title: BMSC_d14_runx2_R2

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
mouse primary MSC osteogenic differentiation d14
ChIP

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
Concatenate replicates.
Align reads with Bowtie 1.2.8
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in logFE mode.
Convert logFE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of log fold enrichment over input from bdgcmp function of MACS2. Bigwig files are available in tar archives on the series record.

source_name: bone marrow_day14_runx2

growth_protocol: Primary MSCs were isolated from femurs and tibias of 6 - 8 weeks old SMAA-mCherry mice. Bone marrow stromal cells attached to plate surface after 72 hours were kept and cultured for additional 4 days before enriching for SMAA-mCherry positive cell by FACS. SMAA-positive MSCs were plated at 1.5 x 10^5 cells per 10 cm culture plate for the expansion in the MSC growth media. BMSCs of passage 6 to 10 were used for all the experiments in this study. All animal work was reviewed and approved by UMASS and/or UVM IACUC (protocol number JL-512).

extract_protocol:
Chromatin were prepared and sheared as previously described [12]. Sheared chromatin was used for immunoprecipitation with Runx2 antibody (M-70, Santa Cruz), Ctcf (07-729, Millipore, Billerica, MA, USA), Smc1a (A300-055A, Bethyl Laboratories, Montgomery, TX, USA), H3K4me (ab8895, Abcam, Cambridge, MA, USA), H3K4me3 (ab1012, Abcam), H3K9me3 (Ab8898, Abcam), H3K9ac (39137, Active Motif), H3K27me3 (07-449, Millipore), H3K27ac (07-360, Millipore), H3K36me3 (ab9050, Abcam), ap300 (sc-585 X, Santa Cruz) or Ezh2 (A304-196A, Bethyl Laboratories) or immunoglobulin G (IgG) (12-370, Millipore) followed by purification using Protein-G Dynabeads (Invitrogen).
Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range. Libraries were sequenced on an Illumina GA-II or Hiseq1500 and single-end 36-base (SE36) sequencing was performed at the NEMO facility at Umass Medical School

treatment_protocol: At day 0, 7, 14, and 21 of differentiation, approximately 5x10^7 MSCs were washed with PBS and then fixed on plate with 1% formaldehyde for 10 minutes at room temperature to crosslink DNA-protein complexes.

tag: tissue

value: bone marrow

tag: cell type

value: mesenchymal stromal cell

tag: markers

value: SMAA-mCherry+

tag: age

value: 6-8 weeks


title: BMSC_d21_runx2_R2

status: Public on May 05 2017

type: SRA

country: USA

description:
mouse primary MSC osteogenic differentiation d21
ChIP

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow_day21_runx2


title: G1_160111_run0456_Mm0h2cR1_male_t0h_DMSO0.0.20pct_rep1

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

library_source: transcriptomic

data_processing:
Basecalling was performed using CASAVA v1.8.2 (Illumina, San Diego, CA). BCL files were converted to FASTQ and demultiplexed using bcl2fastq v1.8 (Illumina, San Diego, CA).
The RNA-seq reads of mixed species were first mapped to a merged genome and annotation including D. grimshawi (dgri_caf1 assembly; Drosophila_grimshawi.GCA_000005155.1.29.dna_sm.genome.fa) D. melanogaster (FlyBase release 6 version 04 ; FlyBase file: dmel-all-chromosome-r6.04.fasta), and A. stephensi (Anopheles-stephensi-Indian_SCAFFOLDS_AsteI2.fa), appended with ERCC sequences (Zook et al., 2012. PMID: 22859977) using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886). The unmapped reads and reads mapping to D. grimshawi or A. stephensi are not reported in this GEO submission or affiliated SRA entry.
Segregated D. melanogaster reads were mapped to the major chromosome arms (chr2L, chr2R, chr3L, chr3R, chr4, chrX, chrY, and chrM) of Drosophila genome assembly release 6 plus ISO1 MT and ERCC sequences using TopHat v2.1.0 (Trapnell et al., 2009. PMID: 19289445) with default options except for the following: Libraries were stranded so mapping was done with --library-type fr-firststrand, and we provided a GTF with known set of gene models (FlyBase r6.09 and ERCC) using -G option.
The ERCC reference was based on the DNA Sequence Library SRM2374 from NIST, the FASTA sequence was corrected according to differences found in (Jiang et al. 2011, PMID: 21816910). We also used the reverse complement of ERCC-00009, ERCC-00014, ERCC-00057, ERCC-00059, ERCC-00099, ERCC-00108, ERCC-00116 for mapping to correct the strand orientation and ERCC-00085 was re-annotated as Subpool C.
Unique alignments were created by keeping only reads that aligned to a single location (NH:i:1) using grep (v2.20). HTseq v0.6.1p1 (Anders et al., 2014. PMID: 25260700) was used to create gene level read counts with default options except (-s reverse) was used to get strand specific read counts.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GeneBank assembly accession: GCA_000001215.4)
Supplementary_files_format_and_content: Tab delimited file containing gene level read counts from Htseq.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole body

growth_protocol: The Drosophila melanogaster w1118 fly stock (FBst0005905) was obtained from the Bloomington Drosophila Stock center (Cook et al., 2010, PMID: 20160480). Flies were grown on Cornmeal, sucrose and yeast media (Agar 10 g/L, Cornmeal 27 g/L, Sugar 43 g/L, Yeast 15 g/L, p-Hydroxy-benzoic acid methyl ester, 2.8 g/ 10.8 ml of Ethanol) obtained from (LabExpress, Ann Arbor, MI) at 25oC at low density (10 female and 5 male parents per vial, transferred to fresh vials daily). After 10 - 11 days post egg laying, adult progeny started to eclose, and flies were removed from the vials and sorted by sex with a fine brush (Robert Simmons, Cranbury, New Jersey. Sapphine S85 or S61), vials were checked every 4 h for newly eclosed flies. We collected 450 virgin w1118 flies per sex, and placed them in batches of 30 per vial with CDF (400kcal/L) for 3 days to age (Lee and Micchelli, 2013, PMID: 23844001).

extract_protocol:
Total RNA isolation followed the RNeasy for spin technology protocol (Qiagen, Valencia, CA). Since these samples were multiplexed with RNA from distantly related species (D. grimshawi and Anopheles stephensi), RNA of the two Drosophila species were mixed with a single Anopheles embryo for repeated bead maceration and a second round of RNA extraction, following the RNeasy protocol as above.
Libraries were prepared using the Truseq PolyA+ stranded mRNA kit (Illumina, San Diego, CA. Cat. No. RS-122-2101 or RS-122-2102), following the manufacturer’s protocol. We used a half reaction size with 100ng total RNA as input for all samples. External RNA Control Consortium (ERCC) spike-ins transcribed from a certified plasmid collection (SRM2374) were added to the Fragment-Prime-Finish Mix during the mRNA fragmentation step.  We used the previously described RNAs from Pool 78A for DMSO treated flies and 78B for control flies (20pg /sample)  (Zook et al., 2012. PMID: 22859977).  Libraries were multiplexed using 24 differently barcoded adapters from TruSeq (Illumina, San Diego, CA). Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing. We sequenced in an Illumina HiSeq2500 (Illumina, San Diego, CA.)

treatment_protocol: Three day post-eclosion flies were anesthetized with CO2 and manually transferred to individual wells in the Whole Animal Feeding Flat (WAFFL, US Application No. 62/080,181, PCT Application No. PCT/US2015/060575) with a fine brush. The top half of the plate (rows A-D) contained females (n= 48) and the bottom half of the plate (rows E-H) contained males (n= 48). One WAFFL was used per time point and each food plate contained all tested concentrations of DMSO. The WAFFLs were sealed using AXYMAT AM-2ML-RD silicone mats (Axygen,Tewksbury MA). Flies were allowed to recover from the anesthetic for at least 3 h before being fed with 8 ul of CDF liquid (400kcal/L) for 24 h provided on a round bottomed No.3799 96-well plate (Costar, Corning, NY), then flies were starved for 6 h by replacing the food with a 96 well plate containing 8 ul of PBS pH 7.4 (Gibco, Life technologies, Grand Island, NY). After starvation, the food plate was change to CDF liquid with 0, 0.1, 0.2, or 0.4% (v/v) DMSO and Sulforhodamine B 0.5 mg/ml (Sigma, St Louis, MO. Cat. No. D2650 and S1402). Flies were allowed to feed for 0, 2, 4 or 8 h. We visually examined flies for a bolus of dyed food in the fly abdomen. A saturated K2SO4 solution (Sigma Aldrich, St Louis, MO) was used to maintain humidity between 95 - 97 % RH in an enclosed chamber which contained the WAFFLs. Relative humidity and temperature of 25oC was measured with a traceable hygrometer (VWR, Randor, PA).                                                                                At each specific end point, the WAFFL was removed from the food plate, blotted on a paper towel to remove leftover food from the bottom and placed at -20oC for 20 min. Once flies were immobilized, the WAFFL was opened and attached to the transfer adapter and receiver plate and then flies were transferred to the receiver plate by centrifugation. The receiver plate then was attached to 96 deep well plate (Axygen, Tewksbury MA. Cat. No. P-DW-11-C-S) then transferred by centrifugation. RLT buffer 600 ul (Qiagen, Valencia, CA) and 100 ul of 1.0 mm dia glass beads (BioSpec Products, Bartlesville, OK) were added to each well, and wells were sealed with two layers of plastic (Applied Biosystems, Warrington, UK). Flies were macerated on MiniBead beater for 1 min x 2 resting on ice (Biospec Products, Bartlesville, OK) and stored at -80oC until RNA extraction. From the treated macerated flies we randomly selected 3 replicates per concentration (n=4), time point (n= 4) and sex (n=2) for a total of 96 samples to be used for preparing libraries.

tag: Sex

value: Male

tag: time (h)

tag: dmso % v/v

tag: developmental stage

value: 3 day old adult

tag: fly line


title: G10_160111_run0456_Mm8h2cR1_male_t8h_DMSO0.0.20pct_rep1


title: F9_160111_run0456_Mm4h1cR3_male_t4h_DMSO0.0.10pct_rep3


title: G11_160111_run0456_Mm8h2cR2_male_t8h_DMSO0.0.20pct_rep2


title: G12_160111_run0456_Mm8h2cR3_male_t8h_DMSO0.0.20pct_rep3


title: BMSC_d21_runx2_R1


title: BMSC_d14_runx2_R1


title: BMSC_d07_runx2_R2

description:
mouse primary MSC osteogenic differentiation d07
ChIP

source_name: bone marrow_day7_runx2


title: G2_160111_run0456_Mm0h2cR2_male_t0h_DMSO0.0.20pct_rep2


title: BMSC_d07_runx2_R1


title: BMSC_d00_runx2_R1

description:
mouse primary MSC osteogenic differentiation d00
ChIP

source_name: bone marrow_day0_runx2


title: BMSC_d21_h3k9me3_R2

source_name: bone marrow_day21_h3k9me3


title: F7_160111_run0456_Mm4h1cR1_male_t4h_DMSO0.0.10pct_rep1


title: F6_160111_run0456_Mm2h1cR3_male_t2h_DMSO0.0.10pct_rep3


title: F8_160111_run0456_Mm4h1cR2_male_t4h_DMSO0.0.10pct_rep2


title: BMSC_d21_h3k9me3_R1


title: H5_160111_run0456_Mm2h4cR2_male_t2h_DMSO0.0.40pct_rep2


title: BMSC_d00_runx2_R2


title: F4_160111_run0456_Mm2h1cR1_male_t2h_DMSO0.0.10pct_rep1


title: F3_160111_run0456_Mm0h1cR3_male_t0h_DMSO0.0.10pct_rep3


title: BMSC_d14_h3k9me3_R1

source_name: bone marrow_day14_h3k9me3


title: G8_160111_run0456_Mm4h2cR2_male_t4h_DMSO0.0.20pct_rep2


title: F12_160111_run0456_Mm8h1cR3_male_t8h_DMSO0.0.10pct_rep3


title: F2_160111_run0456_Mm0h1cR2_male_t0h_DMSO0.0.10pct_rep2


title: BMSC_d07_h3k9me3_R1

source_name: bone marrow_day7_h3k9me3


title: F5_160111_run0456_Mm2h1cR2_male_t2h_DMSO0.0.10pct_rep2


title: F11_160111_run0456_Mm8h1cR2_male_t8h_DMSO0.0.10pct_rep2


title: BMSC_d00_h3k9me3_R1

source_name: bone marrow_day0_h3k9me3


title: BMSC_d07_h3k9me3_R2


title: BMSC_d00_h3k9me3_R2


title: BMSC_d21_h3k9ac_R1

source_name: bone marrow_day21_h3k9ac


title: F1_160111_run0456_Mm0h1cR1_male_t0h_DMSO0.0.10pct_rep1


title: BMSC_d21_h3k9ac_R2


title: BMSC_d14_h3k9ac_R2

source_name: bone marrow_day14_h3k9ac


title: E9_160111_run0456_Mm4h0cR3_male_t4h_DMSO0.0pct_rep3


title: BMSC_d14_h3k9me3_R2


title: E8_151231_run0452_Mm4h0cR2_male_t4h_DMSO0.0pct_rep2


title: BMSC_d14_h3k9ac_R1


title: F10_160111_run0456_Mm8h1cR1_male_t8h_DMSO0.0.10pct_rep1


title: E5_151231_run0452_Mm2h0cR2_male_t2h_DMSO0.0pct_rep2


title: E6_151231_run0452_Mm2h0cR3_male_t2h_DMSO0.0pct_rep3


title: BMSC_d07_h3k9ac_R2

source_name: bone marrow_day7_h3k9ac


title: E4_151231_run0452_Mm2h0cR1_male_t2h_DMSO0.0pct_rep1


title: BMSC_d07_h3k9ac_R1


title: E7_151231_run0452_Mm4h0cR1_male_t4h_DMSO0.0pct_rep1


title: BMSC_d00_h3k9ac_R1

source_name: bone marrow_day0_h3k9ac


title: E3_151231_run0452_Mm0h0cR3_male_t0h_DMSO0.0pct_rep3


title: E2_151231_run0452_Mm0h0cR2_male_t0h_DMSO0.0pct_rep2


title: E12_160111_run0456_Mm8h0cR3_male_t8h_DMSO0.0pct_rep3


title: BMSC_d21_h3k4me_R2

source_name: bone marrow_day21_h3k4me


title: BMSC_d21_h3k4me_R1


title: BMSC_d14_h3k4me_R2

source_name: bone marrow_day14_h3k4me


title: E11_160111_run0456_Mm8h0cR2_male_t8h_DMSO0.0pct_rep2


title: BMSC_d14_h3k4me_R1


title: E10_160111_run0456_Mm8h0cR1_male_t8h_DMSO0.0pct_rep1


title: E1_151231_run0452_Mm0h0cR1_male_t0h_DMSO0.0pct_rep1


title: BMSC_d00_h3k9ac_R2


title: D9_151231_run0452_Mf4h4cR3_female_t4h_DMSO0.0.40pct_rep3

value: Female


title: BMSC_d07_h3k4me_R2

source_name: bone marrow_day7_h3k4me


title: BMSC_d07_h3k4me_R1


title: D8_151231_run0452_Mf4h4cR2_female_t4h_DMSO0.0.40pct_rep2


title: BMSC_d00_h3k4me_R2

source_name: bone marrow_day0_h3k4me


title: BMSC_d00_h3k4me_R1


title: BMSC_d21_h3k4me3_R2

source_name: bone marrow_day21_h3k4me3


title: D5_151231_run0452_Mf2h4cR2_female_t2h_DMSO0.0.40pct_rep2


title: D7_151231_run0452_Mf4h4cR1_female_t4h_DMSO0.0.40pct_rep1


title: D6_151231_run0452_Mf2h4cR3_female_t2h_DMSO0.0.40pct_rep3


title: D4_151231_run0452_Mf2h4cR1_female_t2h_DMSO0.0.40pct_rep1


title: BMSC_d21_h3k4me3_R1


title: BMSC_d14_h3k4me3_R2

source_name: bone marrow_day14_h3k4me3


title: D3_151231_run0452_Mf0h4cR3_female_t0h_DMSO0.0.40pct_rep3

source_name: whole body


title: BMSC_d14_h3k4me3_R1


title: BMSC_d07_h3k4me3_R2

source_name: bone marrow_day7_h3k4me3


title: D11_151231_run0452_Mf8h4cR2_female_t8h_DMSO0.0.40pct_rep2


title: D2_151231_run0452_Mf0h4cR2_female_t0h_DMSO0.0.40pct_rep2


title: D12_151231_run0452_Mf8h4cR3_female_t8h_DMSO0.0.40pct_rep3


title: D10_151231_run0452_Mf8h4cR1_female_t8h_DMSO0.0.40pct_rep1


title: BMSC_d00_h3k4me3_R1

source_name: bone marrow_day0_h3k4me3


title: D1_151231_run0452_Mf0h4cR1_female_t0h_DMSO0.0.40pct_rep1


title: C9_151231_run0452_Mf4h2cR3_female_t4h_DMSO0.0.20pct_rep3


title: BMSC_d21_h3k36me3_R2

source_name: bone marrow_day21_h3k36me3


title: C8_151231_run0452_Mf4h2cR2_female_t4h_DMSO0.0.20pct_rep2


title: BMSC_d21_h3k36me3_R1


title: C7_151231_run0452_Mf4h2cR1_female_t4h_DMSO0.0.20pct_rep1


title: C6_151231_run0452_Mf2h2cR3_female_t2h_DMSO0.0.20pct_rep3


title: BMSC_d14_h3k36me3_R1

source_name: bone marrow_day14_h3k36me3


title: BMSC_d14_h3k36me3_R2


title: BMSC_d07_h3k36me3_R2

source_name: bone marrow_day7_h3k36me3


title: C4_151231_run0452_Mf2h2cR1_female_t2h_DMSO0.0.20pct_rep1


title: C3_151231_run0452_Mf0h2cR3_female_t0h_DMSO0.0.20pct_rep3


title: BMSC_d07_h3k4me3_R1


title: BMSC_d00_h3k36me3_R2

source_name: bone marrow_day0_h3k36me3


title: BMSC_d07_h3k36me3_R1


title: C5_151231_run0452_Mf2h2cR2_female_t2h_DMSO0.0.20pct_rep2


title: BMSC_d00_h3k4me3_R2


title: BMSC_d00_h3k36me3_R1


title: BMSC_d21_h3k27me3_R2

source_name: bone marrow_day21_h3k27me3


title: BMSC_d14_h3k27me3_R2

source_name: bone marrow_day14_h3k27me3


title: BMSC_d21_h3k27me3_R1


title: C2_151231_run0452_Mf0h2cR2_female_t0h_DMSO0.0.20pct_rep2


title: BMSC_d14_h3k27me3_R1


title: C1_151231_run0452_Mf0h2cR1_female_t0h_DMSO0.0.20pct_rep1


title: C11_151231_run0452_Mf8h2cR2_female_t8h_DMSO0.0.20pct_rep2


title: B8_151231_run0452_Mf4h1cR2_female_t4h_DMSO0.0.10pct_rep2


title: B9_151231_run0452_Mf4h1cR3_female_t4h_DMSO0.0.10pct_rep3


title: BMSC_d07_h3k27me3_R2

source_name: bone marrow_day7_h3k27me3


title: BMSC_d00_h3k27me3_R2

source_name: bone marrow_day0_h3k27me3


title: BMSC_d07_h3k27me3_R1


title: BMSC_d00_h3k27me3_R1


title: B7_151231_run0452_Mf4h1cR1_female_t4h_DMSO0.0.10pct_rep1


title: BMSC_d21_h3k27ac_R1

source_name: bone marrow_day21_h3k27ac


title: BMSC_d21_h3k27ac_R2


title: BMSC_d14_h3k27ac_R1

source_name: bone marrow_day14_h3k27ac


title: BMSC_d14_h3k27ac_R2


title: C12_151231_run0452_Mf8h2cR3_female_t8h_DMSO0.0.20pct_rep3


title: B3_151231_run0452_Mf0h1cR3_female_t0h_DMSO0.0.10pct_rep3


title: B5_151231_run0452_Mf2h1cR2_female_t2h_DMSO0.0.10pct_rep2


title: B4_151231_run0452_Mf2h1cR1_female_t2h_DMSO0.0.10pct_rep1


title: BMSC_d07_h3k27ac_R2

source_name: bone marrow_day7_h3k27ac


title: C10_151231_run0452_Mf8h2cR1_female_t8h_DMSO0.0.20pct_rep1


title: B2_151231_run0452_Mf0h1cR2_female_t0h_DMSO0.0.10pct_rep2


title: BMSC_d07_h3k27ac_R1


title: B11_151231_run0452_Mf8h1cR2_female_t8h_DMSO0.0.10pct_rep2


title: BMSC_d00_h3k27ac_R2

source_name: bone marrow_day0_h3k27ac


title: B1_151231_run0452_Mf0h1cR1_female_t0h_DMSO0.0.10pct_rep1


title: BMSC_d00_h3k27ac_R1


title: BMSC_d21_ctcf_R2

source_name: bone marrow_day21_CTCF


title: A8_151231_run0452_Mf4h0cR2_female_t4h_DMSO0.0pct_rep2


title: A9_151231_run0452_Mf4h0cR3_female_t4h_DMSO0.0pct_rep3


title: A7_151231_run0452_Mf4h0cR1_female_t4h_DMSO0.0pct_rep1


title: BMSC_d14_ctcf_R2

source_name: bone marrow_day14_CTCF


title: A6_151231_run0452_Mf2h0cR3_female_t2h_DMSO0.0pct_rep3

source_name: whole body


title: A5_151231_run0452_Mf2h0cR2_female_t2h_DMSO0.0pct_rep2


title: BMSC_d00_ctcf_R2

source_name: bone marrow_day0_CTCF


title: B6_151231_run0452_Mf2h1cR3_female_t2h_DMSO0.0.10pct_rep3


title: BMSC_d00_ctcf_R1


title: Start-seq_dCD2

city: Stanford

first: Kristel

last: Dorighi

state: CA

address: 1291 Welch Rd.

institute: Stanford University

description:
libraries sequenced twice. All four raw files included in SRA records (Two R1 and two R2 files).
processed data files:
dCD-Startseq_F.bedGraph
dCD-Startseq_R.bedGraph

data_processing:
Library strategy: Start-Seq
Paired-end reads for all samples were trimmed for adapter sequence and low quality 3’ ends using cutadapt 1.2.1, discarding those containing reads shorter than 20 nt (-m 20 -q 10), and removing a single nucleotide from the 3’ end of all trimmed reads to allow successful alignment with bowtie 1.1.1
Counts of read-pairs mapping uniquely to each spike-in RNA were determined for each sample, using the same parameters. Mean counts per spike-in for each sample was determined, and least squares linear regression performed against a selected WT sample
The resulting slopes agreed well between replicates and were close to 1, thus reads were normalized solely based on sequencing depth (i.e. per million read pairs uniquely aligned to the mouse genome), by scaling the sample with the higher uniquely mappable read pair count to match the lower
genome build: mm9
processed data files format and content: Combined bedGraphs were generated by summing counts per nucleotide of both replicates for each condition

molecule: total RNA

source_name: embryonic stem cells

growth_protocol: Male mouse embryonic stem cells (R1) were grown at 37°C in 2i+LIF media, a serum free N2B27 based medium supplemented with MEK inhibitor PD0325901 (0.8 mM) and GSK3b inhibitor CHIR99021 (3.3mM), on tissue culture dishes coated with polyL-ornithine (7.5mg/ml) and laminin (5mg/ml), and were plated onto fibronectin (5mg/ml) prior to collection, as previously described (Buecker et al., 2014).

extract_protocol:
Nuclei were extracted and small RNAs selected for library preparation.
TruSeq Small RNA Kit (Illumina)

tag: cell line

value: R1 ESC

tag: strain

tag: genotype

value: Mll3/4 dCD


title: Start-seq_dCD1


title: Start-seq_dKO3

description:
libraries sequenced twice. All four raw files included in SRA records (Two R1 and two R2 files).
processed data files:
dKO-Startseq_F.bedGraph
dKO-Startseq_R.bedGraph

value: Mll3/4 dKO


title: A4_151231_run0452_Mf2h0cR1_female_t2h_DMSO0.0pct_rep1


title: Start-seq_WT1

description:
libraries sequenced twice. All four raw files included in SRA records (Two R1 and two R2 files).
processed data files:
WT-Startseq_F.bedGraph
WT-Startseq_R.bedGraph

value: wild-type


title: BMSC_d14_ctcf_R1


title: dCD_mESC_RNA-seq_rep2

description: processed data file: RNAseq_TPMs.csv

data_processing:
reads were aligned with hisat2 and tabulated with featureCounts against genocode gene models
differential analysis from three biological replicates was performed with DESeq2
genome build: mm9
processed data files format and content: Transcripts per million were computed for each annotated gene and reported in a matrix table for each RNAseq sample submitted.

extract_protocol:
Cells were lysed in Trizol, RNA extracted, mRNAs purified with oligo(dT) beads and reverse transcribed with SuperScriptII.
ChIP DNA, input DNA and cDNA were subject to end repair, A-tailing, adaptor ligation and cleavage with USER enzyme, followed by size selection of 250-500 bp and amplification with NEBNext sequencing primers


title: A1_151231_run0452_Mf0h0cR1_female_t0h_DMSO0.0pct_rep1


title: Start-seq_WT3


title: A12_151231_run0452_Mf8h0cR3_female_t8h_DMSO0.0pct_rep3


title: dCD_mESC_RNA-seq_rep3

description: processed data file: RNAseq_TPMs.csv


title: A10_151231_run0452_Mf8h0cR1_female_t8h_DMSO0.0pct_rep1


title: A11_151231_run0452_Mf8h0cR2_female_t8h_DMSO0.0pct_rep2


title: Start-seq_WT2


title: dCD_mESC_RNA-seq_rep1

description: processed data file: RNAseq_TPMs.csv


title: B10_151231_run0452_Mf8h1cR1_female_t8h_DMSO0.0.10pct_rep1


title: RNAseq_PMA_THP1_rep2

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

description: PMA THP-1 cells RNA-seq technical replicate 2

data_processing:
All samples were sequenced together on an Illumina HiSeq2500 (paired-end, 100), and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed RNA sequencing reads were mapped to gencode v19 transcripts using kallisto. For analysis of differential genes, kallisto outputs were processed using tximport.  Genes with less than 2 counts per million were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: Statistical significance was determined using the glmTreat function in edgeR with a fold change cutoff of 2.

organism: Homo sapiens

source_name: THP-1 cells, + PMA exposure

growth_protocol: THP-1 cells were obtained from ATCC (Lot # 62454382) and grown for multiple passages in T-75 flasks between 2-8 x 105 cells/mL in growth medium containing RPMI-1640 (Corning), 10% fetal bovine serum, and 1% penicillin streptomycin.

extract_protocol:
Approximately 5 million treated or untreated THP-1 cells were collected and washed with 1x ice cold PBS.  RNA was extracted using the Dynabeads mRNA Direct kit according to manufacturer directions.  Sequencing libraries were prepared using the Epicenter ScriptSeq V2 kit according to manufacturer supplied protocol. The resulting libraries were quantified by Qubit, mixed in equal concentrations, and assayed by Bioanalyzer prior to sequencing using Illumina HiSeq 2500 technology.
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For differentiation of THP-1 cells, non-adherent cells were diluted to 2 x 105 cells/mL and grown overnight, and a final concentration of 100 nM PMA was added the following morning. THP-1 derived macrophages were collected after 72 hr exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 minutes followed by cell wash in phosphate buffer saline (PBS) buffer.

tag: pma exposure

value: 72 hr PMA exposure


title: dKO_mESC_RNA-seq_rep2

description: processed data file: RNAseq_TPMs.csv


title: RNAseq_PMA_THP1_rep1

description: PMA THP-1 cells RNA-seq technical replicate 1


title: dKO_mESC_RNA-seq_rep1

description: processed data file: RNAseq_TPMs.csv


title: Start-seq_dKO1


title: RNAseq_Untreated_THP1_rep1

description: untreated THP-1 cells RNA-seq technical replicate 1

source_name: THP-1 cells, - PMA exposure

value: ( - PMA )


title: WT_mESC_RNA-seq_rep2

description: processed data file: RNAseq_TPMs.csv


title: dKO_mESC_RNA-seq_rep3

description: processed data file: RNAseq_TPMs.csv


title: WT_mESC_RNA-seq_rep3

description: processed data file: RNAseq_TPMs.csv


title: BMSC_d21_ctcf_R1


title: MDM-315_H1N1_MOI2_18h_2

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw sequencing reads were aligned to the human hg38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples; gene-level quantification (FPKM normalization)

growth_protocol: Human CD14+ monocytes, isolated from healthy donor blood, were plated at a density of 3 x 10^6 cells in a 10 cm dish and cultured for 10 days in RPMI 1640 + 10% fetal bovine serum, Penicillin-Streptomycin, and 1000U/ml GM-CSF.

extract_protocol:
1 ml Trizol was added to 5-10 x 10^6 cells and the homogenate was incubated at room temperature for 5 minutes. 200 μl chloroform were added per ml of Trizol, shaken vigorously for 15-30 seconds and incubated at room temperature for 15 minutes. Samples were centrifuged for 15 minutes at 4˚C and 12,000 rcf. The aqueous phase was carefully collected in a separate tube. 500 μl isopropanol was added per 1 ml Trizol, inverted to mix and incubated at room temperature for 5-10 minutes. Samples were transferred to Qiagen RNeasy Spin Columns and RNA was isolated according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: For infection, growth medium was replaced with virus diluted to the appropriate concentration in serum-free RPMI 1640 medium at a total volume of 2 mL. Dishes were incubated in a cell culture incubator with gentle rocking every 15 minutes. After 60 minutes, the inoculum was removed and cells were washed twice washed gently with 5 mL serum-free RPMI 1640. 10 mL of RPMI 1640 + 10% fetal bovine serum and Penicillin-Streptomycin was added and cells were incubated for the specified length of time.

value: Human Monocyte-Derived Macrophages (MDM)

tag: donor id

tag: infection

value: A/California/04/09 (H1N1), MOI 2

tag: time point

tag: biological replicate


title: MDM-315_H1N1_MOI0_18h_2

value: uninfected (mock control)


title: MDM-315_H1N1_MOI2_18h_1


title: ATAC-seq_dKO_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie31
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

extract_protocol:
50,000 nuclei were lysed and transposed with the Nextera DNA library preparation kit.
Nextera DNA library preparation Kit (Illumina)


title: Gro-seq_WT

data_processing:
Library strategy: Gro-Seq
reads were trimmed for quality and adapter sequence using Cutadapt 1.2.1, discarding pairs where either mate was trimmed shorter than 15 nt
Read pairs originating from rRNA and tRNA were filtered by aligning against an index consisting of the 45S, 5S, and tRNA transcripts using Bowtie 0.12.8, allowing two mismatches
genome build: mm9
processed data files format and content: BedGraph files were generated from strand-specific 5’-end mapping locations based on spike-normalized reads

extract_protocol:
Nuclei were extracted and nuclear run-on perfomed prior to IP for Br-U RNAs with antibody.
TruSeq Small RNA Kit (Illumina)


title: B12_151231_run0452_Mf8h1cR3_female_t8h_DMSO0.0.10pct_rep3


title: ATAC-seq_dKO_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie30
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: ATAC-seq_WT_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie29
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-315_H1N1_MOI2_12h_1


title: MDM-315_H1N1_MOI2_12h_2


title: MDM-315_H1N1_MOI0_12h_1


title: Input_DNA_WT

data_processing:
reads were trimmed with cutadapt and aligned with bowtie25
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

extract_protocol:
Nuclei were extracted and chromatin sonicated to 250-500bp with a Covaris sonicator and IP was performed with antibody as indicated overnight.
ChIP DNA, input DNA and cDNA were subject to end repair, A-tailing, adaptor ligation and cleavage with USER enzyme, followed by size selection of 250-500 bp and amplification with NEBNext sequencing primers


title: ATAC-seq_WT_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie28
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-315_H1N1_MOI2_06h_2


title: PolII_ChIP-seq_dCD_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie23
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

tag: antibody

value: RNA Pol II (Santa Cruz Biotechnology sc-899)


title: Input_DNA_dCD

data_processing:
reads were trimmed with cutadapt and aligned with bowtie27
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-315_H1N1_MOI2_06h_1

tag: cell type


title: MDM-315_H1N1_MOI2_03h_1


title: PolII_ChIP-seq_dCD_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie24
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: PolII_ChIP-seq_dKO_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie22
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-315_H1N1_MOI0_06h_1


title: PolII_ChIP-seq_dKO_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie21
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-315_H1N1_MOI0_12h_2


title: MDM-315_H1N1_MOI2_03h_2


title: MDM-315_H1N1_MOI0_06h_2


title: MDM-520_H5N1_MOI2_18h_2

value: A/Vietnam/1203/04 (H5N1) HALo, MOI 2


title: H3K27ac_ChIP-seq_dCD_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie18
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

value: H3K27ac (Active Motif 39133)


title: PolII_ChIP-seq_WT_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie20
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: A2_151231_run0452_Mf0h0cR2_female_t0h_DMSO0.0pct_rep2

data_processing:
Basecalling was performed using CASAVA v1.8.2 (Illumina, San Diego, CA). BCL files were converted to FASTQ and demultiplexed using bcl2fastq v1.8 (Illumina, San Diego, CA).
The RNA-seq reads of mixed species were first mapped to a merged genome and annotation including D. grimshawi (dgri_caf1 assembly; Drosophila_grimshawi.GCA_000005155.1.29.dna_sm.genome.fa) D. melanogaster (FlyBase release 6 version 04 ; FlyBase file: dmel-all-chromosome-r6.04.fasta), and A. stephensi (Anopheles-stephensi-Indian_SCAFFOLDS_AsteI2.fa), appended with ERCC sequences (Zook et al., 2012. PMID: 22859977) using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886). The unmapped reads and reads mapping to D. grimshawi or A. stephensi are not reported in this GEO submission or affiliated SRA entry.
Segregated D. melanogaster reads were mapped to the major chromosome arms (chr2L, chr2R, chr3L, chr3R, chr4, chrX, chrY, and chrM) of Drosophila genome assembly release 6 plus ISO1 MT and ERCC sequences using TopHat v2.1.0 (Trapnell et al., 2009. PMID: 19289445) with default options except for the following: Libraries were stranded so mapping was done with --library-type fr-firststrand, and we provided a GTF with known set of gene models (FlyBase r6.09 and ERCC) using -G option.
The ERCC reference was based on the DNA Sequence Library SRM2374 from NIST, the FASTA sequence was corrected according to differences found in (Jiang et al. 2011, PMID: 21816910). We also used the reverse complement of ERCC-00009, ERCC-00014, ERCC-00057, ERCC-00059, ERCC-00099, ERCC-00108, ERCC-00116 for mapping to correct the strand orientation and ERCC-00085 was re-annotated as Subpool C.
Unique alignments were created by keeping only reads that aligned to a single location (NH:i:1) using grep (v2.20). HTseq v0.6.1p1 (Anders et al., 2014. PMID: 25260700) was used to create gene level read counts with default options except (-s reverse) was used to get strand specific read counts.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GeneBank assembly accession: GCA_000001215.4)
Supplementary_files_format_and_content: Tab delimited file containing gene level read counts from Htseq.


title: H3K27ac_ChIP-seq_dCD_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie17
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: H3K27ac_ChIP-seq_dKO_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie15
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: H3K27ac_ChIP-seq_dKO_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie16
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-520_H5N1_MOI0_18h_1

data_processing:
Raw sequencing reads were aligned to the human hg38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples; gene-level quantification (FPKM normalization)


title: MDM-315_H1N1_MOI0_03h_2


title: MDM-520_H5N1_MOI2_12h_2


title: H3K4me1_ChIP-seq_dCD_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie12
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

value: H3K4me1 (abcam ab8895)


title: A3_151231_run0452_Mf0h0cR3_female_t0h_DMSO0.0pct_rep3


title: MDM-520_H5N1_MOI2_12h_1


title: MDM-520_H5N1_MOI0_12h_2


title: H3K27ac_ChIP-seq_WT_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie14
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: H3K4me1_ChIP-seq_dCD_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie11
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: PolII_ChIP-seq_WT_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie19
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: H3K4me1_ChIP-seq_dKO_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie10
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-520_H5N1_MOI0_12h_1


title: MDM-520_H5N1_MOI2_06h_2


title: H3K4me1_ChIP-seq_dKO_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie9
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: H3K4me1_ChIP-seq_WT_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie8
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-520_H5N1_MOI0_06h_2


title: H3K4me1_ChIP-seq_WT_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie7
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-520_H5N1_MOI0_18h_2


title: Start-seq_dKO2

data_processing:
Library strategy: Start-Seq
Paired-end reads for all samples were trimmed for adapter sequence and low quality 3’ ends using cutadapt 1.2.1, discarding those containing reads shorter than 20 nt (-m 20 -q 10), and removing a single nucleotide from the 3’ end of all trimmed reads to allow successful alignment with bowtie 1.1.1
Counts of read-pairs mapping uniquely to each spike-in RNA were determined for each sample, using the same parameters. Mean counts per spike-in for each sample was determined, and least squares linear regression performed against a selected WT sample
The resulting slopes agreed well between replicates and were close to 1, thus reads were normalized solely based on sequencing depth (i.e. per million read pairs uniquely aligned to the mouse genome), by scaling the sample with the higher uniquely mappable read pair count to match the lower
genome build: mm9
processed data files format and content: Combined bedGraphs were generated by summing counts per nucleotide of both replicates for each condition


title: MDM-520_H5N1_MOI0_06h_1


title: MDM-315_H1N1_MOI0_18h_1


title: Mll3/4_ChIP-seq_dKO_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie5
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

value: Mll3/4 (custom)


title: MDM-520_H5N1_MOI2_03h_2


title: MDM-520_H5N1_MOI2_03h_1


title: MDM-520_H5N1_MOI0_03h_2


title: WT_mESC_RNA-seq_rep1

description: processed data file: RNAseq_TPMs.csv

data_processing:
reads were aligned with hisat2 and tabulated with featureCounts against genocode gene models
differential analysis from three biological replicates was performed with DESeq2
genome build: mm9
processed data files format and content: Transcripts per million were computed for each annotated gene and reported in a matrix table for each RNAseq sample submitted.


title: H3K27ac_ChIP-seq_WT_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie13
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-520_H5N1_MOI2_06h_1


title: Mll3/4_ChIP-seq_WT_rep2

data_processing:
reads were trimmed with cutadapt and aligned with bowtie3
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: Liver_Postnatal 7 year_miRNA-seq

city: Chengdu

first: Yihui

last: Liu

state: Sichuan

address: Wen jiang district, Hui Min road #211

department: College of Animal Science & Technology

country: China

institute: Sichuan Agricultural University

data_processing:
The raw reads were performed using a proprietary pipeline, ACGT101-miR program (Illumina), and followed a series of additional filters: After trimming off the sequencing adapters and junk reads, the resulting reads was successively filtered by read length, sequence component. Then the retained reads were searched against the NCBI, Rfam and Repbase database to remove porcine known classes of RNAs (i.e., mRNA, rRNA, tRNA,snRNA, snoRNA and repeats). Then mapping these unique sequences to mirs(miRbase 19.0) and Genome(Sscrofa10.2).
Genome_build: Genome database:Sus scrofa (Sscrofa10.2); miRbase version: V19.0
Supplementary_files_format_and_content: identified miRNAs with details (reads,location,length,etc)

organism: Sus scrofa

source_name: Liver

growth_protocol: The liver tissues were obtained from three male Jinhua pigs at embryonic day 90 (E90), three pigs at postnatal day 30 (30 d) and three pigs at postnatal year 7 (7 y).

extract_protocol:
Total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion, Austin, USA) according to the manufacturer’s protocol. The integrity of total RNA was determined by the Agilent Technologies of Bioanalyzer 2100 and RNA 6000 Nano Labchip Kit (Agilent, CA, USA) with RIN number >6.0.
According to the Illumina EAS Small RNA Sample Prep Protocol. In general, approximately 15 ug of small RNA-enriched total RNA was prepared for High-throughput sequencing. In brief, High-throughput sequencing was performed as following successive step: For each library, the small RNA ranged from 14 to 40 nt were purified by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). Then the modified small RNA was reverse transcribed and amplified by RT-PCR. Finally, the enriched cDNA were sequenced on Genome Analyzer II (GAI, Illumina, San Diego, CA, USA) according to manufacturer instructions.

tag: breed

value: Jinhua

tag: tissue

value: liver

tag: gender

value: male

value: Postnatal 7 year

value: Adult stage


title: MDM-315_H1N1_MOI0_03h_1


title: Liver_Postnatal 30 day_miRNA-seq

tag: age

value: Postnatal 30 day

value: Weaning stage


title: Mll3/4_ChIP-seq_WT_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie2
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

value: R1 ESC

value: wild-type


title: MDM-520_H5N1_MOI0_03h_1

value: Human Monocyte-Derived Macrophages (MDM)


title: MDM-513_H5N1_MOI2_06h_2


title: Liver_Embryo 90 day_miRNA-seq

value: Embryonic 90 day

value: Embryo


title: MDM-513_H5N1_MOI2_06h_1


title: MDM-513_H5N1_MOI2_03h_1


title: MDM-513_H5N1_MOI0_06h_1

value: uninfected (mock control)


title: MDM-513_H5N1_MOI2_03h_2

value: A/Vietnam/1203/04 (H5N1) HALo, MOI 2


title: MDM-513_H5N1_MOI0_03h_1


title: MDM-513_H5N1_MOI0_03h_2


title: MDM-418_H3N2_MOI2_18h_1

value: A/Wyoming/03/03 (H3N2), MOI 2


title: Mll3/4_ChIP-seq_dCD_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie6
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

value: Mll3/4 dCD


title: MDM-418_H3N2_MOI0_18h_2

data_processing:
Raw sequencing reads were aligned to the human hg38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples; gene-level quantification (FPKM normalization)


title: Mll3/4_ChIP-seq_dKO_rep1

data_processing:
reads were trimmed with cutadapt and aligned with bowtie4
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).

value: Mll3/4 dKO

value: Mll3/4 (custom)


title: MDM-418_H3N2_MOI2_12h_1


title: MDM-418_H3N2_MOI2_18h_2


title: MDM-418_H3N2_MOI0_18h_1


title: MDM-418_H3N2_MOI0_12h_1


title: MDM-418_H3N2_MOI0_12h_2


title: MDM-418_H3N2_MOI2_06h_2


title: MDM-513_H5N1_MOI0_06h_2


title: MDM-418_H3N2_MOI0_06h_2


title: MDM-418_H3N2_MOI0_06h_1


title: MDM-418_H3N2_MOI2_03h_2


title: MDM-418_H3N2_MOI0_03h_1


title: Input_DNA_dKO

data_processing:
reads were trimmed with cutadapt and aligned with bowtie26
read coverage was normalized to total aligned reads in a given library
peaks were called with macs2 callpeak routine
normalized density wig tracks were calculated with QuEST
genome build: mm9
processed data files format and content: Visualization tracks were generated with bedtools genomecov (-bg -scale) with scaling factor being 10^6/number aligned reads and converted to bigWig with bedGraphToBigWig (Kent tools).


title: MDM-418_H3N2_MOI0_03h_2


title: MDM-418_H3N2_MOI2_06h_1


title: MDM-418_H3N2_MOI2_03h_1


title: aKOgKO 2

city: Philadelphia

first: Liming

last: Pei

state: PA

address: 3501 Civic Center Blvd. CTRB 6018

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia/University of Pennsylvania

description: ERRa KO/ERRg KO

data_processing:
After QC, clean reads were aligned with reference genome using SOAP2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing gene ID, rpkm and other relevant information

source_name: Heart

extract_protocol:
Hearts were quickly dissected and flash frozen in liquid nitrogen. RNA was harvested using RNAzol reagent.
RNA libraries were prepared at BGI@CHOP using Illumina TruSeq RNA Sample Prep Kit

value: ERRa KO/ERRg KO

value: Heart

value: post natal day 16


title: YJ_r2 (XC)

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline.
For all samples, only reads that passed the Illumina quality control steps were included in subsequent analyses, and reads with multiple copies were considered as a single read for the mapping procedure.
The raw reads were aligned to the Arabidopsis genome (TAIR10) using tophat2. The reads mapped to more than one positions were removed.
The raw counts of gene were generated by perl script.
Genome_build: TAIR10
Supplementary_files_format_and_content: [.txt] tab-delimited file of raw counts

organism: Arabidopsis thaliana

source_name: YJ, young seedlings

growth_protocol: Plants were grown in a growth incubator at 23°C under short day conditions (8 hrs light, 16 hrs dark)

extract_protocol:
Ten-day-old seedlings were used for RNA extraction using Trizol (Invitrogen, 15596– 018), and the extracted RNA was treated with DNase I (Roche, 04716728001).
For Col,  mbd7-3 and mbd7-4, RNA-seq libraries were generated using 2.0 ug of DNaseI-treated RNA and the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat# E7530) according to the manufacturer’s instructions. For YJ, YJ lil-1, LUCH, and LUCH lil-2, Two micrograms of the DNase I- treated RNA were used for RNA-seq library construction with the TruSeq RNA Sample Preparation Kit v2 (Illumina, FC-122-1002). The libraries were sequenced on an Illumina HiSeq 2000 instrument at the genomics core facility at UC Riverside.

tag: genotype/variation

value: wild type (Luciferase transgene in rdr6-11 mutant background)

value: young seedling


title: YJ_r1 (XC)


title: YJ_r3 (XC)


title: aKOgKO 1

description: ERRa KO/ERRg KO


title: aKOgWT 2

description: ERRa KO/ERRg WT

value: ERRa KO/ERRg WT


title: RNAseq_Untreated_THP1_rep2

description: untreated THP-1 cells RNA-seq technical replicate 2

data_processing:
All samples were sequenced together on an Illumina HiSeq2500 (paired-end, 100), and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed RNA sequencing reads were mapped to gencode v19 transcripts using kallisto. For analysis of differential genes, kallisto outputs were processed using tximport.  Genes with less than 2 counts per million were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: Statistical significance was determined using the glmTreat function in edgeR with a fold change cutoff of 2.

value: ( - PMA )


title: aKOgWT 1

description: ERRa KO/ERRg WT


title: MDM-418_H3N2_MOI2_12h_2


title: LUCH_r3 (XC)

source_name: LUCH, young seedlings


title: YJ lil-1_r1 (XC)

source_name: YJ lil-1, young seedlings

value: lil (YJ that has a mutation in LIL gene)


title: LUCH_r1 (XC)


title: MDM-513_H5N1_MOI0_18h_2

value: Human Monocyte-Derived Macrophages (MDM)


title: MDM-513_H5N1_MOI2_18h_1


title: aHetgKO 2

description: ERRa Het/ERRg KO

value: ERRa Het/ERRg KO


title: aHetgKO 1

description: ERRa Het/ERRg KO


title: aHetgWT 1

description: ERRa Het/ERRg WT

value: ERRa Het/ERRg WT


title: MDM-513_H5N1_MOI2_18h_2


title: aHetgWT 2

description: ERRa Het/ERRg WT


title: BMSC_d21_input_R2

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
Concatenate replicates.
Align reads with Bowtie 1.2.8
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in logFE mode.
Convert logFE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of log fold enrichment over input from bdgcmp function of MACS2. Bigwig files are available in tar archives on the series record.

source_name: bone marrow_day21_input

value: bone marrow

value: mesenchymal stromal cell

tag: markers

value: SMAA-mCherry+

value: 6-8 weeks


title: LUCH lil-2_r3 (XC)

source_name: LUCH lil-2, young seedlings

value: lil (LUCH that has a mutation in LIL gene)


title: LUCH lil-2_r2 (XC)


title: LUCH lil-2_r1 (XC)


title: YJ lil-1_r3 (XC)


title: BMSC_d14_input_R2

source_name: bone marrow_day14_input


title: YJ lil-1_r2 (XC)


title: YJ lil-1 (JL)


title: MDM-513_H5N1_MOI2_12h_2

value: A/Vietnam/1203/04 (H5N1) HALo, MOI 2


title: MDM-520_H5N1_MOI2_18h_1


title: MDM-513_H5N1_MOI0_12h_2

value: uninfected (mock control)


title: BMSC_d21_input_R1


title: MDM-513_H5N1_MOI0_18h_1


title: BMSC_d14_input_R1


title: MDM-513_H5N1_MOI2_12h_1


title: mbd7-4 (JL)

source_name: mbd7-4, young seedlings


title: BMSC_d07_input_R2

source_name: bone marrow_day7_input


title: mbd7-3 (JL)

source_name: mbd7-3, young seedlings


title: LUCH_r2 (XC)


title: MDM-513_H5N1_MOI0_12h_1


title: BMSC_d07_input_R1


title: Col (JL)

source_name: Col, young seedlings

value: wild type


title: N36-V600E

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

data_processing:
[raw read cleaning] Illumina TruSeq adapter sequence that may included in raw reads were trimmed by CutAdapt (https://pypi.python.org/pypi/cutadapt).
[mapping on the reference genome] Adapter trimmed reads were mapped by TopHat2 (http://tophat.cbcb.umd.edu) with bowtie2 (http://bowtie-bio.sourceforge.net).
[expression quantification] Normalized gene expression values were calculated by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Thyroid

growth_protocol: Thyrocyte was isolated from normal thyroid tissue. Briefly, normal thyroid tissue was washed five times by PBS (phosphate-buffered saline) and cut into small pieces, followed by treatment with 0.2% collagenase I (Worthington Biochemical, Lakewood, NJ) in HEPES buffer for 6 hours at 32°C. Cell were resuspended in complete F12K media (F12K, Gibco BRL, Bethesda, MD; TSH, 10mU/ml; insulin, 0.01mU/ml; hydrocortisone, 10nM; transferrin, 0.005mg/ml; somatostatin, 10ng/ml; glycyl-L-histidyl-Llysine acetate, 10ng/ml) and placed in 10cm culture dishes.

extract_protocol:
Total RNA was extracted from control and BRAFV600E thyrocyte samples using Macherey-Nagel RNA kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thyrocyte

tag: passages

value: BRAFV600E overexpression


title: BMSC_d00_input_R2

source_name: bone marrow_day0_input


title: N36-Control

value: Normal


title: BMSC_d07_ctcf_R2

source_name: bone marrow_day7_CTCF


title: Col_YJ (JL)

source_name: Col_YJ, young seedlings

value: wild type (Luciferase transgene in rdr6-11 mutant background)

value: young seedling


title: N31-V600E


title: BMSC_d00_input_R1


title: AB1244

status: Public on May 04 2017

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: polyA+ RNA

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Note: read2 not provided by submitter, raw data brokered to SRA as single
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: myeloid

extract_protocol:
Freshly resected surgical specimens were processed, and singlets were sorted based on CD45+ DAPI- CD3- CD19- gating.
Libraries were prepared as described by Jaitin et al., 2014.

tag: Sex

value: female

tag: organ

value: tumor

tag: tumor stage

value: Human lung stage IA adenocarcinoma lesion and adjacent non-involved lung

tag: selection marker

value: singlet DAPI- CD45+ CD3- CD19-/lo


title: N31-Control


title: AB1240

description: polyA+ RNA


title: AB1237

description: polyA+ RNA

value: lung


title: YJ smallRNAseq

data_processing:
Illumina Casava software used for basecalling.
The raw reads of small RNAs were processed by PERL scripts built in house. Briefly, the raw reads were screened with Illumina’s quality control filter. The reads that passed the filter were separated into different bins according to their barcodes (indexes). The adaptor was trimmed for each read. Reads that match known rRNAs, tRNAs, snRNAs, and snoRNAs were removed. Reads of 20–24 nt were selected as the raw small RNA sequences. For Col-0, sde4-3, and nrpe1-11, which are in the Columbia ecotype, the small RNA reads were mapped to the Tair10 Arabidopsis genome with SOAP2. For Ler and top1a, which are in the Landsberg ecotype, the small RNA reads were mapped to a pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt).
Every chromosome of Arabidopsis was divided into continuous 500 bp windows. Small RNAs whose 5’ nucleotide falls into a 500 bp window were counted as those belonging to this window. The number of reads in every window was recorded and served as the abundance of small RNAs in this window. The reads were normalized to RPM (reads per million)
Genome_build: TAIR10, and pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt)
Supplementary_files_format_and_content: txt file, which has two columns chr_postion, RPM (reads per million)

source_name: ten-day-old seedlings

growth_protocol: Arabidopsis thaliana seeds were surface sterilized by either 30% bleach or fumigated in an airtight container with a solution containing 50 mL of 100% bleach and 8% HCl for six hours. After, the seeds were planted on half-strength MS-agar plates containing 1% sucrose (no sucrose was added in plates used for chemical screening to minimize fungal growth), stratified at 4°C for two days and moved into a growth chamber. Plants were grown under continuous light at 23°C. All experiments were performed with ten-day-old seedlings.

extract_protocol: Library was constructed with the Illumina TruSeq-small RNA sample preparation kit per manufacturer’s instructions (Illumina). In brief, gel-purified small RNAs were ligated sequentially to 3’ and 5’ adaptors. Following reverse transcription, PCR amplification of the cDNA resulted in the small RNA library, which was gel-purified and subjected to high throughput sequencing

tag: ecotype

value: Columbia

value: ten-day-old seedlings

tag: genotype


title: AB1238

description: polyA+ RNA


title: AB1239

description: polyA+ RNA


title: AB1241

description: polyA+ RNA


title: YJ lil-1 smallRNAseq

value: lil (YJ that has a mutation in LIL gene)


title: AB1242

description: polyA+ RNA


title: SD_5/6Nx+anti-miR-21_RNASeq_rep2

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

description: pool of 2-3 individuals

data_processing:
Adapter sequences were first removed from the output reads by the tool cutadapt (http://code.google.com/p/cutadapt/).
The trimmed short sequencing reads were aligned to the rat reference (rn5) using Tophat v2.0.10 with mammalian default parameters.
We used the rat Ensembl transcripts (release 76) to guide RABT assembly by Cufflinks v2.0.10.
Cuffdiff was used to determine differences in transcript/isoform abundance between groups.
The Benjamini-Hochberg method was used to control false discovery rate in differential expression analysis.
Genome_build: rn5
Supplementary_files_format_and_content: Gene-level or isoform expression measurements are reported in fragments per kilobase per million reads.

organism: Rattus norvegicus

source_name: Left ventricle tissue_anti-miR-21

growth_protocol: Rats were delivered from Harlan (Envigo) at 9 weeks of age and placed on 0.4% Dyets chow and provided food and water ad libitum.

extract_protocol:
Left ventricle tissues were isolated and flash frozen in liquid nitrogen.   They were then ground into powder under liquid nitrogen which was thawed in Trizol for chloroform-based RNA isolation.
mRNA libraries were constructed for these pools using the Illumina TruSeq Stranded Total RNA Kit.  Samples were multiplexed seven per lane on a 300 Gb flow cell and paired-end sequenced with an Illumina HiSeq 2000.

treatment_protocol: At 10 weeks of age rats were subjected to 5/6Nx surgery; anti-scrambled miR or anti-miR-21-5p was delivered via jugular vein infusion in 3 daily doses at weeks 1 and 4 post-surgery.

value: heart

tag: heart region

value: left ventricle

tag: strain

value: Sprague Dawley

value: male

value: 10 weeks of age at surgery

tag: diet

value: 0.4% Dyets chow


title: AB1235

description: polyA+ RNA


title: AB1236

description: polyA+ RNA


title: SD_5/6Nx+anti-scr_RNASeq_rep1

description: pool of 2-3 individuals

source_name: Left ventricle tissue_anti-scr


title: SD_5/6Nx+anti-scr_RNASeq_rep2

description: pool of 2-3 individuals


title: scFv_DKK1c_2

city: New York

first: Kelley

last: Yan

state: NY

department: Medicine

institute: Columbia University

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 5bp UMI tags were extracted from Read2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

growth_protocol: in vivo modulation of Wnt versus R-spondin in mice

extract_protocol:
epithelial cell preparation from proximal jejunum
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two biological replicates were generated per sample. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al.
Sequencing libraries were loaded at 2.1pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

treatment_protocol: in vivo adenoviral intravenous injection into mice followed by small intestine tissue harvest, dissociation and FACS isolation

value: small intestine

tag: cell type

value: Lgr5-eGFP(+) cells

tag: treatment

value: Ad scFv-DKK1c

tag: condition

value: Wnt GOF


title: SD_Wk7 post-5/6Nx_miRNASeq_rep2

description:
Kriegel_Supplemental Table 3_ 5/6Nx vs. Sham_Wk7_miRNA
pool of 2-3 individuals

data_processing:
Adapter sequences were first removed from the output reads by the tool cutadapt (http://code.google.com/p/cutadapt/); sequences with low quality (base quality < 13) at both ends of reads were further trimmed and trimmed reads with less than 25 bp were removed using the SolexaQA (http://solexaqa.sourceforge.net/).
The trimmed short sequencing reads were aligned to miRbase v20 to identify microRNAs using Bowtie, those that didn't map ewere mapped against Rfam and RepBase.
DESeq was implemented to identify differential expression.
The Benjamini-Hochberg method was used to control false discovery rate in differential expression analysis.
Genome_build: miRbase v20
Supplementary_files_format_and_content: Expression measurements are reported in normalized reads.

source_name: Left ventricle tissue_5/6Nx_7 weeks post surgery

extract_protocol:
Left ventricle tissues were isolated and flash frozen in liquid nitrogen.   They were then ground into powder under liquid nitrogen which was thawed in Trizol for chloroform-based RNA isolation.
Small RNA libraries were constructed for Pools of 2-3 rats, 2 Pools per condition, using the TruSeq Small Sample Preparation RNA Kit.   Samples were multiplexed sequenced with an Illumina HiSeq 2000 using the TruSeq SBS kit v2-HS.

treatment_protocol: At 10 weeks of age rats were subjected to sham or 5/6Nx surgery.

tag: tissue


title: SD_Wk7 post-5/6Nx_miRNASeq_rep1

tag: age


title: scFv_DKK1c_1


title: Rspo2_Fc_1

value: Ad RSPO2

value: RSPO2 GOF


title: Rspo2_Fc_2


title: Rspo1_Fc_2

value: Ad Rspo1

value: Rspo1 GOF


title: SD_Wk7 post-sham_miRNASeq_rep1

source_name: Left ventricle tissue_Sham_7 weeks post surgery


title: SD_Wk5 post-5/6Nx_miRNASeq_rep2

description:
Kriegel_Supplemental Table 3_5/6Nx vs. Sham_Wk5_miRNA
pool of 2-3 individuals

source_name: Left ventricle tissue_5/6Nx_5 weeks post surgery


title: Lgr5_eGFP_neg_2

value: Lgr5-eGFP(-) cells

value: Ad Fc

value: control cell population depleted of ISCs without perturbation


title: AB1243

description: polyA+ RNA

value: female

value: tumor

value: Human lung stage IA adenocarcinoma lesion and adjacent non-involved lung

value: singlet DAPI- CD45+ CD3- CD19-/lo


title: Rspo1_Fc_1


title: SD_Wk5 post-5/6Nx_miRNASeq_rep1

value: heart

value: left ventricle

value: Sprague Dawley

value: male

value: 10 weeks of age at surgery


title: Lgr5_eGFP_neg_1

value: small intestine


title: SD_Wk7 post-sham_miRNASeq_rep2

value: 0.4% Dyets chow


title: Fzd8_Fc_2

value: Lgr5-eGFP(+) cells

value: Ad Fzd8 CRD

value: Wnt LOF


title: SD_Wk4 post-5/6Nx_miRNASeq_rep1

description:
Kriegel_Supplemental Table 3_ 5/6Nx vs. Sham_Wk4_miRNA
pool of 2-3 individuals

source_name: Left ventricle tissue_5/6Nx_4 weeks post surgery


title: SD_Wk5 post-sham_miRNASeq_rep1

source_name: Left ventricle tissue_Sham_5 weeks post surgery


title: LGR5_ECD_1

value: Ad LGR5 ECD

value: Rspo LOF


title: SD_Wk4 post-sham_miRNASeq_rep2

source_name: Left ventricle tissue_Sham_4 weeks post surgery


title: SD_Wk5 post-sham_miRNASeq_rep2


title: LGR5_ECD_2


title: Fc_2

source_name: Fc

value: Ad Fc

value: control intestinal stem cell population without perturbation


title: SD_Wk4 post-5/6Nx_miRNASeq_rep2


title: SD_5/6Nx+anti-miR-21_RNASeq_rep1

description: pool of 2-3 individuals


title: Fc_1


title: SD_Wk4 post-sham_miRNASeq_rep1


title: SD_Wk2 post-5/6Nx_miRNASeq_rep1

description:
Kriegel_Supplemental Table 3_ 5/6Nx vs. Sham_Wk2_miRNA
pool of 2-3 individuals

source_name: Left ventricle tissue_5/6Nx_2 weeks post surgery


title: SD_Wk2 post-5/6Nx_miRNASeq_rep2


title: SD_Wk2 post-sham_miRNASeq_rep2

source_name: Left ventricle tissue_Sham_2 weeks post surgery


title: SD_Wk2 post-sham_miRNASeq_rep1


title: SD_Wk7 post-5/6Nx_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk7
Pool_1_CTTGTA

source_name: Left ventricle tissue

extract_protocol:
Left ventricle tissues were isolated and flash frozen in liquid nitrogen.   They were then ground into powder under liquid nitrogen which was thawed in Trizol for chloroform-based RNA isolation.
mRNA libraries were constructed for these pools using the Illumina TruSeq Stranded Total RNA Kit.   Samples were multiplexed seven per lane on a 300 Gb flow cell and paired-end sequenced with an Illumina HiSeq 2000.


title: SD_Wk7 post-5/6Nx_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk7
Pool_2_CGATGT


title: SD_Wk7 post-sham_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk7
Pool_4_TGACCA


title: mTAL cells expressing GFP-tagged C150S uromodulin isoform replicate 3

city: Milan

first: Luca

last: Rampoldi

address: Via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

description:
log2NormValues.xlsx
C150S_3

data_processing:
Basecalls performed using CASAVA version 1.8
FASTQ files were aligned to mm10 custom fasta (mm10_UMOD.fa) using STAR_2.3.0_r291 aligner with the following parameters --runThreadN 2 --outSAMstrandField "intronMotif" --outSAMunmapped "Within" --readFilesCommand "zcat"
The expression levels were estimated using htseq-count with custom Ensemble mm10 GTF file (included) with the following parameters: --type "exon" --idattr "gene_name" --mode "union"
Differential Expression analysis with limma/voom
Genome_build: UCSC mm10 (Jun 2012) with UMOD human gene added (fasta file included)
Supplementary_files_format_and_content: xlsx file with log2 Normalized Values generated with voomWithQualityWeights function in limma package for expressed genes

source_name: Renal cells

growth_protocol: Cells were grown in DMEM/F12 supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, 5 µg/ml transferrin, 5 ng/ml interferon gamma, 4 µg/ml dexamethasone, 20 nM selenium, 50 µM ascorbic acid and 0,3 g / 500 ml NaHCO3 for 3 days in a 35 mm multiwell dish until they reached confluence. Fresh medium was added 15 hours before RNA extraction.

extract_protocol:
RNA was extracted using 1mL Isol-RNA Lysis Reagent (5Prime) following the manufacturer protocol. Extracted RNA was treated with RNase-free DNase (Qiagen) and cleaned-up using the RNeasy Mini kit (Qiagen).
TruSeq RNA Library Prep Kit v2(Illumina)

value: mTAL

tag: passage

tag: transgene

value: Transduced with lentiviral vector encoding human C150S uromodulin


title: SD_Wk5 post-5/6Nx_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk5
Pool_8_ATGTCA


title: SD_Wk7 post-sham_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk7
Pool_3_GTGAAA


title: Fzd8_Fc_1


title: SD_Wk5 post-sham_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk5
Pool_6_GCCAAT


title: SD_Wk5 post-sham_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk5
Pool_5_ACAGTG


title: SD_Wk5 post-5/6Nx_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk5
Pool_7_CAGATC


title: SD_Wk4 post-5/6Nx_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk4
Pool_4_TGACCA


title: mTAL cells expressing GFP-tagged wild type uromodulin isoform replicate 3

description:
log2NormValues.xlsx
WT_3

value: Transduced with lentiviral vector encoding human wild type uromodulin


title: SD_Wk4 post-sham_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk4
Pool_1_ATGTCA

value: heart


title: SD_Wk4 post-sham_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk4
Pool_2_CGATGT

value: left ventricle


title: SD_Wk2 post-sham_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk2
Pool_10_GTCCGC

value: Sprague Dawley


title: SD_Wk2 post-sham_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk2
Pool_9_CCGTCC

value: male


title: AdRspo1 #3 positive

first: Xiao

last: Li

description: Lgr5-eGFP-IRES-CreER mouse

data_processing:
Sequenced reads were aligned to the mouse reference genome mm9 (UCSC) uisng TopHat with the transcript annotation supplied
The mapped reads was assigned to gene using the tool htseq-count of the Python package HTSeq
The output of Htseq-count was used as input for DESeq2 to perform differential expression analysis, with a FDR of 10% as the cutoff, in addition, a filtering criterion of mean FPKM 1 in at lease one condition was used to define expressed transripts in each differential expression analysis. Cufflinks was used to calculate gene count and perform FPKM normalization.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Lgr5-eGFP+ cells from proximal jejunum

growth_protocol: cells were dissociated from mouse intestine following adenoviral treatment in vivo

extract_protocol:
intestine was harvested, dissociated into a single cell suspension, and cells were FACS isolated
see Extended Methods for full description

treatment_protocol: in vivo adenovirus treatment via intravenous injection

tag: sorted gfp(+) vs gfp(-) cells?

value: GFP+

tag: treatment condition

value: Rspo GOF


title: AdLGR5 ECD#3 positive

description: Lgr5-eGFP-IRES-CreER mouse


title: AdRspo1 #1 positive

description: Lgr5-eGFP-IRES-CreER mouse


title: input for tagged-Reb1 strain

city: Parma

first: Giorgio

last: Dieci

address: Parco Area delle Scienze 23/A

department: Deparment of Life Sciences

institute: University of Parma

data_processing:
Analysis was carried out as in Ferrari et al. 2012 (PMID:22499665) with some variation. Reads were mapped to the Saccaromyces Cerevisiae  (SacCer3) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects. The genome was tiled into 10-bp windows. Each read was extended by 150 bases (we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The input sample was used to estimate the expected counts in a window; the average value for all windows was assigned to windows with zero counts. Finally, we used the Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. We considered all windows with P-values less than 1.0E-8 to have significant peaks. P-value ≤ 1.0E-8 was chosen to give False Discovery Rate (FDR) less than 1%.
Genome_build: SacCer3
Supplementary_files_format_and_content: peaks bed files were generated with the descripted home made script.

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: For ChIP analysis overnight cell cultures pre-grown in YPD medium were diluted into fresh medium to a cell density of 4x106 cells/ml and grown at 30°C until they reached a density of 1.5-2x107 cells/ml before being collected for further analysis.

extract_protocol:
Formaldehyde-fixed cells were disrupted with glass beads and chromatin was extracted, fragmented by sonication and subjected to immunoglobulin G (IgG)-agarose chromatography to purify the DNA fragments associated to TAP-tagged proteins
Ovation® SP Ultralow Library Systems (NuGEN)

tag: sample type

value: TAP-tag


title: ChIP for tagged-Reb1


title: SD_Wk2 post-5/6Nx_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk2
Pool_11_GTGAAA

tag: Sex

value: 10 weeks of age at surgery

value: 0.4% Dyets chow


title: input for tagged-Abf1 strain


title: AdRspo1 #2 positive

description: Lgr5-eGFP-IRES-CreER mouse


title: SD_Wk2 post-5/6Nx_RNASeq_rep2

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk2
Pool_12_CTTGTA


title: ChIP for tagged-Abf1


title: AdLGR5 ECD#1 positive

description: Lgr5-eGFP-IRES-CreER mouse


title: AdFc#2 positive

description: Lgr5-eGFP-IRES-CreER mouse

value: control


title: AdFc#2 negative

description: Lgr5-eGFP-IRES-CreER mouse

source_name: Lgr5-eGFP(-) cells from proximal jejunum

value: GFP(-)


title: mTAL cells expressing GFP-tagged wild type uromodulin isoform replicate 2

description:
log2NormValues.xlsx
WT_2


title: AdFc #1 negative

description: Lgr5-eGFP-IRES-CreER mouse


title: SD_Wk4 post-5/6Nx_RNASeq_rep1

description:
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk4
Pool_3_CCGTCC


title: mTAL cells expressing GFP-tagged wild type uromodulin isoform replicate 1

description:
log2NormValues.xlsx
WT_1


title: mTAL cells expressing GFP-tagged C150S uromodulin isoform replicate 2

description:
log2NormValues.xlsx
C150S_2


title: VcFW Melanin pupa Red region, rep 2

city: ithaca

first: Linlin

last: Zhang

address: 215 TOWER RD

department: Ecology and Evolutionary Department

institute: Cornell University

data_processing:
PCR primers, adaptors and low-quality reads are removed
Trinity was used for assembly
The assembled sequences with putative isoforms identified by Trinity were filtered and only the longest isoform was kept. Cluster database at high identity with tolerance (CD-HIT) was used for further clustering and redundancy removal with minimum similarity cut-off of 95 %.
Filtered reads from each sample were mapped to the assembly using Bowtie.
Supplementary_files_format_and_content: FPKM of the 14 samples

organism: Vanessa cardui

source_name: Fore wings

growth_protocol: V. cardui first instar caterpillars were housed on a 16:8 light:dark at 28 °C.

extract_protocol:
RNA was extracted from each sample using Ambion Purelink RNA Mini Kit (Life Technologies).
Poly-A RNA was isolated with Oligo d(T)25 beads (New England Biolabs, Ipswich, MA) from 1 μg total RNA of each sample and fragmented to size around 350-450 bp. First and second strand cDNA synthesis, end repair, 3′dA tailing and adaptor ligation were performed using NEBNext Ultra RNA library Prep kit for Illumina (New England Biolabs). All samples were tagged with a unique Illumina adapter index. The adapter-ligated sample was size-selected to ~500 bp fragments by AMPure XP beads (Beckman Coulter, Inc.). After 15 PCR cycles, libraries were quantified, multiplexed and sequenced on a Illumina Hiseq 2500 lane as 150 bp paired-end Illumina reads.

treatment_protocol: Hindwings from five different stages were sampled and used in this study including last instar larvae, 72h after pupation, 5d after pupation (pre-pigment pupae), ommochrome development (red/organge ommochorome pigments started to be expressed) and melanin development (black melanin pigments began to show up). Red and Black regions of forewings are disected duiring ommochrome stage. Wings were rapidly dissected in PBS and stored into RNAlater in -80 °C (Life Technologies).

value: fore wings

tag: development stage

value: melanin stage pupa


title: VcFW Melanin pupa Black region, rep 1


title: VcFW Melanin pupa Black region, rep 2


title: VcHW Melanin pupa, rep 2

source_name: Hind wings

value: hind wings


title: VcFW Melanin pupa Red region, rep 1


title: AdLGR5 ECD#2 positive

description: Lgr5-eGFP-IRES-CreER mouse

value: Rspo LOF


title: VcHW Melanin pupa, rep 1


title: mTAL cells expressing GFP-tagged C150S uromodulin isoform replicate 1

description:
log2NormValues.xlsx
C150S_1

value: mTAL

value: Transduced with lentiviral vector encoding human C150S uromodulin


title: VcHW Ommo pupa, rep 2

value: ommochrome stage pupa


title: VcHW Ommo pupa, rep 1


title: WGBS from adult Bl/6 hypothalamus replicate 2

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
QC and adapter trimming (Trimmomatic v0.36) (HEADCROP:6 LEADING:30 TRAILING:30 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7 SLIDINGWINDOW:4:15 MINLEN:16)
Alignment (Bismark v0.15) (--bowtie2 -N 1 -X 1000)
Deduplication (Bismark v0.15)
Methylation calling (Bismark v0.15) (--no_overlap)
Genome_build: mm9
Supplementary_files_format_and_content: Output from bismark methylation extractor (chr,start,end,meth %, methylated, unmethylated)

source_name: bisulfite treated genomic DNA from adult hypothamus

extract_protocol:
Hypothalamus was quickly dissected in ice cold PBS and frozen in liquid nitrogen. Genomic DNA was isolated using Qiagen Blood and Tissue Kit. 0.5% unmethylated Lambda DNA was added as a spike in to calculate conversion rates. 100ng genomic DNA was then bisulfite treated with the EZ DNA Methylation Gold Kit from Zymo Research.
Libraries were constructed with EpiGnome/Truseq DNA Methylation kit from Illumina according to manufacturer's instructions.

value: Bl/6 wildtype

value: hypothalamus region from brain

value: mixed brain cells


title: WGBS from adult Bl/6 hypothalamus replicate 3


title: VcHW 5dAP pupa, rep 1

tag: developmental stage

value: 5d pupa


title: VcHW 5dAP pupa, rep 2


title: VcHW 72hAP pupa, rep 2

value: 72h pupa


title: WGBS from adult Bl/6 hypothalamus replicate 1


title: VcHW Last instar larvae, rep 2

value: last instar larvae


title: Neuron TAB sample 1

data_processing:
Alignment  (bismark)
Methylation calling (bismark)
Genome_build: mm9
Supplementary_files_format_and_content: Output from bismark methylation extractor (chr,start,end,meth %, methylated, unmethylated)

source_name: TAB treated DNA from adult Bl6 mouse FACS sorted NeuN+ neuronal nuclei

extract_protocol:
Total brain nuclei were isolated by sucrose ultracentrifugation and stained with an antibody against NeuN. The stained nuclei were FACS sorted into a NeuN positive fraction.Genomic DNA was isolated with the DNeasy kit from Qiagen.
After genomic DNA isolation, the sample was split in two halves. For TAB sequencing, genomic DNA was sheared, glycosylated and TET1 treated in the laboratory of Prof Chuan He (University of Chicago). Spike ins used for TAB-Sequencing: 1) 0.5% sonicated M.SsI treated lambda DNA was added before sonication (all C on position CpG are methylated); 2) 0.25% 300bp amplified from pUC19 vector was added after sonication ( all C are hydroxymethylated); 3) 0.25% 1.64kb fragment from pUC19 vector was added before sonication (all C are hydroxymethylated; note that this fragment represents a different region than the control in 2)) For regular bisulfite sequencing, the other half of genomic DNA was spiked with 0.5% unmethylated lambda DNA before sonication. After treatments, libraries were prepared with the TruSeq v2 kit from Illumina according to standard recommendations.  Ligation products were size selected (275-400bp), and bisulfite treated (Epitect Bisulfite Kit Qiagen). Fragments were enriched using Pfu Turbo Cx Hotstart Polymerase and Illumina PCR primer cocktail. 2 PCR reactions set up for each sample.  7 PCR cycles were used for enrichment. PCR was pooled and cleaned up with AmPure beads. Total sample volume 20 μl in Resuspension Buffer (Illumina).

value: brain

value: NeuN+ neuronal nuclei


title: Neuron TAB sample 2


title: AdFc #1 positive

description: Lgr5-eGFP-IRES-CreER mouse

value: GFP+

value: control


title: Neuron BS sample 2

source_name: bisulfite treated DNA from adult Bl6 mouse FACS sorted NeuN+ neuronal nuclei


title: VcHW Last instar larvae, rep 1


title: mel_rep7

status: Public on May 03 2017

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: single-cell transcriptomics

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12.  Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12.  Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j.  Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12.  Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12.  Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2.  The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: *txt: Tab-separated text files containing UMI counts per gene and per cell of each sample.
clusters*.txt files generated using Seurat.

source_name: Drop-seq of whole embryo

growth_protocol: Egg lays occurred in 2 hour intervals after 3x 1 hour pre-lays; embryos were aged for 6 hours (D. melanogaster) at room temperature.

extract_protocol: Methanol-fixation was adapted from Stöckius et al. 2009 (Nat. Methods). To avoid cell clumping, 8 volumes (800 µl) of methanol p. a. (pre-chilled to -20˚C) were added drop-wise, while gently mixing or vortexing the cell suspension.  Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1.

value: mixture stage 10 to 17 batch1

tag: fixation

value: 80% methanol/PBS

value: dissociated cells


title: bulk_mel2

description: bulk transcriptomics

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12.  Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12.  Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j.  Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12.  Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12.  Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2.  The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: gene counts
clusters*.txt files generated using Seurat.

source_name: mRNAseq of whole embryo

value: mixture stage 10 to 17 batch2

value: live, not fixed


title: mel_rep4

description: single-cell transcriptomics


title: mel_rep3

description: single-cell transcriptomics


title: Neuron BS sample 1


title: mel_rep6

description: single-cell transcriptomics


title: mel_rep1

description: single-cell transcriptomics


title: mel_rep2

description: single-cell transcriptomics


title: bulk_mel1

description: bulk transcriptomics


title: Methyl-IPS-Rod_M_Y-7602

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Basecalls performed using CASAVA
Whole genome bisulfite sequencing (WGBS) data were mapped to mm9 (MGSCv37) by BSMAP2.74 with the following parameters: -z 33 -f 5 -g 3 -r 0 -m 17 -x 600 –u.
raw methylation status was called by Bis-SNP (Version 0.82.2).
Based on bis-SNP results, beta-value of non-abolished and non-estabilished CG have been extracted and converted to bigwig for visualization.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig

source_name: retina

extract_protocol:
Genomic DNA was isolated from retinal tissues using the DNeasy Blood & Tissue Kit (QIAGEN #69504) according to the manufacturers protocol.
Typically, 2 µg of genomic DNA is used to make WGBS libraries.Whole genome bisulfite sequencing was conducted by the Hudson Alpha research institute for Biotechnology using the Cambridge Epigenetix TrumethylSeq kit (BS workflow) per manufacturer's instructions.

value: mature retinal-derived iPSCs 7602


title: Methyl-mESC-Eb5_E_Y-Eb5

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell


title: Methyl-IPS-Rod_I_Y-8601

value: immature retinal-derived iPSCs 8601


title: Methyl-IPS-Fibr_F_Y-fMG02

source_name: fibroblast-derived iPSCs fMG02

value: derived iPSCs fMG02


title: VcHW 72hAP pupa, rep 1

value: hind wings


title: Methyl-IPS-Fibr_F_N-MEF

source_name: mouse embryonic fibroblasts cell

value: mouse embryonic fibroblasts cell


title: Methyl-IPS-Fibr_F_Y-fMG03

source_name: fibroblast-derived iPSCs fMG03

value: derived iPSCs fMG03


title: S. acidocaldarius Co-IP control RNA

city: Marburg

first: Michael

last: Daume

state: Hessen

address: Karl-von-Frisch-Strasse 10

department: Prokaryotic Small RNA Biology

institute: Max Planck Institute for Terrestrial Microbiology

description: Sample 5

data_processing:
CLC Genomics Workbench 9.5.3
The raw data files were imported using the Illumina Import option (Illumina Pipeline 1.8 and removal of failed reads).
The raw data files were processed by quality score trimming (quality score trimming limit: 0.05; max. number of ambiguities: 2) and NEBNext 3' RNA adapter (AGACGTGTGCTCTTCCGATCT) trimming (strand: minus; action: remove adapter; mismatch cost: 3; gap cost: 5; cutoff internal end matches: 10 ; minimum end matches score: 5). The processed sequences were filtered by length (15 nt cutoff)
The trimmed sequences were mapped to the S. acidocaldarius reference genome (CP000077) using CLC default settings and saved as a read track file. The mapped reads (between 6 to 12 million reads per file) were extracted and sampled to 1.000.000 reads. These 1.000.000 reads were again mapped to the genome using CLC default settings.
Genome_build: S. acidocaldarius reference genome (CP000077)
Supplementary_files_format_and_content: The processed data files are in .wig (wiggle) format. They contain the mapping graphs of the three samples (each 1.000.000 mapped reads) which were created from the coverage plots of the generated read track files. Furthermore, the reference genome (Sulfolobus acidocaldarius DSM 639 (CP000077)) is included as .gkb (genbank) file, which is needed for the illustration of the mapping graph track.
instructions for .wig file importing: When working with CLC Genomics Workbench, import the .gkb file of S. acidocaldarius (genome file) via standard import. Rename the file to "Sulfolobus acidocaldarius DSM 639 (CP000077)" (remove understrikes). This step is critical for the illustration of the mapping graph. Convert the renamed file to a genome track (Toolbox -> Track tools -> Convert to Tracks -> Choose renamed file -> Create sequence track and save). Import the .wig file (via Import -> Tracks) and choose the converted genome track as reference track.

organism: Sulfolobus acidocaldarius

source_name: liquid culture

growth_protocol: Cells were grown in Brock medium to logarithmic phase.

extract_protocol:
Sample 4: Same purification like sample 2 (replicate). Sample 5: Same purification like sample 2, but using a control strain with the untagged l7aegene.
cDNA libraries were prepared according to the NEBNext Small RNA Library Prep Set for Illumina.

value: DSM 639

tag: phase

value: logarithmic phase


title: Methyl-Adult-Rod_M_N-P21

tag: strain

value: postnatal day 21


title: Methyl-Adult-Rod_M_N-P14

value: postnatal day 14


title: Methyl-Adult-Rod_M_N-P7

value: postnatal day 7


title: S. acidocaldarius L7Ae Co-IP small RNA replicate 2

description: Sample 4


title: Methyl-Adult-Rod_I_N-P3

value: postnatal day 3


title: Methyl-Adult-Rod_I_N-P0

value: postnatal day 0


title: Methyl-Adult-Rod_M_N-P10

value: postnatal day 10


title: Methyl-Adult-Rod_E_N-E14.5

value: embryonic day 14.5


title: RNA-IPS-Rod_M_Y-7602

data_processing:
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the mouse genome mm9 (MGSCv37) using in-house software StrongArm.
We required > 30% of exon have > 30x depth. And then classic FPKM have been calculated by cufflink package( version 2.1.1 along with default parameters and “--frag-bias-correct --multi-read-correct“) based on GENCODE annotation vM7.
For Differential Expression analysis between f-iPSC and r-iPSC, we counted reads by HTSEQ(version 0.6.1p1) and used Voom packge(R 3.23, edgeR 3.12.1, limma 3.26.9) for statical tests. CPM(counts per million) have been provided for iPSC RNA-seq
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tab-delimited text files include FPKM or CPM values for each Sample

extract_protocol:
RNA was extracted from freshly isolated retinas using RNeasy Plus Mini kit (Qiagen #74134). Technologies #Q33120)
Libraries were prepared from ~ 500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 2500 sequencers according to the manufacturer’s directions (Illumina.)


title: RNA-IPS-Fibr_F_Y-fG140.04

source_name: fibroblast-derived iPSCs fG140.04

value: fibroblast-derived iPSCs fG140.04


title: RNA-IPS-Fibr_F_Y-fMG03

value: fibroblast-derived derived iPSCs fMG03


title: RNA-IPS-Rod_M_Y-3302

value: mature retinal-derived iPSCs 3302