLV20-37	TAF9-BGHcLV20-38
RBP	TAF9	TAF9
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5825	5826

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-37	BGHcLV20-38
Sample #	75	76
Sample Name	TAF9-BGHcLV20-37	TAF9-BGHcLV20-38
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	324	316
Peak_Molarity	99.00	130.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E9.png	DNA_Library_set45/set1/F9.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_set45/set1/E9.png	RNA_Library_set45/set2/E11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-37	BGHcLV20-38
RBP	TAF9	TAF9
Batch_ID	BGHcLV20	BGHcLV20
WB_result	69.800	73.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	849	850

Sequencing Information

	BGHcLV20-37	BGHcLV20-38
Sample_ID	BGHcLV20-37	BGHcLV20-38
Sample Name	TAF9-BGHcLV20-37	TAF9-BGHcLV20-38
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	96,134,468	87,119,518
total_aligned_reads	93,748,330	84,479,196
unique_aligned_reads	88,562,718	79,827,038
percent_uniqueAligned	0.92124	0.91629
correlation_replicates	0.993975	0.993975
spikein_reads	57,540	44,718
percent_spikeins	0.00060	0.00051
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	480	481

Data Submission Information

	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-38	BGHcLV20-38	BGHcLV20-38	BGHcLV20-38
ENCODE_alias	brenton-graveley:TAF9-BGHcLV20	brenton-graveley:TAF9-BGHcLV20-37	brenton-graveley:L-TAF9-BGHcLV20-37	brenton-graveley:TAF9-BGHcLV20-37_S69_R1_001.fastq.gz	brenton-graveley:TAF9-BGHcLV20-37_S69_R2_001.fastq.gz	brenton-graveley:TAF9-BGHcLV20-HepG2	brenton-graveley:TAF9-BGHcLV20-38	brenton-graveley:L-TAF9-BGHcLV20-38	brenton-graveley:TAF9-BGHcLV20-38_S70_R1_001.fastq.gz	brenton-graveley:TAF9-BGHcLV20-38_S70_R2_001.fastq.gz
ENCODE_accession	ENCSR861BRA	ENCBS815SDI	ENCLB711TMO	ENCFF359OJS	ENCFF126FSB	ENCSR884YQK	ENCBS996LWJ	ENCLB384FAI	ENCFF395VUM	ENCFF822ZKA
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	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-37	BGHcLV20-38	BGHcLV20-38	BGHcLV20-38	BGHcLV20-38
Sample Name	TAF9-BGHcLV20-37	TAF9-BGHcLV20-37	TAF9-BGHcLV20-37	TAF9-BGHcLV20-37	TAF9-BGHcLV20-37	TAF9-BGHcLV20-37	TAF9-BGHcLV20-38	TAF9-BGHcLV20-38	TAF9-BGHcLV20-38	TAF9-BGHcLV20-38
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV45H_library_protocol					LV45H_library_protocol
protocol_URL			L-TAF9-BGHcLV20-37.pdf					L-TAF9-BGHcLV20-38.pdf
ID	2089	2133	2203	2273	2343	7343	2134	2204	2274	2344

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
TAF9-BGHcLV20-37_S69_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	480	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1326
TAF9-BGHcLV20-37_S69_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	480	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1346
TAF9-BGHcLV20-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	480					GRCh38	V40	TAF9-BGHcLV20-37_S69_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGHcLV20-37_S69_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24867
TAF9-BGHcLV20-37_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	480					GRCh38	V40	TAF9-BGHcLV20-37_S69_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGHcLV20-37_S69_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24887
TAF9-BGHcLV20-37_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	480					GRCh38	V40	TAF9-BGHcLV20-37/Aligned.sortedByCoord.out.bam		ENCORE2	25937
TAF9-BGHcLV20-37_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	480					GRCh38	V40	TAF9-BGHcLV20-37/Aligned.sortedByCoord.out.bam		ENCORE2	25957
TAF9-BGHcLV20-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	480					GRCh38	V40	TAF9-BGHcLV20-37/Aligned.sortedByCoord.out.bam		ENCORE2	25977
TAF9-BGHcLV20-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	480					GRCh38	V40	TAF9-BGHcLV20-37/Aligned.sortedByCoord.out.bam		ENCORE2	25997
TAF9-BGHcLV20-38_S70_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	481	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1327
TAF9-BGHcLV20-38_S70_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	481	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1347
TAF9-BGHcLV20-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	481					GRCh38	V40	TAF9-BGHcLV20-38_S70_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGHcLV20-38_S70_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24868
TAF9-BGHcLV20-38_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	481					GRCh38	V40	TAF9-BGHcLV20-38_S70_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGHcLV20-38_S70_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24888
TAF9-BGHcLV20-38_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	481					GRCh38	V40	TAF9-BGHcLV20-38/Aligned.sortedByCoord.out.bam		ENCORE2	25938
TAF9-BGHcLV20-38_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	481					GRCh38	V40	TAF9-BGHcLV20-38/Aligned.sortedByCoord.out.bam		ENCORE2	25958
TAF9-BGHcLV20-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	481					GRCh38	V40	TAF9-BGHcLV20-38/Aligned.sortedByCoord.out.bam		ENCORE2	25978
TAF9-BGHcLV20-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	481					GRCh38	V40	TAF9-BGHcLV20-38/Aligned.sortedByCoord.out.bam		ENCORE2	25998