title: B99_16S rRNA

city: Nanjing City

first: Xingyin

last: Liu

state: Jiangsu Province

address: Long Mian Street No.1

institute: Nanjing Medical University

data_processing:
Library strategy: 16S rRNA DNA-seq
Paired-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence.
Paired-end reads were merged using FLASH (http://ccb.jhu.edu/software/FLASH/). Quality filtering on the raw tags were performed under specific filtering conditions to obtain the high-quality clean tags according to the QIIME (http://qiime.org/index.html) quality controlled process.
The tags were compared with the reference database (Gold database, http://drive5.com/uchime/uchime_download.html) using UCHIME algorithm (UCHIME Algorithm, http://www.drive5.com/usearch/manual/uchime_algo.html) to detect chimera sequences, and then the chimera sequences were removed.
Sequences analysis were performed by Uparse software (http://drive5.com/uparse/). Sequences with ≥97% similarity were assigned to the same OTUs.
For each representative sequence, the GreenGene Database (http://greengenes.lbl.gov/cgi-bin/nph-index.cgi) was used based on RDP classifier (http://sourceforge.net/projects/rdp-classifier/) algorithmto annotate taxonomic information. OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences.
Supplementary_files_format_and_content: For predicted OTU, the sequences of 16S rRNA V4 region are shown in “Autism 16S rRNA OTU.xls”. The assignment and frequency of OTU in each sample are shown in “Autism 16S rRNA OTU assignment and frequency.xls”, the number in "Autism 16S rRNA OTU frequency" is the frequency of each OTU in each sample.

organism: feces metagenome

source_name: Feces

extract_protocol:
Total genome DNA of fecal samples was extracted using the kit (Tiangen Company, Beijing, China). The DNA concentration was performed using Qubit@ 2.0 Fluorometer (Thermo Scientific). DNA quality was also monitored on 1% agarose gels. PCR was performed to produce V4 regions of the 16S rDNA gene using the conserved primers 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’). PCR products and operate electrophoresis on 2% agarose gel for detection. Samples with bright main strip between 400-450bp were chosen for purifing with GeneJET Gel Extraction Kit (Thermo Scientific). PCR fragments were sequenced by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China).
Libraries was sequenced on an Illumina HiSeq platform and 250 bp paired-end reads were generated.

treatment_protocol: Fecal samples were obtained at the homes of each participant, and were immediately frozen in their home freezer. Frozen samples were stored within insulating polystyrene foam containers, and stored at -80 ℃ until analysis. The time span from sampling to delivery to the library as short as possible with a maximum of 24 hours.

tag: tissue

value: human fecal tissue

tag: diagnosis

value: autism spectrum disorder


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F5_ad004

status: Public on Sep 30 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSs

tag: Sex

value: male

tag: age

tag: strain


title: CDTcellplate4_C03

city: Cambridge

first: Ken

last: Dower

state: MA

address: 1 Portland Street

department: Inflammation & Immunology

institute: Pfizer

description: processed data file: rsem.genes.count.matrix

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: hg19; mm10; hg19_mm10
Supplementary_files_format_and_content: human or mouse UMI-collapsed transcripts, gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Transcriptome of single cells

extract_protocol:
Seq-Well, 10x Chrominum V3, Smart-Seq2
Illumina Nextera XT

tag: genome build

tag: sample type

value: Sorted CD4 T Cells from human Peripheral Blood Mononuclear Cells

tag: condition

value: Healthy Primary PBMCs


title: B98_16S rRNA

country: China


title: B97_16S rRNA


title: CDTcellplate4_C02


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F5_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F5_ad002


title: B96_16S rRNA


title: CDTcellplate4_B12


title: CDTcellplate4_C01


title: CDTcellplate4_B11


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad001


title: B95_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad012


title: B94_16S rRNA


title: B92_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad010


title: Non-neoplasticthyroid_2 [RNA]

type: RNA

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using an Illumina BeadArray reader.

data_processing: Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

label: Biotin

molecule: total RNA

label_protocol: According to Illumina whole genome DASL assay

extract_protocol: Total RNA was extracted from snap-frozen tissues with Trizol reagent.

tag: disease

tag: histology

value: M


title: Thyroid_carcinoma_14 [RNA]

value: PTC

value: F


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad006


title: Thyroid_carcinoma_8 [RNA]


title: CDTcellplate4_B10


title: CDTcellplate4_B08


title: Thyroid_carcinoma_3 [RNA]


title: Thyroid_carcinoma_12 [RNA]


title: CDTcellplate4_B09


title: CDTcellplate4_B07


title: B9_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad004


title: B88_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad002


title: Thyroid_carcinoma_15 [RNA]


title: CDTcellplate4_B06


title: CDTcellplate4_B05


title: B87_16S rRNA


title: Thyroid_carcinoma_10 [RNA]


title: B86_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F3_ad012


title: B91_16S rRNA


title: B85_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F4_ad008


title: CDTcellplate4_B04


title: Thyroid_carcinoma_7 [RNA]


title: Thyroid_carcinoma_18 [RNA]


title: CDTcellplate4_B03


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F3_ad007


title: Thyroid_carcinoma_21 [RNA]


title: B81_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F3_ad004


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F3_ad002


title: CDTcellplate4_B02


title: CDTcellplate4_B01


title: Non-neoplasticthyroid_5 [RNA]


title: B80_16S rRNA


title: CDTcellplate4_A11


title: CDTcellplate4_A12


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F3_ad008


title: B77_16S rRNA


title: B79_16S rRNA


title: B8_16S rRNA


title: CDTcellplate4_A10


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F2_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F2_ad012


title: Thyroid_carcinoma_6 [RNA]


title: CDTcellplate4_A09


title: B82_16S rRNA


title: B75_16S rRNA


title: Thyroid_carcinoma_30 [RNA]

value: PTC+PDTC


title: Non-neoplasticthyroid_3 [RNA]


title: Thyroid_carcinoma_4 [RNA]


title: Thyroid_carcinoma_28 [RNA]


title: CDTcellplate4_A07


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F2_ad004


title: B74_16S rRNA


title: CDTcellplate4_A08


title: B73_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F2_ad002


title: CDTcellplate4_A06


title: CDTcellplate4_A05


title: B72_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F2_ad001


title: B71_16S rRNA


title: Thyroid_carcinoma_26 [RNA]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F2_ad008


title: CDTcellplate4_A04


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F12_ad004


title: CDTcellplate4_A03


title: Thyroid_carcinoma_17 [RNA]


title: B7_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F2_ad006


title: Thyroid_carcinoma_1 [RNA]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F12_ad002


title: Thyroid_carcinoma_16 [RNA]


title: Non-neoplasticthyroid_4 [RNA]


title: Thyroid_carcinoma_2 [RNA]


title: CDTcellplate4_A02


title: Thyroid_carcinoma_11 [RNA]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F12_ad001


title: Thyroid_carcinoma_23 [RNA]

value: PDTC+PTC


title: CDTcellplate4_A01


title: B67_16S rRNA


title: B70_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F12_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F11_ad012


title: CDTcellplate1_H12


title: B66_16S rRNA


title: CDTcellplate1_H11


title: CDTcellplate1_H10


title: Thyroid_carcinoma_25 [RNA]

value: PDTC


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F11_ad008


title: CDTcellplate1_H09


title: B63_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F11_ad002


title: B62_16S rRNA


title: B68_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F11_ad001


title: B61_16S rRNA


title: CDTcellplate1_H08


title: CDTcellplate1_H07


title: Non-neoplasticthyroid_1 [RNA]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F10_ad010


title: B60_16S rRNA


title: Thyroid_carcinoma_9 [RNA]


title: Thyroid_carcinoma_13 [RNA]


title: Thyroid_carcinoma_5 [RNA]


title: Thyroid_carcinoma_19 [RNA]


title: CDTcellplate1_H06


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F10_ad008


title: B6_16S rRNA


title: CDTcellplate1_H05


title: B64_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F10_ad006


title: B58_16S rRNA


title: Thyroid_carcinoma_27 [RNA]

value: PDTC+ATC


title: B57_16S rRNA


title: B56_16S rRNA


title: B59_16S rRNA


title: CDTcellplate1_H03


title: CDTcellplate1_H02


title: CDTcellplate1_H01


title: B55_16S rRNA


title: CDTcellplate1_G12


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F1_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F10_ad007


title: CDTcellplate1_H04


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F10_ad002


title: B54_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F1_ad007


title: CDTcellplate1_G11


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F1_ad010


title: B52_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F10_ad001


title: Thyroid_carcinoma_24 [RNA]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F1_ad012


title: Thyroid_carcinoma_29 [RNA]


title: B51_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F1_ad004


title: Thyroid_carcinoma_22 [RNA]


title: CDTcellplate1_G09


title: B50_16S rRNA


title: CDTcellplate1_G08


title: ZC3h12d-KO

city: Tokyo

first: Sachie

last: Hiratsuka

address: 8-1 Kawada-cho Shinjyuku-ku

country: Japan

institute: Tokyo Women's Medical University

description: Male mouse spleen stimulated TCM.

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Transcriptome Array 1.0, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix Power Tools 1.15 software, and obtained normalized intensity values.

label: biotin

source_name: spleen, ZC3h12dKO, TCM-stimulated

label_protocol: The cRNA was amplified, labeled using GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

growth_protocol: Whole spleens were collected and reserved at -80 degrees until total RNA was extracted.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: ZC3h12d male mice were i.p. injected with LTCM at 3 tiles and spleens were collected.

tag: strain/background

tag: genotype/variation

value: ZC3h12d KO

value: spleen

tag: gender

tag: treatment

value: tumor-conditioned medium (TCM)


title: B5_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F1_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F1_ad002


title: Wild-type

description: Male mouse spleen stimulated TCM.

source_name: spleen, wild-type, TCM-stimulated

value: wild-type


title: CDTcellplate1_G07


title: B49_16S rRNA

value: human fecal tissue


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E9_ad007


title: CDTcellplate1_G06


title: CDTcellplate1_G04


title: CDTcellplate1_G10


title: CDTcellplate1_G05


title: B46_16S rRNA

value: autism spectrum disorder


title: CDTcellplate1_G03


title: B44_16S rRNA


title: B45_16S rRNA


title: CDTcellplate1_G02


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E9_ad004

value: SSs


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E9_ad006

value: male


title: B42_16S rRNA


title: CDTcellplate1_G01

value: Sorted CD4 T Cells from human Peripheral Blood Mononuclear Cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E9_ad002


title: B40_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E9_ad008


title: B4_16S rRNA


title: CDTcellplate1_F12

value: Healthy Primary PBMCs


title: CDTcellplate1_F11


title: B48_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E9_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E8_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E9_ad010


title: CDTcellplate1_F10


title: B39_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E8_ad010


title: CDTcellplate1_F09


title: B37_16S rRNA


title: B35_16S rRNA


title: CDTcellplate1_F08


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E8_ad006


title: B34_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E8_ad004


title: CDTcellplate1_F07


title: CDTcellplate1_F06


title: B31_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E8_ad002


title: B30_16S rRNA


title: CDTcellplate1_F04


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E7_ad001


title: B3_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E8_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E8_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E7_ad010


title: CDTcellplate1_F02


title: B28_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E7_ad007


title: CDTcellplate1_F03


title: B36_16S rRNA


title: B27_16S rRNA


title: CDTcellplate1_F01


title: B26_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E7_ad006


title: CDTcellplate1_E11


title: CDTcellplate1_F05


title: CDTcellplate1_E10


title: B25_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E7_ad008


title: CDTcellplate1_E12


title: B24_16S rRNA


title: B23_16S rRNA


title: CDTcellplate1_E09


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E6_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E7_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E6_ad010


title: B22_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E6_ad006


title: CDTcellplate1_E06


title: B21_16S rRNA


title: CDTcellplate1_E08


title: B20_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E5_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E7_ad004


title: CDTcellplate1_E05


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E6_ad008


title: B2_16S rRNA


title: CDTcellplate1_E04


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E5_ad010


title: CDTcellplate1_E03


title: B19_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E5_ad008


title: CDTcellplate1_E02


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E5_ad007


title: B18_16S rRNA


title: B166_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E5_ad002


title: B17_16S rRNA


title: CDTcellplate1_E01


title: CDTcellplate1_D12


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E5_ad012


title: CDTcellplate1_D11


title: B165_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E5_ad004


title: CDTcellplate1_D10


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E4_ad012


title: CDTcellplate1_D08


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E4_ad007


title: CDTcellplate1_D07


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E4_ad002


title: B160_16S rRNA


title: B161_16S rRNA


title: B29_16S rRNA


title: B16_16S rRNA


title: B162_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E3_ad012


title: CDTcellplate1_D04


title: CDTcellplate1_D06


title: B159_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_F11_ad010


title: CDTcellplate1_D05


title: CDTcellplate1_E07


title: B158_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E3_ad010


title: CDTcellplate1_D09


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E3_ad001


title: CDTcellplate1_D03


title: B157_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E3_ad006


title: B164_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E4_ad001


title: B156_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E3_ad004


title: CDTcellplate1_D01


title: CDTcellplate1_D02


title: B155_16S rRNA


title: CDTcellplate1_C12


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E3_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E3_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E2_ad007


title: B153_16S rRNA


title: B151_16S rRNA


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, stranded rRNA depleted RNA seq, replicate 2

city: San Francisco

first: Srivats

last: Venkataramanan

state: California

address: 513 Parnassus Ave, HSW 740

department: Cell and Tissue Biology

institute: University of California, San Francisco

data_processing:
Ribo-seq fastq files were stripped of the adapter sequences using cutadapt. UMI sequences were removed and reads were collapsed to fasta format. Reads shorter than 20 nt were removed. Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs and miRNA (retrieved using the UCSC table browser) using bowtie2 in the ‘local’ alignment mode.
Reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 32 .gtf file. The following parameter were used:--alignEndsType EndToEnd (Ribo-seq and PAR-CLIP) --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.04 (Ribo-seq) --outFilterMismatchNmax 3 (PAR-CLIP and RNA-seq) --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outMultimapperOrder Random (All)
De-novo splice junction discovery was disabled for all datasets.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text or BigWig tracks

source_name: HCT-116 with DDX3X degron, auxin treated, DDX3X R326H transfected, stranded rRNA depleted RNA seq

growth_protocol: HCT116 cells expressing Oryza sativa TIR1 protein and miniAID-tagged DDX3X were grown in McCoy's 5A medium with 10% FBS.

extract_protocol:
Cells were resuspended in TRI reagent (Zymo), and total RNA was extracted using the DIRECTZol RNA Prep kit (Zymo)
TruSeq Stranded Total RNA kit

treatment_protocol: Cells were treated with either DMSO or 500 micromolar Indole-3-acetic-acid for indicated times and either transfected with indicated plasmids or not transfected

tag: cell line background

value: HCT-116 pCMV-OsTIR1 DDX3X-mAID

value: 500 micromolar IAA

value: DDX3X R326H transfected

tag: rna isolation

value: Total RNA


title: B152_16S rRNA

tag: tissue


title: B154_16S rRNA

tag: diagnosis


title: CDTcellplate1_C08


title: CDTcellplate1_C09


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E2_ad001

tag: brain region


title: CDTcellplate1_C10


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E2_ad010

tag: Sex


title: B150_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E2_ad006

tag: age


title: CDTcellplate1_C07


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, stranded rRNA depleted RNA seq, replicate 2

source_name: HCT-116 with DDX3X degron, auxin treated, DDX3X WT transfected, stranded rRNA depleted RNA seq

value: DDX3X WT transfected


title: B15_16S rRNA


title: CDTcellplate1_C06


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, stranded rRNA depleted RNA seq, replicate 1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E2_ad004

tag: strain


title: HCT-116 cells with DDX3X degron, auxin treated, stranded rRNA depleted RNA seq, replicate 2

source_name: HCT-116 with DDX3X degron, auxin treated, stranded rRNA depleted RNA seq


title: CDTcellplate1_C05

tag: genome build


title: B149_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E2_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E12_ad012


title: CDTcellplate1_C11

tag: sample type


title: CDTcellplate1_C04

tag: condition


title: B145_16S rRNA


title: HCT-116 cells with DDX3X degron, DMSO treated, stranded rRNA depleted RNA seq, replicate 2

source_name: HCT-116 with DDX3X degron, DMSO treated, stranded rRNA depleted RNA seq

value: DMSO


title: HCT-116 cells with DDX3X degron, auxin treated, stranded rRNA depleted RNA seq, replicate 1


title: B148_16S rRNA


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, stranded rRNA depleted RNA seq, replicate 1


title: CDTcellplate1_C03


title: HCT-116 cells with DDX3X degron, DMSO treated, stranded rRNA depleted RNA seq, replicate 1


title: B143_16S rRNA


title: B147_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E12_ad010


title: CDTcellplate1_B12


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E12_ad006


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, ribosome profiling, replicate 2

data_processing:
library strategy: ribosome profiling
Ribo-seq fastq files were stripped of the adapter sequences using cutadapt. UMI sequences were removed and reads were collapsed to fasta format. Reads shorter than 20 nt were removed. Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs and miRNA (retrieved using the UCSC table browser) using bowtie2 in the ‘local’ alignment mode.
Reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 32 .gtf file. The following parameter were used:--alignEndsType EndToEnd (Ribo-seq and PAR-CLIP) --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.04 (Ribo-seq) --outFilterMismatchNmax 3 (PAR-CLIP and RNA-seq) --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outMultimapperOrder Random (All)
De-novo splice junction discovery was disabled for all datasets.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text or BigWig tracks

source_name: HCT-116 with DDX3X degron, auxin treated, DDX3X R326H transfected, ribosome profiling

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579404

value: ribosome profiling

tag: adapter sequence

value: TAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC


title: CDTcellplate1_C02


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X R326H transfected, ribosome profiling, replicate 1


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, ribosome profiling, replicate 2

source_name: HCT-116 with DDX3X degron, auxin treated, DDX3X WT transfected, ribosome profiling


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E12_ad004


title: B141_16S rRNA


title: B142_16S rRNA


title: HCT-116 cells with DDX3X degron, auxin treated, DDX3X WT transfected, ribosome profiling, replicate 1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E12_ad001


title: CDTcellplate1_B10


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E12_ad008


title: B14_16S rRNA


title: B144_16S rRNA


title: HCT-116 cells with DDX3X degron, auxin treated, ribosome profiling, replicate 2

source_name: HCT-116 with DDX3X degron, auxin treated, ribosome profiling


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad012


title: B139_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad008


title: CDTcellplate1_C01


title: CDTcellplate1_B09


title: HCT-116 cells with DDX3X degron, auxin treated, ribosome profiling, replicate 1


title: CDTcellplate1_B11


title: B138_16S rRNA


title: CDTcellplate1_B08


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad007


title: CDTcellplate1_B07


title: B137_16S rRNA


title: CDTcellplate1_B06


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad006


title: HCT-116 cells with DDX3X degron, DMSO treated, ribosome profiling, replicate 1

source_name: HCT-116 with DDX3X degron, DMSO treated, ribosome profiling


title: B136_16S rRNA


title: B135_16S rRNA


title: CDTcellplate1_B05


title: CDTcellplate1_B04


title: MDA231ERb_E2+TNFa_rep3

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Reads were mapped using Tophat v2.1.0
Base-calling was performed using Illumina’s RTA version 2.7.7.
Mapped reads were assigned using featureCounts and batch effect correction was performed with RUVseq using a curated set of housekeeping genes to normalize the batches.
A RPKM<1.0 cutoff was used to remove lowly expressed genes.
Genome_build: Hg38

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231-ERβ cells were seeded in 10cm dishes in charcoal-stripped serum-containing medium.

extract_protocol:
RNA was isolated using TRIzol Reagent (Thermo Fischer Scientific) and an miRNeasy Mini kit (Qiagen) following the manufacturer's protocol.
RNA libraries were prepared using 200ng total RNA and the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Cells were treated with doxycyline to induce ERβ expression and vehicle or E2 at the time of seeding. Media was refreshed after 3 days. After a total of 5 days, 20ng/ml TNFα was spiked in for 3 hours

tag: cell line


title: MDA231ERb_E2+TNFa_rep1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad004


title: HCT-116 cells with DDX3X degron, DMSO treated, ribosome profiling, replicate 2


title: CDTcellplate1_B03


title: MDA231ERb_E2_rep3


title: MDA231ERb_E2+TNFa_rep2


title: MDA231ERb_E2_rep2


title: B132_16S rRNA


title: CDTcellplate1_B02


title: MDA231ERb_E2_rep1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E11_ad001


title: CDTcellplate1_B01


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E10_ad012


title: B134_16S rRNA


title: CDTcellplate1_A11


title: B13_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E10_ad010


title: B133_16S rRNA


title: MDA231ERb_TNFa_rep2

value: TNFα+dox


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E10_ad002


title: CDTcellplate1_A09


title: MDA231ERb_TNFa_rep3


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E10_ad001


title: B128_16S rRNA


title: B129_16S rRNA


title: B127_16S rRNA


title: MDA231ERb_TNFa_rep1


title: CDTcellplate1_A10


title: MDA231ERb_veh_rep3

value: veh+dox


title: B126_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E1_ad001


title: CDTcellplate1_A07


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E1_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E10_ad004


title: MDA231ERb_veh_rep2


title: MDA231ERb_veh_rep1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E1_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E1_ad006


title: CDTcellplate1_A05


title: CDTcellplate1_A06


title: CDTcellplate1_A04


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E1_ad004


title: B12_16S rRNA


title: CDTcellplate1_A03


title: B120_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E1_ad002


title: B123_16S rRNA


title: B122_16S rRNA


title: CDTcellplate1_A08


title: CDTcellplate1_A01


title: CDTcellplate1_A02


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E4_ad010


title: B125_16S rRNA


title: B163_16S rRNA


title: B119_16S rRNA


title: B116_16S rRNA


title: B117_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad006


title: B124_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E1_ad008


title: B113_16S rRNA


title: B115_16S rRNA


title: B114_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D8_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad004


title: MDA231ERb_NFkBRNAP_Input_E2+TNFa_rep1

data_processing:
Raw sequencing reads were analyzed using the HiChIP pipeline
Paired-end reads were mapped to the human reference genome (hg38) by Burrows-Wheeler Alignment (BWA) with default settings, and only pairs with at least one of the ends being uniquely mapped were retained for further analysis
Alignments were position sorted and duplicates were removed using the Picard tools
For all samples except KA41-48, peaks were called using the MACS2 algorithm  at FDR ≤ 1%. For samples KA41-KA48 K27me3, peaks were called using SICER.
Genome_build: Hg38
Supplementary_files_format_and_content: Peak files from MACS2 in BED format, and from SICER in TSV format

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Antibodies include: H3K27me3 (Abcam ab 6002), H3K27ac (Abcam ab 4729), NFκB (Cell signaling 8242), RNA Pol II phospho Ser2 (Bethyl, A300-654A)
ChIP-seq libraries were prepared from immunoprecipitated chromatin solutions and input DNA using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI).

treatment_protocol: Cells were treated with doxycyline to induce ERβ expression followed by vehicle or E2 at the time of seeding. Media was refreshed after 3 days. After a total of 5 days, 20ng/ml TNFα was spiked in for 30 minutes. Cells were then harvested via ChIP protocol.

tag: antibody

value: Input (for NFκB and RNAP)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad007


title: MDA231ERb_NFkBRNAP_Input_TNFa_rep2

description: E3-MDA_2-inp-14.FCHWYW5BBXX_L2_ITCTCGGTT

value: TNFα


title: MDA231ERb_NFkBRNAP_Input_E2+TNFa_rep2

description: E3-MDA_4-inp-16.FCHWYW5BBXX_L2_ITCCGTCTT

value: NFκB


title: B109_16S rRNA

value: human fecal tissue

value: autism spectrum disorder


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D8_ad007

value: SSs

value: male


title: B11_16S rRNA


title: B105_16S rRNA


title: MDA231ERb_NFkBRNAP_Input_E2_rep2

description: E3-MDA_3-inp-15.FCHWYW5BBXX_L2_ITAAGCGTT


title: CEMBA190124_6C_1_CEMBA190124_6C_2_E12_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D8_ad001


title: MDA231ERb_NFkBRNAP_Input_TNFa_rep1

description: E2-MDA_2-_inp-6.FCHWYW5BBXX_L1_IGCCAATGT


title: B108_16S rRNA


title: MDA231ERb_NFkBRNAP_Input_E2_rep1


title: B107_16S rRNA


title: B112_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D9_ad008


title: B106_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D8_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad001


title: MDA231ERb_NFkBRNAP_Input_veh_rep1

value: vehicle


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D8_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D8_ad006


title: MDA231ERb_NFkBRNAP_Input_veh_rep2

description: E3-MDA_1-inp-13.FCHWYW5BBXX_L2_ITGGTTGTT


title: B111_16S rRNA


title: B103_16S rRNA


title: Psoriasis5 [5851-Array1]

description: processed data file: Skin_Expression_counts.csv.gz

value: Skin Biopsies

value: Psoriasis


title: Psoriasis5 [5851-Array2]


title: B100_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad007


title: B104_16S rRNA


title: Psoriasis4 [5756-Array1]


title: B1_16S rRNA


title: Psoriasis3 [30696-Array2]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad004


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad002


title: A99_16S rRNA

value: healthy


title: Psoriasis2 [Ski304]


title: B10_16S rRNA


title: A95_16S rRNA


title: B101_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D7_ad006


title: A93_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D6_ad012


title: Psoriasis3 [30696-Array1]


title: CDTcellplate1_A12

value: Sorted CD4 T Cells from human Peripheral Blood Mononuclear Cells

value: Healthy Primary PBMCs


title: Psoriasis1 [Skin301]


title: A92_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D6_ad006


title: Normal3 [NS810]

value: Healthy


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D6_ad001


title: Normal1 [Normal]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D6_ad007


title: Normal2 [NW]


title: Psoriasis4 [5756-Array2]


title: A90_16S rRNA


title: A91_16S rRNA


title: A9_16S rRNA


title: A89_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D6_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D6_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D5_ad007


title: Leprosy1 [Lep1]

value: Leprosy


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D5_ad012


title: Leprosy2 [M10]


title: Leprosy4 [M32]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D5_ad010


title: A88_16S rRNA


title: A97_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D5_ad006


title: A87_16S rRNA


title: Leprosy3 [I63]


title: A86_16S rRNA


title: GA1 [Skin305]

value: Granuloma Annulare


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad012


title: B131_16S rRNA


title: A85_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad001


title: Alopecia1 [Skin302]

value: Alopecia Areata


title: A84_16S rRNA


title: MDA231ERb_me3ac_Input_E2+TNFa_rep1

value: Input (for H3K27)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad007


title: Acne4 [404L]

value: Acne


title: A83_16S rRNA


title: MDA231ERb_me3ac_Input_E2+TNFa_rep2


title: MDA231ERb_me3ac_Input_TNFa_rep2

value: TNFα


title: MDA231ERb_me3ac_Input_TNFa_rep1


title: Acne3 [403L]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad010


title: A82_16S rRNA

value: human fecal tissue


title: Acne2 [Skin308]


title: A80_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad006


title: Acne1 [Skin307]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad004


title: MDA231ERb_me3ac_Input_E2_rep1


title: A8_16S rRNA


title: GA2 [Skin306]


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad002


title: MDA231ERb_me3ac_Input_veh_rep2


title: A78_16S rRNA


title: A77_16S rRNA


title: MDA231ERb_me3ac_Input_veh_rep1


title: A76_16S rRNA


title: MSPB1b: Human iPSCs rep 4

city: Atherton

first: Morteza

last: Roodgar

address: 26 Selby Ln

department: Genetics

institute: Stanford University

description: RNA sequencing_low input_50 cells

data_processing: The RNAseq analysis was conducted using STAR RNA-seq aligner and RSEM transcript quantification software and the pipeline currently used for the ENCODE project (Consortium, 2004; Dobin et al., 2013; Li and Dewey, 2011). For the downstream analysis DeSEQ2 was used for differential expression analysis (Love et al., 2014). The commonly expressed genes among species were used for quantitative cross-species expression comparisons. The gene-gene interaction networks are based on known interactions on string database(Szklarczyk et al., 2016).

source_name: induced pluripotent stem cells_iPSCs

extract_protocol: The rhesus macaque blastocysts on day 5 post IVF was used for immunosurgery to remove zonae pellucidae and trophectoderm as explained elsewhere(Mitalipov et al., 2006). In summary, the zonae pellucidae of rhesus blastocysts will be removed by exposure to 0.5% pronase in TH3 medium for 45 seconds. For immunosurgical isolation of rhesus ICM to remove trophectoderm, zona pellucidae-free rhesus blastocysts were exposed to rabbit anti-rhesus spleen serum for 30 minutes at 37°C from VandeVoort laboratory at UC Davis. Subsequently, the blastocysts were washed in TH3 medium for 3 times and were incubated in guinea pig complement reconstituted with HECM-9 (1:2 vol/vol) at 37°C for 30 minutes(Mitalipov et al., 2006). After the incubation, the trophectoderm was removed mechanically using a small-bore pipette (125μM inner diameter) and the clumps of ICM cells from each blastocyst were washed in PBS and placed in a separate PCR tube containing 5μL of RNAse-free water with 5% RNAse inhibitor. The ICMs were quickly frozen on dry ice and were stored at -80°C for cDNA synthesis and RNA-seq library preparation. The cDNA synthesis and RNA-seq were conducted directly from ICM cells using SMART-Seq V4 Ultra Low input cDNA synthesis kit (Clonetech Inc.). The cDNA concentration was measured using Quibit kit and Bioanalyzer High-Sensitivity DNA kit (Agilent Inc.). The cDNA from each ICM were used for library preparation following Illumina Nextera XT kit protocol (Illumina Inc.). The quality and the quantity of the final library were evaluated using Bioanalyzer High-Sensitivity DNA kit (Agilent Inc.),Kappa kit, and the Agilent 2100 Bioanalyzer instrument. Dual index RNA-seq library from ICMs were pooled together with dual index RNAseq libraries of approximately 50 iPSCs for sequencing with dual index Illumia platform on a HiSeq 4000 sequencing machine. The low input cDNA synthesis and RNA-seq library preparation for ICMs and iPSCs were performed simultaneously on similar number of cells and pooled together to be sequenced in the same batch to minimize the potential batch effects. The sequencing coverage approximately 50 million reads per RNA-seq sample.

tag: cell type

value: iPSCs derived from blood peripheral mononuclear cells

value: untreated


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D4_ad008

value: SSs

value: male


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D3_ad004


title: A72_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D3_ad006


title: MSPB1a: Human iPSCs rep 3

description: RNA sequencing_low input_50 cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D3_ad001


title: A75_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D3_ad002


title: MSPB2a: Human iPSCs rep 1

description: RNA sequencing_low input_50 cells


title: MDA231ERb_me3ac_Input_E2_rep2


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D3_ad008


title: MSPB2b: Human iPSCs rep 2

description: RNA sequencing_low input_50 cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D2_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D2_ad001


title: A70_16S rRNA


title: A71_16S rRNA


title: A7_16S rRNA


title: A67_16S rRNA


title: A68_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D2_ad004


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D2_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D2_ad006


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D2_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D2_ad008


title: A65_16S rRNA


title: A66_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D12_ad012


title: A73_16S rRNA


title: A62_16S rRNA


title: A60_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D12_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D12_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D12_ad006


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D12_ad004


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D11_ad012


title: A61_16S rRNA


title: A59_16S rRNA


title: A6_16S rRNA


title: A58_16S rRNA


title: A69_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D11_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D11_ad007


title: A55_16S rRNA


title: A63_16S rRNA


title: A54_16S rRNA


title: DU145 C1311-treated rep 1

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

data_processing:
Sequencing data were processed to obtain fastq files with bcl2fastq2 Conversion Software v2.19.0 (Illumina, San Diego, USA) including demultiplexing and adapter trimming steps.
The quality of obtained reads was assessed using FastQC (Babraham Institute, Cambridge, United Kingdom) before the analysis, as well as after different processing steps. As all reads were of high quality, they were only soft trimmed and filtered with BBduk (U.S. Department of Energy Joint Genome Institute, Walnut Creek, USA). BBduk tool was also used to filter out fragments originated from rRNAs.
Cleaned reads were mapped to the human reference genome GRCh38 using splice-aware aligner STAR. Unique counts per gene were calculated with in-built option in STAR and used for data visualization and further differential gene expression analysis.
The quality of mapping was assessed with Flagstat module from Samtools as well as RSeQC. Mapped reads were also visually inspected with Integrative Genomics Viewer. Samples size factors were estimated, and counts were normalized using trimmed mean of M-values (TMM).
Differential expression analysis was performed with EdgeR software assuming negative binomial distribution. After model fitting, dispersion estimates were obtained, and general linearized model was applied. Likelihood ratio test (LRT) was used to call differentially expressed genes (DEGs)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw feature counts with relation to genes: gene symbols are in rows, samples in columns – from Sample 1 to Sample 12

source_name: prostate cancer

growth_protocol: Human prostate cancer LNCaP was maintained in RPMI 1640 medium, and DU-145 was maintained in MEM. All media were supplemented with 10% FBS (Biowest, Nuaille, France), 100 U/mL penicillin, and 100 g/mL streptomycin (Sigma-Aldrich). Cells were kept at 37C under a 5% CO2.

extract_protocol:
Total RNA was purified from LNCaP and DU-145 cells with miRVana Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer's instruction. Briefly, samples were lysed in a denaturing lysis solution, and RNA was extracted using Acid-Phenol:Chloroform and fibre-glass filter cartridges. Total RNA was eluted with a low ionic-strength solution provided with the kit. RNA concentration, purity, and integrity were assessed by Qubit (Invitrogen, USA) and Tape Station 2200 (Agilent Technologies, USA).
RNA-seq libraries were constructed from 1 µg of total RNA with RNA integrity number (RIN) > 8, and using the Illumina TruSeq® Stranded Total RNA Library Prep Kit (#20020598, Illumina, USA). Indexed libraries were pooled, clustered with use the cBot and sequenced on the Illumina HiSeq 4000 platform generating 150 bp paired end reads (2 x 75 bp).

treatment_protocol: Imidazoacridinones, C-1311, was synthesized at the Department of Pharmaceutical Technology and Biochemistry, at the Gdansk University of Technology (Poland). Briefly, cells were seeded, left to attach overnight and treated with the C-1311 for 24 hours.

tag: disease

value: carcinoma

tag: morphology

value: epithelial

value: treated with C-1311 for 24 hours


title: DU145 C1311-treated rep 2

tag: treatment


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D12_ad010


title: DU145 C1311-treated rep 3


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D11_ad006


title: DU145 control rep 2


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D11_ad001


title: DU145 control rep 3


title: Sample12816_Atypical

city: Atlanta

first: Arun

last: Boddapati

state: GA

address: 954 Gatewood Road, NE

department: Genomics Core

institute: Yerkes National Primate research center

data_processing:
Raw NGS reads were trimmed to remove adapters and low-quality regions using Trimmomatic v0.33 and were aligned to the human hg38 reference genome and Gencode release 26 annotation using STAR v2.5.2b. Read and alignment quality were assessed using MultiQCv1.1 to aggregate QC metrics from Picard (http://broadinstitute.github.io/picard/), FastQC v0.11.5, FastQ screen v0.9.3 and RseQC v1.1.8. Gene-level expression was quantified using RSEM v1.3.0
Genome_build: Human - hg38
Supplementary_files_format_and_content: Text files generated using RSEM v1.3.0  containing raw counts and FPKM values.

source_name: atypical MBC (CD21-CD27-)

growth_protocol: Cell culture protocol: Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were further sorted into subsets by staining with fluorophore conjugated antibodies and FACS

extract_protocol:
Cells were lysed with RLT buffer (Qiagen) and RNA was isolated using the Qiagen AllPrep 96 kit as per manufacturer's instructions except treatment with 27 units DNAse I to removegenomic DNA contamination. cDAN was synthesized using SMART-Seq v4 Ultra Low Input RNA kit
600 pg sheared cDNA was used as input into the low Inout Library Prep kit v2 (Clonetech/Takara Bio) and prepared following manufacturer's protocol Final NGS libraries were assessed on a BioAnalyzer 2100 using High Sensitivity Chips. The libraries were normalized to 0.5 nM, pooled equally and prepared for sequencing on the NextSeq (illumina, San Diego) following manufacturer's guidelines  for two mid-output 2X76 cycles.

tag: subject status

value: adult living in Malaria-endemic Mali

tag: subject id

value: Patient 3

value: 24 years

value: Male

value: Blood

value: Peripheral mononuclear blood cells (PBMCs)

tag: cell subset

value: atypical MBC (CD21-CD27-)


title: Sample12815_AcMBC

source_name: activated memroy B cell (AcMBC- CD21-CD27+)

tag: tissue


title: A53_16S rRNA

source_name: Feces

tag: diagnosis

value: healthy


title: A52_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D10_ad012

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: Sex

tag: age


title: Sample12814_CMBC

source_name: classical memory B cell (CMBC- CD21+CD27+)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D10_ad010

tag: strain


title: A51_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D10_ad008


title: Sample128123_Naive

source_name: Naïve B cells (CD21+CD27-)

value: Naïve B cells (CD21+CD27-)


title: LNCaP C-1311-treated rep 3

value: LNCaP


title: A50_16S rRNA

value: human fecal tissue


title: A57_16S rRNA


title: Sample12812_Atypical

value: Patient 2

value: 26 years


title: A5_16S rRNA


title: LNCaP C-1311-treated rep 2


title: LNCaP C-1311-treated rep 1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D10_ad006

value: SSs

value: male


title: Sample12811_AcMBC

value: activated memroy B cell (AcMBC- CD21-CD27+)


title: Sample12810_CMBC

value: classical memory B cell (CMBC- CD21+CD27+)


title: A47_16S rRNA


title: LNCaP control rep 2

value: carcinoma

value: epithelial

value: untreated


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D10_ad004


title: A46_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D10_ad002


title: DU145 control rep 1


title: LNCaP control rep 1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D11_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D10_ad001


title: Sample12808_Atypical

value: adult living in Malaria-endemic Mali

value: Patient 1

value: 24 years

value: Male


title: LNCaP control rep 3


title: A45_16S rRNA

value: healthy


title: Sample12807_AcMBC

value: Blood

value: Peripheral mononuclear blood cells (PBMCs)


title: Sample12806_CMBC


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D1_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D1_ad001


title: Sample12805_Naive

value: Naïve B cells (CD21+CD27-)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D1_ad007


title: A35_16S rRNA

value: human fecal tissue


title: A43_16S rRNA


title: A40_16S rRNA


title: A34_16S rRNA


title: A49_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D1_ad006


title: A33_16S rRNA


title: Sample12809_Naive

value: Patient 2

value: 26 years


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D1_ad004

value: SSs

value: male


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D1_ad002


title: A32_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_D1_ad008


title: A3_16S rRNA


title: OVCAR3-DAB2IP O/E 3

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

data_processing:
NextSeq read sequences were cleaned using Trimmomatic version 0.32 with the paramaters “2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17” to remove adapter sequences and perform quality trimming.
Custom perl scripts along with FASTX-Toolkit version 0.0.13.2 with the following parameters, “-l 17 -v -M 1 -i “ was also used to look for partial adapters within the read.
FASTX-Toolkit was then used to reverse complement the reads.
The resulting reads were mapped against GRCh38.p5 using TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100”. Tophat uses Bowtie, which is based on the Burrows-Wheeler transform algorithm, for sequence alignment and allows for mapping across exon junctions
Read counts for each gene were created using custom perl scripts and Gencode v24 as the annotation
Custom perl scripts were used for estimation of transcript abundances based on Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Initial differential expression analysis was carried out using the DESeq2 package (version 1.12.4) in R/Bioconductor (R version 3.3.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include RPKM values for each sample

growth_protocol: OVCAR3 cell were grown in DMEM, supplemented with 10% FBS, antibiotic-antimycotic, MEM vitamins and MEM nonessential amino acids

extract_protocol:
RNA was harvested from the adipocytes using the RNAEasy kit (Qiagen)
RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina #RS-122-2101) according to manufacter's protocol.
Poly-A tail mRNA library

treatment_protocol: In triplicate, OVCAR3 cells were transfected with empty vector or DAB2IP overexpressing vector

value: ovarian cancer cell line

tag: passages

tag: genotype/variation

value: DAB2IP O/E


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C9_ad012


title: OVCAR3-DAB2IP O/E 2

tag: cell line


title: A29_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C9_ad001


title: OVCAR3-DAB2IP O/E 1


title: A28_16S rRNA


title: m6A_IP2

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
All samples of N6-methyladenosine–sequencing (m6A-seq) and RNA-Binding Protein Immunoprecipitation sequencing (RIP-seq) studies were performed by Illumina Hiseq 4000 with single-end 50-bp read length
The deep sequencing data were aligned to human reference genome version 38 (GRCh38) using hisat2 with default setting
For m6A peaks calling, we scanning the longest isoform for each gene in 100-bp sliding window with 10-bp step to obtain read counts in each window. To reduce the influence of the sequencing depth and bias from potential inaccurate gene structure annotation, we exclude windows with less than five read counts in m6A-IP sample. The read counts in each window in each gene were normalized by the median read counts of all window of corresponding gene. m6A-enriched peaks (windows) were identified by FDR < 0.05 and log2-transformation of enrichment score >= 1. FDR was adjusted by Fisher exact test p value which assessed the differential windows between m6A-IP and input samples. Window enrichment score were calculated by (IP_C × Input_MedC)/(IP_MedC × Input_C). IP_C: read counts of the m6A-IP sample in the current peak; IP_MedC: median read counts of the m6A-IP sample in all windowns on the current isoform; Input_C: read counts of the input sample in the current peak; Input_MedC: median read counts of input sample in all windows on the current isoform.  The motifs of m6A peaks was identified by HOMER command findMotifsGenome.pl with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: excel file containing m6A peak

source_name: human cell line

growth_protocol: MDA-MB-231Br cells were grown in DMEM medium with 10% FBS and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
total RNA was extracted using Direct-zol (Zymo) from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Breast Cancer Cell

tag: antibody

value: m6A antibody (Synaptic Systems, 202003)


title: OVCAR3-empty vector 3

tag: cell type

value: empty vector


title: A27_16S rRNA


title: m6A_IP1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C9_ad006


title: A26_16S rRNA


title: OVCAR3-empty vector 1


title: OVCAR3-empty vector 2


title: m6A_Input1


title: m6A_Input2


title: RIPZ

data_processing:
All samples were sequenced by Illumina HiSeq 4000 with single-end 50-bp read length. The deep sequencing data were mapped to human genome version 38 (GRCh38).
All samples of RNA-Binding Protein Immunoprecipitation sequencing (RIP-seq) studies were performed by Illumina Hiseq 4000 with single-end 50-bp read length. The deep sequencing data were aligned to human reference genome version 38 (GRCh38) using hisat2 with default setting. After reads were mapped with hisat2, stringtie6 was  used to calculate the fragments per kilobase per million (FPKM) of each gene which represent their transcriptional expression level
Genome_build: hg38
Supplementary_files_format_and_content: excel file containing processed FPKM from input and IP samples

value: anti-YTHDF3 antibody:Santa Cruz Biotechnology #sc-377121


title: A23_16S rRNA


title: A31_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C8_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C8_ad012


title: PEM59: MODS-8d

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

description:
MODS-8d
Total RNA was isolated form the whole blood

data_processing:
RNA-Seq reads were mapped on Hg38 transcriptome using the ENSEMBL GRCh38.p3 annotation with the STAR aligner
Normalized count was obtained from the STAR aligner
Genome_build: UCSC human reference genome (hg38)
Supplementary_files_format_and_content: CSV file includes human ensembl_gene_id and normalized counts (TPM) for each gene in individual samples

source_name: Whole Blood

extract_protocol:
The total RNA was extracted using the PAXgene Blood RNA kit, following the manufacturer’s instructions. Quality and quantity of RNA were checked using a 2100 Bioanalyzer (Agilent Technologies, CA, USA) and the samples with an RNA integrity number ≥ 7 were sequenced.
Ribo-depleted RNA was used for Library preparation and paired end sequencing was performed using Illumina platform (Nextera sequencing) and sequencing chemistry according to the manufacturer’s instructions (Life Technologies, USA).

value: Whole Blood

tag: age (months)

tag: race

value: White

tag: gender

tag: disease

value: Multiple organ dysfunction syndrome (MODS)

tag: disease stage

value: 8days post treatment


title: A22_16S rRNA

value: healthy


title: PEM54: MODS-8d

value: Black

value: female


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C9_ad007


title: RIPSZ


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C8_ad007


title: InputZ


title: PEM38: MODS-8d

value: Hispanic White


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C8_ad006


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C9_ad010


title: A21_16S rRNA

value: human fecal tissue


title: PEM37: MODS-8d


title: InputSZ


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C9_ad002

value: SSs


title: A20_16S rRNA


title: A2_16S rRNA


title: PEM41: MODS-8d

value: male


title: PEM17: MODS-8d


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C8_ad002


title: A25_16S rRNA


title: PEM03: MODS-8d


title: A17_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C8_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C7_ad012


title: A169_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C7_ad010


title: PEM16: ECMO-8d

description:
ECMO-8d
Total RNA was isolated form the whole blood

value: East Asian

value: Multiple organ dysfunction syndrome (MODS) patients at extra corporeal membrane oxygenation (ECMO)  support


title: PEM55: ECMO-8d


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C7_ad004


title: A168_16S rRNA


title: PEM36: ECMO-8d


title: A167_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C7_ad002


title: A166_16S rRNA


title: PEM51: ECMO-8d


title: PEM09: MODS-8d


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C8_ad004


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C7_ad008


title: A19_16S rRNA


title: A165_16S rRNA


title: A18_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C7_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C6_ad012


title: PEM61: MODS-72h

description:
MODS-72h
Total RNA was isolated form the whole blood

value: 72h post treatment


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C6_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C6_ad007


title: PEM58: MODS-72h


title: PEM46: MODS-72h


title: A162_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C6_ad004


title: A161_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C6_ad002


title: PEM14: MODS-72h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C6_ad006


title: A16_16S rRNA


title: A159_16S rRNA


title: PEM40: MODS-72h


title: A164_16S rRNA


title: A163_16S rRNA


title: PEM42: MODS-72h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C5_ad012


title: A158_16S rRNA


title: PEM22: MODS-72h


title: A160_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C5_ad007


title: A157_16S rRNA


title: PEM07: MODS-72h


title: A156_16S rRNA


title: A155_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C5_ad001


title: PEM39: MODS-72h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C5_ad006


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C5_ad010


title: PEM28: MODS-72h


title: PEM12: MODS-72h


title: A154_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C5_ad004


title: PEM29: MODS-72h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C6_ad008


title: PEM43: MODS-72h


title: A153_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C5_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C4_ad012


title: PEM06: MODS-72h


title: PEM30: MODS-72h


title: PEM63: ECMO-72h

description:
ECMO-72h
Total RNA was isolated form the whole blood


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C4_ad007


title: A149_16S rRNA


title: A150_16S rRNA


title: A151_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C4_ad006


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C4_ad010


title: PEM21: ECMO-72h


title: PEM53: ECMO-72h


title: PEM35: ECMO-72h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C4_ad002


title: A148_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C4_ad004


title: PEM25: ECMO-72h


title: A147_16S rRNA


title: A145_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C3_ad001


title: A144_16S rRNA


title: A152_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C3_ad007


title: A143_16S rRNA


title: PEM19: CT

description:
CT
Total RNA was isolated form the whole blood

value: Control


title: PEM34: CT


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C3_ad010


title: A142_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C3_ad006


title: PEM49: MODS-72h

value: Hispanic Black


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C3_ad004


title: A141_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C4_ad008


title: A146_16S rRNA


title: PEM60: MODS-0h

description:
MODS-0h
Total RNA was isolated form the whole blood


title: PEM20: CT


title: A140_16S rRNA


title: PEM56: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C3_ad002


title: PEM24: CT


title: PEM48: MODS-0h


title: A14_16S rRNA


title: A137_16S rRNA


title: PEM44: MODS-0h


title: PEM45: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad007


title: A136_16S rRNA


title: PEM13: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad012


title: PEM05: MODS-8d


title: PEM15: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad006


title: PEM32: MODS-0h


title: PEM31: MODS-0h


title: PEM18: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad004


title: A135_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad002


title: A132_16S rRNA


title: A131_16S rRNA


title: A133_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C2_ad008


title: A129_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad012


title: A130_16S rRNA


title: PEM11: MODS-0h


title: PEM08: MODS-0h


title: A139_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad010


title: PEM02: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C3_ad008


title: DNA_guide_barcode_association_spike2

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington

description:
amplicon-derived DNA
unique_barcode_guide_associations.txt.gz

data_processing:
These were the processing steps for the unique_barcode_guide_associations.txt.gz processed data file: Reads were aligned with bowtie2 version 2.3.5. First two bowtie indices were built with default parameters, one index based on the amplicon sequence where the barcode positions were replaced with ‘N’s and another index based on the amplicon sequence with one version per guide. The read fragment fastq files including the barcode segment was aligned to the barcode-specific bowtie index with ‘--n-ceil L,18,0.15’ and otherwise default parameters. The read fragment fastq files containing the gRNA sequence were aligned to the gRNA-specific bowtie index with default parameters. From the bam output of these alignments, for each read we extracted the gRNA fragment which the read aligned to and the random barcode sequence. We excluded read fragments with Ns in the barcode and fragments that had barcodes paired with multiple guides.
These were the processing steps for the transMPRA_construct_counts.txt.gz processed data file: Before aligning reads to the construct, overlapping reads were merged with pear version 0.9.10 with the flags ‘-n 240 -m 260’ and otherwise default parameters. For alignment we constructed a bowtie2 (version 2.2.5) index with default parameters using a fasta file generated from the construct sequence with a distinct sequence for each enhancer and ‘N’ values at the random barcode region. The bowtie2 alignment was performed with ‘--threads 4’, ‘--n-ceil L,18,0.15’, and the pear-merged reads as the input. Following read alignment we summarized each read by the enhancer it best aligns to as well as the random barcode sequence. We used the file of unique guide and barcode pairs described above to perfectly match barcodes to guides. Finally, reported counts were already collapsed by UMI.
Genome_build: NA
Supplementary_files_format_and_content: The unique barcode guide file contains the aligned guide in the first column, followed by the unique 18-bp random barcode identifier, and finally the reverse complement of the 18-bp barcode identifier.
Supplementary_files_format_and_content: The transMPRA construct counts file contains the enhancer identifier, the construct guide, the barcode identifier, the number of reads aligning to that particular construct, the assay, the time of cell harvest post transfection, the library transfection condition, the replicate number, the sample identifier, the unique construct identifier, followed by the target gene knockdown.

organism: synthetic construct

source_name: amplicon

growth_protocol: Standard K562 growth conditions were applied, specifically: The cells were grown at 37°C and cultured in RPMI 1640 with L-Glutamine (GIBCO) along with 10% FBS and 1% penicillin-streptomycin (GIBCO).

extract_protocol:
Following our experimental design at day 5 and day 10 post transfection, cells were harvested, genomic DNA and total RNA were extracted using the AllPrep DNA/RNA mini kit (Qiagen 80204). We extracted mRNA from total RNA with the Oligotex Direct mRNA mini kit (Qiagen 72022).
We used a One-Step RT-PCR kit (Thermofisher 12595025) with custom primers to produce cDNA from the mRNA and subsequently ran 3 cycles of PCR which included a P5 adapter, sample-specific p5 index (8 bp), UMI (10bp) and P7 adapter. RT-PCR products were cleaned with AMPure XP beads (Beckman Coulter A63880). Next, we amplified the library using P5/P7 primers. Finally, the resulting PCR-amplified cDNA library was pooled at an equimolar ratio then size-selected on a 1.5%-agarose gel. DNA was processed with a similar two-step PCR approach. First, we PCR amplified the DNA for 3 cycles, which incorporated a P5 adapter, sample-specific p5 index (8 bp), UMI (10 bp), and P7 adapter. PCR products were cleaned with AMPure XP beads (Beckman Coulter A63880). Next, we amplified the library using P5/P7 primers. Finally, the resulting PCR-amplified DNA library was pooled at an equimolar ratio and then size-selected on an agarose gel. All RNA and DNA libraries were pooled and sequenced on an Illumina NextSeq instrument. Paired-end reads of 150 base pairs were sequenced from the forward and reverse end of the amplified fragment.
OTHER: RNA-seq and DNA-seq

treatment_protocol: Cells were electroporated with the transMPRA library and piggyBac transposase.

tag: condition

tag: time harvested


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad008


title: PEM50: MODS-0h

tag: tissue


title: A126_16S rRNA

data_processing:
Library strategy: 16S rRNA DNA-seq
Paired-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence.
Paired-end reads were merged using FLASH (http://ccb.jhu.edu/software/FLASH/). Quality filtering on the raw tags were performed under specific filtering conditions to obtain the high-quality clean tags according to the QIIME (http://qiime.org/index.html) quality controlled process.
The tags were compared with the reference database (Gold database, http://drive5.com/uchime/uchime_download.html) using UCHIME algorithm (UCHIME Algorithm, http://www.drive5.com/usearch/manual/uchime_algo.html) to detect chimera sequences, and then the chimera sequences were removed.
Sequences analysis were performed by Uparse software (http://drive5.com/uparse/). Sequences with ≥97% similarity were assigned to the same OTUs.
For each representative sequence, the GreenGene Database (http://greengenes.lbl.gov/cgi-bin/nph-index.cgi) was used based on RDP classifier (http://sourceforge.net/projects/rdp-classifier/) algorithmto annotate taxonomic information. OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences.
Supplementary_files_format_and_content: For predicted OTU, the sequences of 16S rRNA V4 region are shown in “Autism 16S rRNA OTU.xls”. The assignment and frequency of OTU in each sample are shown in “Autism 16S rRNA OTU assignment and frequency.xls”, the number in "Autism 16S rRNA OTU frequency" is the frequency of each OTU in each sample.

tag: diagnosis


title: A125_16S rRNA


title: DNA_guide_barcode_association_spike1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad007

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

tag: brain region

tag: Sex


title: PEM04: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad004

tag: age

tag: strain


title: PEM27: MODS-0h


title: A122_16S rRNA


title: PEM26: MODS-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad006


title: A124_16S rRNA


title: A123_16S rRNA


title: PEM57: ECMO-0h

description:
ECMO-0h
Total RNA was isolated form the whole blood


title: A121_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad002


title: A128_16S rRNA


title: PEM47: ECMO-0h


title: A12_16S rRNA


title: PEM23: ECMO-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C11_ad012


title: PEM52: ECMO-0h


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C11_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C11_ad007


title: A118_16S rRNA


title: A120_16S rRNA


title: A117_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C11_ad004


title: B164_metagenomic

data_processing:
Library strategy: Metageomic-seq
Sequencing results pretreatment. Preprocessing the Raw Data obtained from the Illumina HiSeq sequencing platform using Readfq V8.0 was conducted to acquire the Clean Data for subsequent analysis. Considering the possibility of host pollution may exist in samples, Clean Data need to be blast to the host database which default using Bowtie2.2.4 software.
Metagenome Assembly. To the samples taken from non-complex environment, such as intestine, faeces and so on, the Clean Data is assembled and analyst by SOAP denovo software the parameters are as follows: -d 1, -M 3, -R, -u, -F, -K 55. All samples’ Clean Data are compared to each Scaffolds respectively by Bowtie 2.2.4 software to acquire the PE reads not used and the parameters are: --end-to-end, --sensitive, -I 200, -X 400. All the reads not used in the forward step of all samples are combined and then use the software of SOAPdenovo (V2.04) / MEGAHIT (v1.0.4-beta) for mixed assembly with the parameters same as single assembly
Gene prediction and abundance analysis. The Scaftigs (≥ 500 bp) assembled from both single and mixed are all predicted the ORF by Meta Gene Mark software. For ORF predicted, CD-HIT software is adopted to redundancy and obtain the unique initial gene catalogue. The Clean Data of each sample is mapped to initial gene catalogue using Bowtie 2.2.4. The basic information statistic, core-pan gene analysis, correlation analysis of samples and venn figure analysis of number of genes are all based on the abundance of each gene in each sample in gene catalogue.
Taxonomy prediction. DIAMOND software V0.9.9 is used to blast the Unigenes to the sequences of Bacteria, Fungi, Archaea and Viruses which are all extracted from the NR database. Choosing the result of which the e value ≤ the smallest e value * 10 to take the LCA algorithm which is applied to system classification of MEGAN software to make sure the species annotation information of sequences. The table containing the number of genes and the abundance information of each sample in each taxonomy hierarchy (kingdom, phylum, class, order, family, genus, species) are obtained based on the LCA annotation result and the gene abundance table.
Common functional database annotations. Adopt DIAMOND software (V0.9.9) to blast Unigenes to functional database with the parameter setting of blastp, -e 1e-5. Functional database exclude KEGG, eggNOG, CAZy database. Statistic of the relative abundance of different functional hierarchy, the relative abundance of each functional hierarchy equal the sum of relative abundance annotated to that functional level. Based on the function annotation result and gene abundance table, the gene number table of each sample in each taxonomy hierarchy is obtained. Based on the abundance table of each taxonomy hierarchy, not only the counting of annotated gene numbers, the exhibition of the general relative abundance situation, the exhibition of abundance cluster heat map and the decrease-dimension analysis of PCA and NMDS are conducted, but also the Anosim analysis of the difference between groups (inside) based on functional abundance, comparative analysis of metabolic pathways, the Metatat and LEfSe analysis of functional difference between groups are performed.
Resistance gene annotation. Use DIAMOND software (V0.9.9) to align the Unigenes to ARDB database with the parameter setting are blastp，-e 1e-5. Filter the aligned result and choose the identity value bigger than the lowest identity value from the aligned result of each sequence, which the database required to make sure the resistance gene annotation is reliable. Based on the abundance of resistance genes, the abundance bar charts, the abundance cluster heat map and the resistance genes’ number difference between groups are displayed. In the same way, the resistance genes’ abundance distribution in each samples, the species attribution analysis of resistance genes and the resistance mechanism of resistance genes analysis are also conducted.
Supplementary_files_format_and_content: For predicted genes, the CDS sequences of unigenes are shown in “Unigenes.CDS.cdhit.fa”, and the frequency of unigenes in each sample are shown in “Unigenes.readsNum.xls”. For predicted protein, the amino acid sequences of unigenes are shown in “Unigenes.protein.cdhit.fa”, and the frequency of protein in each sample are shown in “Unigenes.protein.table.txt”. For predicted taxa annotation and frequency, the processed data are shown in “Unigenes.absolute.xls”. Considering elementary of samples, the taxa annotation of each sample are show in “Unigenes.absolute,sample,xls”.

source_name: Human feces

extract_protocol:
Total genome DNA of fecal samples was extracted using the kit (#DP328, Tiangen Biotech Co. Ltd., Beijing, China). A total amount of 1μg DNA per sample was used as input material for the DNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, the DNA sample was fragmented by sonication to a size of 350 bp, then DNA fragments were end polished, A-tailed, and ligated with the full-length adaptor for Illumina sequencing with further PCR amplification. At last, PCR products were purified (AMPure XP system) and libraries were analysed for size distribution by Agilent2100 Bioanalyzer and quantified using real-time PCR.

treatment_protocol: Fecal samples were obtained at the homes of each participant, and were immediately frozen in their home freezer. Frozen samples were stored within insulating polystyrene foam containers, and stored at -80 ℃ until analysis. The time span from sampling to delivery to the hospital was intended to be as short as possible with a maximum of 24 hours.

value: feces

value: Autism spectrum disorder


title: PEM01: ECMO-0h

value: Whole Blood

value: White


title: PEM10: ECMO-0h


title: A119_16S rRNA

extract_protocol:
Total genome DNA of fecal samples was extracted using the kit (Tiangen Company, Beijing, China). The DNA concentration was performed using Qubit@ 2.0 Fluorometer (Thermo Scientific). DNA quality was also monitored on 1% agarose gels. PCR was performed to produce V4 regions of the 16S rDNA gene using the conserved primers 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’). PCR products and operate electrophoresis on 2% agarose gel for detection. Samples with bright main strip between 400-450bp were chosen for purifing with GeneJET Gel Extraction Kit (Thermo Scientific). PCR fragments were sequenced by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China).
Libraries was sequenced on an Illumina HiSeq platform and 250 bp paired-end reads were generated.


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C11_ad006

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: A116_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C12_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C11_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C10_ad012


title: A113_16S rRNA


title: A114_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C10_ad007


title: A115_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C10_ad008


title: A112_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C10_ad006


title: B156_metagenomic


title: B143_metagenomic


title: A110_16S rRNA


title: B152_metagenomic


title: A111_16S rRNA


title: B141_metagenomic


title: B142_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C10_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C10_ad002


title: A109_16S rRNA


title: A11_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C1_ad012


title: B132_metagenomic


title: A108_16S rRNA


title: B158_metagenomic


title: B120_metagenomic


title: B115_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C11_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C1_ad001


title: A106_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C1_ad010


title: KP panc Atg7_KO +Atg7 tumor rep3

city: New York

first: Xiphias

middle: Ge

last: Zhu

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Reads were mapped to the mouse transcriptome (mm10, Ensembl annotations) using STAR (v2.7).
FeatureCounts (v1.6) was used to count exonic reads (with -O option) and DESeq2 v1.20 (R v3.5.1) was used to normalize and compare samples.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include TPM values for each sample.

source_name: KP pancreas cancer cells

extract_protocol:
Cells were harvested, tumors were homogenized and RNA was isolated by Qiagen Rneasy kit and 1ug of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared using standard Illumina protocols

tag: growth protocol

value: Subcutaneous tumor

tag: genotype

value: Atg7_KO expressing Atg7 cDNA

tag: treatment


title: B114_metagenomic


title: A105_16S rRNA

value: healthy


title: A104_16S rRNA


title: B127_metagenomic


title: B106_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C1_ad006


title: B111_metagenomic


title: KP panc Atg7_KO +Atg7 tumor rep1


title: B103_metagenomic


title: A102_16S rRNA


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C1_ad004


title: KP panc Atg7_KO +Vector tumor rep3

value: Atg7_KO expressing empty vector


title: KP panc Atg7_KO +Vector tumor rep2


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C1_ad002


title: A100_16S rRNA


title: B99_metagenomic


title: KP panc Atg7_KO +Vector tumor rep1


title: A101_16S rRNA


title: B94_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_C1_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B9_ad012


title: KP panc Atg7_KO +Atg7 +TNF rep3

value: In vitro

value: 24hrs with 100 ng/mL TNFalpha


title: A10_16S rRNA

value: human fecal tissue


title: B37_metagenomic


title: KP panc Atg7_KO +Atg7 +TNF rep2


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B9_ad001

value: SSs

value: male


title: KP panc Atg7_KO +Atg7 tumor rep2


title: A1_16S rRNA


title: B36_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B9_ad006


title: KP panc Atg7_KO +Atg7 +TNF rep1


title: KP panc Atg7_KO +Atg7 -TNF rep3


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B9_ad004


title: B29_metagenomic


title: KP panc Atg7_KO +Atg7 -TNF rep2


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B9_ad002


title: B28_metagenomic


title: KP panc Atg7_KO +Vector +TNF rep3


title: B13_metagenomic


title: B14_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B8_ad012


title: B7_metagenomic


title: KP panc Atg7_KO +Vector +TNF rep1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B8_ad001


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B9_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B8_ad007


title: B6_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B8_ad010


title: KP panc Atg7_KO +Vector -TNF rep3


title: B5_metagenomic


title: KP panc Atg7_KO +Atg7 -TNF rep1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B8_ad006


title: KP panc Atg7_KO +Vector -TNF rep2


title: KP panc Atg7_KO +Vector -TNF rep1


title: B8_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B8_ad004


title: KP panc Atg7_KO +Vector +TNF rep2


title: B2_metagenomic


title: A165_metagenomic

value: healthy control


title: A149_metagenomic


title: B3_metagenomic


title: B1_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B7_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B7_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B8_ad008


title: A164_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B7_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B7_ad001


title: C57BL/6 1

city: Los Angeles

first: Benjamin

middle: Pierre

last: Hurrell

address: 1450 Biggy Street

department: MMI

institute: University of Southern California

description: BH181207 - sample 18

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR (v3.5.3) with default parameter settings
Gencode M20 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

source_name: sorted ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated ILC2s after 3 i.n. injections of 0.5µg rm-IL33

tag: background strain

value: wildtype

value: lung

tag: cell type

value: 6 weeks


title: ICAM-1 KO 1

description: BH181207 - sample 22

value: ICAM-1 KO


title: ICAM-1 KO 2

description: BH181207 - sample 23


title: C57BL/6 2

description: BH181207 - sample 20


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B7_ad004


title: A142_metagenomic

value: feces


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B7_ad002


title: A144_metagenomic


title: A115_metagenomic


title: A114_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B6_ad012


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B7_ad008


title: ESC2_OHT

city: Bethesda

first: Eros

last: Lazzerini Denchi

state: MD

address: 9000 Rockville Pike building 37, room 2144B

institute: National Cancer Institute

data_processing:
fastq files were aligned to version 98 of mouse reference genome GRCm38 using Salmon
Transcript abundance files (txi) files generated in Salmon were analyzed using DESeq2 using tximport
Multifactor analysis using the pasilla package was used to compare cell type and treatment
Differentially expressed genes were identified by linear modeling  using the pasilla package: genotype + cell type
Wald test was used to evaluate p-values
Genome_build: version 98 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes counts per million (CPM) values for each Sample ...

source_name: Mouse ES

growth_protocol: Cells were plated in 10 cm plates and placed in a 5% CO2 37 °C incubator for 96hrs

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were either left unstimulated, or stimulated with OHT for 3 days

value: OHT

value: ESC


title: FLICs_OHT

source_name: Differentiated ES (FLICS)

value: FLICs


title: ESC_OHT


title: ESC2

value: wild-type

value: untreated


title: FLICs

description: FLICs


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B6_ad001


title: ESC

description: ESC


title: A113_metagenomic

city: Nanjing City

first: Xingyin

last: Liu

institute: Nanjing Medical University


title: A109_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B6_ad006

city: La Jolla

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute


title: A93_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B6_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B6_ad004


title: A101_metagenomic


title: A87_metagenomic


title: A89_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B6_ad008


title: A78_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B5_ad012


title: DNA methylation in 293FT with shLuc and mock treatment (4w)_rep2

type: genomic

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

institute: Hoshi University

description: Normal cells

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System.

data_processing: The data were analyzed using GenomeStudio Methylation Module Software.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were maintained in DMEM medium.

extract_protocol: Genomic DNA was extracted by standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).

treatment_protocol: cells with TET3 knockdown were treated with NOC18 (or mock treated) for 4, 10, and 20 weeks

tag: cell line

tag: shRNA

value: shLuc

tag: agent

value: mock

tag: time point


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B6_ad002


title: DNA methylation in 293FT with shLuc and NOC18 treatment (4w)_rep2

description: Normal cells


title: DNA methylation in 293FT with shTET3#2 and NOC18 treatment (10w)

description: Normal cells


title: DNA methylation in 293FT with shTET3#2 and mock treatment (10w)

description: Normal cells


title: A76_metagenomic


title: DNA methylation in 293FT with shLuc and mock treatment (4w)_rep3

description: Normal cells


title: DNA methylation in 293FT with shLuc and NOC18 treatment (4w)_rep3

description: Normal cells


title: A73_metagenomic


title: DNA methylation in 293FT with shTET3#3 and NOC18 treatment (4w)

description: Normal cells


title: DNA methylation in 293FT with shTET3#3 and mock treatment (10w)

description: Normal cells


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B5_ad007


title: A71_metagenomic


title: DNA methylation in 293FT with shTET3#2 and mock treatment (4w)

description: Normal cells


title: DNA methylation in 293FT with shTET3#1 and mock treatment (20w)

description:
Normal cells
sh_SAMPLE 10
Raw data file: non-normalized_data_sh.txt

tag: time


title: DNA methylation in 293FT with shLuc and NOC18 treatment (20w)

description:
Normal cells
sh_SAMPLE 11
Raw data file: non-normalized_data_sh.txt

value: TET3 knockdown


title: A69_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B5_ad002


title: A68_metagenomic


title: DNA methylation in 293FT with shTET3#3 and mock treatment (4w)

description: Normal cells


title: DNA methylation in 293FT with shTET3#2 and NOC18 treatment (4w)

description: Normal cells


title: DNA methylation in 293FT with shTET3#3 and NOC18 treatment (10w)

description: Normal cells


title: DNA methylation in 293FT with shTET3#1 and NOC18 treatment (20w)

description:
Normal cells
sh_SAMPLE 12
Raw data file: non-normalized_data_sh.txt


title: A67_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B5_ad004


title: DNA methylation in 293FT with shLuc and NOC18 treatment (4w)_rep1

description:
Normal cells
sh_SAMPLE 6
Raw data file: non-normalized_data_sh.txt


title: DNA methylation in 293FT with shTET3#1 and mock treatment (4w)

description:
Normal cells
sh_SAMPLE 7
Raw data file: non-normalized_data_sh.txt


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B5_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B5_ad006


title: A59_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B5_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B4_ad007


title: DNA methylation in 293FT with shTET3#1 and NOC18 treatment (4w)

description:
Normal cells
sh_SAMPLE 8
Raw data file: non-normalized_data_sh.txt


title: A54_metagenomic


title: A53_metagenomic


title: A52_metagenomic


title: DNA methylation in 293FT with shTET3#1 and mock treatment (10w)

description:
Normal cells
sh_SAMPLE 3
Raw data file: non-normalized_data_sh.txt


title: NCC – CTCF HiChIP rep2

city: Buffalo

first: Brandon

last: Decker

address: 955 Main St

department: Pathology and Anatomical Sciences

institute: University at Buffalo

description:
HiChIP Genomic DNA
NCC_CTCF_HiChIP_combined.bedpe

data_processing:
HiC Pro v2.11.1
Preprocessing and identifying valid chromatin interaction pairs.
The 2 biological replicates for each condition were processed together by HiC Pro.
Default Settings
Hichipper v0.7.3
Binning valid interaction pairs to calculate interaction strength.
Default Settings (EACH ALL)
ESC and NCC of the same condition were normalized to same number of valid interaction pairs (sampled) prior to running Hichipper.
Genome_build: mm10

source_name: Neuronal Committed Cells

growth_protocol: ES cells were routinely generated by re-plating adherent cultures on bovine skin gelatin coated plastic in DMEM media supplemented with 100U/mL Leukemia Inhibitory Factor (LIF).

extract_protocol:
Cells grown on 10 cm plates in culture  were fixed in 1% formaldehyde, scraped into collection tubes, and then prepared using the Hi-C (Rao et. al. 2014) or HiChIP (Mumbach et. al. 2016) protocols.
Libraries were constructed using Illumina tn5 transposase on HiC and HiChIP interaction libraries followed by PCR amplification using a multiplex bar-coded PCR primer set.

treatment_protocol: ES cells were induced into neural differentiation by washing cells with DPBS and then administering 1 uM Retinoic Acid in LIF-free media to cells for 48 hours.

value: ES-derived neural committed cells

tag: chip antibody

value: CTCF (ab70303 Abcam)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B4_ad010

value: SSs

value: male


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B4_ad006


title: NCC – FGFR1 HiChIP rep1

description:
HiChIP Genomic DNA
NCC_FGFR1_HiChIP_combined.bedpe

value: FGFR1 (ab10646 Abcam)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B4_ad001


title: A51_metagenomic

address: Long Mian Street No.1

tag: tissue

value: healthy control


title: A31_metagenomic

tag: diagnosis


title: NCC – Hi-C rep1

description:
HiC Genomic DNA
NCC_HiC_combined.bedpe


title: NCC – Hi-C rep2

description:
HiC Genomic DNA
NCC_HiC_combined.bedpe


title: ESC – CTCF HiChIP rep2

description:
HiChIP Genomic DNA
ESC_CTCF_HiChIP_combined.bedpe

source_name: Embryonic Stem Cells

value: ES cells


title: DNA methylation in 293FT with shLuc and mock treatment (20w)

description:
Normal cells
sh_SAMPLE 9
Raw data file: non-normalized_data_sh.txt


title: A6_metagenomic


title: ESC – CTCF HiChIP rep1


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B4_ad002

address: 10010 North Torrey Pines Road

tag: brain region


title: A9_metagenomic


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B3_ad012

tag: Sex


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B3_ad001

tag: age


title: DNA methylation in 293FT with shLuc and mock treatment (4w)_rep1

description:
Normal cells
sh_SAMPLE 5
Raw data file: non-normalized_data_sh.txt


title: SAMPLE 8: DNA methylation in WT #4-5 NOC18 10w

description: Normal cells

source_name: 293FT with  NOC18 treatment

treatment_protocol: cells were treated with NOC18 (or mock treated) for 10 weeks

value: 293FT wild type


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B3_ad006

tag: strain


title: ESC – FGFR1 HiChIP rep2

description:
HiChIP Genomic DNA
ESC_FGFR1_HiChIP_combined.bedpe


title: NCC – FGFR1 HiChIP rep2


title: SAMPLE 7: DNA methylation in WT #4-5 mock 10w

description: Normal cells


title: A3_metagenomic

value: feces


title: A5_metagenomic


title: DNA methylation in 293FT with shLuc and mock treatment (10w)

description:
Normal cells
sh_SAMPLE 1
Raw data file: non-normalized_data_sh.txt


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B3_ad004


title: ESC – FGFR1 HiChIP rep1


title: NCC – CTCF HiChIP rep1


title: ESC – Hi-C rep2

description:
HiC Genomic DNA
ESC_HiC_combined.bedpe


title: SAMPLE 6: DNA methylation in WT #4-4 NOC18 10w

description: Normal cells


title: ESC – Hi-C rep1

description:
HiC Genomic DNA
ESC_HiC_combined.bedpe


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B2_ad012


title: DNA methylation in 293FT with shTET3#1 and NOC18 treatment (10w)

description:
Normal cells
sh_SAMPLE 4
Raw data file: non-normalized_data_sh.txt


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B2_ad002


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B3_ad002


title: DNA methylation in 293FT with shLuc and NOC18 treatment (10w)

description:
Normal cells
sh_SAMPLE 2
Raw data file: non-normalized_data_sh.txt


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B2_ad004


title: SAMPLE 2: DNA methylation in TKO #4-20 NOC18 10w

description: Normal cells

source_name: 293FT with TET triple KO (TET1, TET2, TET3) and NOC18 treatment


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad010


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B2_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad007


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad012


title: SAMPLE 1: DNA methylation in TKO #4-20 mock 10w

description: Normal cells

source_name: 293FT with TET triple KO (TET1, TET2, TET3)


title: SAMPLE 4: DNA methylation in TKO #4-22 NOC18 10w

description: Normal cells

value: 293FT with TET triple KO (TET1, TET2, TET3)


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad008


title: CEMBA190124_6C_1_CEMBA190124_6C_2_B12_ad006


title: D.7 Itk-/- LMN4 rep3

city: Ithaca

first: sabrina

last: solouki

address: 530 Campus Rd.

department: Immunology and Infectious Disease

institute: Cornell university

description:
D7LMN4_FPKM.txt
d7-WT-LMN4C

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts and cuffnorm v2.2.1 was used to generate FPKM values for annotated genes.
Genes with FPKM and annotation were further analyzed in Genespring for PCA, clustering, and differential gene expression. GSEA was also used to analyze biological pathways and enriched genes based on ratios.
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: text file with FPKM

source_name: CD44lowCD122low CD8+ T cells from Spleen; CD45.1-CD45.2+ post-adoptive transfer

extract_protocol:
CD8+ T cells were sorted from spleens, pelleted, frozen at -80C. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Directional RNA-seq libraries were prepared from 50ng total RNA per sample using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation, by the RNA Sequencing Core at Cornell University.

treatment_protocol: Infection with Listeria monocytogenes expressing N4 OVA or T4 OVA peptide variant

value: CD8+ T cells

tag: donor mouse strain

tag: recipient mouse strain

tag: itk genotype

value: Itk-/-

tag: timepoint

value: day 7

tag: listeria treatment