AGGF1 RNA-Seq in HepG2


RBP	AGGF1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	AGGF1-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR326OZZ
Batch_ID	BGHcLV05
Pool ID	Pool-181119
Local_Set_Name	set41_spikeins
ENCODE_KD_Exp_ID	ENCSR666QJU
ENCODE_CN_Exp_ID	ENCSR805TIZ
Rep1	AGGF1-BGHcLV05-5D
Rep2	AGGF1-BGHcLV05-6D
CN1	NT-BGHcLV05-1D
CN2	NT-BGHcLV05-2D
Rep1_qPCR	65.9
Rep2_qPCR	53.3
Rep1_WB	94.5
Rep2_WB	96.2
Antibody Cat#	A303-634A
Antibody Lot#	A303-634A
Antibody DCC ID	ENCAB191KLA
Status	Released
Project	ENCODE4
ID	887

	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6
idx	41	78	42	79
TRCN#_or_BGC#	BGC#0000023	BGC#0000023	BGC#0000023	BGC#0000023
shRNA_or_gRNA_sequence	CTCAGTAAAATACTCCAACG	CTCAGTAAAATACTCCAACG	CTCAGTAAAATACTCCAACG	CTCAGTAAAATACTCCAACG
PAM
Name	AGGF1_2	AGGF1_2	AGGF1_2	AGGF1_2
Sample_ID	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	AGGF1	AGGF1	AGGF1	AGGF1
qPCR_result	65.9		53.3
Ave_qPCR	59.6
RT-qPCR_primer-F	gaaggatggtggaggaatga
RT-qPCR_primer-R	atgaggatggtttgcctgtc
protein_conc	4146	0	4034	0
WB_result	94.5		96.2
Ave_WB	95.3
WB_DONE_date	7/20/16		WES
MW	81kDa
IP	1IP		1IP
antibody_Cat#	A303-634A		A303-634A
Antibody DCC ID	ENCAB191KLA		ENCAB191KLA
submitted_to_DCC_date	10/26/16
Rep1_TPM	15	0	0	0
Rep2_TPM	14	0	0	0
Action	Ready		Ready
Library_start_date	08/15/16		08/15/16
repeat_library	5/11/17		5/11/17
Note
ID	6182	6221	6183	6222

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6	BGHcLV05-6
Sample #			79			80
Sample Name	AGGF1-BGHcLV05-5	AGGF1-BGHcLV05-5B	AGGF1-BGHcLV05-5D	AGGF1-BGHcLV05-6	AGGF1-BGHcLV05-6B	AGGF1-BGHcLV05-6D
Sample_Name_Alias	AGGF1_BGHcLV05-5	AGGF1-BGHcLV05-5B		AGGF1_BGHcLV05-6	AGGF1-BGHcLV05-6B
Index Well Position	S11	S25	S25	S12	S27	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-08-15	2017-05-11	2018-11-19	2016-08-15	2017-05-11	2018-11-19
Lib_ID	Lib-160815	Lib-170511	Lib-181119	Lib-160815	Lib-170511	Lib-181119
Tecan_Location
Tecan
Tecan_date
Size_bp			293			304
Peak_Molarity			59.40			43.20
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/C1.png	DNA_Library_set39/set2/G7.png	DNA_Library_set41/set1/G9.png	DNA_Library_cLV04/set1/B1.png	DNA_Library_set39/set2/H7.png	DNA_Library_set41/set1/H9.png
RIN	8.9	8.9	8.9	9.1	9.1	9.1
libSample_RNA_Well	RNA_Library_cLV04-05/set1/C7.png	RNA_Library_cLV04-05/set1/C7.png	RNA_Library_cLV04-05/set1/C7.png	RNA_Library_cLV04-05/set1/D7.png	RNA_Library_cLV04-05/set1/D7.png	RNA_Library_cLV04-05/set1/D7.png
SampleQC_method			TapeStation			TapeStation
SampleQC_date			2022-03-01			2022-03-01
Sample_ID	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6	BGHcLV05-6
RBP	AGGF1	AGGF1	AGGF1	AGGF1	AGGF1	AGGF1
Batch_ID	BGHcLV05	BGHcLV05	BGHcLV05	BGHcLV05	BGHcLV05	BGHcLV05
WB_result	94.500	94.500	94.500	96.200	96.200	96.200
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B	D		B	D
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE3	ENCODE3	ENCODE4
ID	3012	3046	3256	3013	3047	3257

Sequencing Information

	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6	BGHcLV05-6
Sample_ID	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6	BGHcLV05-6
Sample Name	AGGF1_BGHcLV05-5	AGGF1-BGHcLV05-5B	AGGF1-BGHcLV05-5D	AGGF1_BGHcLV05-6	AGGF1-BGHcLV05-6B	AGGF1-BGHcLV05-6D
Pool ID	Pool-161129	Pool-170911	Pool-181119	Pool-161129	Pool-170911	Pool-181119
LocalServer_folder	BGHcLV05	set39_H	set41_spikeins	BGHcLV05	set39_H	set41_spikeins
total_reads	57,579,706	62,692,058	144,652,908	37,073,956	38,686,288	224,872,970
total_aligned_reads	49,179,688	54,976,814	122,234,898	30,200,948	32,706,986	180,769,824
unique_aligned_reads	46,081,710	51,648,774	114,834,024	28,082,198	30,783,604	169,782,036
percent_uniqueAligned	0.80031	0.82385	0.79386	0.75746	0.79572	0.75501
correlation_replicates	0.529885	0.996161	0.996501	0.529885	0.996161	0.996501
spikein_reads	121,416	22	205,264	173,406	8	218,176
percent_spikeins	0.00211		0.00142	0.00468		0.00097
original_ReadLength	100	100	100	100	100	100
QC_Status	BadCorrelation	Submitted	Submitted	BadCorrelation	Submitted	Submitted
ID	1665	1697	1969	1666	1698	1970

	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6
ENCODE_alias	brenton-graveley:AGGF1-BGHcLV05-B	brenton-graveley:AGGF1-BGHcLV05-HepG2_A	brenton-graveley:AGGF1-BGHcLV05-D	brenton-graveley:L-AGGF1-BGHcLV05-5D	brenton-graveley:AGGF1-BGHcLV05-HepG2	brenton-graveley:AGGF1-BGHcLV05-5B	brenton-graveley:L-AGGF1-BGHcLV05-6D	brenton-graveley:AGGF1-BGHcLV05-6B
ENCODE_accession	ENCSR437GYG	ENCSR718VYC	ENCSR666QJU	ENCLB710LCN	ENCSR326OZZ	ENCBS048KGW	ENCLB644OBV	ENCBS010LBN
object_type	experiment	experiment	experiment	library	gene_silencing_series	biosample	library	biosample
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
Sample_ID	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-5	BGHcLV05-6	BGHcLV05-6
Sample Name	AGGF1-BGHcLV05-5B	AGGF1-BGHcLV05-5B	AGGF1-BGHcLV05-5D	AGGF1-BGHcLV05-5D	AGGF1-BGHcLV05-5D	AGGF1-BGHcLV05-5B	AGGF1-BGHcLV05-6D	AGGF1-BGHcLV05-6B
Selected	Yes	No	Yes	Yes	Yes	No	Yes	No
Status	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2019-03-13	2022-03-07	2019-03-13
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
				LV41_library_protocol_spikeins			LV41_library_protocol_spikeins
protocol_URL				L-AGGF1-BGHcLV05-5D.pdf			L-AGGF1-BGHcLV05-6D.pdf
ID	3215	6581	7380	7408	7415	7438	7409	7439

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
AGGF1-BGHcLV05-5B_ACTGAT_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1697	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE3	22270
AGGF1-BGHcLV05-5B_ACTGAT_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1697	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE3	22294
AGGF1-BGHcLV05-5B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1697					GRCh38	V40	AGGF1-BGHcLV05-5B_ACTGAT_ACBE67ANXX_L004_001.R1.fastq.gz,AGGF1-BGHcLV05-5B_ACTGAT_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22318
AGGF1-BGHcLV05-5B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1697					GRCh38	V40	AGGF1-BGHcLV05-5B/Aligned.sortedByCoord.out.bam		ENCORE2	22342
AGGF1-BGHcLV05-5B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1697					GRCh38	V40	AGGF1-BGHcLV05-5B/Aligned.sortedByCoord.out.bam		ENCORE2	22366
AGGF1-BGHcLV05-5B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1697					GRCh38	V40	AGGF1-BGHcLV05-5B/Aligned.sortedByCoord.out.bam		ENCORE2	22390
AGGF1-BGHcLV05-5B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1697					GRCh38	V40	AGGF1-BGHcLV05-5B/Aligned.sortedByCoord.out.bam		ENCORE2	22414
AGGF1-BGHcLV05-5B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1697					GRCh38	V40	AGGF1-BGHcLV05-5B_ACTGAT_ACBE67ANXX_L004_001.R1.fastq.gz,AGGF1-BGHcLV05-5B_ACTGAT_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22438
AGGF1_BGHcLV05-5_GGCTAC_L002_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1665	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23134
AGGF1_BGHcLV05-5_GGCTAC_L002_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1665	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23146
AGGF1_BGHcLV05-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1665					GRCh38	V40	AGGF1_BGHcLV05-5_GGCTAC_L002_001.R1.fastq.gz,AGGF1_BGHcLV05-5_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	23158
AGGF1_BGHcLV05-5_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1665					GRCh38	V40	AGGF1_BGHcLV05-5/Aligned.sortedByCoord.out.bam		ENCORE2	23170
AGGF1_BGHcLV05-5_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1665					GRCh38	V40	AGGF1_BGHcLV05-5/Aligned.sortedByCoord.out.bam		ENCORE2	23182
AGGF1_BGHcLV05-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1665					GRCh38	V40	AGGF1_BGHcLV05-5/Aligned.sortedByCoord.out.bam		ENCORE2	23194
AGGF1_BGHcLV05-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1665					GRCh38	V40	AGGF1_BGHcLV05-5/Aligned.sortedByCoord.out.bam		ENCORE2	23206
AGGF1_BGHcLV05-5_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1665					GRCh38	V40	AGGF1_BGHcLV05-5_GGCTAC_L002_001.R1.fastq.gz,AGGF1_BGHcLV05-5_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	23218
AGGF1-BGHcLV05-5D_S2_R1_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1969	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R1_001.fastq.gz	ENCORE2	27405
AGGF1-BGHcLV05-5D_S2_R2_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1969	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R2_001.fastq.gz	ENCORE2	27433
AGGF1-BGHcLV05-5D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1969					GRCh38	V40	AGGF1-BGHcLV05-5D_S2_R1_001.fastq.gz,AGGF1-BGHcLV05-5D_S2_R2_001.fastq.gz		ENCORE2	27461
AGGF1-BGHcLV05-5D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1969					GRCh38	V40	AGGF1-BGHcLV05-5D/Aligned.sortedByCoord.out.bam		ENCORE2	27489
AGGF1-BGHcLV05-5D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1969					GRCh38	V40	AGGF1-BGHcLV05-5D/Aligned.sortedByCoord.out.bam		ENCORE2	27517
AGGF1-BGHcLV05-5D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1969					GRCh38	V40	AGGF1-BGHcLV05-5D/Aligned.sortedByCoord.out.bam		ENCORE2	27545
AGGF1-BGHcLV05-5D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1969					GRCh38	V40	AGGF1-BGHcLV05-5D/Aligned.sortedByCoord.out.bam		ENCORE2	27573
AGGF1-BGHcLV05-5D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1969					GRCh38	V40	AGGF1-BGHcLV05-5D_S2_R1_001.fastq.gz,AGGF1-BGHcLV05-5D_S2_R2_001.fastq.gz		ENCORE2	27601
AGGF1-BGHcLV05-6B_ATTCCT_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1698	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE3	22271
AGGF1-BGHcLV05-6B_ATTCCT_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1698	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1B_CGTACG_ACBE67ANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2B_GAGTGG_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE3	22295
AGGF1-BGHcLV05-6B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1698					GRCh38	V40	AGGF1-BGHcLV05-6B_ATTCCT_ACBE67ANXX_L004_001.R1.fastq.gz,AGGF1-BGHcLV05-6B_ATTCCT_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22319
AGGF1-BGHcLV05-6B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1698					GRCh38	V40	AGGF1-BGHcLV05-6B/Aligned.sortedByCoord.out.bam		ENCORE2	22343
AGGF1-BGHcLV05-6B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1698					GRCh38	V40	AGGF1-BGHcLV05-6B/Aligned.sortedByCoord.out.bam		ENCORE2	22367
AGGF1-BGHcLV05-6B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1698					GRCh38	V40	AGGF1-BGHcLV05-6B/Aligned.sortedByCoord.out.bam		ENCORE2	22391
AGGF1-BGHcLV05-6B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1698					GRCh38	V40	AGGF1-BGHcLV05-6B/Aligned.sortedByCoord.out.bam		ENCORE2	22415
AGGF1-BGHcLV05-6B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1698					GRCh38	V40	AGGF1-BGHcLV05-6B_ATTCCT_ACBE67ANXX_L004_001.R1.fastq.gz,AGGF1-BGHcLV05-6B_ATTCCT_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22439
AGGF1_BGHcLV05-6_CTTGTA_L002_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1666	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23135
AGGF1_BGHcLV05-6_CTTGTA_L002_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1666	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23147
AGGF1_BGHcLV05-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1666					GRCh38	V40	AGGF1_BGHcLV05-6_CTTGTA_L002_001.R1.fastq.gz,AGGF1_BGHcLV05-6_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	23159
AGGF1_BGHcLV05-6_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1666					GRCh38	V40	AGGF1_BGHcLV05-6/Aligned.sortedByCoord.out.bam		ENCORE2	23171
AGGF1_BGHcLV05-6_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1666					GRCh38	V40	AGGF1_BGHcLV05-6/Aligned.sortedByCoord.out.bam		ENCORE2	23183
AGGF1_BGHcLV05-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1666					GRCh38	V40	AGGF1_BGHcLV05-6/Aligned.sortedByCoord.out.bam		ENCORE2	23195
AGGF1_BGHcLV05-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1666					GRCh38	V40	AGGF1_BGHcLV05-6/Aligned.sortedByCoord.out.bam		ENCORE2	23207
AGGF1_BGHcLV05-6_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1666					GRCh38	V40	AGGF1_BGHcLV05-6_CTTGTA_L002_001.R1.fastq.gz,AGGF1_BGHcLV05-6_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	23219
AGGF1-BGHcLV05-6D_S3_R1_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1970	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R1_001.fastq.gz	ENCORE2	27406
AGGF1-BGHcLV05-6D_S3_R2_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1970	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1D_CGTACG_HJMKJBCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2D_S1_R2_001.fastq.gz	ENCORE2	27434
AGGF1-BGHcLV05-6D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1970					GRCh38	V40	AGGF1-BGHcLV05-6D_S3_R1_001.fastq.gz,AGGF1-BGHcLV05-6D_S3_R2_001.fastq.gz		ENCORE2	27462
AGGF1-BGHcLV05-6D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1970					GRCh38	V40	AGGF1-BGHcLV05-6D/Aligned.sortedByCoord.out.bam		ENCORE2	27490
AGGF1-BGHcLV05-6D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1970					GRCh38	V40	AGGF1-BGHcLV05-6D/Aligned.sortedByCoord.out.bam		ENCORE2	27518
AGGF1-BGHcLV05-6D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1970					GRCh38	V40	AGGF1-BGHcLV05-6D/Aligned.sortedByCoord.out.bam		ENCORE2	27546
AGGF1-BGHcLV05-6D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1970					GRCh38	V40	AGGF1-BGHcLV05-6D/Aligned.sortedByCoord.out.bam		ENCORE2	27574
AGGF1-BGHcLV05-6D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1970					GRCh38	V40	AGGF1-BGHcLV05-6D_S3_R1_001.fastq.gz,AGGF1-BGHcLV05-6D_S3_R2_001.fastq.gz		ENCORE2	27602