title: H3K27me3_gastrocnemius_09

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

data_processing:
Reads were aligned to mm10 using ‘bwa’
Unmapped reads, reads with a MAPQ smaller then 1, duplicate reads and those that mapped outside of chr 1-19 and Chr X were removed using ‘samtools
Peak calling was done with EPIC2 software using the following parameters: fragment size = 200; window size = 200; g =2 for H3K4me3 and H3K27ac, g=3 for H3K27me3, FDR < 0.05, e=100
Genome_build: mm10
Supplementary_files_format_and_content: Binarized file produced by bwa containing sequence alignment data.
Supplementary_files_format_and_content: Text file containing enriched regions coordinates

source_name: Gastrocnemius

growth_protocol: Mice were multi-housed and provided ad libitum access to a chow diet LabDiet 5001 (LabDiet, Saint Louis, MO) prior to the start of the study. At 6 months of age, mice were singly housed and placed on a modified AIN-93 diet. Food intake was set at 11.2 kcal/day, which was fed ~ 1 hr prior to lights out and water was provided ad lib

extract_protocol:
Extracted chromatin was immunoselected with anti-H3K4me3 (#39159, Lot 22119006, Active Motif, Carlsbad, CA, USA), anti-H3K27ac (ab4729, Lot. GR3231887-1; Abcam, Cambridge, UK) and H3K27me3 (07-449, Lot. 3091919; Millipore, Temecula, CA, USA) antibodies following the procedure already described without limited reversal of crosslining (LRC) step. The bound fractions were decrosslinked, and purified DNA was used for library preparation.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were sacrificed at the age of 13 months by exsanguination under isoflurane anesthesia, and brain cortexes and gastrocnemius muscle isolated and immediately snap frozen in liquid nitrogen.

value: PSAPP

value: 13 months

value: Gastrocnemius


title: H3K27me3_gastrocnemius_10

status: Public on Jan 05 2022

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: age

tag: tissue

tag: antibody


title: Input DNA, Frog eye, Unoperated animal, Replicate 1

city: Albany

first: Ben

middle: Gregory

last: Szaro

state: NY

address: 1400 Washington Avenue

department: Biological Sciences

country: USA

institute: University at Albany, SUNY

data_processing:
For histone ChIP-Seq and 5hmC DIP-Seq: Adapter sequences and barcodes were removed using Trimmomatic and FastX Tookit, and low-quality reads (quality score Q < 30) were filtered from the data using Trim Galore! (v0.3.7) with Cutadapt (v1.9). Read alignments were performed against the Xenopus laevis genome (v.9.1) using Bowtie2 (v2.2.9), with the --very-sensitive preset option. BAM alignment files were converted into the bigWig files using bam2bigwig.
Supplementary_files_format_and_content: All processed files are in the bigWig (bw) format. Bisulfite-seq files represent methylation in CpG context and are combined for the three biological replicates for each condition. ChIP-Seq and 5hmC DIP-seq files represent alignments for each read and are provided separately for each biological replicate.

organism: Xenopus laevis

source_name: 6 frog eyes from unoperated animals

growth_protocol: All animals used in this study were purchased from Xenopus Express, Inc (Brooksville, FL). Prior to surgery, they were acclimated to the lab for at least one week, under a 12L:12D photoperiod, in tanks of condition water at 22C, and fed every other day.

extract_protocol:
5hmC MeDIP-Seq: Eyes for optic nerve crush studies were rapidly dissected and then homogenized immediately, pooling six eyes for each biological replicate.Total DNA, along with RNA, was isolated using the RNA/DNA/Protein Purification kit from Norgen Biotek Corp. with DNase I treatment, following manufactuer's protocols. For histone ChIP-Seq: Eyes and hindbrain were frozen on dry ice immediately upon dissection. Dissected tissues were frozen immediately on dry ice and stored at  80°C for later processing. Tissues were thawed while homogenizing them in PBS containing protease inhibitor cocktail, in 2-ml Pyrex glass homogenizers. After low-speed centrifugation (1,300 rpm for 5 min at 4°C), pellets were resuspended and cross-linked in PBS with 1% formaldehyde for 10 min at room temperature. Cross-linking reactions were quenched with glycine. Samples were subsequently prepared for lysis and sonication in a Diagenode Standard Bioruptor (Chromatin Shearing and Optimization kit, Diagenode #C01020010). Sonication was performed at the high-power setting for 30 cycles of 30 seconds on and 30 seconds off. This was repeated until the sheared chromatin was 150-350 bp in size, as verified by gel electrophoresis. Immunoprecipitation was done using 5 μg of antibody and 50 μl of DiaMag protein A-coated magnetic beads.
For histone ChIP-seq: Samples for ChIP-seq were prepared using the Manual iDEAL ChIP-seq kit for histones (Diagenode #C1010051) according to the manufacturer’s protocols, and the following antibodies: H3K4me3 (Abcam ab8580; lot GR3201240-1), H3K27ac (Abcam ab4729; lot GR3205523-1), H3K27me3 (Abcam MsMAb ab6002; lot GR275911-8), H3K9me3 (Abcam RbPAb ab8898; lots GR3176466-4/GR250850-1). Samples were subsequently prepared for lysis and sonication in a Diagenode Standard Bioruptor (Chromatin Shearing and Optimization kit, Diagenode #C01020010). Sonication was performed at the high-power setting for 30 cycles of 30 seconds on and 30 seconds off. This was repeated until the sheared chromatin was 150-350 bp in size, as verified by gel electrophoresis. Immunoprecipitation was done using 5 μg of antibody and 50 μl of DiaMag protein A-coated magnetic beads. Barcoded DNA libraries were prepared from the immunoprecipitated DNA, as well as from equal amounts of pre-IP DNA from sheared chromatin, using the NEBNext Ultra II DNA Library Prep kit for Illumina sequencing. Sequencing (Illumina NextSeq500) was performed at the University at Albany Center for Functional Genomics core facility (75 bp, single end reads). 5hmC MeDIP: Genomic DNA (1 μg each) was sonicated for 14 cycles of 15 seconds on and 90 seconds off, using a Diagenode Standard Bioruptor to produce fragments of 200--600 bp in length, which was verified by gel electrophoresis. The sheared DNA was then subjected to 5hmC-IP using the kit’s 5hmC antibody and its non-specific IgG control antibody, overnight at 4°C, according to the manufacturer's instructions (hMeDIP Kit, Diagenode #C02010031, mouse monoclonal mAb). The immunoprecipitated DNA was washed and released from the antibody complex by proteinase-K digestion and resuspended in 100 μl of DNA-IP buffer (DIB) provided by the kit. Library preparation and sequencing was then performed as for histone ChIP-Seq.

treatment_protocol: Unilateral orbital optic nerve crushes (Zhao and Szaro 1994, doi: 10.1002/cne.903430112) and complete spinal cord transections (Gibbs and Szaro 2018, doi: 10.1101/pdb.prot101030) were performed on fully anesthetized animals (MS222).

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile frog

tag: surgery

value: unoperated

tag: Sex

value: not determined


title: Input DNA, Tadpole hindbrain, Unoperated, Replicate 2

source_name: 5 unoperated tadpoles, age-matched with 1 week, spinal cord transected tadpoles

value: stage 53 tadpole


title: Input DNA, Tadpole hindbrain, Unoperated, Replicate 1


title: Input DNA, Frog hindbrain, Spinal cord transected, Replicate 1

source_name: 5 frogs, 1 week after spinal cord transection

value: spinal cord transection


title: SAMPLE 114 [Genotype 114]

type: genomic

city: Brandon

first: James

middle: Raymond

last: Tucker

state: MB

address: 2701 Grand Valley Rd.

country: Canada

institute: Agriculture and Agri-Food Canada

hyb_protocol: not provided

scan_protocol: Illuina iScan instrument

data_processing: Illumina Genome Studio software was used for clustering

label: Cy3, Cy5

organism: Hordeum vulgare

source_name: leaf tissue

label_protocol: not provided

growth_protocol: Seeds of barley were surface sterilized with dilute bleach solution (6% per vol) then germinated on cotton balls.

extract_protocol: Qiagen, 96 well DNeasy protocol as per manufacturers instructions

treatment_protocol: leaves were cut and placed in liquid nitorgen then freeze dried.

value: leaf

tag: genotype

value: barley genotype 114


title: SAMPLE 115 [Genotype 115]

value: barley genotype 115


title: SAMPLE 111 [Genotype 111]

value: barley genotype 111


title: SAMPLE 112 [Genotype 112]

value: barley genotype 112


title: H10B6_3-AL-CL_13

city: Lausanne

first: Joanito

last: Liberti

address: Biophore

country: Switzerland

institute: University of Lausanne

library_source: transcriptomic

data_processing:
Trimmomatic was used to remove adapters and low-quality bases with the following parameters: LEADING: 10 (trim the leading nucleotides until quality > 10), TRAILING: 10 (trim the trailing nucleotides until quality > 10), SLIDINGWINDOW: 4:20 (trim the window of size four for reads with local quality below a score of 20), and MINLEN: 80 (discard reads shorter than 80 bases).
Reads were aligned with STAR v.2.5.4b to the honeybee genome (Apis mellifera assembly HAv3.1).
Mapped reads were converted into raw read counts with the htseq-count script (http://www.huber.embl.de/users/anders/HTSeq/doc/count.html).
Genome_build: Amel_HAv3.1
Supplementary_files_format_and_content: Separate .txt file for each sample contaning counts of reads mapped to individual genes

molecule: total RNA

organism: Apis mellifera

growth_protocol: We collected pupae from each of 10 hives and kept them in an incubator at 70% RH and 34.5 °C in the dark for two days. We transferred newly emerged adult bees in sterile cages built with a 100 mm petri dish and an inverted sterile plastic cup of 3 dl.

extract_protocol:
RNA extractions of brain regions were performed with the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer’s specifications, including a DNase treatment (Qiagen) to remove genomic DNA.
RNA-sequencing libraries were prepared with the KAPA stranded mRNA kit (Roche) following the manufacturer’s protocol, except that we appended TruSeq unique dual indexes (UDIs, Illumina) instead of the adapters provided by the kit to better control for index hopping during sequencing.

treatment_protocol: Four cages from each of the ten hives were randomly assigned to one of four treatments. Bees were either (i) kept microbiota-depleted (MD) or colonized with (ii) the gut homogenate (CL) inoculum (iii) the community of 13 strains (CL_13) inoculum, or (iv) the two strains of Bifidobacterium asteroides (CL_Bifi) inoculum. Colonizations were performed three days after pupae extraction.

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

tag: treatment

value: Colonized with a community of 13 different gut microbiota strains (CL_13)

tag: hive


title: H3K27me3_gastrocnemius_05


title: SAMPLE 116 [Genotype 116]

value: barley genotype 116


title: H3K27me3_gastrocnemius_08

value: PSAPP


title: SAMPLE 117 [Genotype 117]

value: barley genotype 117


title: H10B6_3-MB-CL_13

value: mushroom bodies (MB) region of the brain


title: H3K27me3_gastrocnemius_07

value: 13 months

value: Gastrocnemius


title: H10B6_3-OL-CL_13

value: optic lobes (OL) region of the brain


title: H10B5_5-OL-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: H10B5_5-MB-CL_Bifi


title: SAMPLE 110 [Genotype 110]

value: barley genotype 110


title: H10B5_5-AL-CL_Bifi


title: Input DNA, Tadpole hindbrain, Spinal cord transected, Replicate 2

source_name: 5 tadpoles, 1 week after spinal cord transection

value: albino, Xenopus Express

value: stage 53 tadpole

value: spinal cord transection

value: not determined


title: Input DNA, Tadpole hindbrain, Spinal cord transected, Replicate 1


title: H3K27me3_gastrocnemius_04


title: H3K27me3_gastrocnemius_06


title: H3K27me3_gastrocnemius_03


title: SAMPLE 113 [Genotype 113]

value: leaf

value: barley genotype 113


title: H3K27me3 IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 2

source_name: 6 unoperated frog eyes, 11 days after contralateral orbital optic nerve crush

value: 1-3 mos. postmetamorphic juvenile frog

value: optic nerve crush, unoperated eye


title: H10B2_4-AL-MD

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Microbiota-depleted (MD)


title: SAMPLE 107 [Genotype 107]

value: barley genotype 107


title: H3K27me3 IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 1


title: SAMPLE 106 [Genotype 106]

value: barley genotype 106


title: H3K27me3 IP, Frog eye, Optic nerve crush, Operated eye, Replicate 2

source_name: 6 operated frog eyes, 11 days after orbital optic nerve crush

value: optic nerve crush, operated eye


title: SAMPLE 108 [Genotype 108]

value: barley genotype 108


title: H10B2_4-MB-MD

value: mushroom bodies (MB) region of the brain


title: SAMPLE 105 [Genotype 105]

value: barley genotype 105


title: H3K27me3_gastrocnemius_01

value: PSAPP

value: 13 months

value: Gastrocnemius


title: H10B2_4-OL-MD

value: optic lobes (OL) region of the brain


title: H3K27me3 IP, Frog eye, Optic nerve crush, Operated eye, Replicate 1

value: albino, Xenopus Express

value: not determined


title: H3K27me3 IP, Frog eye, Unoperated animal, Replicate 2

value: unoperated


title: H3K27ac_gastrocnemius_10


title: H3K27me3_gastrocnemius_02


title: H10B1_6-AL-CL

value: Colonized with a gut homogenate (CL)


title: H3K27me3 IP, Frog eye, Unoperated animal, Replicate 1

value: 1-3 mos. postmetamorphic juvenile frog


title: H3K27ac_gastrocnemius_09


title: H3K27ac_gastrocnemius_08


title: SAMPLE 104 [Genotype 104]

value: leaf

value: barley genotype 104


title: SAMPLE 103 [Genotype 103]

value: barley genotype 103


title: H10B1_6-OL-CL


title: H10B1_6-MB-CL


title: H3K27ac_gastrocnemius_05


title: H3K27ac_gastrocnemius_07


title: H3K27me3 IP, Frog hindbrain, Unoperated, Replicate 1

source_name: 5 unoperated frogs


title: Input DNA, Frog eye, Unoperated animal, Replicate 2


title: H3K27ac_gastrocnemius_06


title: H3K27me3 IP, Frog hindbrain, Spinal cord transected, Replicate 2

value: spinal cord transection


title: H3K27me3 IP, Frog hindbrain, Spinal cord transected, Replicate 1


title: H9B4_7-MB-CL_Bifi


title: SAMPLE 102 [Genotype 102]

value: barley genotype 102


title: SAMPLE 101 [Genotype 101]

value: barley genotype 101


title: H3K27me3 IP, Frog hindbrain, Unoperated, Replicate 2


title: H3K27ac_gastrocnemius_04


title: SAMPLE 100 [Genotype 100]

value: barley genotype 100


title: H3K27ac_gastrocnemius_03


title: H9B4_7-AL-CL_Bifi

value: antennal lobes and subaesophageal ganglion (AL) region of the brain


title: SAMPLE 98 [Genotype 98]

value: barley genotype 98


title: H9B3_5-AL-CL


title: H3K27me3 IP, Tadpole hindbrain, Unoperated, Replicate 1

value: stage 53 tadpole


title: H3K27me3 IP, Tadpole hindbrain, Spinal cord transected, Replicate 2


title: H3K27me3 IP, Tadpole hindbrain, Unoperated, Replicate 2


title: H9B3_5-MB-CL

value: mushroom bodies (MB) region of the brain


title: H3K27ac_gastrocnemius_02

value: PSAPP

value: 13 months

value: Gastrocnemius


title: H3K27ac_gastrocnemius_01


title: H9B3_5-OL-CL

value: optic lobes (OL) region of the brain


title: H3K27me3 IP, Tadpole hindbrain, Spinal cord transected, Replicate 1

value: albino, Xenopus Express

value: not determined


title: H9B1_3-AL-CL_13

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: SAMPLE 97 [Genotype 97]

value: leaf

value: barley genotype 97


title: SAMPLE 96 [Genotype 96]

value: barley genotype 96


title: H3K4me3_gastrocnemius_10


title: H3K27ac IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 2

value: 1-3 mos. postmetamorphic juvenile frog

value: optic nerve crush, unoperated eye


title: SAMPLE 99 [Genotype 99]

value: barley genotype 99


title: H9B1_3-MB-CL_13


title: H3K4me3_gastrocnemius_09


title: SAMPLE 94 [Genotype 94]

value: barley genotype 94


title: SAMPLE 95 [Genotype 95]

value: barley genotype 95


title: H3K4me3_gastrocnemius_08


title: H8B3_3-AL-CL_13

value: antennal lobes and subaesophageal ganglion (AL) region of the brain


title: H3K4me3_gastrocnemius_07


title: H3K27ac IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 1


title: H3K27ac IP, Frog eye, Optic nerve crush, Operated eye, Replicate 1

value: optic nerve crush, operated eye


title: SAMPLE 93 [Genotype 93]

value: barley genotype 93


title: H8B3_3-MB-CL_13

value: mushroom bodies (MB) region of the brain


title: H9B1_3-OL-CL_13


title: H3K27ac IP, Frog eye, Optic nerve crush, Operated eye, Replicate 2


title: H3K27ac IP, Frog eye, Unoperated animal, Replicate 2

value: unoperated


title: SAMPLE 109 [Genotype 109]

value: barley genotype 109


title: H3K4me3_gastrocnemius_06

value: PSAPP

value: 13 months

value: Gastrocnemius


title: SAMPLE 90 [Genotype 90]

value: leaf

value: barley genotype 90


title: H8B3_3-OL-CL_13

value: optic lobes (OL) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: SAMPLE 92 [Genotype 92]

value: barley genotype 92


title: H3K4me3_gastrocnemius_05


title: SAMPLE 91 [Genotype 91]

value: barley genotype 91


title: H3K27ac IP, Frog eye, Unoperated animal, Replicate 1

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile frog

value: not determined


title: H3K4me3_gastrocnemius_04


title: H8B2_3-MB-CL

value: Colonized with a gut homogenate (CL)


title: H3K27ac IP, Frog hindbrain, Spinal cord transected, Replicate 2

value: spinal cord transection


title: H3K4me3_gastrocnemius_02


title: H8B2_3-OL-CL


title: H3K27ac IP, Frog hindbrain, Unoperated, Replicate 1


title: H3K27ac IP, Frog hindbrain, Unoperated, Replicate 2


title: H8B1_3-AL-CL_Bifi

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: H3K4me3_gastrocnemius_01


title: SAMPLE 88 [Genotype 88]

value: barley genotype 88


title: H8B1_3-MB-CL_Bifi

value: mushroom bodies (MB) region of the brain


title: SAMPLE 87 [Genotype 87]

value: barley genotype 87


title: H3K27ac IP, Frog hindbrain, Spinal cord transected, Replicate 1


title: H3K4me3_gastrocnemius_03

value: PSAPP

value: 13 months

value: Gastrocnemius


title: H9B4_7-OL-CL_Bifi

value: optic lobes (OL) region of the brain


title: H3K27me3_cortex_09

source_name: Brain cortex

value: Brain cortex


title: SAMPLE 86 [Genotype 86]

value: leaf

value: barley genotype 86


title: SAMPLE 89 [Genotype 89]

value: barley genotype 89


title: H8B2_3-AL-CL


title: SAMPLE 84 [Genotype 84]

value: barley genotype 84


title: SAMPLE 83 [Genotype 83]

value: barley genotype 83


title: H3K27ac IP, Tadpole hindbrain, Unoperated, Replicate 1

value: albino, Xenopus Express

value: stage 53 tadpole

value: unoperated

value: not determined


title: SAMPLE 81 [Genotype 81]

value: barley genotype 81


title: H3K27me3_cortex_08


title: H8B5_3-MB-MD

value: mushroom bodies (MB) region of the brain

value: Microbiota-depleted (MD)


title: H8B5_3-AL-MD

value: antennal lobes and subaesophageal ganglion (AL) region of the brain


title: SAMPLE 85 [Genotype 85]

value: barley genotype 85


title: H3K27ac IP, Tadpole hindbrain, Spinal cord transected, Replicate 2

value: spinal cord transection


title: H3K27me3_cortex_07

value: PSAPP

value: 13 months


title: H3K27me3_cortex_06

value: Brain cortex


title: H8B5_3-OL-MD

value: optic lobes (OL) region of the brain


title: H7B4_9-MB-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: SAMPLE 80 [Genotype 80]

value: leaf

value: barley genotype 80


title: H3K27me3_cortex_05


title: H3K9me3 IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 2

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile frog

value: optic nerve crush, unoperated eye


title: H3k27me3_cortex_02


title: SAMPLE 78 [Genotype 78]

value: barley genotype 78


title: H7B4_9-AL-CL_Bifi


title: H3K27me3_cortex_04


title: H3K9me3 IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 1

value: not determined


title: SAMPLE 79 [Genotype 79]

value: barley genotype 79


title: H3K27me3_cortex_01


title: H3K27me3_cortex_03


title: SAMPLE 76 [Genotype 76]

value: barley genotype 76


title: H7B3_4-AL-MD

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Microbiota-depleted (MD)


title: H7B3_4-OL-MD


title: H7B2_3-AL-CL

value: Colonized with a gut homogenate (CL)


title: H3K9me3 IP, Frog eye, Optic nerve crush, Operated eye, Replicate 1

value: optic nerve crush, operated eye


title: SAMPLE 77 [Genotype 77]

value: barley genotype 77


title: H3K27ac_cortex_07

value: PSAPP

value: 13 months

value: Brain cortex


title: H7B3_4-MB-MD

value: mushroom bodies (MB) region of the brain


title: H3K9me3 IP, Frog eye, Optic nerve crush, Operated eye, Replicate 2


title: SAMPLE 75 [Genotype 75]

value: leaf

value: barley genotype 75


title: H3K27ac_cortex_06


title: SAMPLE 73 [Genotype 73]

value: barley genotype 73


title: H3K9me3 IP, Frog hindbrain, Unoperated, Replicate 2

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile frog

value: unoperated


title: H3K27ac_cortex_09


title: H3K9me3 IP, Frog eye, Unoperated animal, Replicate 2

value: not determined


title: H8B1_3-OL-CL_Bifi

value: optic lobes (OL) region of the brain

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: H3K9me3 IP, Frog eye, Unoperated animal, Replicate 1


title: H3K27ac_cortex_08


title: H3K27ac_cortex_05


title: H3K9me3 IP, Frog hindbrain, Spinal cord transected, Replicate 1

value: spinal cord transection


title: SAMPLE 71 [Genotype 71]

value: barley genotype 71


title: SAMPLE 74 [Genotype 74]

value: barley genotype 74


title: H3K9me3 IP, Frog hindbrain, Unoperated, Replicate 1


title: SAMPLE 70 [Genotype 70]

value: barley genotype 70


title: H7B2_3-OL-CL

value: Colonized with a gut homogenate (CL)


title: H7B2_3-MB-CL


title: H3K27ac_cortex_04

value: PSAPP

value: 13 months


title: H3K27ac IP, Tadpole hindbrain, Unoperated, Replicate 2

value: stage 53 tadpole


title: H7B1_3-MB-CL_13

value: mushroom bodies (MB) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: H3K9me3 IP, Tadpole hindbrain, Unoperated, Replicate 2


title: H7B1_3-AL-CL_13

value: antennal lobes and subaesophageal ganglion (AL) region of the brain


title: H7B1_3-OL-CL_13


title: H3K9me3 IP, Frog hindbrain, Spinal cord transected, Replicate 2

value: albino, Xenopus Express


title: SAMPLE 72 [Genotype 72]

value: leaf

value: barley genotype 72


title: SAMPLE 82 [Genotype 82]

value: barley genotype 82


title: H3K27ac_cortex_03

value: Brain cortex


title: H6B6_2-AL-MD

value: Microbiota-depleted (MD)


title: H3K9me3 IP, Tadpole hindbrain, Unoperated, Replicate 1

value: unoperated

value: not determined


title: H6B6_2-MB-MD


title: H3K9me3 IP, Tadpole hindbrain, Spinal cord transected, Replicate 2

value: spinal cord transection


title: H6B6_2-OL-MD

value: optic lobes (OL) region of the brain


title: H3K9me3 IP, Tadpole hindbrain, Spinal cord transected, Replicate 1


title: H3K27ac_cortex_01


title: H3K4me3_cortex_09


title: H6B5_4-AL-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: H3K4me3_cortex_08

value: PSAPP


title: SAMPLE 68 [Genotype 68]

value: barley genotype 68


title: SAMPLE 69 [Genotype 69]

value: barley genotype 69


title: H3K4me3 IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 1

value: 1-3 mos. postmetamorphic juvenile frog

value: optic nerve crush, unoperated eye


title: SAMPLE 67 [Genotype 67]

value: barley genotype 67


title: H3K4me3 IP, Frog eye, Optic nerve crush, Unoperated eye, Replicate 2

value: albino, Xenopus Express


title: H3K4me3_cortex_07

value: 13 months


title: H6B5_4-OL-CL_Bifi


title: H6B5_4-MB-CL_Bifi

value: mushroom bodies (MB) region of the brain


title: H3K4me3_cortex_06


title: H3K4me3 IP, Frog eye, Optic nerve crush, Operated eye, Replicate 2

value: optic nerve crush, operated eye


title: H6B4_3-AL-CL

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with a gut homogenate (CL)


title: H3K27ac IP, Tadpole hindbrain, Spinal cord transected, Replicate 1

value: stage 53 tadpole


title: SAMPLE 65 [Genotype 65]

value: leaf

value: barley genotype 65


title: SAMPLE 63 [Genotype 63]

value: barley genotype 63


title: H6B4_3-OL-CL

value: optic lobes (OL) region of the brain


title: SAMPLE 61 [Genotype 61]

value: barley genotype 61


title: H3K4me3 IP, Frog eye, Unoperated animal, Replicate 2

value: unoperated

value: not determined


title: H3K4me3_cortex_05

value: PSAPP

value: Brain cortex


title: SAMPLE 62 [Genotype 62]

value: barley genotype 62


title: H6B4_3-MB-CL


title: SAMPLE 64 [Genotype 64]

value: barley genotype 64


title: H3K4me3 IP, Frog eye, Optic nerve crush, Operated eye, Replicate 1

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile frog


title: H6B2_5-OL-CL_13

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: H3K4me3 IP, Frog hindbrain, Spinal cord transected, Replicate 2

value: spinal cord transection


title: SAMPLE 59 [Genotype 59]

value: barley genotype 59


title: SAMPLE 60 [Genotype 60]

value: barley genotype 60


title: H3K4me3 IP, Frog hindbrain, Unoperated, Replicate 2


title: H3K4me3 IP, Frog hindbrain, Spinal cord transected, Replicate 1


title: H3K4me3_cortex_02

value: 13 months


title: H5B5_6-AL-MD

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Microbiota-depleted (MD)


title: H3K4me3_cortex_03


title: H5B5_6-MB-MD

value: mushroom bodies (MB) region of the brain


title: H3K4me3 IP, Frog hindbrain, Unoperated, Replicate 1


title: H3K4me3 IP, Tadpole hindbrain, Unoperated, Replicate 2

value: stage 53 tadpole


title: H3K4me3 IP, Tadpole hindbrain, Unoperated, Replicate 1

value: unoperated


title: H3K4me3_cortex_01


title: H6B2_5-MB-CL_13


title: H5B5_6-OL-MD

value: optic lobes (OL) region of the brain


title: MIR29cb2-KO rep1

city: Shanghai

first: Yun

last: Liao

address: Xianxia

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone

extract_protocol:
Bone was collected flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone

tag: background strain

value: female


title: MIR29cb2-KO rep2


title: MIR29cb2-KO rep3


title: H3K27ac_cortex_02

value: PSAPP

value: Brain cortex


title: H3K4me3 IP, Tadpole hindbrain, Spinal cord transected, Replicate 2

value: albino, Xenopus Express

value: not determined


title: H5B4_4-AL-CL

value: Colonized with a gut homogenate (CL)


title: H3K4me3 IP, Tadpole hindbrain, Spinal cord transected, Replicate 1

value: spinal cord transection


title: H5B4_4-MB-CL


title: Abisporus csRNA-input rep2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: abisporus-tsr.txt

data_processing:
For csRNA-seq, sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the appropriate genome using STAR with default parameters[PMID: 23104886]. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded. Transcription Start Regions (TSRs), representing loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findcsRNATSS.pl tool, which uses short input RNA-seq, traditional total RNA-seq, and annotated gene locations to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (Duttke et al. for more details[PMID:31649059]). Replicate experiments were first pooled to form meta-experiments for each condition prior to identifying TSRs. Annotation information, including gene assignments, promoter distal, stable transcript, and bidirectional annotations are provided by findcsRNATSS.pl.
For RNA-seq, reads from accession GSE171286 were downloaded and aligned to the C. immitis genome (ASM14933v2)  using STAR with default parameters. Reference-guided transcranscript assembly was performed using StringTie2 (Kovaka et al. 2019) with the Ensembl gene annotation (GTF file) and additional parameters “-m 100 --rf”. Assembled transcripts were compared to the existing C. immitis annotation using cuffcompare.
Genome_build: C. immitis (ASM14933v2), S. cerevisiae (R64-1-1/sacCer3), S. pombe (ASM294v2), A. bisporus (gca_000300555/Agabi_varbur_1)
Supplementary_files_format_and_content: Tab-delimited Text file describing TSR positions and annotations, GTF formated transcript definition files

organism: Agaricus bisporus

source_name: Agaricus bisporus fruiting body

growth_protocol: C. immitis R.S. strain was grown as mycelia or spherules as previously described (Viriyakosol et al. 2013). To grow mycelia, 2×10^6 arthroconidia/ml were incubated in 250 ml flat-bottom Erlenmeyer flasks (Corning) in 50 ml GYE media. Flasks were cultured in a 30°C incubator without shaking for 5 days. To grow spherules, arthroconidia were washed 2 times in modified Converse media (Converse 1956). The spores were inoculated at 4×106 arthroconidia/ml into a 250 ml baffled Erlenmeyer flask containing 50 ml of modified Converse media. Flasks were set up and grown on a shaker at 160 rpm, in 14% CO2 at 42°C. Four flasks were harvested 2 days after inoculation and the remaining four flasks after 8 days. Fresh Converse media was not added.  The spherules did not rupture and release endospores within that time in this culture system. Saccharomyces cerevisiae (strain RYH2863) was grown as described previously (Neal et al. 2018). Schizosaccharomyces pombe (strain TH972) was generously provided by Tony Hunter (SALK Institute for Biological Sciences) and grown in Yeast Extract with Supplements (YES)(Leverson et al. 2002). White and brown ecotypes of Agaricus bisporus, better known as ‘Champignon’ or ‘crimini mushroom’ were kindly provided by Monterey Mushroom farms.

extract_protocol:
Trizol extraction after tissue homogenisation
For RNA-Seq, strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Yeast Ribo-Zero rRNA Removal Kit (Illumina) and then using the TruSeq Stranded total RNA-Seq kit (Illumina) according to manufacturer's instructions. Then 100 bases were sequenced from both ends using a HiSeq 4000 according to the manufacturer's instructions (Illumina).    csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen) and RNAs were 5’dephosporylation by quickCIP (NEB). Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500.
csRNA-seq, sRNA-seq, total RNA-seq

treatment_protocol: untreated

value: white

tag: tagtreatment

value: untreated

tag: method

value: sRNA-seq (csRNA-seq input)


title: WT rep3

value: WT


title: WT rep1


title: H3K4me3 IP, Frog eye, Unoperated animal, Replicate 1

value: 1-3 mos. postmetamorphic juvenile frog


title: SAMPLE 54 [Genotype 54]

value: leaf

value: barley genotype 54


title: SAMPLE 55 [Genotype 55]

value: barley genotype 55


title: Abisporus csRNA-input rep1

description: abisporus-tsr.txt


title: SAMPLE 57 [Genotype 57]

value: barley genotype 57


title: H3K4me3_cortex_04

value: 13 months


title: Abisporus csRNA-seq rep3

description: abisporus-tsr.txt

value: csRNA-seq


title: H5B2_3-MB-CL_Bifi

value: mushroom bodies (MB) region of the brain

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: GPIDay25

city: San Diego

first: David

last: Muench

state: CA

address: 10290 Campus Point Drive

institute: Eli Lilly and Company

data_processing:
10X Genomics Cell Ranger v3.1
Gene-cell UMI matrix was generated for downstream analyses. Low-quality cells were removed based on their unique feature counts and mitochondrial gene content. Data was normalized and log transformed using the default setting of Seurat (version 3.1.4).
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, there is one mtx file with filtered gene expressing UMI counts for each sample, one tsv file containing gene names, and one tsv file with cell barcodes.

molecule: polyA RNA

source_name: Hind paw synovium

growth_protocol: Immediately following sacrifice, murine synovial cells were isolated, FACS sorted for viable single cells, and loaded onto a 10X Genomics Chromium.

extract_protocol:
Freshly sorted synovial cells were combined with reagents from the 3' GEM Kit v3.1 (10X Genomics) and each sample was loaded on an individual lane of a 10X Genomics Cromium for targeted capture of 10,000 cells each. Following single cell partioning, cDNA was generated and further processed according to the manufacturer's recommended protocol.
Following the amplification and size selection of cDNA according to the manufacturer's recommended protocol (10X Genomics 3' GEM Kit v3.1 and 3' GEM Library Kit v3.1), each sample was indexed using the i7 Multiplex Kit (10X Genomics) and then pooled at an equimolar ratio for sequencing.

treatment_protocol: For GPI-induced arthritis experiments, mice were randomly allocated to groups for the subsequent induction of arthritis as previously described (Schubert et al., 2004) and the investigators were blinded to this allocation during scoring. Briefly, 7 mg of human recombinant GPI protein was diluted with ice cold DPBS and 1.75 mL Complete Freund?s Adjuvant (Sigma) to a final volume of 3.5 mL (2 mg/mL) and emulsified using a Bead Ruptor Elite (Omni International). Under isoflurane anesthesia, DBA/1 mice hind flanks were shaved and injected sub-cutaneously with 100 uL of emulsion on each side of the base of the tail (total 400 ug GPI per mouse, 'day 0').

value: Synovium

tag: disease state

value: Arthritis, Day 25


title: GPIDay14

value: Arthritis, Day 14


title: GPIDay6

value: Arthritis, Day 6


title: Abisporus csRNA-seq rep2

description: abisporus-tsr.txt

value: white


title: H5B2_3-AL-CL_Bifi

value: antennal lobes and subaesophageal ganglion (AL) region of the brain


title: SAMPLE 53 [Genotype 53]

value: barley genotype 53


title: Abisporus csRNA-seq rep1

description: abisporus-tsr.txt

value: brown

value: untreated


title: H5B1_3-AL-CL_13

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: WT rep2

value: bone

value: WT

value: female


title: Naive1

value: Steady-state


title: H5B4_4-OL-CL

value: optic lobes (OL) region of the brain

value: Colonized with a gut homogenate (CL)


title: SAMPLE 49 [Genotype 49]

value: leaf

value: barley genotype 49


title: SAMPLE 66 [Genotype 66]

value: barley genotype 66


title: H6B2_5-AL-CL_13


title: SAMPLE 50 [Genotype 50]

value: barley genotype 50


title: H5B1_3-MB-CL_13

value: mushroom bodies (MB) region of the brain


title: H5B2_3-OL-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: SAMPLE 51 [Genotype 51]

value: barley genotype 51


title: Naive2

value: Synovium


title: SAMPLE 48 [Genotype 48]

value: barley genotype 48


title: Day 7 post AMI rep 4

first: Yaozu

last: Xiang

address: 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
Illumina Casava v1.8 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.4.0j with parameters --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM --runThreadN 10
Transcripts per million (TPM) were evaluated by a statistical method RSEM (RNA-Seq by Expectation Maximization) using a generative model of RNA-seq reads and the EM algorithm, taking read mapping uncertainty into account and achieving the most accurate abundance estimates
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart

extract_protocol:
Total RNA was isolated from the heart of mouse for analysis using the miRNeasy Mini Kit (1038703, QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were anesthetized by spontaneous inhalation and maintained under general anesthesia with 1–2% isoflurane. Animals were mechanically ventilated using a rodent ventilator (Harvard Apparatus) connected to an endotracheal tube. The heart was exposed by a left side limited thoracotomy and the LAD was ligated with a 6-0 polyester suture 1 mm from the apex of the normally positioned left auricle and samples were analyzed 0,1,7 days after injury.

value: Heart

value: Day 7 post AMI


title: SAMPLE 47 [Genotype 47]

value: barley genotype 47


title: SAMPLE 46 [Genotype 46]

value: barley genotype 46


title: SAMPLE 44 [Genotype 44]

value: barley genotype 44


title: Day 7 post AMI rep 3


title: H4B6_2-AL-CL

value: antennal lobes and subaesophageal ganglion (AL) region of the brain


title: SAMPLE 45 [Genotype 45]

value: barley genotype 45


title: Ptch1cKO-4

city: Boston

first: Zach

last: Herbert

state: MA

address: 450 Brookline Ave

department: Molecular Biology Core Facilities

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to mm10 reference genome using STAR (v2.5)
Raw gene counts calculated by STAR
Genome_build: mm10

source_name: tdTomato+ astrocytes from P23-P25 cortex

extract_protocol:
Somatosensory cortex from postnatal brains were dissected out and astrocytes were sorted out based on tdTomato fluorescence, followed by RNA extraction using Qiagen kits
cDNA was generated using NoGEN Ultralow System v2 and exome capture performed using Illumina TruSeq RNA exome capture reagents
RNA Exome Sequencing

treatment_protocol: 10-15 μL of 20 mg/ml tamoxifen was injected intraperitoneally for three consecutive days (P12-P14) in order to induce effective cre recombination.

tag: mouse line

value: Glast-CreERT2; Ptch1fl/fl; Ai14

value: Somatosensory cortex

tag: developmental stage

value: P23-P25 (P12-P14 tamoxifen injection)


title: Ptch1cKO-3


title: Day 7 post AMI rep 2


title: Ptch1cKO-1


title: H5B1_3-OL-CL_13

value: optic lobes (OL) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: H4B6_2-MB-CL

value: mushroom bodies (MB) region of the brain

value: Colonized with a gut homogenate (CL)


title: Day 7 post AMI rep 1


title: Ptch1cKO-2


title: SAMPLE 43 [Genotype 43]

value: leaf

value: barley genotype 43


title: WT-4

value: Glast-CreERT2; Ai14


title: SAMPLE 56 [Genotype 56]

value: barley genotype 56


title: Day 1 post AMI rep 4

value: Heart

value: Day 1 post AMI


title: H4B6_2-OL-CL


title: WT-3


title: Day 1 post AMI rep 3


title: WT-2


title: H4B5_2-AL-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: Day 1 post AMI rep 2


title: WT-1


title: Day 1 post AMI rep 1


title: SAMPLE 52 [Genotype 52]

value: barley genotype 52


title: SAMPLE 40 [Genotype 40]

value: barley genotype 40


title: SAMPLE 41 [Genotype 41]

value: barley genotype 41


title: SAMPLE 42 [Genotype 42]

value: barley genotype 42


title: RNAseq_shCtrl_Rep4

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

institute: University of Turin

data_processing:
After quality controls with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), raw reads were aligned to the GRCm38 mouse genome reference (mm10) using HiSat2 v2.2.0 with options: -N 1 -L 20 -i S,1,0.5 -D 25 -R 5 --pen-noncansplice 20 --mp 1,0 --sp 3,0. Pre-built indexes based on the Ensembl transcript annotation (release 84) for guided alignment to transcriptome were retrieved from the HiSat2 web site (https://cloud.biohpc.swmed.edu/index.php/s/grcm38_tran/download). Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using GENCODE comprehensive gene annotation (release M23 – GRCm38.p6 https://www.gencodegenes.org/mouse/release_M23.html). Multi-mapped reads were excluded from quantification. Gene expression counts were next analysed using the edgeR package.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of raw read counts per gene/samples.

source_name: Mouse Embryonic Stem Cells

growth_protocol: E14 mouse ESCs were grown on 0.1% gelatin-coated plates and maintained in high-glucose DMEM (Invitrogen) supplemented with 18% EmbryoMax® FBS (Millipore), 0.1 mM non-essential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), 0.1 mM 2-mercaptoethanol, 1000 U/mL Leukemia Inhibitory Factor (LIF; Millipore), 25 U/mL penicillin, and 25 μg/mL streptomycin. Cells were routinely tested to be free of mycoplasma.

extract_protocol:
RNA samples were extracted directly from cultured cells using Trizol reagent (Invitrogen) followed by isopropanol precipitation, and sample quality control was performed with Agilent Bioanalyzer 2100. All of the samples had an RNA integrity number ranging from 9.9 to 10.
For RNA-seq library preparation, 1 μg of total RNA was depleted of ribosomal RNA using the RiboMinus Eukaryote System v2 kit (Invitrogen), following manufacturer instructions. Ribo-RNA was resuspended in 17 μL of EFP buffer (Illumina), heated to 94 °C for 8 min, and used as input for the first-strand synthesis, using the TruSeq RNA Sample Prep kit, following manufacturer instructions. Poly(A) RNA-seq library was performed by using the TruSeq RNA Sample Prep kit, following the manufacturer’s instructions.

treatment_protocol: Transient transfection was performed using Lipofectamine 2000 Transfection Reagent (Invitrogen) for mouse ESCs in accordance to the recommendations of the manufacturer. For Smad7 knockdown, cells were transfected twice with 5 μg of the specific shRNA construct, and maintained in growth medium for 48 hours.

tag: cell type

value: ESC

tag: shRNA

value: shCtrl


title: Sham rep 4

tag: strain

value: Sham


title: Sham rep 3


title: H4B5_2-OL-CL_Bifi

value: optic lobes (OL) region of the brain


title: H4B4_7-MB-MD

value: mushroom bodies (MB) region of the brain

value: Microbiota-depleted (MD)


title: Sham rep 2


title: RNAseq_shCtrl_Rep1


title: RNAseq_shCtrl_Rep3


title: H4B4_7-OL-MD


title: Sham rep 1


title: RNAseq_shCtrl_Rep2


title: H4B3_4-AL-CL_13

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: H4B4_7-AL-MD


title: H4B5_2-MB-CL_Bifi


title: RNAseq_sh2-Smad7_Rep4


title: SAMPLE 38 [Genotype 38]

value: leaf

value: barley genotype 38


title: SAMPLE 37 [Genotype 37]

value: barley genotype 37


title: SAMPLE 39 [Genotype 39]

value: barley genotype 39


title: H4B3_4-MB-CL_13


title: SAMPLE 35 [Genotype 35]

value: barley genotype 35


title: SAMPLE 36 [Genotype 36]

value: barley genotype 36


title: SAMPLE 34 [Genotype 34]

value: barley genotype 34


title: RNAseq_sh2-Smad7_Rep3


title: NIH3T3-EGFP-H3mm18-Doxplus-D48-4 (ATAC-seq)

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
For ATAC-seq analysis, raw sequencing data were trimmed using Cutadapt (version 2.6) wapper, Trim Galore! (version 0.6.6), with the options:  --paired --2colour 20.
The reads were mapped by the aligning software bowtie2 (version 2.3.5.1) to the reference genome (UCSC mm10, Bowtie 2 index), and the uniquely mapped reads were retained.
ATAC-seq signal tracks (bigWig) were generated using  the software deepTools (version 3.3.0) with the options: bamCoverage --centerReads --binSize 100 --normalizeUsing CPM --smoothLength 1000.
We counted reads of ChIL-seq and ATAC-seq within 5kb±TSS regions of the first exon by the software bedtools (version 2.29.2) with “multicov” option.
Genome_build: GRCm38/mm10

source_name: NIH3T3 cell line (Dox inducible H3mm18)

growth_protocol: NIH3T3 cells were grown in DMEM supplemented with 10% calf serum.

extract_protocol: Sequencing was performed in an Illumina NovaSeq 6000 system with 51 cycles for both read 1 and read 2 using NovaSeq 6000 S2 Reagent Kit for ATAC-seq

treatment_protocol: Introduction of MyoD into NIH3T3 cells was carried out using the retroviral vector MyoD-T2A-3xNLS-mKO2.

value: NIH3T3 cell line (Dox inducible H3mm18)

value: Differentiated for 48 hours


title: NIH3T3-EGFP-H3mm18-Doxplus-D48-3 (ATAC-seq)


title: NIH3T3-EGFP-H3mm18-Doxplus-D48-2 (ATAC-seq)


title: RNAseq_sh1-Smad7_Rep2

value: ESC


title: H4B3_4-OL-CL_13


title: NIH3T3-EGFP-H3mm18-Doxminus-D48-4 (ATAC-seq)


title: ChIP_Mock

data_processing:
Following quality controls (performed with FastQC v0.11.2), sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3 –q 20). Trimmed reads were next analysed with the ENCODE Transcription Factors and Histone Modifications ChIP-seq pipeline 2 (v1.6.1, available from https://github.com/ENCODE-DCC/chip-seq-pipeline2), using default software and parameter settings for the ‘Transcription Factors’ processing mode. Briefly, reads were aligned to the mouse reference genome (UCSC mm10) using Bowtie2. Duplicated, multi-mapping and poor-quality alignments were discarded, and peak calling was performed using MACS2, using the input DNA as control library. Signal tracks were generated as fold enrichment over control for both individual and pooled replicates using MACS2. To determine a consensus set of Smad7 putative genomic binding sites conserved across biological replicates, the Irreproducible Discovery Rate (IDR) procedure was carried out, as implemented in the ENCODE pipeline. Starting from overlapped peak calls in individual libraries (with SPP peak caller at FDR < 0.01 and using the mock bioChIP-seq as control), the conservative (i.e. from the comparison of true replicates) and optimal set of IDR thresholded (IDR < 0.05) peaks was retained as the final set of Smad7 binding sites.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BigWig files containing ChIP-seq signal as fold enrichment over control; BED/regionPeak file of replicated peak calls.

extract_protocol:
4×107 ESCs expressed Bio-Smad7 protein were harvested, cross-linked with 1% formaldehyde for 10 min, quenched with 0.125 M glycine for 5 min, and then washed twice in cold 1×PBS. Cells were lysed in Isotonic Buffer (20 mM HEPES, 100 mM NaCl, 250 mM Sucrose, 5 mM MgCl2, 5 µM ZnCl2, pH 7.5) supplemented with 1% NP-40 and anti-protease. Cell lysates were centrifuged at 1,000 rpm for 5 min at 4°C to isolate the nuclei. Nuclei were suspended in 1 mL of 0.15 % SDS Lysis Buffer (20 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 0.15 % SDS, 1 % Triton X-100, pH 8.0) supplemented with anti-protease and subjected for sonication to shear chromatin fragments to an average size between 100bp and 400bp on the Pico Bioruptor® (Diagenode) (2 runs of 10 cycles [30 sec ‘‘ON’’, 30 sec ‘‘OFF’’]) at high power setting. Fragmented chromatin was centrifuged at 13,000 rpm for 15 min at 4°C.  50 µL MyOneTM Streptavidin T1 Dynabeads (Thermo-Fisher Scientific) were saturated with PBS/1% BSA at RT for 1 hour and then incubated with the sample at 4°C overnight on a rotator. After incubation, Dynabeads were washed twice with 1 mL of Washing Buffer I (2 % SDS), once with 1 mL of Washing Buffer II (50 mM HEPES, 500 mM NaCl, 0.1% Sodium Deoxycholate, 1% Triton X-100, 1 mM EDTA, pH 7.5), once with 1 mL Washing Buffer III (10 mM Tris-HCl, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1 mM EDTA, pH 8.0), and once with 1 mL of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). All the washing steps were performed at RT for 8 mins on a rotator. The chromatin was eluted in 250 µL SDS Elution Buffer (1% SDS, 50 mM Tris-HCl, 10 mM EDTA, pH 8.0) followed by reverse cross-linking at 65°C overnight. After decrosslinking, the ChIP DNA was purified using QIAQuick PCR Purification Kit (Qiagen) according to the manufacturer’s instructions. For the reference sample, BirA-ESCs without tagged protein were used.
The purified ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix (NEB) following the manufacturer’s protocol. Libraries were pooled and sequenced on an Illumina Next500 Platforms using the 75bp high output sequencing kit.

tag: Stage


title: ChIP_BioSmad7_rep2


title: SAMPLE 32 [Genotype 32]

tag: tissue

value: barley genotype 32


title: NIH3T3-EGFP-H3mm18-Doxplus-D48-1 (ATAC-seq)


title: H3B5_2-AL-CL_13


title: H3B6_2-MB-MD


title: SAMPLE 33 [Genotype 33]

value: barley genotype 33


title: H3B6_2-AL-MD


title: NIH3T3-EGFP-H3mm18-Doxminus-D48-3 (ATAC-seq)


title: SAMPLE 31 [Genotype 31]

value: barley genotype 31


title: RNAseq_sh1-Smad7_Rep1


title: SAMPLE 58 [Genotype 58]

value: barley genotype 58


title: H3B6_2-OL-MD

value: optic lobes (OL) region of the brain

value: Microbiota-depleted (MD)


title: ChIP_BioSmad7_rep1


title: H3B5_2-MB-CL_13

value: mushroom bodies (MB) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: RiboTag wt-3

city: New York

first: Maria

last: Passarelli

state: New York

address: Rockefeller University, 1230 York Ave

institute: Rockefeller University

description:
ribosome-associated mRNA
ribotag_deseq2_result.csv

data_processing:
Library strategy: Ribo-seq
Reads were aligned to tRNA space using bowtie2-2.4.1 (charged tRNA profiling) or to mm10 using STAR v2.5.2a (RNA-Seq, Ribo-Seq, polysome profiling, riboTag).
tRNA reads that were aligned to tRNA probes in tRNA space were counted using samtools.
Polysome profiling, RNA-Seq, Ribo-Seq and RiboTag reads that were aligned to coding sequences were counted using featureCounts or htseq-count (Ribo-Seq)
Differentially expressed transcripts were determined using DESeq2 or xtail (Ribo-Seq)
Genome_build: mm10
Supplementary_files_format_and_content: differential gene expression by deseq2 or xtail, .csv or .txt

source_name: PyMT Tumor

growth_protocol: All cells were maintained in DMEM supplemented with 10% FBS.HCC1806 cells were maintained in RPMI supplemented with 10% FBS, sodium pyruvate, and HEPES.

extract_protocol:
RNA was extracted using 0.3M NaOAc lysis buffer and phenol chloroform extraction (charged tRNA profiling), or as previously described (polysome profiling - Gandin et al 2014, ribosome profiling: McGlincy & Ingolia 2017, RiboTag: Sanz et al 2009)
charged tRNA profiling libraries were conducted as previously described (Goodarzi et al, 2016). RNA-Seq, polysome profiling and RiboTag libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina). Ribo-Seq libraries were constructed as described previously (McGlincy and Ingolia, 2017).

value: Lars wt; rpl22HA fl/wt; MMTV-Cre+; MMTV-PyMT+


title: H3B5_2-OL-CL_13


title: NIH3T3-EGFP-H3mm18-Doxminus-D48-2 (ATAC-seq)


title: SAMPLE 28 [Genotype 28]

value: leaf

value: barley genotype 28


title: NIH3T3-EGFP-H3mm18-Doxminus-D48-1 (ATAC-seq)


title: SAMPLE 27 [Genotype 27]

value: barley genotype 27


title: SAMPLE 26 [Genotype 26]

value: barley genotype 26


title: SAMPLE 30 [Genotype 30]

value: barley genotype 30


title: RiboTag wt-2


title: H3B3_4-AL-CL_Bifi

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: SAMPLE 29 [Genotype 29]

value: barley genotype 29


title: NIH3T3-EGFP-H3mm18-Doxplus-UI-4 (ATAC-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: Before retroviral infection (UnInfected, UI)


title: RiboTag wt-1


title: NIH3T3-EGFP-H3mm18-Doxplus-UI-2 (ATAC-seq)


title: H3B3_4-MB-CL_Bifi


title: NIH3T3-EGFP-H3mm18-Doxplus-UI-1 (ATAC-seq)


title: RiboTag Lars Het-3

value: Lars fl/wt; rpl22HA fl/wt; MMTV-Cre+; MMTV-PyMT+


title: H3B1_3-AL-CL

value: Colonized with a gut homogenate (CL)


title: H3B3_4-OL-CL_Bifi

value: optic lobes (OL) region of the brain


title: RiboTag Lars Het-2


title: H3B1_3-MB-CL


title: NIH3T3-EGFP-H3mm18-Doxplus-UI-3 (ATAC-seq)


title: SAMPLE 25 [Genotype 25]

value: barley genotype 25


title: RiboTag Lars Het-1


title: NIH3T3-EGFP-H3mm18-Doxminus-UI-4 (ATAC-seq)


title: SAMPLE 24 [Genotype 24]

value: barley genotype 24


title: SAMPLE 23 [Genotype 23]

value: barley genotype 23


title: H2B5_1-AL-MD

value: Microbiota-depleted (MD)


title: RiboSeq RPF-Pool

description:
ribosome protected fragments
riboSeq_4T0shLars_xtail_result.txt

tag: cell line

value: breast cancer cell line


title: NIH3T3-EGFP-H3mm18-Doxminus-UI-3 (ATAC-seq)


title: RNA-Seq 4T07 shLars4-2

description:
total RNA
riboSeq_4T0shLars_xtail_result.txt

data_processing:
Reads were aligned to tRNA space using bowtie2-2.4.1 (charged tRNA profiling) or to mm10 using STAR v2.5.2a (RNA-Seq, Ribo-Seq, polysome profiling, riboTag).
tRNA reads that were aligned to tRNA probes in tRNA space were counted using samtools.
Polysome profiling, RNA-Seq, Ribo-Seq and RiboTag reads that were aligned to coding sequences were counted using featureCounts or htseq-count (Ribo-Seq)
Differentially expressed transcripts were determined using DESeq2 or xtail (Ribo-Seq)
Genome_build: mm10
Supplementary_files_format_and_content: differential gene expression by deseq2 or xtail, .csv or .txt


title: H3B1_3-OL-CL


title: NIH3T3-EGFP-H3mm18-Doxminus-UI-2 (ATAC-seq)


title: RNA-Seq 4T07 shLars4-1


title: SAMPLE 22 [Genotype 22]

value: leaf

value: barley genotype 22


title: NIH3T3-EGFP-H3mm18-Doxminus-UI-1 (ATAC-seq)

extract_protocol: Sequencing was performed in an Illumina NovaSeq 6000 system with 51 cycles for both read 1 and read 2 using NovaSeq 6000 S2 Reagent Kit for ATAC-seq.


title: RNA-Seq 4T07 shLars3-2


title: SAMPLE 21 [Genotype 21]

value: barley genotype 21


title: H2B5_1-MB-MD

value: mushroom bodies (MB) region of the brain


title: RNA-Seq 4T07 shLars3-1


title: SAMPLE 20 [Genotype 20]

value: barley genotype 20


title: Scer RNA-seq rep1

description: scer-tsr.txt

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

value: untreated

value: ribo-0 total RNA-seq


title: H2B5_1-OL-MD


title: H2B4_3-AL-CL_13

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: siSlc25a26_3

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
BGI used BGISEQ platform for RNA-Seq
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT
The clean reads were align to the reference genome sequnence using Bowtie2
Genome_build: NCBI, Rattus_norvegicus , GCF_000001895.5_Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Neonatal rat ventricular myocytes (NRVMs)

growth_protocol: NRVMs were maintained in DMEM supplemented with 1% Insulin-Transferrin-Selenium (ITS-G, BD Biosciences, CA, USA), 100 U/mL penicillin and 100 μg/ml streptomycin.

extract_protocol:
RNA of NRVMs extracted according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

treatment_protocol: NRVMs were first transfected with siSlc25a26 or siNeg, then treated with PE for 36h after 12h.

value: Sprague-Dawley (SD) Rat


title: RNA-Seq 4T07 shCtrl-2

value: shCtrl


title: SAMPLE 19 [Genotype 19]

value: barley genotype 19


title: SAMPLE 18 [Genotype 18]

value: barley genotype 18


title: RNA-Seq 4T07 shCtrl-1


title: H2B4_3-MB-CL_13


title: polysome profiling shLars4-high-3

description:
polysome-associated mRNA
polysome_4T07shLars_H_L_deseq2_result.txt

tag: fraction

value: high-translated mRNAs (3+ polysomes)


title: H2B4_3-OL-CL_13

value: optic lobes (OL) region of the brain


title: siSlc25a26.PE_3

value: treated with PE for 36 hours


title: siSlc25a26_2


title: SAMPLE 17 [Genotype 17]

value: barley genotype 17


title: SAMPLE 16 [Genotype 16]

value: leaf

value: barley genotype 16


title: polysome profiling shLars4-high-2

value: breast cancer cell line


title: SAMPLE 15 [Genotype 15]

value: barley genotype 15


title: siSlc25a26.PE_2


title: polysome profiling shLars4-high-1


title: H2B3_3-MB-CL

value: mushroom bodies (MB) region of the brain

value: Colonized with a gut homogenate (CL)


title: H2B3_3-OL-CL


title: siSlc25a26_1

value: untreated


title: polysome profiling shLars4-low-3

value: low-translated mRNAs (1-2 polysomes)


title: siSlc25a26.PE_1


title: H2B1_4-AL-CL_Bifi

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: siNeg.PE_3

value: Sprague-Dawley (SD) Rat

value: siNeg


title: siNeg.PE_2


title: SAMPLE 12 [Genotype 12]

value: barley genotype 12


title: polysome profiling shLars4-low-2


title: SAMPLE 10 [Genotype 10]

value: barley genotype 10


title: H2B1_4-OL-CL_Bifi

value: optic lobes (OL) region of the brain


title: SAMPLE 14 [Genotype 14]

value: barley genotype 14


title: polysome profiling shLars4-low-1


title: SAMPLE 13 [Genotype 13]

value: barley genotype 13


title: SAMPLE 11 [Genotype 11]

value: leaf

value: barley genotype 11


title: polysome profiling shLars3-high-3

value: breast cancer cell line

value: high-translated mRNAs (3+ polysomes)


title: H1B6_4-AL-CL


title: polysome profiling shLars3-high-2


title: siNeg_3


title: SAMPLE 8 [Genotype 8]

value: barley genotype 8


title: siNeg_1


title: polysome profiling shLars3-low-3


title: H1B6_4-OL-CL

value: Colonized with a gut homogenate (CL)


title: SAMPLE 7 [Genotype 7]

value: barley genotype 7


title: polysome profiling shLars3-high-1


title: SAMPLE 6 [Genotype 6]

value: barley genotype 6


title: siNeg_2

value: untreated


title: SAMPLE 9 [Genotype 9]

value: barley genotype 9


title: polysome profiling shLars3-low-2

value: low-translated mRNAs (1-2 polysomes)


title: H1B6_4-MB-CL

value: mushroom bodies (MB) region of the brain


title: H1B5_3-AL-CL_13

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: polysome profiling shLars3-low-1


title: catfish_liver_BxC_rep2

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

description: Illumina mRNA-seq

data_processing:
FastQC (version 0.11.5) software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.39), and masked for low-complexity or low-quality sequence.
The ramaining high-quality clean reads were mapped to the channel catfish reference genome using TopHat (version 2.1.1)
Bedtools (version 2.29.0) was conducted to calculate the number of aligned reads of each gene overlapping its exons.
edgeR was used to calculate log2-fold change (log2FC), |log2FC| >1.5 and FDR < 0.05 was used as cutoff for generating DEGs.
Genome_build: Ictalurus punctatus genome (GenBank assembly accession GCA_001660625.1 IpCoco_1.2)
Supplementary_files_format_and_content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene and every sample

organism: Ictalurus punctatus x Ictalurus furcatus

source_name: Liver

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA)
The RNA integrity was evaluated with the LabChip GX Touch HT (PerkinElmer, MA, USA). The RNA library preparation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, MA, USA). Enriched RNAs were fragmented for 10 minutes at 94 °C. The first strand cDNA synthesis, second strand cDNA synthesis, end repair and adaptor ligation according to the manufacturer’s protocol. The library PCR amplification were performed with 16 cycle PCR. The average size of the RNA libraries was approximately 350 bp (including the adapters). The RNA sequencing libraries were checked using the LabChip GX Touch HT (PerkinElmer, MA, USA) and quantified by using Qubit 3.0 Fluorometer (Invitrogen, CA, USA).

value: B x C (female Blue catfish x male Channel catfish)

value: liver


title: Dark replicate 2_D.3

city: East Lansing

first: Eva

last: Farre

state: MI

address: 612 Wilson Road, Plant Biology, Room 166

department: Plant Biology

institute: Michigan State University

data_processing:
Read quality control and trimming were carried out using FastQC.
Reads were mapped to the N. oceanica CCMP1779 v2.0 genome annotation (JGI) using TopHat.
The transcriptome was then assembled using Cufflinks.
Cuffnorm was used to calculate FPKM (Fragments Per Kilobase Million) values.
We determined differentially expressed genes using Cuffdiff.
Genome_build: N. oceanica CCMP1779 v2.0 genome annotation (JGI)
Supplementary_files_format_and_content: LI_analysis_FPKM_TPM.csv: Comma-separated text file includes FPKM, TPM for each sample as well as log2(fold_change), p- and q-values comparing dark and light treatments.

organism: Nannochloropsis oceanica

source_name: Nannochloropsis oceanica

growth_protocol: Cells were grown under 12 h light:12 h dark cycles at 22°C under agitation (100 rpm). Light intensity during light periods was 30 μmol s-1 m-2.

extract_protocol:
RNA was extracted from ground frozen pellets using the Omega eZNA Plant RNA kit (Omega Biotek).
Illumina TruSeq Stranded mRNA Library.

treatment_protocol: Before harvesting, cells were transferred to darkness at ZT 12 and kept in the dark for 36 h. Cells were given a 5 min blue or red light pulse (20 μmol s-1 m-2) or kept in the dark. All cells were then kept in the dark for 15 min before harvesting. Cells were collected at 4,000 g for 10 min at 4°C, the cell pellet was resuspended in 1.5 ml f/2 media and transferred to 2 ml tubes. The cells were centrifuged again at 18,000 g for 10 min at 4°C and flash frozen in liquid nitrogen. Black or amber tubes were used to prevent light exposure during harvesting.

value: dark


title: SAMPLE 5 [Genotype 5]

source_name: leaf tissue

value: leaf

value: barley genotype 5


title: H1B5_3-OL-CL_13

value: optic lobes (OL) region of the brain


title: siNeg.PE_1

value: Sprague-Dawley (SD) Rat

value: siNeg

value: treated with PE for 36 hours


title: Red light replicate 2_R.3

value: red light


title: SAMPLE 4 [Genotype 4]

value: barley genotype 4


title: polysome profiling shCtrl-high-3

value: breast cancer cell line

value: shCtrl

value: high-translated mRNAs (3+ polysomes)


title: SAMPLE 3 [Genotype 3]

value: barley genotype 3


title: H1B3_5-AL-CL_Bifi

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)


title: catfish_liver_BxC_rep1

description: Illumina mRNA-seq

value: B x C (female Blue catfish x male Channel catfish)


title: H1B5_3-MB-CL_13

value: mushroom bodies (MB) region of the brain

value: Colonized with a community of 13 different gut microbiota strains (CL_13)


title: catfish_liver_CxB_rep2

description: Illumina mRNA-seq

value: C x B (female Channel catfish x male Blue catfish)

value: liver


title: SAMPLE 2 [Genotype 2]

value: leaf

value: barley genotype 2


title: Red light replicate 1_R.2


title: catfish_liver_CxB_rep1

description: Illumina mRNA-seq


title: Blue light replicate 2_B.3

value: blue light


title: polysome profiling shCtrl-low-3

value: low-translated mRNAs (1-2 polysomes)


title: polysome profiling shCtrl-high-2


title: Blue light replicate 1_B.1


title: polysome profiling shCtrl-high-1


title: M9 Min KDG, RNA, replicate 1

city: Ann Arbor

first: Lydia

last: Freddolino

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description:
LFC in processed data file is log2( second condition abundance / first condition abundance ); e.g., “glu2_vs_glu1” indicates log2(glu1 / glu2)
glu2_vs_kdg_deseq.csv
kdg_vs_glu1_deseq.csv

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
We performed gene-level quantitation with htseq-count, using union mode for scoring and all mode for non-unique assignments
Differential expression calling was then performed using deseq2 with default settings
Genome_build: U00096.3
Supplementary_files_format_and_content: .gr files: Occupancies (expressed as log2(chip/input) for ChIP samples, and robust z-scores (as defined in https://doi.org/10.1101/2020.01.29.924811) for IPOD samples. The first column gives a location and the second column gives the corresponding value
Supplementary_files_format_and_content: .csv files for RNA: Tabular output from DeSeq2, using as a sign convention log(cond2/cond1), where cond1 is the first condition listed and log2 the second condition listed in the file name
Supplementary_files_format_and_content: .bed files: Occupancies (expressed as log2(chip/input) for ChIP samples, and robust z-scores (as defined in https://doi.org/10.1101/2020.01.29.924811) for IPOD samples. Standard bed-formatted files

organism: Escherichia coli

source_name: Culture lysate

growth_protocol: Overnight cultures (in M9 minimal media + 0.02% glucose) were back diluted to an OD600 0.003 in fresh, prewarmed M9 minimal medium including 0.2% glucose at 37°C. After growth to an OD of 0.2, the Glu #1 sample was harvested. Remaining cells were diluted to an OD of ~0.1 in M9 ninimal medium including 0.2% 5-keto D-gluconic acid, and grown to an OD of 0.2, at which point the KDG sample was harvested. Remaining cells were diluted in M9 minimal media plus 0.2% glucose to an OD of 0.003, and grown to an OD of 0.2, at which point the Glu #2 sample was harvested.

extract_protocol:
The pellet was resuspended in 100 μl of TE and treated with 177kU (1 μl) Ready-lyse lysozyme solution (Lucigen: Catalog #R1804) and 0.2 mg (10 μl) proteinase K (Thermo Fisher Scientific: Catalog #EO0492), incubated for 10 min at room temperature with vortexing every 2 min. The RNA was purified using RNA Clean and Concentrator kit-5 (Zymo: Catalog #R1014), treated with 5 units of Baseline-ZERO DNase (Epicentre: Catalog #DB0715K) in the presence of RNAse inhibitor (NEB: Catalog #M0314L) for 30 min at 37°C. RNA was purified again using RNA Clean and Concentrator kit-5 (Zymo: Catalog #R1014). RNA was flash-frozen in a dry ice-ethanol bath and stored at −80°C.
rRNA depletion was performed using the bacterial rRNA depletion kit following manufacturer instructions (New England Biolabs (NEB): Catalog #E7850L). The only modification performed was the last step, where instead of a bead clean up, we used the RNA Clean and Concentrator kit-5 (Zymo: Catalog #R1014).  Sequencing preparation was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer instructions (NEB: Catalog #E7420L) for rRNA-depleted RNA.  Random primers were used, and RNA was considered intact for the NEBNext Ultra protocol. Slight modifications to the protocol are as follows. To purify cDNA, the Oligo clean & concentrator was used (Zymo: Catalog #D4061). Following adapter ligation, DNA was puri- fied using DNA Clean & Concentrator-5 (Zymo: Catalog #D4014).

treatment_protocol: Upon the harvest points noted under ‘growth protocol’, 1 mL of sample was preserved in Qiagen RNAprotect bacterial reagent following the manufacturer’s instructions

value: wild type

tag: media

value: M9 minimal media + KDG

tag: time of harvest

value: logarithmic phase (after growth in glucose)


title: polysome profiling shCtrl-low-2

value: breast cancer cell line

value: shCtrl


title: H1B1_6-AL-MD

tag: treatment

value: Microbiota-depleted (MD)


title: M9 Min KDG, RNA, replicate 2

tag: genotype


title: SAMPLE 1 [Genotype 1]

value: barley genotype 1


title: H1B3_5-MB-CL_Bifi

value: Colonized with two strains of Bifidobacterium asteroides (CL_Bifi)

tag: hive


title: H2B3_3-AL-CL

value: antennal lobes and subaesophageal ganglion (AL) region of the brain

value: Colonized with a gut homogenate (CL)


title: non-HF-8E2

city: Beijing

first: Shan

last: He

address: Jingyuan Road No.5

institute: Beijing Chaoyang Hospital Jingxi Branch

data_processing:
Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8) used for basecalling
Sequence quality was examined using the FastQC software
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown.
The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT to assess the coding potential of those sequences. Use rMATS to detect alternative splicing events and plots.
Genome_build: GRCh37
Supplementary_files_format_and_content: excel files for the FPKM of transcript and gene in samples

organism: Homo sapiens

source_name: epicardial adipose tissue

extract_protocol:
Total RNA was extracted from freshly frozen epicardial adipose tissue using a QIAGEN miRNAeasy Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Isolated total RNA was subjected to ribosomal RNA deletion using a Ribo-Zero Magnetic Kit (EpiCentre, Madison, WI), randomly fragmented and then used to construct RNA sequencing library using KAPA Stranded RNA-Seq Library Prep Kit for Illumina.
The RNA fragments were primed with random hexametric primers to synthesize the first cDNA strand, and the second cDNA strand was incorporated with dUTP instead of dTTP. The resulting cDNA were amplified in situ using TruSeq SR Cluster Kit v3-cBot-HS. The strand-specific libraries were qualified on the Agilent 2100 Bioanalyzer and subsequently sequenced on the Illumina HiSeq 6000 platform.

value: epicardial adipose tissue

tag: group

value: control


title: H2B1_4-MB-CL_Bifi

value: mushroom bodies (MB) region of the brain


title: H1B3_5-OL-CL_Bifi

value: optic lobes (OL) region of the brain


title: Jmjd3f/f;Olig2Cre;mTmG

city: Buffalo

first: Soo-Kyung

last: Lee

address: 109 Cooke Hall

department: Department of Biological Sciences

institute: University at Buffalo, The State University of New York

data_processing:
Raw sequencing cell barcodes were filtered to distinguish between valid cell barcodes from empty cell barcodes using an algorithm in Cellranger count v2.1.1.
Filtered reads were aligned to mm10, using STAR v2.4.0 with a default setting.
Gene-barcode count matrix was read using a function Read10X in an R package Seurat v2.3.0 for downstream analysis.
Gene-barcode matrix was normalized using a global-scaling normalization method LogNormalize in Seurat v2.3.0, in which gene expression for each cell was normalized by the total expression, multiplied by a scale factor 10,000, and then log-transformed.
For visualization, t-distributed stochastic neighbor embedding (tSNE) technique was used with the perplexity parameter, an expected number of neighbors, set to the default value 30.
Graph-based clustering approach in Seurat was used within a function FindClusters in Seurat v2.3.0 to group cells together with a resolution parameter 0.6.
Genome_build: mm10
Supplementary_files_format_and_content: comma delimited gene-barcode count matrix with genes in rows and barcodes in columns

extract_protocol:
Spinal cords were dissected from E12.5 embryos and isolated cells were subjected to FACS sorting to collect GFP+ cells. Single cell suspension were then subjected to 10x genomics.
RNA libraries were prepared for sequencing using standard Illumina protocols using Chromium Single Cell 3’ Gel Bead Kit, Chromium Single Cell 3’ Chip Kit and Chromium Single Cell 3’ Library Kit.

tag: strain background

tag: age

tag: genotype/variation

value: Spinal cord

value: Spinal cord GFP+ cells


title: H1B1_6-OL-MD

data_processing:
Trimmomatic was used to remove adapters and low-quality bases with the following parameters: LEADING: 10 (trim the leading nucleotides until quality > 10), TRAILING: 10 (trim the trailing nucleotides until quality > 10), SLIDINGWINDOW: 4:20 (trim the window of size four for reads with local quality below a score of 20), and MINLEN: 80 (discard reads shorter than 80 bases).
Reads were aligned with STAR v.2.5.4b to the honeybee genome (Apis mellifera assembly HAv3.1).
Mapped reads were converted into raw read counts with the htseq-count script (http://www.huber.embl.de/users/anders/HTSeq/doc/count.html).
Genome_build: Amel_HAv3.1
Supplementary_files_format_and_content: Separate .txt file for each sample contaning counts of reads mapped to individual genes

extract_protocol:
RNA extractions of brain regions were performed with the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer’s specifications, including a DNase treatment (Qiagen) to remove genomic DNA.
RNA-sequencing libraries were prepared with the KAPA stranded mRNA kit (Roche) following the manufacturer’s protocol, except that we appended TruSeq unique dual indexes (UDIs, Illumina) instead of the adapters provided by the kit to better control for index hopping during sequencing.


title: H1B1_6-MB-MD


title: M9 Min KDG, IPOD, replicate 1

description:
wt_minkdg_v6rz_chipsub.gr
wt_minkdg_v6rz_chipsub.bed

extract_protocol:
DNA samples: Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA. RNA: RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
DNA samples: NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup (see the accompanying paper for details).


title: Dark replicate 1_D.1

value: dark


title: tumor plus triple combination, mouse 10

type: RNA

city: Heidelberg

first: Hamed

last: Alborzinia

address: Im Neuenheimer Feld 280

department: Stem cells and Cancer (DFKZ)

country: Germany

institute: DKFZ

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_treated_10

hyb_protocol: Affy Clariom S Human was used for this experiment. Subsequent hybridization was performed according to the manufacturer's instruction.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and photomultiplier tube settings at 430

data_processing: Raw CEL-files were RMA-normalized using the oligo package from Bioconductor, probes were filtered by low expression and duplicates

label: biotin

source_name: human cancer cell line SK-N-DZ_isolated from xenograft mouse model

label_protocol: 500 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step to synthesize biotin-labeled cRNA

growth_protocol: cells were isolated from orthotopic xenograft mouse model

extract_protocol: Total RNA was isolated using the RNA isolation Mini Kit (Qiagen) according to the manufacturers’ protocols. The quality of total RNA was confirmed by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer. The RNA is turned into a double stranded cDNA. This is done through reverse transcription.

treatment_protocol: We treated the mice with the combination of IKE and PPG together with genetic targeting of GPX4 activity

value: SK-N-DZ

value: human neuroblastoma cancer cell line

value: tumor plus triple combination


title: tumor plus triple combination, mouse 9

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_treated_9


title: Jmjd3f/+;Olig2Cre;mTmG


title: M9 Min KDG, Input, replicate 2

description:
wt_minkdg_chip_vs_inp_lograt.gr
wt_minkdg_chip_vs_inp_lograt.bed
wt_minkdg_v6rz_chipsub.gr
wt_minkdg_v6rz_chipsub.bed

value: wild type

value: M9 minimal media + KDG

value: logarithmic phase (after growth in glucose)


title: non-HF-4E2


title: HK27

city: Chicago

first: Nissim

last: Hay

state: IL

address: 900 South Ashland Ave

department: BMG

institute: University of Illinois Chicago

description: Single cell RNA-seq was performed using Drop-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against genome version GRCh37.p13 hg19 (From Ensembl) and corresponding gene model is extracted from Ensembl version 74.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell

source_name: MMTV-PyMT; HK2 f/f ; UBC-Cre ERT2

growth_protocol: Spontaneous tumor growth driven by MMTV-PyMT

extract_protocol:
Drop-seq on the single cell suspension
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)

treatment_protocol: Sytemic HK2 KO was induced by ERT2Cre upon Tamoxifen treatment

value: mammary tumor with systemic HK2 deletion

tag: timepoint

value: 3 months after palpable tumor devloped

value: HK2 knockout


title: M9 Min KDG, IPOD, replicate 2


title: HK2_6


title: polysome profiling shCtrl-low-1

value: breast cancer cell line

value: shCtrl

value: low-translated mRNAs (1-2 polysomes)


title: non-HF-7E2

value: epicardial adipose tissue

value: control


title: HK2_5


title: non-HF-2E2


title: tumor plus triple combination, mouse 6

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_treated_6

tag: cell type


title: HK2_4


title: tumor plus vehicle, mouse 5

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_control_5

value: tumor plus vehicle


title: non-HF-3E2


title: tumor plus triple combination, mouse 8

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_treated_8


title: M9 Min KDG, RNA polymerase ChIP, replicate 2

description:
wt_minkdg_chip_vs_inp_lograt.gr
wt_minkdg_chip_vs_inp_lograt.bed


title: M9 Min Glu #2, RNA, replicate 1

description:
LFC in processed data file is log2( second condition abundance / first condition abundance ); e.g., “glu2_vs_glu1” indicates log2(glu1 / glu2)
glu2_vs_glu1_deseq.csv
glu2_vs_kdg_deseq.csv

value: M9 minimal media + glucose

value: logarithmic phase (after growth in KDG)


title: HFpEF-11E2

value: HFpEF


title: M9 Min KDG, RNA polymerase ChIP, replicate 1


title: HFpEF-12E2


title: HK23_CB


title: HK22_CB


title: M9 Min Glu #2, IPOD, replicate 2

description:
wt_minglu2_v6rz_chipsub.gr
wt_minglu2_v6rz_chipsub.bed


title: M9 Min Glu #2, IPOD, replicate 1


title: HFpEF-10E2


title: tumor plus triple combination, mouse 7

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_treated_7

value: SK-N-DZ

value: human neuroblastoma cancer cell line


title: tumor plus vehicle, mouse 4

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_control_4


title: metl-9 mut infected (P.A14)_1

first: Guan

last: Jialiang

state: Beijing

address: China, Beijing, Haidian district, Peking University, 1000871

institute: Peking University

data_processing:
raw sequencing data was aligned to C. elegans genome reference (ce11) by HISAT2 (version 2.1.0) with default settings
duplicated reads or reads with low mapping quality (<30) were removed using samtools version 1.9
the filtered reads were counted at the gene level using featureCount version 1.6.3
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files containing gene expression counts

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were fed on OP50 (normal food) on nematode growth medium (NGM) at 20℃ until L4.

extract_protocol:
Total RNA were extracted by Trizol reagent and chloroform extraction.
1)mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA (For total RNA extracted from human whole blood, globin mRNA are depleted ); 2)RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 3)End repair, add A and adaptor ligation; 4)PCR; 5)Circularization and make DNB; 6) Sequencing on DNBSEQ platform

treatment_protocol: L4 wroms were washed off plates by M9 and clean up 3 times by M9, then transfer to slow-killing plate (SK) with OP50 or P.A14, and maintained at 20℃ for 2 hrs before samples collection. SK plate were seeded with OP50 or P.A14 48 hrs before use, and maintained at 37℃, 24 hrs before use, plates were moved to 20 ℃.

value: metl-9 mut

value: P.A14 infected

tag: developmental period


title: tumor plus vehicle, mouse 3

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_control_3


title: tumor plus vehicle, mouse 2

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_control_2


title: tumor plus vehicle, mouse 1

description:
Gene expression data from xenograft tumors treated with triple combinaton described in summary
SK-N-DZ_control_1


title: M9 Min KDG, Input, replicate 1

tag: strain

value: wild type

value: M9 minimal media + KDG

value: logarithmic phase (after growth in glucose)


title: HFpEF-6E2


title: HFpEF-1E2


title: WT8

source_name: MMTV-PyMT; HK2 f/f

value: mammary tumor

value: 3 months after palpable tumor devloped

value: Wild type


title: metl-9 mut normal condition (OP50)_1

value: normal condition


title: Treated_3

city: Hangzhou

first: Yuhan

last: Shu

address: Ling Yin Street, Road 38 West Lake District

institute: Zhejiang University

data_processing:
We performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Cutadapt software was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software  to map reads to the genome,(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2,and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: Ensembl v96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: differential expression genes between treated and control

source_name: colon cancer cells

growth_protocol: Cells were maintained in high glucose dulbecco's modified eagle medium (DMEM, HyClone) and supplemented with 10% FBS, 100 units/ml penicillin, 100 mg/ml streptomycin, 1 mM sodium pyruvate and 1 mM nonessential amino acids.

extract_protocol:
Total RNA was extracted using  Trizol buffer (Beyotime, Shanghai, China)  following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SW620 cells were seeded in 6-cm dishes overnight and treated with 12.5μM DHOK for 24 h in a 5% CO2 incubator.

value: 14,15β-dihydroxyklaineanone for 24h


title: metl-9 mut normal condition (OP50)_2


title: HK21_CB

value: mammary tumor with systemic HK2 deletion

value: HK2 knockout


title: WT6

source_name: MMTV-PyMT; UBC-Cre ERT2


title: M9 Min Glu #2, RNA polymerase ChIP, replicate 2

description:
wt_minglu2_chip_vs_inp_lograt.gr
wt_minglu2_chip_vs_inp_lograt.bed

value: M9 minimal media + glucose


title: WT7


title: metl-9 KO infected (P.A14)_2

value: metl-9 KO


title: M9 Min Glu #2, RNA, replicate 2

value: logarithmic phase (after growth in KDG)


title: Treated_2


title: WT5


title: metl-9 mut infected (P.A14)_2


title: M9 Min Glu #2, Input, replicate 1

description:
wt_minglu2_chip_vs_inp_lograt.gr
wt_minglu2_chip_vs_inp_lograt.bed
wt_minglu2_v6rz_chipsub.gr
wt_minglu2_chip_vs_inp_lograt.bed


title: M9 Min Glu #2, Input, replicate 2

description:
wt_minglu2_chip_vs_inp_lograt.gr
wt_minglu2_chip_vs_inp_lograt.bed
wt_minglu2_v6rz_chipsub.gr
wt_minglu2_v6rz_chipsub.bed


title: metl-9 KO infected (P.A14)_1


title: M9 Min Glu #2, RNA polymerase ChIP, replicate 1


title: control_3


title: M9 Min Glu #1, RNA, replicate 2

description:
LFC in processed data file is log2( second condition abundance / first condition abundance ); e.g., “glu2_vs_glu1” indicates log2(glu1 / glu2)
glu2_vs_glu1_deseq.csv
kdg_vs_glu1_deseq.csv

value: logarithmic phase


title: PyMT4_CB


title: PyMT3_CB


title: metl-9 KO normal condition (OP50)_2


title: metl-9 KO normal condition (OP50)_1


title: M9 Min Glu #1, RNA, replicate 1


title: control_1


title: PyMT2_CB


title: Treated_1


title: wild-type infected (P.A14)_2

value: wild-type (bristol)


title: D481_LLN_Flu_CMV_CD8

first: Donna

last: Farber

address: 650 West 168th Street

institute: Columbia University Medical Center

description:
DM044_S16
201028_NS500289_0872_AH27F2BGXH_DM044_S16

data_processing:
RTA (Illumina) for base calling on Illumina Illumina Novaseq 6000
extract UMIs and barcodes with "umi_tools extract"
align reads with STAR
assign alignments to genes with featureCounts
sort & index bam with samtools
make count matrix from bam with "umi_tools count", pandas, and scipy
Genome_build: GRCm38
Supplementary_files_format_and_content: plate_matrix.csv: raw gene counts for each barcode
Supplementary_files_format_and_content: plate_meta.csv: barcode, well, and cell type table

source_name: Lung-draining lymph node CD8 T cells

extract_protocol:
lysis buffer 0.2% Triton X-100, 1 U/uL SUPERaseIN, 2mM dNTPs, 2uM well-specific RT primer
pooled 3' end scRNA-Seq

treatment_protocol: Mononuclear cells were thawed,  dead cells were removed, and cells were left to rest overnight (5% CO2, 37C). Cells were then stimulated by the addition of individual virus-specific peptide megapools (1ug/mL) for 24 hrs. Antigen-responsive cells were stained using the IFN-gamma Secretion Assay – Detection Kit, human (Miltenyi Biotec, cat# 130-054-202) then stained with fluorochrome-conjugated antibodies to label cell surface markers. IFN-gamma+ CD69+ CD8+ T cells were sorted using BD Influx Cell Sorter directly into 96-well plates containing 7.5 μl of lysis buffer [0.2% Triton X-100 (Sigma), SUPERaseIN (1 U/μl) (Thermo Fisher Scientific), 2 mM deoxyribonucleotides (dNTPs) (Thermo Fisher Scientific), and 2 μM reverse transcriptase (RT) primer (Integrated DNA Technologies)].

value: Lung-draining lymph node CD8 T cells

tag: stimulation condition

value: Flu or CMV stimulated CD8


title: M9 Min Glu #1, IPOD, replicate 2

description:
wt_minglu1_v6rz_chipsub.bed
wt_minglu1_v6rz_chipsub.gr

value: wild type


title: wild-type infected (P.A14)_1

value: P.A14 infected


title: PyMT1_CB

description: Single cell RNA-seq was performed using Drop-seq


title: M9 Min Glu #1, IPOD, replicate 1


title: wild-type normal condition (OP50)_2


title: _Mar1_Flu_II

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

data_processing:
Sequenced reads were trimmed for adaptor sequence, low-quality base calls using Skewer v0.2.2 with parameters -m pe -l 36 -q 15 -Q 15
Reads were mapped to CBS138 whole genome using TopHat v2.1.1 with parameters -p 12 -g 1 --b2-very-sensitive --library-type fr-firststrand
Reads counts per feature (ORF) were obtained with the htseq-count script from HTSeq (v 0.7.1) using parameters -m union -s reverse -t gene -i Name
Genome_build: CBS138 whole genome
Supplementary_files_format_and_content: Table with read counts for each feature (ORF)

organism: Nakaseomyces glabratus

source_name: ∆mar1_1h fluconazole exposure

growth_protocol: Cells were grown in minimal medium and exposed to fluconazole stress for 1h or not (control). Cells were pelleted and frozen at -80ºC until RNA extraction

extract_protocol:
Ambion Ribopure-Yeast RNA kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 1h fluconazole exposure


title: D481_Lung_Flu_CMV_CD8

description:
DM034_S6
201028_NS500289_0872_AH27F2BGXH_DM034_S6

source_name: Lung CD8 T cells

value: Lung CD8 T cells


title: M9 Min Glu #1, Input, replicate 2

description:
wt_minglu1_chip_vs_inp_lograt.bed
wt_minglu1_chip_vs_inp_lograt.gr
wt_minglu1_v6rz_chipsub.bed
wt_minglu1_v6rz_chipsub.gr


title: _Mar1_Flu_I


title: _Mar1_control_II

value: control


title: wild-type normal condition (OP50)_1


title: D481_Spleen_Flu_CMV_CD8

description:
DM029_S1
201028_NS500289_0872_AH27F2BGXH_DM029_S1

source_name: Spleen CD8 T cells

value: Spleen CD8 T cells


title: M9 Min Glu #1, RNA polymerase ChIP, replicate 2

description:
wt_minglu1_chip_vs_inp_lograt.bed
wt_minglu1_chip_vs_inp_lograt.gr


title: _Mar1_control_I


title: D481_BM_Flu_CMV_CD8

description:
DM039_S11
201028_NS500289_0872_AH27F2BGXH_DM039_S11

source_name: Bone marrow CD8 T cells

value: Bone marrow CD8 T cells