TAF9 RNA-Seq in K562

General Information


RBP	TAF9
Cell_Line	K562
Method	CRISPR
Exp_Name	TAF9-BGKcLV19-K562
ENCODE_series_ID	ENCSR154LSO
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR490PSG
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	TAF9-BGKcLV19-53
Rep2	TAF9-BGKcLV19-54
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	98.48
Rep2_qPCR	98.18
Rep1_WB	97.4
Rep2_WB	99.0
Antibody Cat#	PA5-40919
Antibody Lot#
Antibody DCC ID	ENCAB320JFK
Status	Released
Project	ENCODE4
ID	61

Experiment Information (Status: Released)

	BGKcLV19-53	BGKcLV19-54
idx	727	728
TRCN#_or_BGC#	BGC#0000491	BGC#0000491
shRNA_or_gRNA_sequence	TTGTCTTACAGGTACACCAG	TTGTCTTACAGGTACACCAG
PAM	GGG	GGG
Name	TAF9_70	TAF9_70
Sample_ID	BGKcLV19-53	BGKcLV19-54
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	TAF9	TAF9
qPCR_result	98.48	98.18
Ave_qPCR
RT-qPCR_primer-F	CGAAGTACCGACCCGAGTTA
RT-qPCR_primer-R	TTTTTCCAACCCCTGGTGTA
protein_conc	4042	3798
WB_result	97.4	99.0
Ave_WB	98.2
WB_DONE_date	11/15/19
MW	29KD
IP	Rabbit / I
antibody_Cat#	PA5-40919
Antibody DCC ID	ENCAB320JFK
submitted_to_DCC_date	11/16/20
Rep1_TPM	276.5	0
Rep2_TPM	293.2	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4847	4848

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TAF9	Product_ID: PA5-40919 Lot_ID: TL2693011 Source: Thermo Fisher Target Name: TAF9-human

Experiment Status

	BGKcLV19-53	BGKcLV19-54
Sample_ID	BGKcLV19-53	BGKcLV19-54
Sample Name
Sample Name	TAF9-BGKcLV19-53	TAF9-BGKcLV19-54
RBP	TAF9	TAF9
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5715	5716

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-53	BGKcLV19-54
Sample #	29	30
Sample Name	TAF9-BGKcLV19-53	TAF9-BGKcLV19-54
Sample_Name_Alias
Index Well Position	G03	H03
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	302	297
Peak_Molarity	40.00	99.40
libSampleQC_DNA_Well	DNA_Library_set45/set1/G3.png	DNA_Library_set45/set1/H3.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set45/set1/G3.png	RNA_Library_set45/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-53	BGKcLV19-54
RBP	TAF9	TAF9
Batch_ID	BGKcLV19	BGKcLV19
WB_result	97.400	99.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	803	804

Sequencing Information

	BGKcLV19-53	BGKcLV19-54
Sample_ID	BGKcLV19-53	BGKcLV19-54
Sample Name	TAF9-BGKcLV19-53	TAF9-BGKcLV19-54
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	56,882,756	94,669,502
total_aligned_reads	49,933,646	86,451,162
unique_aligned_reads	45,628,770	78,795,516
percent_uniqueAligned	0.80215	0.83232
correlation_replicates	0.995425	0.995425
spikein_reads	33,538	47,346
percent_spikeins	0.00059	0.00050
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	434	435

Data Submission Information

	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-54	BGKcLV19-54	BGKcLV19-54	BGKcLV19-54
ENCODE_alias	brenton-graveley:TAF9-BGKcLV19	brenton-graveley:TAF9-BGKcLV19-53	brenton-graveley:L-TAF9-BGKcLV19-53	brenton-graveley:TAF9-BGKcLV19-53_S23_R1_001.fastq.gz	brenton-graveley:TAF9-BGKcLV19-53_S23_R2_001.fastq.gz	brenton-graveley:TAF9-BGKcLV19-K562	brenton-graveley:TAF9-BGKcLV19-54	brenton-graveley:L-TAF9-BGKcLV19-54	brenton-graveley:TAF9-BGKcLV19-54_S24_R1_001.fastq.gz	brenton-graveley:TAF9-BGKcLV19-54_S24_R2_001.fastq.gz
ENCODE_accession	ENCSR490PSG	ENCBS463TWT	ENCLB885PFO	ENCFF267TXK	ENCFF274BAQ	ENCSR154LSO	ENCBS306DAG	ENCLB691ZNK	ENCFF698QFJ	ENCFF285CLM
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	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-53	BGKcLV19-54	BGKcLV19-54	BGKcLV19-54	BGKcLV19-54
Sample Name	TAF9-BGKcLV19-53	TAF9-BGKcLV19-53	TAF9-BGKcLV19-53	TAF9-BGKcLV19-53	TAF9-BGKcLV19-53	TAF9-BGKcLV19-53	TAF9-BGKcLV19-54	TAF9-BGKcLV19-54	TAF9-BGKcLV19-54	TAF9-BGKcLV19-54
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		TAF9-BGKcLV19-53.pdf	L-TAF9-BGKcLV19-53.pdf				TAF9-BGKcLV19-54.pdf	L-TAF9-BGKcLV19-54.pdf
ID	2101	2157	2227	2297	2367	7344	2158	2228	2298	2368

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-BGKcLV19-53_S23_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	434	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1256
TAF9-BGKcLV19-53_S23_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	434	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1306
TAF9-BGKcLV19-53_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	434					GRCh38	V40	TAF9-BGKcLV19-53_S23_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGKcLV19-53_S23_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25249
TAF9-BGKcLV19-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	434					GRCh38	V40	TAF9-BGKcLV19-53_S23_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGKcLV19-53_S23_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27203
TAF9-BGKcLV19-53_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	434					GRCh38	V40	TAF9-BGKcLV19-53/Aligned.sortedByCoord.out.bam		ENCORE2	27253
TAF9-BGKcLV19-53_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	434					GRCh38	V40	TAF9-BGKcLV19-53/Aligned.sortedByCoord.out.bam		ENCORE2	27303
TAF9-BGKcLV19-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	434					GRCh38	V40	TAF9-BGKcLV19-53/Aligned.sortedByCoord.out.bam		ENCORE2	27353
TAF9-BGKcLV19-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	434					GRCh38	V40	TAF9-BGKcLV19-53/Aligned.sortedByCoord.out.bam		ENCORE2	27403
TAF9-BGKcLV19-54_S24_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	435	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1257
TAF9-BGKcLV19-54_S24_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	435	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1307
TAF9-BGKcLV19-54_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	435					GRCh38	V40	TAF9-BGKcLV19-54_S24_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGKcLV19-54_S24_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25250
TAF9-BGKcLV19-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	435					GRCh38	V40	TAF9-BGKcLV19-54_S24_R1_001.filtered.trimmed.paired.fastq.gz,TAF9-BGKcLV19-54_S24_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27204
TAF9-BGKcLV19-54_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	435					GRCh38	V40	TAF9-BGKcLV19-54/Aligned.sortedByCoord.out.bam		ENCORE2	27254
TAF9-BGKcLV19-54_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	435					GRCh38	V40	TAF9-BGKcLV19-54/Aligned.sortedByCoord.out.bam		ENCORE2	27304
TAF9-BGKcLV19-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	435					GRCh38	V40	TAF9-BGKcLV19-54/Aligned.sortedByCoord.out.bam		ENCORE2	27354
TAF9-BGKcLV19-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	435					GRCh38	V40	TAF9-BGKcLV19-54/Aligned.sortedByCoord.out.bam		ENCORE2	27404