title: H4K16ac_interphase_ChIPSeq_Rep1

description:
1041
H4K16ac_Async_Mitotic_Union_Peaks.bed.gz

value: estradiol

value: interphase


title: H4K16ac_interphase_ChIPSeq_Rep2

status: Public on Apr 10 2019

type: SRA

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

country: USA

institute: Pennsylvania State University

description:
1043
H4K16ac_Async_Mitotic_Union_Peaks.bed.gz

library_source: genomic

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters  --barcode-mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Peaks called with Sicer V1.1 using parameters mm9 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: Bed3+2 format. Peaks were called for all  ChIP-seq replicates separately using HOMER findPeaks (v4.9.1, parameters:  -style histone) using cell-cycle-matched sequenced ChIP input. Peaks were  required to be called in at least 2 replicates, and peak sets for each  factor were merged between interphase and mitosis using BedTools merge  (v2.22.0, default parameters). For BRD4, mitosis peaks needed to be present  in at least 2 of the 6 combined nocodazole and ro3306 replicates. Peaks  were excluded if they contained >50% overlap with repeat regions and any  overlap with blacklist regions. Columns 4 and 5 are rpkm intensities  extracted from these peak regions during interphase and mitosis. All  intensities were scaled by qPCR-derived scaling factors.

molecule: genomic DNA

organism: Mus musculus

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 cells are a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., 1997) in which GATA1-ER is stably expressed. G1E-ER4 cells are induced to differentiate through the addition of estradiol to the culture medium. G1E-ER4 cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s ChIP-seq Sample Preparation Kit. SPRIselect (Beckman Coulter) beads were used obtain an average library target size of 338 bp (range 302-436 bp), followed by real-time qPCR quantification using the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Single-end sequencing (1x50bp or 1x75 bp) was performed on the Illumina NextSeq 500 in high-output mode using Illumina sequencing reagents according to Illumina instructions.

treatment_protocol: Cells were induced to mature with 100 nM estradiol to activate GATA1-ER. For the mitosis conditions, nocodazole (200 ng/ml) was added after 6h of estradiol induction to synchronize cells in mitosis. At 13h following the addition of E2, cells were fixed with 1% formaldehyde and used for ChIP.

tag: strain

tag: cell line

value: G1E ER4

tag: cell type

value: ES-derived erythroid progenitor cells

tag: treatment

tag: mitotic phase

tag: chip antibody

value: Millipore 07-370


title: H3K27ac_mitosis_ChIPSeq_Rep2

description:
1596
H3K27ac_Async_Mitotic_Union_Peaks.bed.gz

value: estradiol, nocodazole

value: mitosis

value: Active Motif 39685


title: H3K122ac_interphase_ChIPSeq_Rep2

description:
1039
H3K122ac_Async_Mitotic_Union_Peaks.bed.gz

value: Abcam ab33309


title: H4K16ac_mitosis_ChIPSeq_Rep2

description:
1044
H4K16ac_Async_Mitotic_Union_Peaks.bed.gz


title: JNJ_24h_Rep1

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

description:
SMB21 cells treated with JNJ for 24 hours
sample name:
Sample 10

library_source: transcriptomic

data_processing:
A minimum of 30 million reads was generated, yielding a minimum of 26 million uniquely mapped reads.
Sequenced reads were trimmed for adaptor sequence.
Sequencing reads were aligned to the mm9 reference genome assembly and gene counts were quantified using the STAR aligner version 2.5.1b.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited processed data file contains gene counts as determined by the STAR aligner.

molecule: total RNA

growth_protocol: SMB21 cells were kept in culture using DMEM/F12 mix supplemented with B-27.

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit (Qiagen).
Single-end RNA-seq libraries were prepared using Ilumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according the manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on two Illumina NextSeq 500 runs with single-end 75bp reads.

treatment_protocol: SMB21 cells were treated with the HDAC inhibitor JNJ (Quisinostat) or DMSO for indicated periods, Alternatively, SMB21 cells were treated with a virus coding for shRNA against luciferase, Hdac1 or Hdac2. Cells were selected with puromycin.

value: medulloblastoma

tag: tissue

value: cell line derived from brain


title: H3K27ac_mitosis_ChIPSeq_Rep1

description:
1590
H3K27ac_Async_Mitotic_Union_Peaks.bed.gz


title: H3K122ac_mitosis_ChIPSeq_Rep2

description:
1040
H3K122ac_Async_Mitotic_Union_Peaks.bed.gz


title: H3K14ac_mitosis_ChIPSeq_Rep1

description:
1034
H3K14ac_Async_Mitotic_Union_Peaks.bed.gz

value: Millipore 07-353


title: H3K14ac_interphase_ChIPSeq_Rep1

description:
1033
H3K14ac_Async_Mitotic_Union_Peaks.bed.gz


title: H3S10ph_mitosis_ChIPSeq_Rep2

description:
1032
H3S10ph_Async_Mitotic_Union_Peaks.bed.gz

value: Abcam ab5176


title: H3S10ph_mitosis_ChIPSeq_Rep1

description:
1030
H3S10ph_Async_Mitotic_Union_Peaks.bed.gz


title: H3K27ac_interphase_ChIPSeq_Rep1

description:
1588
H3K27ac_Async_Mitotic_Union_Peaks.bed.gz


title: H3S10ph_interphase_ChIPSeq_Rep2

description:
1031
H3S10ph_Async_Mitotic_Union_Peaks.bed.gz


title: H3K14ac_mitosis_ChIPSeq_Rep2

description:
1036
H3K14ac_Async_Mitotic_Union_Peaks.bed.gz


title: H3K122ac_mitosis_ChIPSeq_Rep1

description:
1038
H3K122ac_Async_Mitotic_Union_Peaks.bed.gz


title: H2AZ_interphase_ChIPSeq_Rep1

description:
1025
H2AZ_Async_Mitotic_Union_Peaks.bed.gz

value: Abcam ab4174


title: H2AZ_mitosis_ChIPSeq_Rep2

description:
1028
H2AZ_Async_Mitotic_Union_Peaks.bed.gz


title: H3S10ph_interphase_ChIPSeq_Rep1

description:
1029
H3S10ph_Async_Mitotic_Union_Peaks.bed.gz


title: H2AZ_interphase_ChIPSeq_Rep2

description:
1027
H2AZ_Async_Mitotic_Union_Peaks.bed.gz


title: H3_interphase_ChIPSeq_Rep2

description:
1023
H3_Async_Mitotic_Union_Peaks.bed.gz

value: Abcam ab1791


title: H3_mitosis_ChIPSeq_Rep1

description:
1022
H3_Async_Mitotic_Union_Peaks.bed.gz


title: H3_interphase_ChIPSeq_Rep1

description:
1021
H3_Async_Mitotic_Union_Peaks.bed.gz


title: H2AZ_mitosis_ChIPSeq_Rep1

description:
1026
H2AZ_Async_Mitotic_Union_Peaks.bed.gz


title: H3K122ac_interphase_ChIPSeq_Rep1

description:
1037
H3K122ac_Async_Mitotic_Union_Peaks.bed.gz


title: Pol2_mitosis_noc_JQ1_Rep2

description:
1847
Pol2_Async_Mitotic_Union_Peaks.bed.gz

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters  --barcode-mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Peaks called with Sicer V1.1 using parameters mm9 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: Brd4 Bed3+2 format. Peaks were called for all ChIP-seq replicates separately using HOMER findPeaks (v4.9.1, parameters: -style histone) using cell-cycle-matched sequenced ChIP input. Peaks were required to be called in at least 2 replicates, and peak sets for each factor were merged between interphase and mitosis using BedTools merge (v2.22.0, default parameters). For BRD4, mitosis peaks needed to be present in at least 2 of the 6 combined nocodazole and ro3306 replicates. Peaks were excluded if they contained >50% overlap with repeat regions and any overlap with blacklist regions. Columns 4 and 5 are rpkm intensities  extracted from these peak regions during interphase and mitosis. All  intensities were scaled by qPCR-derived scaling factors.
Supplementary_files_format_and_content: Pol2 Bed3+2 format.  Regions are 2.5kb long centered on gene TSS  that have a TSS-proximal Type 2 BRD4 peak. Columns 5 and 6 are rpkm  intensities extracted from these peak regions during mitosis with DMSO (col  5) or JQ1 (col 6) treatment. All intensities were scaled by library  normalization.

treatment_protocol: G1E-ER4 cells were induced by addition of 100 nM estradiol for 13 hours total. At 5 hours post-induction, cells were arrested in pro-metaphase by addition of either 10 uM ro3306 (2 replicates of BRD4 ChIP-seq) or 200 ng/ml nocodazole (3 replicates of BRD4 ChIP-seq, 2 replicates for all other targets). Nocodazole-treated populations were fixed with 1% room temperature formaldehyde for 10 minutes at 13 hours post-induction. Treatment with the CDK1 inhibitor ro3306 (Vassilev et al., 2006) arrested cells at the late G2/mitosis checkpoint, and so at 13 hours post-induction, ro3306 was washed out and cells were grown in media for 30 minutes at 37 degrees before formaldehyde fixation so that mitotic cells could be collected.

value: estradiol, nocodazole, JQ1

value: Cell Signaling 14958


title: Pol2_mitosis_noc_Rep2

description:
1846
Pol2_Async_Mitotic_Union_Peaks.bed.gz


title: H3_mitosis_ChIPSeq_Rep2

description:
1024
H3_Async_Mitotic_Union_Peaks.bed.gz


title: Brd4_mitosis_noc_JQ1_Rep1

description:
1591
Brd4_Async_Mitotic_Union_Peaks.bed.gz

value: Bethyl A301-985A


title: Brd4_mitosis_noc_Rep3

description:
1589
Brd4_Async_Mitotic_Union_Peaks.bed.gz


title: Brd4_mitosis_ro3306_Rep2

description:
995
Brd4_Async_Mitotic_Union_Peaks.bed.gz

value: estradiol, ro3306


title: Brd4_interphase_Rep2

description:
992
Brd4_Async_Mitotic_Union_Peaks.bed.gz

value: G1E ER4

value: estradiol

value: interphase


title: Brd4_interphase_Rep1

description:
991
Brd4_Async_Mitotic_Union_Peaks.bed.gz

value: ES-derived erythroid progenitor cells


title: Brd4_mitosis_noc_Rep2

description:
993
Brd4_Async_Mitotic_Union_Peaks.bed.gz

value: estradiol, nocodazole

value: mitosis


title: Brd4_interphase_Rep3

description:
1587
Brd4_Async_Mitotic_Union_Peaks.bed.gz


title: Brd4_mitosis_ro3306_Rep1

description:
462
Brd4_Async_Mitotic_Union_Peaks.bed.gz


title: IF3

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Fastq files were pseudoalign and quantified through Kallisto version 0.43.
Processed files were analysed with Sleuth version 0.30
Genome_build: mm10
Supplementary_files_format_and_content: Processed files generated using Kallisto version 0.43.0.

source_name: Folicular Cells

extract_protocol:
RNA was isolated using RNAClean XP beads (Agentcourt, A63987) on a magnetic stand (DynaMag, Invitrogen 12331D). Reverse transcription primers were: P1-RNA-TSO: Biot-rArArUrGrArUrArCrGrGrCrGrArCrCrArCrCrGrArUrNrNrNrNrNrNrGrGrG, P1-T31: Biot-AATGATACGGCGACCACCGATCG31T, P1-PCR: Biot-GAATGATACGGCGACCACCGAT. RNA was eluted for 1 min in RT- cDNA synthesis mix 1 (0. 5 μl P1-T31 (20uM), 0.3 μl RNasin plus (Promega, N2615), 1.5 μl 10 mM dNTP, 3.5 μl 10 mM Tris pH 7.5- 0.5% IGEPAL CA-630 (Sigma) and 1.7 μl RNase free ddH2O) and the beads pipetted up and down ten times. The eluted sample was then incubated for 3 min at 72°C, followed by 1 min on ice, then 7.5 μl of mix 2 was added (3 μl 5X FS Buffer SS, 0.375 μl 100 mM DTT, 0.375 μl RNasin plus, 0.5 μl P1-RNA-TSO (40uM), 0.75 μl Maxima RT Minus H (Thermo Scientific, EP0751), 1.8 μl 5M Betaine (Sigma, B0300), 0.9 μl 50 mM MgCl2 and 0.175 μl RNase free ddH2O. Reverse transcription (RT) occurred during a thermal cycle of one cycle (90 min at 42 °C), 10 cycles (2 min at 50°C, 2 min at 42°C) and one cycle (15 min 70 °C), and the product was kept at 4 °C. The cDNA was then amplified using 15 μl of the RT product, 20 μl 2x KAPA HiFi HS Ready Mix (Kapabiosystems, KK2601), 1.5 μl P1-PCR (10uM), and 3.5 μl RNase free ddH2O. Amplification occurred during following cycle: One cycle of 3 min at 98 °C, 20 cycles (15 sec at 98 °C, 20 sec at 67 °C, 6 min at 72 °C), one cycle (5 min at 72 °C), and the product was kept at 4 °C. 20 μl of PCR product were cleaned up using 16 μl RNAClean XP beads. The cDNA was eluted in 20 μl RNase free ddH2O and kept at -20 °C.
Isolated amplicons were confirmed to be 1500-2000 bp long by a High Sensitivity DNA Assay (Bioanalyzer). Concentration of all sample was measured on a Qubit fluorometer (Thermo Fisher), all samples were adjusted to 0.1 ng/μl with ddH2O, and 2.5 μl cDNA were subjected to Nextera XT DNA Library preparation (Illumina) using a Nextera XT Index Kit (Illumina, FC-131-1002) and according to the manufacturer’s protocol, except that all volumes were used at 0.5 x of the indicated volumes. Sample quality was again verified by Bioanalyzer, sample concentrations measured on the Qubit fluorometer and adjusted to a concentration of 4.54 ng/ μl. All samples were pooled at equal contribution and run in multiple lanes. Sequencing was performed using 76 base single-end reading on a NextSeq instrument (Illumina).

value: Ileum Lymph Node

tag: cell number

value: Not applicable

tag: cd11b status


title: IF1


title: IL3

source_name: Lymphatic Endothelial Cells


title: IL2


title: Brd4_mitosis_noc_Rep1

description:
529
Brd4_Async_Mitotic_Union_Peaks.bed.gz


title: DL3

value: Duodenum Lymph Node


title: IL1


title: DL2


title: IF2


title: DF3


title: DF2


title: Pol2_mitosis_noc_Rep1

description:
1844
Pol2_Async_Mitotic_Union_Peaks.bed.gz


title: Pol2_mitosis_noc_JQ1_Rep1

description:
1845
Pol2_Async_Mitotic_Union_Peaks.bed.gz


title: DF1


title: CL3

value: Cecal-Colonic Lymph Node


title: CF3


title: CL2


title: CL1


title: CF2


title: CF1


title: 3cLn_Cd11b+

description: 4 technical replicates included. Each SRR represents a technical replicate of the same sample, that was resequenced.

source_name: Dendritic Cells

value: Positive


title: 4cLn_Cd11b+


title: 4dLn_Cd11b+


title: 3dLn_Cd11b+


title: 2iLn_Cd11b+


title: 3cLn_Cd11b-

value: Negative


title: 2cLn_Cd11b+


title: 4iLn_Cd11b+


title: 1cLn_Cd11b+


title: 3iLn_Cd11b+


title: 4iLn_Cd11b-


title: 2dLn_Cd11b+


title: 1dLn_Cd11b+


title: 4cLn_Cd11b-


title: 2iLn_Cd11b-


title: 1iLn_Cd11b+


title: 2cLn_Cd11b-


title: 1cLn_Cd11b-


title: DL1


title: 3iLn_Cd11b-


title: 3dLn_Cd11b-


title: 4dLn_Cd11b-


title: 1iLn_Cd11b-


title: DW019_ApcTT

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Raw FASTQ files were analyzed on the Galaxy server (usegalaxy.org).
Transcripts were quantified using Salmon* (Galaxy version 0.9.1). * Patro et al, Nat Methods 14, 417-419 (2107). Doi: 10.1038/nmeth.4197.
Differential expression was analyzed using the DESeq2 ** package (Galaxy version 2.11.40.2). ** Love et al, Genome Biol. 15, 550 (2014). Doi: 10.1186/s13059-014-0550-8.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: comma separated file, including read counts for each sample

molecule: polyA RNA

source_name: mouse colon

extract_protocol:
RNA was isolated using an Absolutely RNA Miniprep Kit (Agilent) according to the manufacturer's instructions.
Poly-A RNA-seq libraries were generated at the University of Virginia Genome Analysis and Technology Core with Illumina barcodes and single end 75bp sequence generated on an Illumina NextSeq 500.
RNA-seq, poly A selection, 75bp single end reads.

tag: tissue type

value: colon tumor

tag: genotype

value: Apc heterozygous; Tgif1;Tgif2 null

tag: Sex

value: male


title: DW018_ApcTT


title: DW017_ApcTT


title: 1dLn_Cd11b-


title: 2dLn_Cd11b-


title: DW016_ApcTT


title: DW011_Apc

value: Apc heterozygous


title: DW012_Apc


title: DW009_Apc


title: DW008_Apc

value: female


title: DW014_ApcTT


title: DW015_ApcTT


title: DW007_Apc


title: DW005_WT

value: normal colon

value: wild type


title: DW010_Apc


title: DW006_Apc


title: DW003_WT


title: DW001_WT


title: DW002_WT


title: DW013_ApcTT


title: 14MC

type: RNA

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v:2.5) Lumi package

label: biotin

organism: Homo sapiens

source_name: Liver Tissue

label_protocol: Total RNA was labled with the Kit according to manufacturers suggested protocol.

extract_protocol: For total RNA extraction, cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen) using a pestle and nuclease-free 1.5-ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines, and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: machine

value: ORGANOX

tag: time

value: POST


title: DW004_WT


title: 14MB

value: PRE


title: 13CC

value: CONTROL


title: 14MA


title: 14CB


title: 13MC


title: 11CB


title: 12MC


title: 13MB


title: 11CC


title: 10 nM 1,25(OH)2 D, 3 h treated, VDR IP, lane 2 of sequencing

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

description: Vit D VDR 2

data_processing:
Base calling was done with th Illumina Bustard base caller.  Results were converted to Illumina 1.9 encoded FASTQ format using the perl script "solexa2fastq.pl" written by James Bonfield in 2006. A program "FastQC" was then run to observe read quality and to ensure that FASTQ filex were properly formatted.
Reads from multiple lanes of sequencing for the same sample were combined.
Alignment to human reference genome version hg19 using Bowtie v 1.1.1 with the arguments: “bowtie –n 1 –m 1 –k 1 –e 70 –best”
Statistically significant ChIP-seq peaks were identified using Model-based Analysis of ChIP-Seq data (MACS) version 2 with the following arguments: macs2 callpeak –bw 150 –keep-dup 1 –g hs –qvalue=0.01 –m 5 50 –bdg. Otherwise, default parameters were used.
Genome_build: hg19
Supplementary_files_format_and_content: tdf files were created for visualization in the IGV genome viewer; these are from the alignments of the pooled lanes for the samples.  The IgG control IP was used as background that was subtracted from the peaks for the vehicle or vitamin D treatment groups
Supplementary_files_format_and_content: Excel file with information about the peaks: (column) (1) Chromosome, (2) Gene symbol, (3) Gene description, (4) location relative to gene, (5) Distance to TSS, (6) Peak start, (7) peak end, (8) peak width, (9) peak height vehicle, (10) peak height vitamin D, (11) DR3 motif in peak (1= yes), (12) peak overlaps a TSS (1=yes).

source_name: RWPE1 cells

growth_protocol: RWPE cells were grown to 80% confluence in Defined Keratinocyte-Serum Free medium supplemented with growth factors as described by Rhim JS et al. (1994) Proc Natl. Acad. Sci. 91:11874-78.

extract_protocol:
Immune complexes from immunoprecipitations of formalin-fixed, sonicated samples were collected with a 50% slurry of protein G for 1 h at 4oC. Cross-links were reversed overnight in 1% SDS, 0.1 M NaHCO3, and 0.2 M NaCl at 65oC.   DNA was purified using Qiagen QIAquick Spin Kits.
We used methods originally reported in Robertson G. et al. (2007) Nature Methods 4:651-7.  Briefly, 100-300 bp fragments of the immunoprecipitated were eluted from 12%  PAGE gels and the DNA was recovered using a QIAquick PCR purification kit.  DNA ends were repaired using a 1:5 mix of T4 and Klenow DNA polymerases, phenol–chloroform–isoamyl alcohol (pH 8.0) extracted, and precipitated with 100% EtOH, mussel glycogen (Invitrogen) and 7.5 M NH4OAc. We recovered the precipitate by centrifugation at 20,200g for 15 min at 4 °C. We added a single adenine base to the DNA using Klenow exo– (3′ and 5′ exo minus; Illumina), phenol–chloroform–isoamyl alcohol extracted, and precipitated as above.. The DNA pellet was washed twice with 70% EtOH and resupended in 10 ml of LoTE buffer. Adapters (Illumina) were ligated to ends of the single adenine–tailed DNA following the manufacturer's instructions with the exception that we diluted the adaptor oligonucleotide mix (Illumina) 1/10 before use. We recovered the DNA using a QIAquick PCR Purification Kit (Qiagen) and we enriched the adaptor-modified DNA fragments by PCR using Phusion polymerase (Finnzymes) and PCR primer 1.1 and 2.1 (Illumina) following the manufacturer's instructions (separate 10- and 15-cycle reactions were run). After cycling, we purified the reactions using a QIAquick MiniElute kit (Qiagen) according to the manufacturer's instructions, with 15 μl of elution buffer heated to 50 °C. We quantified the DNA quality with an Agilent DNA 1000 series II assay and a Nanodrop 7500 spectrophotometer using a 1.5-μl aliquot that was diluted to 10 nM.

treatment_protocol: Treatments were prepared in Defined Keratinocyte-Serum Free Medium supplemented with growth factors.   1,25(OH)2 D was prepared in absolute ethanol and was provided to cells at 10 nM.  An equal volume of ethanol was used as a negative control.  After 3 hours cells were harvested for the ChIP assay.

value: HPV-18 immortalized, non-tumorigenic prostate epithelial cell line

tag: agent

value: vitamin D

value: anti-VDR polyclonal antibody (C-20, sc-1008, Santa Cruz Biotechnology)

tag: number of reads


title: 9CB


title: 9MC


title: 9CC


title: 7MC


title: 13MA


title: 14CC


title: 9MB


title: 12MB


title: 10 nM 1,25(OH)2 D, 3 h treated, VDR IP, lane 1 of sequencing

description: Vit D VDR 1


title: 11MC


title: 8CB


title: 10CB


title: 11MB


title: 8CC


title: 10CC


title: 13CB


title: 12MA


title: 1%_DKO_RNAseq_2

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
ChIP-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and mapped to human genome (hg19) using bowtie2 (version 2.2.3), filtering out alignments with mapping quality less than 10. Duplicate alignments were removed using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). The ChIP-seq peaks were called using MACS2 (version 2.0.10), with a q-value threshold of 0.05 and using the random background of ChIP samples as controls.
Genome_build: hg19
Supplementary_files_format_and_content: [ChIP-Seq] Bigwig, bed
[RNA-Seq] FPKMs

source_name: MDA-MB-231 cells

growth_protocol: Cells were cultured with DMEM+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen). Chromatin was isolated using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology), sonicated to 200-300 bp in length, and subjected to immunoprecipitation overnight with respective antibodies. The ChIP DNA was eluted, decrosslinked, and purified.
mRNA-seq libraries were prepared with a TruSeq Stranded mRNA Library Prep kit (Illumina). ChIP-seq libraries were prepared with a KAPA Hyper Library Preparation kit.

treatment_protocol: Cells were exposed to 20% or 1% O2 for 24 hrs

value: MDA-MB-231 cells

value: HIF-1/2alpha knockout


title: vehicle treated, VDR IP, lane 2 of sequencing

description: Vehicle VDR 2

value: vehicle


title: vehicle treated, VDR IP, lane 1 of sequencing

description: Vehicle VDR 1


title: Pooled vehicle and vitamin D treated, IgG control IP, lane 2 of sequencing

description: IgG 2

value: vehicle and vitamin D

value: anti-IgG polyclonal antibody (12-370, Millipore Sigma)


title: 7MB


title: 6MB


title: 6MC


title: Input_async_ChIPseq (Histones)

value: G1E ER4

value: ES-derived erythroid progenitor cells

value: asynchronous


title: Input_mitotic_ChIPseq (Histones)

value: mitosis


title: Input_mitotic_ChIPseq (TFs)


title: Input_async_ChIPseq (TFs)


title: H3K14ac_interphase_ChIPSeq_Rep2

description:
1035
H3K14ac_Async_Mitotic_Union_Peaks.bed.gz

value: estradiol

value: interphase

value: Millipore 07-353


title: Pooled vehicle and vitamin D treated, IgG control IP, lane 1 of sequencing

description: IgG 1


title: 5MC

value: ORGANOX

value: POST


title: 4MB

value: PRE


title: 7CB

value: CONTROL


title: 6CB


title: iNampt-CKO-3

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

country: Japan

institute: Tokushima University Graduate School of Biomedical Sciences

description: iNampt-conditional knockout mice-3

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent DNA Microarray Scanner (G2505C) Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Kidneys

label_protocol: Agilent Low Input Quick Amp Labeling Kit, one-color labeling protocol

growth_protocol: Mice in the control and Nampt CKO groups were sacrificed and their whole kidneys were harvested.

extract_protocol: RNA was prepared using miRNeasy Mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Whole kidneys were harvested for microarray analysis using the SurePrint G3 Mouse GE 8x60K Microarray according to the Agilent standard protocols.

tag: gender

value: male

tag: genotype/variation

value: iNampt-conditional knockout


title: iNampt-CKO-1

description: iNampt-conditional knockout mice-1

tag: strain


title: 5MB


title: Cont-1

description: Control mice-1

value: Control


title: iNampt-CKO-2

description: iNampt-conditional knockout mice-2


title: 4CC


title: 7CC


title: 3MC


title: 4CB


title: 4MC


title: 6CC


title: 3MA


title: Cont-3

description: Control mice-3


title: Cont-2

description: Control mice-2


title: shHdac2_Rep1

description:
SMB21 cells treated with virus coding for shRNA targeting Hdac2
sample name:
Sample 19

tag: cell line

tag: cell type

value: medulloblastoma

value: cell line derived from brain


title: 2CC


title: Root segment above and below young lateral roots, replicate 3

city: Brookings

first: Sen

last: Subramanian

state: SD

address: 1390 College Avenue

department: Agronomy, Horticulture, and Plant Science

institute: South Dakota State University

data_processing:
Sequence quality assessment using FastQC
Sequences trimmed using prinseq-lite v0.19.5 (minimum phred quality score = 20, window size of 5, no Ns, and minimum post trimming length = 25)
All YLR, all ABYLR, and rep1 of ELR libraries had to be sequenced twice due to technical reasons. The trimmed outputs from both rounds for the same sample/replicate were merged by appending the fastq files
Reads were mapped to Gmax v1.1_189 Phytozome v9.0 using tophat v2.0.5 (no transcriptome, genome read, no read and segment mismatches, no deletions and insertions, maximum intron length -5000, and library type- fr-second strand)
Mapped reads were assembled using cuffmerge (cufflinks v2.0.2)
Differential expression analysis using cuffdiff (FDR <0.05)
Genome_build: Gmax_v1.1_189
Supplementary_files_format_and_content: Matrix of normalized expression values (FPKM) for all transcripts in all tissues and replicates

organism: Glycine max

source_name: dissected root segment above and below young lateral roots

growth_protocol: Soybean (Glycine max) Williams 82 cv. Seeds were surface-sterilized, sown in a mixture of autoclaved vermiculite and perlite (2:1 ratio). Seedlings were grown in a growth chamber (Conviron, Manitoba, Canada) at 25'C and 16/8 hrs light cycle, and watered with nitrogen free plant nutrient solution for both nodule and root tissue harvest. All growth conditions including watering were identical between plants used for LR and nodule harvests except rhizobium inoculation. All growth conditions including watering were identical between plants used for LR and nodule harvests except rhizobium inoculation.

extract_protocol:
Total RNA was isolated using Trizol using the protocol recommended by the manufacturer with slight modifications - using twice the recommended amount of trizol. A tissue lyser (QIAGEN, Hilden, Germany) was used for tissue homogenization.
RNA quality was checked using a Bioanalyzer (Agilent Technologies, Santa Clara, CA), and library was prepared using ScriptSeqª v2 RNA-Seq Library Preparation Kit (Epicentre, Madison, WI) according to the manufacturers recommendation.

treatment_protocol: For inoculation Bradyrhizobium diazoefficiens cells were resuspended in N-PNS to a concentration of OD 0.08 OD at 600nm and applied to the roots. EN and MN and control tissues were harvested at 5-7dpi and 14-16 dpi respectively. ELR and YLR and their controls were harvested from uninoculated plants. ELR and YLR tissues and controls were harvested 5-7 days after germination.

value: root

tag: cultivar

value: Williams 82


title: Young lateral roots, replicate 1

source_name: dissected young lateral roots

value: lateral root

tag: developmental stage

value: young


title: Young lateral roots, replicate 3

tag: tissue


title: Young lateral roots, replicate 2


title: Root segment above and below young lateral roots, replicate 1


title: Root segment above and below emerging lateral roots, replicate 3

source_name: dissected root segment above and below emerging lateral roots


title: 3MB


title: Root segment above and below emerging lateral roots, replicate 2


title: 2CB


title: 1MB


title: Root segment above and below young lateral roots, replicate 2


title: C2.I5.02_X_C2.I5.pool

city: Sao Paulo

first: Carlos

middle: T

last: Hotta

state: SP

address: Av. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

description: Comparison between RNA Internode 5 C2C502 time point sample and RNA pool sample.

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: Raw and background corrected data

organism: Saccharum hybrid cultivar SP80-3280

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

extract_protocol: modified Trizol method

treatment_protocol: NO

value: Internode 5

tag: variety

tag: collect


title: Root segment above and below emerging lateral roots, replicate 1


title: C2.I5.00_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C500 time point sample and RNA pool sample.


title: 1MC


title: C2.I1.26_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C126 time point sample and RNA pool sample.

value: Internode 1


title: Emerging lateral roots, replicate 3

source_name: dissected emerging lateral roots

value: emerging


title: C2.I1.10_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C110 time point sample and RNA pool sample.


title: C2.I5.06_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C506 time point sample and RNA pool sample.


title: 1CC


title: Emerging lateral roots, replicate 1


title: C2.I1.08_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C108 time point sample and RNA pool sample.


title: C2.I1.16_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C116 time point sample and RNA pool sample.


title: C2.I5.08_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C508 time point sample and RNA pool sample.


title: C2.I1.22_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C122 time point sample and RNA pool sample.


title: C2.I1.14_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C114 time point sample and RNA pool sample.


title: C2.I1.18_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C118 time point sample and RNA pool sample.


title: C2.I5.04_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C504 time point sample and RNA pool sample.


title: C2.I1.12_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C112 time point sample and RNA pool sample.


title: C2.I5.10_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C510 time point sample and RNA pool sample.


title: 1CB


title: Root segment above and below mature nodules, replicate 2

source_name: dissected root segment above and below mature nodules


title: Emerging lateral roots, replicate 2


title: C2.I1.20_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C120 time point sample and RNA pool sample.


title: C2.I1.pool_X_C2.I1.04

description: Swap of comparison between Internode 1 RNA pool sample and C2C104 time point RNA sample.


title: Root segment above and below mature nodules, replicate 1


title: C2.I1.24_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C124 time point sample and RNA pool sample.


title: Mature nodules, replicate 3

source_name: dissected mature nodules

value: nodule

value: mature


title: Root segment above and below mature nodules, replicate 3


title: C2.I1.06_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C106 time point sample and RNA pool sample.


title: Mature nodules, replicate 1


title: Root segment above and below emerging nodules, replicate 3

source_name: dissected root segment above and below emerging nodules


title: C2.I1.04_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C104 time point sample and RNA pool sample.


title: C2.I1.pool_X_C2.I1.06

description: Swap of comparison between Internode 1 RNA pool sample and C2C106 time point RNA sample.


title: C2.I1.pool_X_C2.I1.02

description: Swap of comparison between Internode 1 pool RNA sample and C2C102 time point RNA sample.


title: Root segment above and below emerging nodules, replicate 2


title: Emerging nodules, replicate 3

source_name: dissected emerging nodules


title: Emerging nodules, replicate 1


title: Emerging nodules, replicate 2


title: C2.I1.pool_X_C2.I1.00

description: Swap of comparison between Internode 1 pool RNA sample and C2C100 time point RNA sample.


title: C2.I1.02_X_C2.I1.pool

description: Comparison between RNA Internode 1 C2C102 time point sample and RNA pool sample.


title: C2.I1.00_X_C2.I1.pool

description: Comparison between Internode 1 pool sample and C2C100 time point sample.


title: C2.F1.pool_X_C2.F1.26

description: Swap of comparison between Leaf 1 pool sample and C2F126 time point sample.

value: Leaf 1


title: Root segment above and below emerging nodules, replicate 1


title: C2.F1.pool_X_C2.F1.18

description: Swap of comparison between Leaf 1 pool sample and C2F118 time point sample.


title: C2.F1.pool_X_C2.F1.12

description: Swap of comparison between Leaf 1 pool sample and C2F112 time point sample.


title: C2.F1.pool_X_C2.F1.08

description: Swap of comparison between Leaf 1 pool sample and C2F108 time point sample.


title: C2.F1.pool_X_C2.F1.10

description: Swap of comparison between Leaf 1 pool sample and C2F110 time point sample.


title: C2.F1.pool_X_C2.F1.16

description: Swap of comparison between Leaf 1 pool sample and C2F116 time point sample.


title: C2.F1.pool_X_C2.F1.20

description: Swap of comparison between Leaf 1 pool sample and C2F120 time point sample.


title: C2.I5.pool_X_C2.I5.26

description: Swap of comparison between Internode 5 pool sample and C2C526 time point sample.


title: C2.F1.pool_X_C2.F1.22

description: Swap of comparison between Leaf 1 pool sample and C2F122 time point sample.


title: C2.F1.pool_X_C2.F1.02

description: Swap of comparison between Leaf 1 pool sample and C2F102 time point sample.


title: C2.F1.pool_X_C2.F1.06

description: Swap of comparison between Leaf 1 pool sample and C2F106 time point sample.


title: C2.F1.pool_X_C2.F1.04

description: Swap of comparison between Leaf 1 pool sample and C2F104 time point sample.


title: C2.F1.pool_X_C2.F1.24

description: Swap of comparison between Leaf 1 pool sample and C2F124 time point sample.


title: C2.F1.pool_X_C2.F1.14

description: Swap of comparison between Leaf 1 pool sample and C2F114 time point sample.


title: C2.I5.pool_X_C2.I5.24

description: Swap of comparison between Internode 5 pool sample and C2C524 time point sample.


title: C2.F1.pool_X_C2.FI.00

description: Swap of comparison between Leaf 1 pool sample and C2F100 time point sample.


title: TUBE-1

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway, Suite 747

department: Department of Neurology and Neuroscience

institute: Institute for Cell Engineering, Johns Hopkins University

data_processing:
After sequencing run the Illumina Real Time Analysis (RTA) module was used to perform image analysis, base calling, and the BCL Converter (bcl2fastq v2.17.1.14) were followed to generate FASTQ files which contain the sequence reads.
Read-level Q/C was performed by FastQC (v0.11.5). Pair-end reads of cDNA sequences are aligned back to the human genome (UCSC hg19 from Illumina iGenome) by the spliced read mapper TopHat (v2.0.9) with default option with “--mate-innder-dist 160” and “--library-type fr-firststrand” parameters based on known transcripts of Ensembl Build GRCh37.75.
To achieve gene-level expression profile, the properly paired and mapped reads are achieved by “samtools sort –n” option, and these reads are counted by htseq-count v0.9.1 (with intersection-strict mode and stranded option) according to gene annotation (Ensembl Build GRCh37.75) and RPKM is calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: human embryonic stem cell

growth_protocol: hESCs (H9, WiCell) and hiPSCs were cultured using standard protocols. The hESC lines and hiPSC lines were cultured with mouse embryonic fibroblasts (MEFs) (AppliedStemCell) pre-plated at 12,000–15,000 cells/cm2. Medium contained DMEM/F12, 20% knockout serum replacement, 1 mM L-glutamine, 100 μM MEM non-essential amino acids, and 0.1 mM β-mercaptoethanol. 10 ng/mL of FGF-2 was added after sterile filtration, and cells were fed daily, and passaged weekly, using 6 U/mL dispase or mechanically.

extract_protocol:
Trizol Method
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA RiboZero Gold sample Prep Kit (RS-122-2303) following the manufacturer’s protocol. The concentration of RNA was measured by Qubit (Life Technologies). Quality of RNAseq library was measured by LabChipGX (Caliper) using HT DNA 1K/12K/HiSens Labchip. The final cDNA libraries were sequenced using HiSeq 3000 for high-throughput DNA sequencing.

value: human embryonic stem cell

value: multinucleated myotubes


title: MYOG-3

value: MYOG::EGFP+ myoblast cells


title: TUBE-3


title: MYOG-1


title: C2.I5.pool_X_C2.I5.20

description: Swap of comparison between Internode 5 pool sample and C2C520 time point sample.


title: PAX7-1

value: PAX7::EGFP+ putative skeletal muscle stem/precursor cells


title: PAX7-3


title: C2.I5.pool_X_C2.I5.12

description: Swap of comparison between Internode 5 pool sample and C2C512 time point sample.


title: C2.I5.pool_X_C2.I5.10

description: Swap of comparison between Internode 5 pool sample and C2C510 time point sample.


title: C2.I1.pool_X_C2.I1.24

description: Swap of comparison between Internode 1 pool sample and C2C124 time point sample.


title: C2.I5.pool_X_C2.I5.18

description: Swap of comparison between Internode 5 pool sample and C2C518 time point sample.


title: C2.I1.pool_X_C2.I1.18

description: Swap of comparison between Internode 1 pool sample and C2C118 time point sample.


title: MSGN1-2

value: MSGN1::EGFP+ presomite cells


title: C2.I1.pool_X_C2.I1.16

description: Swap of comparison between Internode 1 pool sample and C2C116 time point sample.


title: C2.I5.pool_X_C2.I5.04

description: Swap of comparison between Internode 5 pool sample and C2C504 time point sample.


title: C2.I1.pool_X_C2.I1.22

description: Swap of comparison between Internode 1 pool sample and C2C122 time point sample.


title: C2.I5.pool_X_C2.I5.00

description: Swap of comparison between Internode 5 pool sample and C2C500 time point sample.


title: C2.I5.pool_X_C2.I5.16

description: Swap of comparison between Internode 5 pool sample and C2C516 time point sample.


title: C2.I1.pool_X_C2.I1.26

description: Swap of comparison between Internode 1 pool sample and C2C126 time point sample.


title: C2.I5.pool_X_C2.I5.14

description: Swap of comparison between Internode 5 pool sample and C2C514 time point sample.


title: C2.I1.pool_X_C2.I1.14

description: Swap of comparison between Internode 1 pool sample and C2C114 time point sample.


title: C2.I5.pool_X_C2.I5.08

description: Swap of comparison between Internode 5 pool sample and C2C508 time point sample.


title: OCT4-2

value: OCT4::EGFP+ embryonic stem cells


title: C2.I1.pool_X_C2.I1.12

description: Swap of comparison between Internode 1 pool sample and C2C112 time point sample.


title: MSGN1-1


title: C2.I5.pool_X_C2.I5.02

description: Swap of comparison between Internode 5 pool sample and C2C502 time point sample.


title: C2.I5.pool_X_C2.I5.22

description: Swap of comparison between Internode 5 pool sample and C2C522 time point sample.


title: C2.I1.pool_X_C2.I1.20

description: Swap of comparison between Internode 1 pool sample and C2C120 time point sample.


title: C2.I1.pool_X_C2.I1.10

description: Swap of comparison between Internode 1 pool sample and C2C110 time point sample.


title: OCT4-1


title: PA-Xwt1_rep3

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

data_processing:
Base calling was done using Bcl2fastq by Illumina
Alignment using Tophat2.1.1, default settings except for --library-type fr-firststrand; used hg19 gtf as reference
RPKM calculated using Cufflinks2.2.1, default setting except -u, --library-type fr-firststrand; used hg19 gtf as reference
Custom pipeline to convert the RPKM to attomoles using ERCC spike-in mix as reference
Average of replicates using custom pipeline
Calculation of relative RNA levels in infected vs.mock infected o PA-X expression vs. control samples
Genome_build: hg19; PR8 sequences downloaded from FluDB
Supplementary_files_format_and_content: tab delimited files listing Refseq ID, ratio vs. control and standard deviation for each PA-X overexpression line or ratio vs. mock infectedand standard deviation  for each flu infection strain; only RNAs present at at least 1 FPKM in all control and mock infected samples are included

source_name: A549 cells

growth_protocol: A459 and derivative PA-X-inducible cell lines were grown in DMEM+10% FBS.

extract_protocol:
Total RNA was harvested using the Qiagen Rneasy kit
Library were constructed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human (Illumina) following the manufacturer's protocol.
RNA-seq (stranded)

treatment_protocol: Samples were collected either after 18 hrs if doxycyline treatment, for the PA-X inducible cell lines and A549 control, or 15 hrs of infection with A/PuertoRico/8/1934 H1N1 (wt or PA-X mutant strains), or mock infection as a control..

tag: ectopic expression

value: dox-inducible PR8 PA-X wt  (stable line #1)

tag: treatment

value: 0.2 ug/ml doxycycline for 18 hrs


title: A549_rep3


title: PA-Xmut8_rep3

value: dox-inducible PR8 PA-X D108A catalytic mutant (stable line #8)


title: mock_rep4

tag: infection

value: mock infected - 15 hrs


title: PR8-PA(deltaX)_rep4

value: A/PuertoRico/8/1934 H1N1 - 15 hrs

tag: influenza a strain

value: PA(deltaX) - mutations in frameshifting site in PR8 segment 3 and L201Stop mutation in PA-X


title: Mature nodules, replicate 2

value: Williams 82


title: PR8-PA(fs)_rep3

value: PA(fs) - mutations in frameshifting site in PR8 segment 3


title: wtPR8_rep3

value: wild-type


title: mock_rep3


title: PA-Xwt1_rep2


title: PR8-PA(X9)_rep3

value: PA(X9) - L201Stop mutation in PA-X


title: PA-Xwt10_rep2

value: dox-inducible PR8 PA-X wt  (stable line #10)


title: C2.I1.pool_X_C2.I1.08

description: Swap of comparison between RNA Internode 1 C2C108 time point sample and RNA pool sample.

value: Internode 1


title: PA-Xmut8_rep2


title: C2.F1.18_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F118 time point sample and RNA pool sample.

value: Leaf 1


title: C2.F1.12_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F112 time point sample and RNA pool sample.


title: C2.F1.24_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F126 time point sample and RNA pool sample.


title: C2.F1.20_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F120 time point sample and RNA pool sample.


title: C2.F1.26_X_C2.F1.pool


title: PA-Xmut2_rep2

value: dox-inducible PR8 PA-X D108A catalytic mutant (stable line #2)


title: C2.F1.06_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F106 time point sample and RNA pool sample.


title: C2.F1.10_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F110 time point sample and RNA pool sample.


title: C2.I5.pool_X_C2.I5.06

description: Swap of comparison between Internode 5 pool sample and C2C506 time point sample.

value: Internode 5


title: PR8-PA(X9)_rep2


title: C2.F1.14_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F114 time point sample and RNA pool sample.


title: A549_rep2


title: C2.F1.00_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F100 time point sample and RNA pool sample.


title: C2.F1.16_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F116 time point sample and RNA pool sample.


title: mock_rep2


title: PR8-PA(deltaX)_rep2


title: C2.F1.04_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F104 time point sample and RNA pool sample.


title: wtPR8_rep1


title: wtPR8_rep2


title: PA-Xwt10_rep1


title: PR8-PA(fs)_rep1


title: C2.F1.08_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F108 time point sample and RNA pool sample.


title: PA-Xwt1_rep1


title: PA-Xmut8_rep1


title: mock_rep1


title: C2.F1.02_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F102 time point sample and RNA pool sample.


title: C2.F1.22_X_C2.F1.pool

description: Comparison between RNA Leaf 1 C2F122 time point sample and RNA pool sample.


title: A549_rep1


title: C2.I5.24_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C524 time point sample and RNA pool sample.


title: C2.I5.20_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C520 time point sample and RNA pool sample.


title: E7.5 exVE cells Rep 1

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
Bulk RNA-seq data was aligned to the mm38 mouse genome using STAR and reads that mapped to multiple genomic locations were filtered out.
Gene expression counts for each sample were determined using the summarizeOverlaps function of the GenomicRanges package using Ensembl annotations.
Genome_build: mm38
Supplementary_files_format_and_content: Vector of unnormalized gene expression counts in  gzipped csv format

source_name: E7.5 exVE cells Rep 1

growth_protocol: Mice were maintained under a 12 hr light-dark cycle and checked for vaginal plugs in the morning. All embryos for this study were obtained by natural matings of virgins 6-8 weeks of age. Embryos at noon on the day of detecting copulation plugs were estimated at E0.5.  Uteri were flushed with flushing and holding medium (FHM, Millipore) as previously described. Embryos were subsequently washed in 2-3 drops of FHM and kept in drops of FHM covered with mineral oil (Sigma) on ice prior to single-cell dissociation. Post-implantation embryos were dissected in DMEM/F12 (Life Technologies)/5% Newborn calf serum (Life Technologies) and staged according to Downs and Davies 6 or by somite number.

extract_protocol:
13ss (E8.75) embryos were used as the terminal end point of this study since this is the latest time one can confidently assign cells in the gut tube with a VE-vs.-DE identity using either the Afp-GFP reporter  or the Ttr-Cre  driver crossed to a Cre reporter, since by 18-20ss (E9.0) both Afp and Ttr genes, and cis-regulatory elements used in the respective transgenic lines of mice, become activated in gut endoderm derivatives including the emergent liver. To obtain single cells from 13ss gut tubes, Afp-GFPTG/+ embryos were dissected out of the uterus, and extra- embryonic membranes and heads were removed. Torsos washed in three drops of DMEM/F12 on ice and subjected to Pancreatin/Trypsin treatment (2.5% Pancreatin / 0.5% Trypsin in PBS) for 5 min (exact time was batch dependent and empirically tested) on ice and then washed in three drops of DMEM/F12, 10% Newborn calf serum on ice. Gut tubes were dissected out using Tungsten needles (FST Cat No. 10130-10) and washed in cold DMEM/F12. Gut tubes were then incubated for 20 min at 37°C in Accutase/0.25% Trypsin (1:2) for the dissociation of single cells. To obtain single cells from definitive and visceral endoderm cell from stages E7.5 and visceral endoderm cells from E6.5, embryos were washed in three drops of DMEM/F12 on ice and subjected to Pancreatin/Trypsin treatment (2.5% Pancreatin / 0.25% Trypsin in PBS) for 3 min (E7.5) and 45s (E6.5) on ice and then washed in three drops of DMEM/F12, 10% Newborn calf serum on ice. The endoderm layer was removed from the rest of the tissue using Tungsten needles and subsequently washed in cold DMEM/F12 and incubated for 20 min at 37°C in Accutase/0.25% Trypsin (1:2). For E5.5 (defined as the stage when the DVE/AVE was distally positioned, observed as a thickening of the emVE epithelium), whole embryos were collected, and Reichert’s membrane removed with Tungsten needles. Embryos were washed in cold DMEM/F12 and then incubated in 0.25% Trypsin for 5 min at 37°C. To dissociate the tissue into a single cell suspension, DMEM/F12, 20% Newborn calf serum, 4mM EDTA were added in 1:1 ratio. Cell clumps were dissociated into single cells using a mouth pipet and 75mm glass capillaries. Subsequently, the single cell suspension was filtered through a FlowMI cell strainer (40μm) to remove debris. Single cells were spun down at 450g for 4 min at room temperature and then cell numbers were determined using a Neubauer hemocytometer. For pre-implantation embryo dissociations, embryos were incubated in 0.5% Trypsin-EDTA (Invitrogen) at 37°C for 3 minutes before transferring to PBS supplemented with 0.5mM EDTA (Invitrogen) and 4% BSA (Sigma) for mechanical dissociations. Trypsin-treated embryos were dissociated by repeated pipetting (trituration) using pulled capillaries (Sutter Instruments) attached to a mouth pipet.
RNA concentration and quality were assessed, and cDNA libraries construction and sequencing were done by the Genomics and Epigenomics Core Facility at Weill Medical College, Cornell University, New York

value: Extraembryonic visceral endoderm


title: E7.5 emVE cells Rep 1

source_name: E7.5 emVE cells Rep 1

value: Embryonic visceral endoderm


title: E8.75 Gut tube posterior Rep 2

source_name: E8.75 Gut tube posterior Rep 2

value: Posterior gut tube


title: E7.5 exVE cells Rep 2

source_name: E7.5 exVE cells Rep 2


title: E7.5 emVE cells Rep 2

source_name: E7.5 emVE cells Rep 2


title: C2.I5.26_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C526 time point sample and RNA pool sample.


title: C2.I5.22_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C522 time point sample and RNA pool sample.


title: C2.I5.14_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C514 time point sample and RNA pool sample.


title: C2.I5.16_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C516 time point sample and RNA pool sample.


title: E8.75 Gut tube posterior Rep 1

source_name: E8.75 Gut tube posterior Rep 1

value: Posterior  gut tube


title: E8.75 Gut tube mid gut - posterior Rep 1

value: Mid - posterior gut tube


title: PA-Xmut2_rep1

value: 0.2 ug/ml doxycycline for 18 hrs


title: E8.75 Gut tube anterior - mid gut Rep 1

source_name: E8.75 Gut tube anterior - mid gut Rep 1

value: Anterior - Mid gut tube


title: E8.75 Gut tube bulk tissue Rep 1

source_name: E8.75 Gut tube bulk tissue Rep 1

value: Gut tube


title: E8.75 Gut tube anterior - mid gut Rep 2

source_name: E8.75 Gut tube anterior - mid gut Rep 2

value: Anterior -Mid gut tube


title: lepr-5fu

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices.

source_name: Lepr-cre;LoxP-tdTomato

extract_protocol:
RNeasy Micro Kit - QIAGEN
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

treatment_protocol: 150 mg kg−1 5-FU (Sigma-Aldrich, F6627-5G) or PBS control; day four after injection.

value: bone marrow

value: non-hematopoietic Lepr+

tag: age


title: E8.75 Gut tube dissociated cells Rep 2

source_name: E8.75 Gut tube dissociated cells Rep 2


title: E8.75 Gut tube anterior Rep 2

source_name: E8.75 Gut tube anterior Rep 2

value: Anterior gut tube


title: E8.75 Gut tube dissociated cells Rep 1

source_name: E8.75 Gut tube dissociated cells Rep 1


title: E8.75 Gut tube bulk tissue Rep 2

source_name: E8.75 Gut tube bulk tissue Rep 2


title: vecad-5fu

source_name: VEcad-cre;LoxP-tdTomato

value: non-hematopoietic VEcad+


title: lepr-ctrl

value: PBS


title: E8.75 Gut tube mid gut - posterior Rep 2


title: LSK-VEcad-Dll4I3COIN

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

source_name: bone marrow

treatment_protocol: 1,000 μg tamoxifen (Sigma, T5648) intraperitoneally every day for 10 days

tag: genotype

tag: source

value: hematopoietic progenitors

value: 10 weeks


title: vecad-ctrl


title: E8.75 Gut tube anterior Rep 1

source_name: E8.75 Gut tube anterior Rep 1


title: LSK-CTRL

value: VEcad


title: 5FU-treat-vecad

value: 14 weeks


title: C2.I5.18_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C518 time point sample and RNA pool sample.

value: Internode 5


title: 5FU-cntrl-col23

value: non-hematopoietic Col2.3+

value: 5, 14 weeks


title: 5FU-treat-lepr

value: 18, 22 weeks


title: niche-vecad

value: 12 weeks


title: 5FU-cntrl

value: non-hematopoietic Lepr+ and VEcad+

value: 6-22 weeks


title: niche-lepr

value: non-hematopoietic LepR+


title: 5FU-treat-col23

value: bone marrow


title: Foxp1 cKO aTreg 2

city: Shanghai

first: Jinyi

last: Tang

address: Yueyang road 320

country: China

institute: IPS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were cleaned for trimming adaptor sequence, low-quality sequence (Q<20) from the 3' end, and filtering the reads with the length less than 20.
Cleaned reads were then mapped to mm10 whole genome using HISAT2 (version 2.0.5) with the default parameters for paired-end data.
Fragments Per Kilobase of transcript per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
HTSeq was used to count the reads for each gene. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using TMM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample.

extract_protocol:
Two populations from Foxp3-YFP-Cre and Foxp1fl/fl Foxp3-YFP-Cre mice were isolated respectively by cell sorting (rTreg: CD4positiveYFPpositiveCD44lowCD62Lhigh, aTreg: CD4positiveYFPpositiveCD44highCD62Llow)
Total RNA were extracted using Trizol(Thermo),  and sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Spleen and peripheral lymph nodes were harvested in Foxp3-YFP-Cre and Foxp1fl/fl Foxp3-YFP-Cre mice in 6-8 weeks. For RNAseq, We have four samples, WT rTreg, WT aTreg, cKO rTreg, cKO aTreg and  2 replicates for each sample.

value: Spleen and peripheral lymph nodes

value: Foxp1fl/fl Foxp3-YFP-Cre


title: niche-col23

value: 16 weeks


title: H28815R_C

city: Chicago

first: Michelle

last: Ward

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
RNA-seq reads from each species were trimmed and mapped to each genome (hg19 or panTro3) using Tophat2 (version 2.0.11) (Kim et al. 2013).
The number of reads falling into orthologous meta-exons across 30,030 Ensembl genes from hg19, panTro3 and rheMac3 (Blekhman et al. 2010) was determined using featureCounts within subread (version 1.5.0) (Liao et al. 2014).
Only autosomal genes are retained.
Genome_build: hg19 & panTro3
Supplementary_files_format_and_content: RNA-seq counts for orthologous autosomal genes for all individuals

source_name: induced pluripotent stem cell-derived cardiomyocytes

growth_protocol: Human and chimpanzee iPSC-derived cardiomyocytes were maintained in Cardiomyocyte Maintenance Media  [500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (S1200-500, Genemate), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1M HEPES (SH3023701, ThermoFisher Scientific), 5 mL Glutamax (35050-061, ThermoFisher Scientific), 5 mL Penicillin/Streptomycin)].

extract_protocol:
RNA was extracted from ~1.5 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA) in species-balanced batches. Samples had a median RIN score of 9.1
Samples were combined into 4 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit.  Libraries were sequenced on the HiSeq3000/4000 following the manufacturer's protocols.

treatment_protocol: Four conditions per sample were collected per individual: A- normoxia at 10% oxygen, B- hypoxia at 1% oxygen for 6 hours, C- re-oxygenation at 10% oxygen for 6 hours and D- re-oxygenation at 10% oxygen for 24 hours.

tag: Sex

value: Male

tag: population

value: Caucasian


title: H28815R_D


title: Foxp1 cKO rTreg 2

tag: strain


title: Foxp1 cKO rTreg 1


title: H28815R_A

tag: cell line

value: normoxia


title: H28815R_B

value: hypoxia


title: WT aTreg 2


title: H28815_C


title: 3B: TWIST1 KO #3 PAX7-2

source_name: human embryonic stem cell

value: human embryonic stem cell

tag: cell type


title: WT aTreg 1


title: H28815_D


title: H28815_B


title: 3A: TWIST1 KO #3 PAX7-1


title: WT rTreg 2


title: Foxp1 cKO aTreg 1


title: 1B: TWIST1 KO #1 PAX7-2


title: H28815_A


title: 1A: TWIST1 KO #1 PAX7-1


title: TUBE-5

value: multinucleated myotubes


title: MYOG-5

value: MYOG::EGFP+ myoblast cells


title: PAX7-5

value: PAX7::EGFP+ putative skeletal muscle stem/precursor cells


title: PAX7-4


title: MYOG-4


title: H28126_D


title: H28126_B


title: H28126_A


title: MSGN1-4

value: MSGN1::EGFP+ presomite cells


title: MSGN1-3


title: OCT4-3

value: OCT4::EGFP+ embryonic stem cells


title: H28126_C


title: H25237R_D

value: Female


title: H25237R_C


title: H25237R_A


title: H25237_A


title: H25237_B


title: H25237_D


title: H24280_C


title: H24280_D


title: new hair cells 1

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were trimmed using Trimmomatic and mapped to the mouse reference genome (mm10) using TopHat (Trapnell and Schatz, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: excle file with average FPKM value, fold change and p value for each genes

source_name: Atoh1 overexpression-induced new hair cells

growth_protocol: the mice were maitained at 37°C in the Shanghai Medical Experimental Animal center.

extract_protocol:
extraction of total RNA using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to the manufacturer's protocol
Sequencing library were prepared with SMART-Seq v4 Ultra Low Input RNA Kit and Illumina mRNA-Seq Sample Prep Kit.

treatment_protocol: Sox2-CreER+/Atoh1-HA+/Atoh1-eGFP+/tdTomato+ fourth positive mice were sacrificed at P7, and the cochlear epithelium was dissected and trypsinized with pre-warmed 0.25% trypsin/EDTA (Invitrogen) at 37°C for 5 min. Soybean trypsin inhibitor (Worthington Biochem) was added to terminate the reaction followed by mechanical trituration with blunt tips and pipetting up and down ~100 times. Suspended cells were percolated through a 40 µm cell strainer (BD Biosciences) before FACS. The original HCs were labeled with enhanced green fluorescent protein (eGFP+ cells), new HCs were co-labeled with enhanced green fluorescent protein and tdTomato red fluorescent protein (eGFP+/tdTomato+ cells), and SCs were labeled with tdTomato red fluorescent protein (tdTomato+ cells). The original HCs, new HCs, and SCs were sorted on a BD FACS Aria III (BD Biosciences) using the tdTomato and GFP channels.

value: cochlea hair cells


title: new hair cells 2


title: TUBE-4


title: original hair cells 2

source_name: original hair cells


title: H24280_B


title: WT rTreg 1


title: original hair cells 1


title: H22422_C


title: H22422_D


title: OCT4-4


title: H24280_A


title: Dux_KO_late_2-cell_replicate3

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were first trimmed to remove adaptor sequences and low-quality bases using Trimgalore (version 0.4.5).
Reads (>35bp) were aligned to mm9 reference genome using HISAT2 (version 2.1.0) (Kim et al., 2015) and RPKM values for each gene were computed using Cufflinks (version 2.2.1) (Trapnell et al., 2010).
For differential gene expression analyses, TEtranscripts (version 1.5.1) (Jin et al., 2015) was used to generate read counts for genes and repeats and DESeq package (Anders and Huber, 2010) was used to compute false discovery rate using the ‘nbinomTest’ function.
The RNA-seq bigwig tracks were generated using deeptools (version 3.0.2) (Ramirez et al., 2014) and visualized as the custom tracks in the Integrative Genomic Viewer genome browser (Robinson et al., 2011)
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files that can be uploaded to a genome browser to view the RNA-seq signal intesnity at different genomic loci

extract_protocol:
Dux WT/KO 1-cell and 2-cell embryos were collected by in vitro fertilization (IVF). 1-cell embryos were collected at 12 hours post fertilization (hpf) and 2-cell embryos were collected at 30 hpf.
SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 643890) was used for reverse transcription and cDNA amplification (11 cycles).  cDNA were then fragmented, adaptor-ligated and amplified using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions.  Single-end 100bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).

value: B6/DBA mixed

value: 2-cell embryo

tag: genotype/variation

value: Dux knockout (KO)


title: Dux_KO_late_2-cell_replicate2

tag: developmental stage


title: Dux_KO_late_2-cell_replicate1


title: H22422_B


title: H25237R_B


title: H25237_C


title: H22422_A


title: Dux_WT_late_2-cell_replicate3

value: Dux wildtype (WT)


title: Dux_WT_late_2-cell_replicate2


title: Dux_WT_late_2-cell_replicate1


title: Anti-IgM, T330m, rep2

city: Suita, Osaka

first: Mariko

last: Okada

address: 3-2 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

data_processing:
Base calling and quality scoring was performed by using Illumina RTA v1.18.64.
FASTQ file generation and de-multiplexing was performed by using Illumina bcl2fastq v1.8.4.
The RNA-seq reads were trimmed to remove the adaptor and low-quality sequences by using Trimmomatic v0.36.
The trimmed reads were mapped to the mouse reference genome sequence using STAR v2.7.0e.
Quantification of gene expression was performed by using RSEM v1.3.1.
The parameters of STAR and RSEM softwares were set according to the ENCODE Consortium pipeline (Long RNA-seq Data Processing Pipeline; https://www.encodeproject.org/pipelines/ENCPL002LSE).
Genome_build: GRCm38.p6 with Gencode vM20 gene-annotation dataset
Supplementary_files_format_and_content: Tab-delimited text files include gene ID, transcript ID, gene length, expected read counts and TPM values.

source_name: Splenic B cell

growth_protocol: The mouse splenic B cells were purified by depleting CD43+ cells with magnetic beads using AutoMACS (Miltenyi Biotec). The purified B Cells were cultured in Iscove’s modified Dulbecco’s medium containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was collected using the NucleoSpin RNA plus kit (MACHEREY-NAGEL GmbH & Co.). Quality control was performed with the 2100 Bioanalyzer system (Agilent; RNA integrity numbers > 8).
RNA libraries were prepared for sequencing using the standard Illumina protocols (TruSeq Stranded mRNA Sample Prep Kit).

treatment_protocol: The purified B Cells were stimulated with 10 µg/ml of anti-IgM. Total RNA was extracted every 15 minutes from 0 time to 6 hours after stimulation.

value: wild type

tag: gender

value: pooled male and female

value: 8-12 weeks

tag: tissue

value: Spleen

value: B cells

tag: time point


title: Anti-IgM, T345m, rep2


title: Anti-IgM, T345m, rep1


title: Anti-IgM, T330m, rep1


title: Dux_KO_late_1-cell_replicate2

value: 1-cell embryo


title: Anti-IgM, T315m, rep2


title: H21792R_B

value: Caucasian

value: hypoxia


title: Anti-IgM, T285m, rep2


title: Anti-IgM, T315m, rep1


title: H21792_D


title: Anti-IgM, T360m, rep2


title: Anti-IgM, T360m, rep1


title: Anti-IgM, T300m, rep2


title: Dux_WT_late_1-cell_replicate2


title: Anti-IgM, T285m, rep1


title: Dux_KO_late_1-cell_replicate1


title: Dux_WT_late_1-cell_replicate1


title: Anti-IgM, T270m, rep2


title: Anti-IgM, T300m, rep1


title: H3K4me2 ChIP-seq Plasma cell

city: La Jolla

first: Kees

last: Murre

state: CALIFORNIA

address: 9500 gilman drive, NSB 5114A

department: Biology

institute: UCSD

description: used for Fig. 3 and Supplementary Fig. 3

data_processing:
TCC processing: Reads were mapped by bowtie and processed by HOMER to create tag directory with default setting. Read numbers of naïve and plasma cells were down-sampled by HOMER, using getRandomReads.pl by reducing the total number of reads to match the smaller sample size (naïve B cells). Interactions were called by HOMER using 1 Mb bins and a threshold p=10-5 with the other options set as default. Raw TCC matrices were generated by HOMER with -raw option using 1 Mb bins for the whole genome. The raw matrices were KR-normalized.
ATAC processing: Reads were mapped to mouse genome build mm9 using TopHat. ATAC peaks were called by MACS 1.4 with default settings for broad peak.
ChIP processing: Reads were mapped to mouse genome build mm9 using TopHat and converted to track plots by IGV.
RNA-seq processing: Single-end sequencing reads were mapped to mouse genome build mm9 using TopHat. Transcript quantification was performed using Kallisto with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The TCC matrix is a tab-separated matrix. The values are the KR normalized read numbers. The RNA reads table is the table output by kallisto. The ChIP peak.bed files are output by MACS1.4. The tdf files are outputs of igv toTDF

source_name: in vitro activated, sorted plasma cells

growth_protocol: Splenocytes were incubated with CD23-biotin (eBioscience, clone B3B4, cat. 13-0232-81) and purified using anti-biotin microbeads (Miltenyi Biotec, cat. 130-090-485) on MACs LS columns. Selected cells were cultured at 0.5 million/mL in 24-well plates in RPMI media containing 10% FBS, 2% PSG, and B-me.

extract_protocol:
CD23+ MACs purified cells were activated in vitro for 3 days with LPS. On day 3, cells were harvested, and fixed in PBS containing 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. GFP+ cells were sorted on a BD FACsAriaII. Fixed cells were stored at -80 degrees until use.
Cells were fixed for 10 min in PBS containing 1% formaldehyde. Formaldehyde was quenched by incubation for 10 min with 0.2 M glycine. Cells were washed twice with PBS and pellets were frozen in liquid nitrogen. Nonspecific binding was blocked in 30 μl protein G Dynabeads (Life Technologies) by incubation with 0.5% BSA (wt/vol) in PBS. Magnetic beads were bound with 6 μg of the appropriate antibody. Crosslinked cells were lysed in lysis buffer 1 (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% TritonX-100) and were washed with lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA and0.5 mM EGTA). Cells were resuspended and then were sonicated in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine). Lysates were cleared by centrifugation, and Triton X-100 was added at a final concentration of 1%. Lysates were then incubated overnight at 4 °C with the previously prepared magnetic beads. Beads were washed once with RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and 1 mM EDTA), once with RIPA 500 buffer (50 mM Tris-HCl, pH 8.0, 500 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and 1 mM EDTA), once with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate and 1 mM EDTA) and finally twice with TE buffer (10 mM Tris, pH 8.0, and 1 mM EDTA). Bound complexes were eluted from the beads by incubation for 30 min at 65°C with shaking in elution buffer (10 mM Tris-HCl, pH 8.0, 0.5% SDS, 300 mM NaCl and 5 mM EDTA). Crosslinks were reversed by incubation overnight at 65 °C. RNA and protein were digested in the supernatants with RNase A and proteinase K, and DNA was purified with ChIP DNA Clean and Concentrator Columns (Zymoresearch). Libraries were prepared with the NEBNext primer set and were selected by size by 8% PAGE. Libraries were run on Illumina HiSeq 2500.

treatment_protocol: Cultured CD23+ cells were stimulated with 10ug/mL LPS for 3 days (Sigma).

value: in vitro activated, sorted plasma cells

value: Blimp-GFP mice

tag: chip antibody


title: H21792_C

tag: treatment


title: H21792_B


title: Anti-IgM, T255m, rep1


title: Anti-IgM, T255m, rep2


title: Anti-IgM, T270m, rep1


title: H21792R_C


title: H21792R_D


title: H21792_A

value: normoxia


title: Anti-IgM, T240m, rep2


title: H3K4me2 ChIP-seq Naïve B

source_name: CD23+ MACs-purified Naïve B

extract_protocol:
CD23+ MACs purified cells were collected. Cells were fixed in PBS containing 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use.
Cells were fixed for 10 min in PBS containing 1% formaldehyde. Formaldehyde was quenched by incubation for 10 min with 0.2 M glycine. Cells were washed twice with PBS and pellets were frozen in liquid nitrogen. Nonspecific binding was blocked in 30 μl protein G Dynabeads (Life Technologies) by incubation with 0.5% BSA (wt/vol) in PBS. Magnetic beads were bound with 6 μg of the appropriate antibody. Crosslinked cells were lysed in lysis buffer 1 (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% TritonX-100) and were washed with lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA and0.5 mM EGTA). Cells were resuspended and then were sonicated in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine). Lysates were cleared by centrifugation, and Triton X-100 was added at a final concentration of 1%. Lysates were then incubated overnight at 4 °C with the previously prepared magnetic beads. Beads were washed once with RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and 1 mM EDTA), once with RIPA 500 buffer (50 mM Tris-HCl, pH 8.0, 500 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100 and 1 mM EDTA), once with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate and 1 mM EDTA) and finally twice with TE buffer (10 mM Tris, pH 8.0, and 1 mM EDTA). Bound complexes were eluted from the beads by incubation for 30 min at 65°C with shaking in elution buffer (10 mM Tris-HCl, pH 8.0, 0.5% SDS, 300 mM NaCl and 5 mM EDTA). Crosslinks were reversed by incubation overnight at 65 °C. RNA and protein were digested in the supernatants with RNase A and proteinase K, and DNA was purified with ChIP DNA Clean and Concentrator Columns (Zymoresearch). Libraries were prepared with the NEBNext primer set and were selected by size by 8% PAGE. Libraries were run on Illumina HiSeq 2500.

value: CD23+ MACs-purified Naive B

value: WT


title: Anti-IgM, T225m, rep2


title: H3K36me3 ChIP-seq Plasma cell


title: H20961_D

value: Male


title: H21792R_A

value: Female


title: Anti-IgM, T240m, rep1


title: Anti-IgM, T225m, rep1


title: H3K36me3 ChIP-seq Naïve B


title: TCC Plasma cell

description: used for Fig. 1-6

data_processing:
Library strategy: TCC
TCC processing: Reads were mapped by bowtie and processed by HOMER to create tag directory with default setting. Read numbers of naïve and plasma cells were down-sampled by HOMER, using getRandomReads.pl by reducing the total number of reads to match the smaller sample size (naïve B cells). Interactions were called by HOMER using 1 Mb bins and a threshold p=10-5 with the other options set as default. Raw TCC matrices were generated by HOMER with -raw option using 1 Mb bins for the whole genome. The raw matrices were KR-normalized.
ATAC processing: Reads were mapped to mouse genome build mm9 using TopHat. ATAC peaks were called by MACS 1.4 with default settings for broad peak.
ChIP processing: Reads were mapped to mouse genome build mm9 using TopHat and converted to track plots by IGV.
RNA-seq processing: Single-end sequencing reads were mapped to mouse genome build mm9 using TopHat. Transcript quantification was performed using Kallisto with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The TCC matrix is a tab-separated matrix. The values are the KR normalized read numbers. The RNA reads table is the table output by kallisto. The ChIP peak.bed files are output by MACS1.4. The tdf files are outputs of igv toTDF

source_name: ex vivo sorted plasma cells

extract_protocol:
CD23+ MACs purified cells were activated in vitro for 3 days with LPS. On day 3, cells were harvested, and fixed in PBS containing 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. GFP+ cells were sorted on a BD FACsAriaII. Fixed cells were stored at -80 degrees until use.
We used TCC to generate genome-wide contact maps essentially as described by Kalhor et al. Nature Biotechnology, 2012. Ten million CD23+ follicular B cells were isolated from spleens of WT mice. Cells were fixed in 1% formadehyde and quenched with 0.2M glycine. Cells were lysed in buffer containing SDS. Digestion was performed with Mbo1 (NEB). After ligation, libraries were amplified using Phusion HotStart II for experimentally determined numbers of PCR cycles with the following program: 98ºC /30 seconds, x-cycles [98ºC/10 seconds, 65ºC for 30 seconds, 72ºC for 20 seconds], 72ºC for 5 minutes. Fragments between 300 and 600 bp were selected. DNA was paired-end sequenced with Illumina HiSeq 2500.

value: ex vivo sorted plasma cells


title: H20961_B


title: Anti-IgM, T195m, rep1


title: Anti-IgM, T195m, rep2


title: Anti-IgM, T180m, rep2


title: H20682_D


title: Anti-IgM, T180m, rep1


title: Anti-IgM, T165m, rep1


title: RNA-seq Plasma cell

description: used for Fig. 1,2,3

extract_protocol:
Harvested bone marrow was processed and stained with antibodies. CD138+B220-IgD-CD4-CD8-Gr1-Ter119- plasma cells were sorted on a BD FACsAria Fusion.
Total RNA was isolated using RNeasy Mini kit (Qiagen). RNA was treated with TURBO DNase (Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA purification kit (Life Technologies). cDNA was generated with the First-strand synthesis kit (Life Technologies) using random hexamers in the presence of actinomycin D. Second-strand synthesis was performed with dUTP instead of dTTP. Sonicated cDNA was ligated to adaptors (NEBNext primer kit). The resulting DNA was treated with uracil-N-glycolsylase prior to PCR amplification with the indexing primers (NEBNext primer kit).


title: Anti-IgM, T150m, rep2


title: RNA-seq Naïve B

description: used for Fig. 1,2,3

source_name: ex vivo sorted naive B cells

extract_protocol:
Harvested spleens were processed and stained with antibodies. CD23+IgD+ cells were sorted on a BD FACsAria Fusion.
Total RNA was isolated using RNeasy Mini kit (Qiagen). RNA was treated with TURBO DNase (Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA purification kit (Life Technologies). cDNA was generated with the First-strand synthesis kit (Life Technologies) using random hexamers in the presence of actinomycin D. Second-strand synthesis was performed with dUTP instead of dTTP. Sonicated cDNA was ligated to adaptors (NEBNext primer kit). The resulting DNA was treated with uracil-N-glycolsylase prior to PCR amplification with the indexing primers (NEBNext primer kit).

value: ex vivo sorted naive B cells


title: H20682_C


title: Anti-IgM, T165m, rep2

value: wild type


title: ATAC-seq Plasma cell

description: used for Fig. 2,3

data_processing:
TCC processing: Reads were mapped by bowtie and processed by HOMER to create tag directory with default setting. Read numbers of naïve and plasma cells were down-sampled by HOMER, using getRandomReads.pl by reducing the total number of reads to match the smaller sample size (naïve B cells). Interactions were called by HOMER using 1 Mb bins and a threshold p=10-5 with the other options set as default. Raw TCC matrices were generated by HOMER with -raw option using 1 Mb bins for the whole genome. The raw matrices were KR-normalized.
ATAC processing: Reads were mapped to mouse genome build mm9 using TopHat. Duplicated reads were removed by picard-tools. ATAC peaks were called by MACS 1.4 with default settings for broad peak.
ChIP processing: Reads were mapped to mouse genome build mm9 using TopHat and converted to track plots by IGV.
RNA-seq processing: Single-end sequencing reads were mapped to mouse genome build mm9 using TopHat. Transcript quantification was performed using Kallisto with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The TCC matrix is a tab-separated matrix. The values are the KR normalized read numbers. The RNA reads table is the table output by kallisto. The ChIP peak.bed files are output by MACS1.4. The tdf files are outputs of igv toTDF

source_name: ex vivo sorted B220- BM plasma cells

extract_protocol:
Harvested bone marrow was processed and stained with antibodies. CD138+B220-IgD-CD4-CD8-Gr1-Ter119- plasma cells were sorted on a BD FACsAria Fusion.
50,000 cells were used for library preparation.  Cells were lysed, then treated with transposition mix (Nextera DNA Sample Preparation Kit) for 30 min at 37 degrees. Library fragments were amplified with 1x NEB Next PCR Master Mix and custom Nextera PCR primers. The number of cycles of PCR amplification was determined by q-PCR. 200-800 bps of libraries were selected using SPRI beads. Libraries were sequenced on a HiSeq 4000 system as paired-end reads.

value: ex vivo sorted B220- BM plasma cells


title: Anti-IgM, T135m, rep2

value: pooled male and female

value: 8-12 weeks


title: Anti-IgM, T210m, rep1

value: Spleen

value: B cells


title: H20682_B

value: Caucasian


title: Anti-IgM, T150m, rep1


title: Anti-IgM, T120m, rep2


title: Anti-IgM, T135m, rep1


title: ATAC-seq Naïve B

description: used for Fig. 2,3

extract_protocol:
Harvested spleens were processed and stained with antibodies. CD23+IgD+ cells were sorted on a BD FACsAria Fusion.
50,000 cells were used for library preparation.  Cells were lysed, then treated with transposition mix (Nextera DNA Sample Preparation Kit) for 30 min at 37 degrees. Library fragments were amplified with 1x NEB Next PCR Master Mix and custom Nextera PCR primers. The number of cycles of PCR amplification was determined by q-PCR. 200-800 bps of libraries were selected using SPRI beads. Libraries were sequenced on a HiSeq 4000 system as paired-end reads.


title: Anti-IgM, T210m, rep2


title: Anti-IgM, T120m, rep1


title: H20682_A


title: C2.I5.12_X_C2.I5.pool

description: Comparison between RNA Internode 5 C2C512 time point sample and RNA pool sample.

extract_protocol: modified Trizol method

value: Internode 5

tag: variety

tag: collect


title: LMPP_KO_3

description:
counts.LMPP.raw.csv.gz
counts.LMPP.normalized.csv.gz

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: bone marrow VEc-Dll4i3COIN lymphoid-primed multipotential progenitor

extract_protocol:
RNeasy Micro Kit - QIAGEN
SMART-Seq v4 Ultra Low Input RNA Kit - Clontech

value: bone marrow

tag: age

value: 24 weeks


title: Anti-IgM, T105m, rep2

tag: genotype


title: TCC Naïve B

description: used for Fig. 1-6

extract_protocol:
CD23+ MACs purified cells were collected. Cells were fixed in PBS containing 1% formaldehyde for 10 mins. Formaldehyde was quenched with 0.2 M glycine for 10 mins. Fixed cells were stored at -80 degrees until use.
We used TCC to generate genome-wide contact maps essentially as described by Kalhor et al. Nature Biotechnology, 2012. Ten million CD23+ follicular B cells were isolated from spleens of WT mice. Cells were fixed in 1% formadehyde and quenched with 0.2M glycine. Cells were lysed in buffer containing SDS. Digestion was performed with Mbo1 (NEB). After ligation, libraries were amplified using Phusion HotStart II for experimentally determined numbers of PCR cycles with the following program: 98ºC /30 seconds, x-cycles [98ºC/10 seconds, 65ºC for 30 seconds, 72ºC for 20 seconds], 72ºC for 5 minutes. Fragments between 300 and 600 bp were selected. DNA was paired-end sequenced with Illumina HiSeq 2500.


title: C8861_D

organism: Pan troglodytes

value: Chimpanzee


title: H20961_A

value: normoxia


title: Anti-IgM, T105m, rep1


title: C8861_C


title: Anti-IgM, T90m, rep2


title: LMPP_KO_1

tag: source


title: Anti-IgM, T75m, rep2


title: LMPP_CNTRL_3

source_name: bone marrow cntrl lymphoid-primed multipotential progenitor


title: Anti-IgM, T75m, rep1


title: C8861_B

tag: Sex

value: hypoxia


title: LMPP_CNTRL_2


title: Anti-IgM, T60m, rep2


title: Anti-IgM, T60m, rep1


title: Anti-IgM, T45m, rep2


title: C4955_D

value: Male

tag: population


title: Anti-IgM, T30m, rep1

tag: strain


title: LMPP_CNTRL_1


title: Anti-IgM, T15m, rep2


title: Anti-IgM, T30m, rep2


title: Anti-IgM, T45m, rep1


title: DLL4_2_CD144pos

description:
counts.BM.raw.csv.gz
counts.BM.normalized.csv.gz

value: non-hematopoietic CD144+ Dll4+

value: 4-12 weeks


title: C4955_B

tag: cell line


title: Anti-IgM, T15m, rep1

tag: cell type


title: DLL4_1_CD144pos


title: LMPP_KO_2


title: C4955_A


title: T0, rep2


title: T0, rep1


title: Anti-IgM, T90m, rep1


title: C40300_D

value: Female


title: C8861_A


title: DLL1_2_CD144neg

source_name: Dll-mCherry

value: non-hematopoietic CD144- Dll1+


title: DLL1_1_CD144pos

value: non-hematopoietic CD144+ Dll1+


title: DLL1_1_CD144neg


title: C40300_B


title: C40300_C


title: C40300_A


title: C40280R_D


title: Vecad_4

description:
counts.niche.raw.csv.gz
counts.niche.normalized.csv.gz

value: non-hematopoietic VEcad+


title: Vecad_3


title: C40280R_C


title: C40280R_B


title: Vecad_1


title: C4955_C


title: C40280_D


title: C40280R_A


title: Lepr_4

source_name: Lepr-cre;LoxP-tdTomato

value: non-hematopoietic LepR+


title: Lepr_3


title: DLL1_2_CD144pos


title: H20961_C


title: C40280_A


title: Col2.3_4

value: non-hematopoietic Col2.3+


title: Lepr_1


title: Lepr_2


title: C40280_B


title: C40210R_D


title: Col2.3_3


title: Patient 19 Recurrent

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

institute: University of Louisville

description: Sample name/patient number:  63

data_processing:
QA/QC of raw fastq files was performed using FastQC v 0.10.1
Raw fastq sequences were aligned to the hg38 genome using tophat2 v2.0.13 using the Ensembl gtf
Genome_build: hg38
Supplementary_files_format_and_content: FPKM_geneMatrix_NORMALIZED.txt represents normalized FPKM values using cuffnorm v2.2.1

source_name: Epidermis

extract_protocol:
RNAs were isolated using a Qiagen RNeasy kit according to the manufacturer’s instructions (Qiagen) or TRIzol (Invitrogen). After total RNA extraction, magnetic beads with oligo dT were used to isolate polyA enriched mRNA.
Libraries were constructed by BGI using their standard RNA transcriptome sequencing protocol.

treatment_protocol: All patients had not been treated systemically for at least 4 weeks or topical treatment for at least 2 weeks prior to the study entry. Patients were treated with topical halomethasone monohydrate 0.05% cream daily for 2 weeks. Skin lesion severity was evaluated by PASI (psoriasis area and severity index) score. Typical lesions that represented the overall skin condition before and after treatment as well as relapse (4 weeks after treatment) were taken.

value: Epidermis

tag: treatment stage

value: Post treatment


title: Patient 21 Recurrent

description: Sample name/patient number:  65


title: Patient 18 Recurrent

description: Sample name/patient number:  62


title: Col2.3_2

city: New York


title: C40210R_C


title: C40210R_B


title: Vecad_2

source_name: VEcad-cre;LoxP-tdTomato


title: Patient 21 Posttreatment

description: Sample name/patient number:  60

value: Glucocorticoid treatment


title: Patient 20 Posttreatment

description: Sample name/patient number:  59


title: C40210R_A


title: Patient 17 Posttreatment

description: Sample name/patient number:  56


title: Patient 18 Posttreatment

description: Sample name/patient number:  57


title: C40210_D


title: C40210_C


title: Patient 19 Posttreatment

description: Sample name/patient number:  58


title: C40280_C


title: Patient 21 Pretreatment

description: Sample name/patient number:  55

value: Pre treatment


title: Patient 19 Pretreatment

description: Sample name/patient number:  53


title: C40210_B


title: C40210_A


title: Patient 20 Recurrent

description: Sample name/patient number:  64


title: Patient 17 Pretreatment

description: Sample name/patient number:  51


title: Patient 18 Pretreatment

description: Sample name/patient number:  52


title: C3649_D


title: sRNA-seq-T3

city: Hefei

first: chaoling

last: Wei

state: Anhui

address: 130 West Changjiang Road

institute: Anhui Agricultural University

data_processing:
The raw reads of sRNA-seq was generated from the Illumina GAIIX system and the degradome sequencing was sequenced on Illumina Hiseq2500
In sRNA-seq, the raw reads were filtered using the Illumina pipeline filter (Solexa 0.3), and then further processed with the in-house program (ACGT101-v4.2-miR, LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences ranging from 18 to 26 nt in length were compared with known plant miRNAs in miRBase (Release 22; http://www.mirbase.org), using BLAST searches to identify known miRNAs with no more than two mismatches. After the analyses, known miRNAs were categorized into four groups (1a, 1b, 2a, and 3a).
In degradome sequencing ,raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software and processed to remove adaptor sequences and low-quality sequencing reads. The unique sequencing reads with lengths of 20 nt and 21 nt were then used to identify potentially cleaved targets with a public software package (CleaveLand3.0 pipeline)
Genome_build: Camellia sinensis var. sinensis (Sequence Read Archive database accession No. SRA536878, http://pcsb.ahau.edu.cn:8080/CSS/)
Supplementary_files_format_and_content: precursors and mature miRNA sequences,tab-delimited text files include RPKM values for each Sample

organism: Camellia sinensis

source_name: Leaf

growth_protocol: Three-year-old cuttings were planted in pots (30-cm diameter, 35-cm height) and grown in a green house maintained at 23 ± 3 °C with 65 ± 5% room humidity and a 16/8 h (day/light) photoperiod. All experimental plants were irrigated once a day and fertilized once a month. Healthy Shuchazao cuttings with uniform growth (25−30 cm in height) were selected for experiments.

extract_protocol:
Total RNA was isolated from each frozen sample using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. The quantity and quality of the total RNA were determined using a Bioanalyzer 2100 (Agilent, CA, USA) and the RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Equal quantities of total RNA from C. gloeosporioides- and mock-inoculated leaves collected at four days post infection (4dpi) were used to prepare the sRNA libraries using the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA). We performed single-end sequencing (36 bp) on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) using the vendor’s recommended protocol.

treatment_protocol: The pathogenic C. gloeosporioides was originally isolated from diseased leaves of Shuchazao at the field of Anhui Agricultural University, Hefei, China. C. gloeosporioides was cultured on potato dextrose agar and incubated at 25 °C ± 2 °C in darkness for 10 days to promote sporulation. Conidia were harvested and suspended in sterile water. The conidia concentration was determined using a hemocytometer and adjusted to 1×10^5 mL-1 for inoculation.

value: Shuchazao

value: gloeosporioides-inoculated

tag: developmental stage

value: mature leaf


title: sRNA-seq-T2


title: sRNA-seq-T1


title: Col2.3_1

value: bone marrow


title: C3649_C

source_name: induced pluripotent stem cell-derived cardiomyocytes

value: Male

value: Chimpanzee


title: C3649_B

value: hypoxia


title: Patient 17 Recurrent

description: Sample name/patient number:  61


title: sRNA-seq-CK3

value: control


title: sRNA-seq-CK2


title: C3649_A

value: normoxia


title: sRNA-seq-CK1


title: C3647R_D

value: Female


title: Oxibendazole control Male

city: Lexington

first: Martin

middle: K

last: Nielsen

state: KY

address: 1400 Nicholasville Road

institute: University of Kentucky

data_processing:
Adaptor trimming and quality control were performed using TrimGalore Version 0.4.4 (Babraham Bioinformatics).
Reads were subsequently aligned to the Parascaris univalens reference genome (Wang et al., 2017) using STAR Version 2.5b (Dobin et al., 2013).
Reads were annotated to the Parascaris reference transcriptome (Wang et al., 2017) using Cufflinks (Release 2.2.1) (Trapnell et al., 2012).
Read counts were normalized as fragments per kilobase of exon per million mapped reads (FPKM) and differential gene expression analysis was performed on normalized read counts.
Genome_build: Parascaris univalens reference genome (doi:10.1101/gr.225730.117)
Supplementary_files_format_and_content: *genes.fpkm_tracking

organism: Parascaris sp.

source_name: Whole worm

growth_protocol: Worms were maintained as described my Scare et al. (2018). Briefly, worms were kept in tissue culture flasks in 200 mL of RPMI-1640 at 37C in an air incubator. Media was changed every 12 hours.

extract_protocol:
Whole worms were ground to a fine powder. 1 mL TRIzol reagent used for RNA isolation following the manufacturer's instructions.
RNA samples were sent to the University of Louisville CGeMM DNA Core Facility for library preparation and sequencing. Libraries were prepared with Illumina’s TruSeq stranded total RNA library kit (Illumina, San Diego, CA, USA) with Ribo-Zero Gold depletion. Libraries were sequenced using the NextSeq 500 High Output v2 75 cycles kit. Samples were run in 1x75 base pair configuration, generating up to 400 million reads total, approximately 40 million reads per sample.

treatment_protocol: No treatment given, but worm was snap frozen at the same time as the oxibendazole treated worm.

tag: isolate

value: University of Kentucky, Main Chance Farm, barn 10

value: Whole body

value: Adult

value: Oxibendazole control


title: Patient 20 Pretreatment

description: Sample name/patient number:  54

tag: tissue

value: Epidermis


title: C3647R_B

extract_protocol:
RNA was extracted from ~1.5 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA) in species-balanced batches. Samples had a median RIN score of 9.1
Samples were combined into 4 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit.  Libraries were sequenced on the HiSeq3000/4000 following the manufacturer's protocols.


title: Allogeneic transplant - MC-deficient mouse 5

first: Ethan

middle: Jesse

last: Strattan

address: 900 South Limestone Street, Wethington Building, CTW453

department: Hematology/BMT

description: Total RNA was extracted from skin taken from the nape of the neck. RNA was assessed for quality by Bioanalyzer and 100ng was loaded into the Nanostring Myeloid Innate Immunity Panel.

hyb_protocol: In the NanoString kit, individual mRNA molecules are directly hybridized with barcoded fluorescent molecules per the manufacturer's instructions.

scan_protocol: Samples were scanned by a Nanostring Sprint system and number of barcoded spots was counted directly.

data_processing: Data was assessed using the NanoString nSolver software, which normalizes the readouts to a panel of ~20 housekeeping genes.

source_name: skin after bone marrow transplant

label_protocol: RNA was assessed for quality by Agilent Bioanalyzer, then measured by QuBit and 100ng was loaded into the NanoString Myleoid Innate Immunity kit.

extract_protocol: Skin in RNAlater solution was transferred to 1ml of Trizol, then minced and homogenized. Trizol extraction of RNA was performed as per the manufacturer's instructions. RNA was assessed for quality by Agilent Bioanalyzer, then measured by QuBit and 100ng was loaded into the Myleoid Innate Immunity kit.

treatment_protocol: Recipient mice were irradiated with 850cGy ionizing radiation, then injected IV with 5e6 LP/J bone marrow cells and 2e6 LP/J splenocytes. GVHD symptoms were allowed to progress for 7 weeks, then mice were euthanized by CO2 and skin was isolated from the nape of the neck and stored in RNAlater solution at -20C

tag: transplant type

value: Allogeneic


title: Allogeneic transplant - MC-deficient mouse 3


title: Allogeneic transplant - MC-deficient mouse 4


title: Oxibendazole control Female