EIF3H RNA-Seq in HepG2


RBP	EIF3H
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF3H-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR097WJI
Batch_ID	BGHcLV05
Pool ID	Pool-181119
Local_Set_Name	set41_spikeins
ENCODE_KD_Exp_ID	ENCSR733MVT
ENCODE_CN_Exp_ID	ENCSR805TIZ
Rep1	EIF3H-BGHcLV05-15D
Rep2	EIF3H-BGHcLV05-16D
CN1	NT-BGHcLV05-1D
CN2	NT-BGHcLV05-2D
Rep1_qPCR	83.8
Rep2_qPCR	77.1
Rep1_WB	68.8
Rep2_WB	73.9
Antibody Cat#	A301-754A
Antibody Lot#	A301-754A
Antibody DCC ID	ENCAB957ITF
Status	Released
Project	ENCODE4
ID	888

	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16
idx	51	90	52	91
TRCN#_or_BGC#	BGC#0000033	BGC#0000033	BGC#0000033	BGC#0000033
shRNA_or_gRNA_sequence	TGGGTCTGGTTGTAGAAGAT	TGGGTCTGGTTGTAGAAGAT	TGGGTCTGGTTGTAGAAGAT	TGGGTCTGGTTGTAGAAGAT
PAM
Name	EIF3H_2	EIF3H_2	EIF3H_2	EIF3H_2
Sample_ID	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	EIF3H	EIF3H	EIF3H	EIF3H
qPCR_result	83.8		77.1
Ave_qPCR	80.5
RT-qPCR_primer-F	gcacacagaggatgatgctg
RT-qPCR_primer-R	ataccagcccacgtgaagat
protein_conc	4067	0	3845	0
WB_result	68.8		73.9
Ave_WB	71.4
WB_DONE_date	7/19/16		wes
MW	40 kDa
IP	1
antibody_Cat#	A301-754A		A301-754A
Antibody DCC ID	ENCAB957ITF		ENCAB957ITF
submitted_to_DCC_date	10/26/16
Rep1_TPM	77	0	0	0
Rep2_TPM	92	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	6194	6231	6195	6232

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16	BGHcLV05-16
Sample #			81			82
Sample Name	EIF3H-BGHcLV05-15	EIF3H-BGHcLV05-15B	EIF3H-BGHcLV05-15D	EIF3H-BGHcLV05-16	EIF3H-BGHcLV05-16B	EIF3H-BGHcLV05-16D
Sample_Name_Alias	EIF3H_BGHcLV05-15	EIF3H-BGHcLV05-15B		EIF3H_BGHcLV05-16	EIF3H-BGHcLV05-16B
Index Well Position	S20	S01	S01	S21	S02	S02
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			288			288
Peak_Molarity			52.20			63.00
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/H1.png	DNA_Library_set39/set2/A8.png	DNA_Library_set41/set1/A10.png	DNA_Library_cLV04/set2/B1.png	DNA_Library_set39/set2/B8.png	DNA_Library_set41/set1/B10.png
RIN	9.2	9.2	9.2	9.1	9.1	9.1
libSample_RNA_Well	RNA_Library_cLV04-05/set1/A8.png	RNA_Library_cLV04-05/set1/A8.png	RNA_Library_cLV04-05/set1/A8.png	RNA_Library_cLV04-05/set1/B8.png	RNA_Library_cLV04-05/set1/B8.png	RNA_Library_cLV04-05/set1/B8.png
SampleQC_method			TapeStation			TapeStation
SampleQC_date			2022-03-01			2022-03-01
Sample_ID	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16	BGHcLV05-16
RBP	EIF3H	EIF3H	EIF3H	EIF3H	EIF3H	EIF3H
Batch_ID	BGHcLV05	BGHcLV05	BGHcLV05	BGHcLV05	BGHcLV05	BGHcLV05
WB_result	68.800	68.800	68.800	73.900	73.900	73.900
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	3018	3048	3258	3019	3049	3259

Sequencing Information

	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16	BGHcLV05-16
Sample_ID	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16	BGHcLV05-16
Sample Name	EIF3H_BGHcLV05-15	EIF3H-BGHcLV05-15B	EIF3H-BGHcLV05-15D	EIF3H_BGHcLV05-16	EIF3H-BGHcLV05-16B	EIF3H-BGHcLV05-16D
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	67,020,772	76,530,742	143,009,524	46,557,816	63,590,884	134,106,758
total_aligned_reads	46,213,238	67,402,560	115,813,516	30,767,360	56,598,932	102,419,308
unique_aligned_reads	43,068,330	63,338,010	108,596,398	28,343,542	53,029,950	95,979,750
percent_uniqueAligned	0.64261	0.82762	0.75936	0.60878	0.83392	0.71570
correlation_replicates	0.640040	0.997608	0.996538	0.640040	0.997608	0.996538
spikein_reads	82,376	96	195,656	174,230	4	161,784
percent_spikeins	0.00123		0.00137	0.00374		0.00121
original_ReadLength	100	100	100	100	100	100
QC_Status	BadCorrelation	Submitted	Submitted	BadCorrelation	Submitted	Submitted
ID	1671	1699	1971	1672	1700	1972

	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16
ENCODE_alias	brenton-graveley:EIF3H-BGHcLV05-B	brenton-graveley:EIF3H-BGHcLV05-HepG2_A	brenton-graveley:EIF3H-BGHcLV05-D	brenton-graveley:L-EIF3H-BGHcLV05-15D	brenton-graveley:EIF3H-BGHcLV05-HepG2	brenton-graveley:EIF3H-BGHcLV05-15B	brenton-graveley:L-EIF3H-BGHcLV05-16D	brenton-graveley:EIF3H-BGHcLV05-16B
ENCODE_accession	ENCSR964YLV	ENCSR587GQL	ENCSR733MVT	ENCLB865GAI	ENCSR097WJI	ENCBS443YFV	ENCLB899QXE	ENCBS731URN
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	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-15	BGHcLV05-16	BGHcLV05-16
Sample Name	EIF3H-BGHcLV05-15B	EIF3H-BGHcLV05-15B	EIF3H-BGHcLV05-15D	EIF3H-BGHcLV05-15D	EIF3H-BGHcLV05-15D	EIF3H-BGHcLV05-15B	EIF3H-BGHcLV05-16D	EIF3H-BGHcLV05-16B
Selected	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes
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		LV39_biosample_protocol	LV41_library_protocol_spikeins	LV39_biosample_protocol
protocol_URL				L-EIF3H-BGHcLV05-15D.pdf		EIF3H-BGHcLV05-15B.pdf	L-EIF3H-BGHcLV05-16D.pdf	EIF3H-BGHcLV05-16B.pdf
ID	3216	6687	7381	7410	7417	7440	7411	7441

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
EIF3H-BGHcLV05-15B_ATCACG_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1699	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	22272
EIF3H-BGHcLV05-15B_ATCACG_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1699	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	22296
EIF3H-BGHcLV05-15B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1699					GRCh38	V40	EIF3H-BGHcLV05-15B_ATCACG_ACBE67ANXX_L004_001.R1.fastq.gz,EIF3H-BGHcLV05-15B_ATCACG_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22320
EIF3H-BGHcLV05-15B_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	1699					GRCh38	V40	EIF3H-BGHcLV05-15B/Aligned.sortedByCoord.out.bam		ENCORE2	22344
EIF3H-BGHcLV05-15B_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	1699					GRCh38	V40	EIF3H-BGHcLV05-15B/Aligned.sortedByCoord.out.bam		ENCORE2	22368
EIF3H-BGHcLV05-15B_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	1699					GRCh38	V40	EIF3H-BGHcLV05-15B/Aligned.sortedByCoord.out.bam		ENCORE2	22392
EIF3H-BGHcLV05-15B_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	1699					GRCh38	V40	EIF3H-BGHcLV05-15B/Aligned.sortedByCoord.out.bam		ENCORE2	22416
EIF3H-BGHcLV05-15B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1699					GRCh38	V40	EIF3H-BGHcLV05-15B_ATCACG_ACBE67ANXX_L004_001.R1.fastq.gz,EIF3H-BGHcLV05-15B_ATCACG_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22440
EIF3H_BGHcLV05-15_GTGGCC_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1671	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23140
EIF3H_BGHcLV05-15_GTGGCC_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1671	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23152
EIF3H_BGHcLV05-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1671					GRCh38	V40	EIF3H_BGHcLV05-15_GTGGCC_L003_001.R1.fastq.gz,EIF3H_BGHcLV05-15_GTGGCC_L003_001.R2.fastq.gz		ENCORE2	23164
EIF3H_BGHcLV05-15_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	1671					GRCh38	V40	EIF3H_BGHcLV05-15/Aligned.sortedByCoord.out.bam		ENCORE2	23176
EIF3H_BGHcLV05-15_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	1671					GRCh38	V40	EIF3H_BGHcLV05-15/Aligned.sortedByCoord.out.bam		ENCORE2	23188
EIF3H_BGHcLV05-15_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	1671					GRCh38	V40	EIF3H_BGHcLV05-15/Aligned.sortedByCoord.out.bam		ENCORE2	23200
EIF3H_BGHcLV05-15_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	1671					GRCh38	V40	EIF3H_BGHcLV05-15/Aligned.sortedByCoord.out.bam		ENCORE2	23212
EIF3H_BGHcLV05-15_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1671					GRCh38	V40	EIF3H_BGHcLV05-15_GTGGCC_L003_001.R1.fastq.gz,EIF3H_BGHcLV05-15_GTGGCC_L003_001.R2.fastq.gz		ENCORE2	23224
EIF3H-BGHcLV05-15D_S4_R1_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1971	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	27409
EIF3H-BGHcLV05-15D_S4_R2_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1971	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	27437
EIF3H-BGHcLV05-15D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1971					GRCh38	V40	EIF3H-BGHcLV05-15D_S4_R1_001.fastq.gz,EIF3H-BGHcLV05-15D_S4_R2_001.fastq.gz		ENCORE2	27465
EIF3H-BGHcLV05-15D_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	1971					GRCh38	V40	EIF3H-BGHcLV05-15D/Aligned.sortedByCoord.out.bam		ENCORE2	27493
EIF3H-BGHcLV05-15D_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	1971					GRCh38	V40	EIF3H-BGHcLV05-15D/Aligned.sortedByCoord.out.bam		ENCORE2	27521
EIF3H-BGHcLV05-15D_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	1971					GRCh38	V40	EIF3H-BGHcLV05-15D/Aligned.sortedByCoord.out.bam		ENCORE2	27549
EIF3H-BGHcLV05-15D_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	1971					GRCh38	V40	EIF3H-BGHcLV05-15D/Aligned.sortedByCoord.out.bam		ENCORE2	27577
EIF3H-BGHcLV05-15D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1971					GRCh38	V40	EIF3H-BGHcLV05-15D_S4_R1_001.fastq.gz,EIF3H-BGHcLV05-15D_S4_R2_001.fastq.gz		ENCORE2	27605
EIF3H-BGHcLV05-16B_CGATGT_ACBE67ANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1700	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	22273
EIF3H-BGHcLV05-16B_CGATGT_ACBE67ANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1700	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	22297
EIF3H-BGHcLV05-16B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1700					GRCh38	V40	EIF3H-BGHcLV05-16B_CGATGT_ACBE67ANXX_L004_001.R1.fastq.gz,EIF3H-BGHcLV05-16B_CGATGT_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22321
EIF3H-BGHcLV05-16B_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	1700					GRCh38	V40	EIF3H-BGHcLV05-16B/Aligned.sortedByCoord.out.bam		ENCORE2	22345
EIF3H-BGHcLV05-16B_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	1700					GRCh38	V40	EIF3H-BGHcLV05-16B/Aligned.sortedByCoord.out.bam		ENCORE2	22369
EIF3H-BGHcLV05-16B_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	1700					GRCh38	V40	EIF3H-BGHcLV05-16B/Aligned.sortedByCoord.out.bam		ENCORE2	22393
EIF3H-BGHcLV05-16B_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	1700					GRCh38	V40	EIF3H-BGHcLV05-16B/Aligned.sortedByCoord.out.bam		ENCORE2	22417
EIF3H-BGHcLV05-16B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1700					GRCh38	V40	EIF3H-BGHcLV05-16B_CGATGT_ACBE67ANXX_L004_001.R1.fastq.gz,EIF3H-BGHcLV05-16B_CGATGT_ACBE67ANXX_L004_001.R2.fastq.gz		ENCORE2	22441
EIF3H_BGHcLV05-16_GTTTCG_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1672	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23141
EIF3H_BGHcLV05-16_GTTTCG_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1672	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23153
EIF3H_BGHcLV05-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1672					GRCh38	V40	EIF3H_BGHcLV05-16_GTTTCG_L003_001.R1.fastq.gz,EIF3H_BGHcLV05-16_GTTTCG_L003_001.R2.fastq.gz		ENCORE2	23165
EIF3H_BGHcLV05-16_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	1672					GRCh38	V40	EIF3H_BGHcLV05-16/Aligned.sortedByCoord.out.bam		ENCORE2	23177
EIF3H_BGHcLV05-16_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	1672					GRCh38	V40	EIF3H_BGHcLV05-16/Aligned.sortedByCoord.out.bam		ENCORE2	23189
EIF3H_BGHcLV05-16_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	1672					GRCh38	V40	EIF3H_BGHcLV05-16/Aligned.sortedByCoord.out.bam		ENCORE2	23201
EIF3H_BGHcLV05-16_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	1672					GRCh38	V40	EIF3H_BGHcLV05-16/Aligned.sortedByCoord.out.bam		ENCORE2	23213
EIF3H_BGHcLV05-16_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1672					GRCh38	V40	EIF3H_BGHcLV05-16_GTTTCG_L003_001.R1.fastq.gz,EIF3H_BGHcLV05-16_GTTTCG_L003_001.R2.fastq.gz		ENCORE2	23225
EIF3H-BGHcLV05-16D_S5_R1_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1972	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	27410
EIF3H-BGHcLV05-16D_S5_R2_001.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1972	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	27438
EIF3H-BGHcLV05-16D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1972					GRCh38	V40	EIF3H-BGHcLV05-16D_S5_R1_001.fastq.gz,EIF3H-BGHcLV05-16D_S5_R2_001.fastq.gz		ENCORE2	27466
EIF3H-BGHcLV05-16D_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	1972					GRCh38	V40	EIF3H-BGHcLV05-16D/Aligned.sortedByCoord.out.bam		ENCORE2	27494
EIF3H-BGHcLV05-16D_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	1972					GRCh38	V40	EIF3H-BGHcLV05-16D/Aligned.sortedByCoord.out.bam		ENCORE2	27522
EIF3H-BGHcLV05-16D_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	1972					GRCh38	V40	EIF3H-BGHcLV05-16D/Aligned.sortedByCoord.out.bam		ENCORE2	27550
EIF3H-BGHcLV05-16D_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	1972					GRCh38	V40	EIF3H-BGHcLV05-16D/Aligned.sortedByCoord.out.bam		ENCORE2	27578
EIF3H-BGHcLV05-16D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1972					GRCh38	V40	EIF3H-BGHcLV05-16D_S5_R1_001.fastq.gz,EIF3H-BGHcLV05-16D_S5_R2_001.fastq.gz		ENCORE2	27606