TFIP11 RNA-Seq in K562

General Information


RBP	TFIP11
Cell_Line	K562
Method	shRNA
Exp_Name	TFIP11-BGKLV19-K562
ENCODE_series_ID	ENCSR352PIE
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR911DGK
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	TFIP11_BGKLV19_55B
Rep2	TFIP11_BGKLV19_56B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	50.6
Rep2_qPCR	53.4
Rep1_WB	50.0
Rep2_WB	46.2
Antibody Cat#	A302-548A
Antibody Lot#	A302-548A
Antibody DCC ID	ENCAB593XBQ
Status	Released
Project	ENCODE3
ID	484

Experiment Information (Status: Released)

	BGKLV19-55	BGKLV19-56
idx	262	263
TRCN#_or_BGC#	TRCN0000074507	TRCN0000074507
shRNA_or_gRNA_sequence	CCTGGGTTGGAAGTCGATGTT	CCTGGGTTGGAAGTCGATGTT
PAM
Name	TFIP11	TFIP11
Sample_ID	BGKLV19-55	BGKLV19-56
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	TFIP11	TFIP11
qPCR_result	50.6	53.4
Ave_qPCR	52.0
RT-qPCR_primer-F	gcacatccatctgtcaagga
RT-qPCR_primer-R	tgtgggtgagataggcaatg
protein_conc	3247	4024
WB_result	50.0	46.2
Ave_WB	48.1
WB_DONE_date	4/13/2015
MW
IP	1	1
antibody_Cat#	A302-548A	A302-548A
Antibody DCC ID	ENCAB593XBQ	ENCAB593XBQ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	10.9089242	0
Rep2_TPM	10.7920978	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	287	288

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TFIP11	Product_ID: A302-548A Lot_ID: 1 Source: Bethyl Labs Target Name: TFIP11-human

Experiment Status

	BGKLV19-55	BGKLV19-56
Sample_ID	BGKLV19-55	BGKLV19-56
Sample Name	TFIP11_BGKLV19_55B	TFIP11_BGKLV19_56B
Sample Name	TFIP11_BGKLV19_55B	TFIP11_BGKLV19_56B
RBP	TFIP11	TFIP11
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	702	703

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-55	BGKLV19-56
Sample #
Sample Name	TFIP11-BGKLV19-55B	TFIP11-BGKLV19-56B
Sample_Name_Alias	TFIP11_BGKLV19_55B	TFIP11_BGKLV19_56B
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G11.png	DNA_Library_LV18-19/set1/H11.png
RIN	9.5	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C6.png	RNA_Library_LV19-21-24/set1/D6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-55	BGKLV19-56
RBP	TFIP11	TFIP11
Batch_ID	BGKLV19	BGKLV19
WB_result	50.000	46.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2386	2387

Sequencing Information

	BGKLV19-55	BGKLV19-56
Sample_ID	BGKLV19-55	BGKLV19-56
Sample Name	TFIP11_BGKLV19_55B	TFIP11_BGKLV19_56B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	44,740,000	28,380,000
total_aligned_reads	41,821,810	26,501,332
unique_aligned_reads	38,274,364	24,248,228
percent_uniqueAligned	0.85548	0.85441
correlation_replicates	0.995542	0.995542
spikein_reads	292,254	174,556
percent_spikeins	0.00653	0.00615
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1028	1029

Data Submission Information

	BGKLV19-55	BGKLV19-55
ENCODE_alias	brenton-graveley:TFIP11_BGKLV19	brenton-graveley:TFIP11-BGKLV19-K562
ENCODE_accession	ENCSR911DGK	ENCSR352PIE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-55	BGKLV19-55
Sample Name	TFIP11_BGKLV19_55B	TFIP11_BGKLV19_55B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2899	7006

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
TFIP11_BGKLV19_55B_ATGTCA_L007_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1028	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15144
TFIP11_BGKLV19_55B_ATGTCA_L007_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1028	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15202
TFIP11_BGKLV19_55B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1028					GRCh38	V40	TFIP11_BGKLV19_55B_ATGTCA_L007_R1_001.fastq.gz,TFIP11_BGKLV19_55B_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	15260
TFIP11_BGKLV19_55B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1028					GRCh38	V40	TFIP11_BGKLV19_55B/Aligned.sortedByCoord.out.bam		ENCORE2	15331
TFIP11_BGKLV19_55B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1028					GRCh38	V40	TFIP11_BGKLV19_55B/Aligned.sortedByCoord.out.bam		ENCORE2	15389
TFIP11_BGKLV19_55B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1028					GRCh38	V40	TFIP11_BGKLV19_55B/Aligned.sortedByCoord.out.bam		ENCORE2	15447
TFIP11_BGKLV19_55B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1028					GRCh38	V40	TFIP11_BGKLV19_55B/Aligned.sortedByCoord.out.bam		ENCORE2	15505
TFIP11_BGKLV19_55B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1028					GRCh38	V40	TFIP11_BGKLV19_55B_ATGTCA_L007_R1_001.fastq.gz,TFIP11_BGKLV19_55B_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	16402
TFIP11_BGKLV19_56B_CCGTCC_L007_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1029	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15145
TFIP11_BGKLV19_56B_CCGTCC_L007_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1029	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15203
TFIP11_BGKLV19_56B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1029					GRCh38	V40	TFIP11_BGKLV19_56B_CCGTCC_L007_R1_001.fastq.gz,TFIP11_BGKLV19_56B_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	15261
TFIP11_BGKLV19_56B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1029					GRCh38	V40	TFIP11_BGKLV19_56B/Aligned.sortedByCoord.out.bam		ENCORE2	15332
TFIP11_BGKLV19_56B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1029					GRCh38	V40	TFIP11_BGKLV19_56B/Aligned.sortedByCoord.out.bam		ENCORE2	15390
TFIP11_BGKLV19_56B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1029					GRCh38	V40	TFIP11_BGKLV19_56B/Aligned.sortedByCoord.out.bam		ENCORE2	15448
TFIP11_BGKLV19_56B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1029					GRCh38	V40	TFIP11_BGKLV19_56B/Aligned.sortedByCoord.out.bam		ENCORE2	15506
TFIP11_BGKLV19_56B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1029					GRCh38	V40	TFIP11_BGKLV19_56B_CCGTCC_L007_R1_001.fastq.gz,TFIP11_BGKLV19_56B_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	16403