title: Time series in DD conditions in the OE1 line [OE-1_13_A]

description:
OE-1_13_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: 7785496089_R01C01

status: Public on May 24 2019

type: genomic

city: Hefei

first: Chao

last: Yang

address: #69 Meishan Road, Hefei230032, Anhui, China

country: China

institute: First Affiliated Hospital of Anhui Medical University

hyb_protocol: The whole genome genotyping was conducted at Chinese National Human Genome  Center at Shanghai, China. Approximately 200ng of genomic DNA was used for  genotyping analysis. Briefly, each sample was whole-genome amplified, fragmented,  precipitated and resuspended in appropriate hybridization buffer.

scan_protocol: After  hybridization, the BeadChip oligonucleotides were extended by a single labeled base,  which was detected by fluorescence imaging with an Illumina Bead Array Reader.

data_processing:
Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).
Processed data file includes: Genotype: AA,AB,BB,or NC (no call), GC Score, Theta, R, B Allele Freq and Log R ratio

label: not provided

molecule: genomic DNA

organism: Homo sapiens

source_name: Public control

label_protocol: not provided

extract_protocol: Genomic DNA was extracted from peripheral blood lymphocytes by standard  procedures (Miller et al, 1988) using Flexi Gene DNA kits (QIAGEN, Germany)

tag: gender

value: Unknown

tag: tissue

value: Whole blood

tag: disease state

value: Chronic inflammatory skin disease


title: Tfh17_1

type: SRA

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

country: USA

institute: Stanford University

description: Ensemble RNA-seq

library_source: transcriptomic

data_processing:
Adapter trimming by cutadapt (version 1.17)
Aligned to the GRCh38 reference genome using STAR (version 2.6.1a)
Filter multi-mapping reads with samtools (version 1.7)
Count using featureCounts (version 1.6.2) using Ensembl GRCh38 GTF transcript annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: text file with raw read counts

molecule: polyA RNA

source_name: Primary T cell sorted from peripheral blood

growth_protocol: Sorted from PBMCs

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit (Clontech);
Nextera XT DNA Library Prep Kit (Illumina)

tag: cell type

value: Tfh17 CD4+ T cell

tag: donor

tag: disease status

value: healthy


title: Tfh1_2

description: Ensemble RNA-seq

value: Tfh1 CD4+ T cell


title: 7785488092_R05C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Time series in DD conditions in the Wt [Wt_19_C]

type: RNA

city: Paris

first: Angela

last: Falciatore

address: 15 rue de l'ecole de Medicine

department: UMR 7238, LCQB

country: France

institute: CNRS

description:
Wt_19_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.

hyb_protocol: For each hybridization, 100 ng of was used. Hybridization and washes were performed according to manufacturer’s protocols (http://www.nanostring.com) by the Plateforme nanostring, Institut Curie, Paris, France.

scan_protocol: Scanning was performed according to manufacturer’s protocols (http://www.nanostring.com) by the Plateforme nanostring, Institut Curie, Paris, France.

data_processing: Raw data were normalized using the internal spike-in control probes, then RNA counts were normalized using the geometric mean of three reference genes (rps, tbp and actin12) and presented as the log2 ratio between the gene and the normalizers expression.

molecule: total RNA

organism: Phaeodactylum tricornutum

source_name: Cellular culture, preadapted to 16L:8D cycles

label_protocol: Un-labeled total RNA has been hybridized using biotin and fluorescence tag labeled gene-specific probes.

growth_protocol: The Wt CCMP632 strain of Phaeodactylum tricornutum Bohlin (Pt1 8.6) and the OE-1 line were routinely grown in f/2 medium (Guillard, 1975) at 18°C under white fluorescent lights (Philips TL-D De Luxe Pro 950) in 16L:8D cycles under 40 µmol m-2 s-1 of photons. Cultures were kept in exponential growth phase diluting them every three days with fresh medium and their axenicity assessed through contamination tests. Triplicate cultures of each treatment were grown in 1000 ml Erlenmeyers, shaked at 100 rpm to prevent settling of cells.

extract_protocol: 100 ml of culture (10^8 total cells) were filtered (grade 589/2, Whatman, 28414108), washed with PBS and flash frozen in liquid nitrogen. Total RNA was extracted by adding TriPure isolation Reagent (Roche, 11667165001) to the frozen filters and following the manufacturer’s instructions, with a further purification by ammonium acetate precipitation as described in Huysman et al., 2013. The recovered RNA was then quantified using a spectrophotometer and its integrity checked on 2% agar gel.

treatment_protocol: Cell culture was pre-adapted to 16L:8D regime and put in DD condition. Sampling started at the beginning of the day (time point 1), sampling every 3 hours for 24 hours.

tag: strain/background

tag: genotype/variation

value: Wild type

value: Culture

tag: light-dark cycle

value: Continuous darkness

tag: time point


title: Time series in DD conditions in the Wt [Wt_22_C]

description:
Wt_22_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Tfh1_1

description: Ensemble RNA-seq


title: Tfh1_3

description: Ensemble RNA-seq


title: Time series in DD conditions in the Wt [Wt_13_C]

description:
Wt_13_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the OE1 line [OE-1_4_A]

description:
OE-1_4_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.

treatment_protocol: bHLH1a overexpressing line cell culture was pre-adapted to 16L:8D regime and put in DD condition. Sampling started at the beginning of the day (time point 1), sampling every 3 hours for 24 hours.

value: bHLH1a Overexpressing


title: 7785488092_R04C01


title: Time series in DD conditions in the Wt [Wt_7_C]

description:
Wt_7_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_10_C]

description:
Wt_10_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: 7785488092_R03C02


title: Time series in DD conditions in the OE1 line [OE-1_1_A]

description:
OE-1_1_A
Raw data: OE-1_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_25_B]

description:
Wt_25_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: 7785488092_R03C01


title: Tfh1-17_1

description: Ensemble RNA-seq

value: Tfh1-17 CD4+ T cell


title: Time series in DD conditions in the Wt [Wt_22_B]

description:
Wt_22_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_25_C]

description:
Wt_25_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Naive_4

description: Ensemble RNA-seq

value: Naive CD4+ T cell


title: Time series in DD conditions in the Wt [Wt_19_B]

description:
Wt_19_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: 7785488092_R02C02


title: Time series in DD conditions in the Wt [Wt_13_B]

description:
Wt_13_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_16_C]

description:
Wt_16_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_16_B]

description:
Wt_16_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Naive_3

description: Ensemble RNA-seq


title: 7785488092_R02C01


title: 7785488092_R04C02


title: Time series in DD conditions in the Wt [Wt_10_B]

description:
Wt_10_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Naive_2

description: Ensemble RNA-seq


title: 7785488092_R01C02


title: Tfh1-17_3

description: Ensemble RNA-seq


title: Time series in DD conditions in the Wt [Wt_4_C]

description:
Wt_4_C
Raw data: Wt_C.xlsx
Replica 3/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_1_B]

description:
Wt_1_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_25_A]

description:
Wt_25_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_4_B]

description:
Wt_4_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.


title: Tfh1-17_2

description: Ensemble RNA-seq


title: 7785488092_R01C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: Time series in DD conditions in the Wt [Wt_22_A]

description:
Wt_22_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_19_A]

description:
Wt_19_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Library NK94

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

description: snDrop-seq data

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
First, paired-end reads were filtered out if read 1 had more than 4 non-T bases in the last 10 bases (to remove all non poly T-captured contaminated reads), or had one or more bases with poor quality score (less than 10). And cell barcode and UMI information were then inferred from the first 12 bases and the next 8 bases of read 1 respectively. The right mate of each read pair was trimmed to remove any portion of the SMART adaptor sequence or large stretches of polyA tails (6 consecutive bp or greater).
The trimmed reads were then aligned to the human genome (GENCODE GRCH38) using STAR v2.5 with the default parameter settings
Reads mapping to intronic or exonic regions of genes as per the GENCODE gene annotation were both recorded. One further correction step to fix barcode synthesis errors was performed by inserting N at last base of the cell barcode for reads which had identical first 11 bases of the cell barcode and same last T base of UMI.
Digital expression matrix was then generated with genes as rows and cells as columns. UMI counts were assigned for each gene of each cell by collapsing UMI reads which had only 1 edit distance
Genome_build: GENCODE GRCH38
[UCSD-WU_Single_Nuclei_Cluster_Annotated_Raw_UMI_Matrix.tsv]  Includes UMI counts for each sample passing QC filtering.  The column headers are in the format:  "[clusterID]_[libraryID]_[cell_barcode]".
[UCSD-WU_Single_Nuclei_Cluster_Annotations.csv]  Includes lusterID annotations.

source_name: adult kidney

extract_protocol:
Frozen kidney tissue was treated with nuclear extraction buffer, isolated nuclei was stained with DAPI.
Nuclei were loaded at the concentration of 100 nuclei/ml, and co-encapsulated in droplets with barcoded beads purchased from ChemGenes Corporation, Wilmington MA (Cat. # Macosko201110). When encapsulation was complete, droplets were heated to lyze the nuclei membrane, and were then broken by perfluorooctanol, following which beads were harvested, and hybridized RNA was reverse transcribed. Beads hybridized with RNA from individual nuclei was harvested, pooled and reverse transcribed. cDNA was then PCR amplified for 16 cycles with primer, buffer and cycle conditions identical to original Dropseq protocol and libraries were prepared by Nextera XT tagmentation according to Illumina's instructions and indexed with different Nextera index 1 primers
snDrop-seq and Nextera

tag: experiment

tag: barcode

tag: ppid

tag: region

value: Cortex

tag: tissue collection

value: donor kidney from MAT

tag: tissue processing

value: Dry-ice frozen, 7x40uM Sections - RNAlater

tag: Sex

value: F

tag: source

value: Washington University

value: mixed sample (non-demultiplexed)


title: 7787539026_R06C02

tag: gender

value: Unknown

tag: tissue

value: Whole blood


title: Time series in DD conditions in the Wt [Wt_10_A]

description:
Wt_10_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.

tag: cell type


title: 7787539026_R06C01

tag: disease state

value: Chronic inflammatory skin disease


title: Time series in DD conditions in the Wt [Wt_16_A]

description:
Wt_16_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: Time series in DD conditions in the Wt [Wt_13_A]

description:
Wt_13_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.


title: 7787539026_R05C02


title: Library NK93

description: snDrop-seq data


title: Library NK92

description: snDrop-seq data

value: Nephrectomy

value: University of Michigan


title: Time series in DD conditions in the Wt [Wt_7_B]

description:
Wt_7_B
Raw data: Wt_B.xlsx
Replica 2/3. Time point 0 corresponds to the light onset.

value: Wild type


title: Library NK91

description: snDrop-seq data


title: Time series in DD conditions in the Wt [Wt_7_A]

description:
Wt_7_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.

value: Culture


title: Time series in DD conditions in the Wt [Wt_4_A]

description:
Wt_4_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.

value: Continuous darkness


title: 7787539026_R05C01


title: Naive_1

description: Ensemble RNA-seq

tag: donor

tag: disease status

value: healthy


title: 7787539026_R04C02


title: Time series in DD conditions in the Wt [Wt_1_A]

description:
Wt_1_A
Raw data: Wt_A.xlsx
Replica 1/3. Time point 0 corresponds to the light onset.

tag: strain/background

tag: genotype/variation


title: Library NK90

description: snDrop-seq data


title: 7787539026_R04C01


title: Library NK89

description: snDrop-seq data


title: Time series in DD conditions [DD_24_C]

description:
DD_24_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx

hyb_protocol: For each hybridization, 100 ng of was used. Hybridization and washes were performed according to manufacturer’s protocols (http://www.nanostring.com) by the UCL Nanostring facility, London, UK.

scan_protocol: Scanning was performed according to manufacturer’s protocols (http://www.nanostring.com) by the UCL Nanostring facility, London, UK.

growth_protocol: The wild-type CCMP632 strain of Phaeodactylum tricornutum Bohlin (Pt1 8.6) was routinely grown in f/2 medium (Guillard, 1975) at 18°C under white fluorescent lights (Philips TL-D De Luxe Pro 950) in 16L:8D cycles under 40 µmol m-2 s-1 of photons. Cultures were kept in exponential growth phase diluting them every three days with fresh medium and their axenicity assessed through contamination tests. Triplicate cultures of each treatment were grown in 1000 ml Erlenmeyers, shaked at 100 rpm to prevent settling of cells.

treatment_protocol: Cell culture was pre-adapted to 16L:8D regime and then split and put in LD and DD conditions. Sampling started at the beginning of the night (time point -8), sampling every 4 hours for 32 hours.

tag: light-dark cycle

tag: time point


title: Time series in DD conditions [DD_16_C]

description:
DD_16_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: Library NK88

description: snDrop-seq data

tag: experiment

tag: barcode


title: Time series in DD conditions [DD_20_C]

description:
DD_20_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: Time series in DD conditions [DD_12_C]

description:
DD_12_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: 7787539026_R03C02


title: Time series in DD conditions [DD_4_C]

description:
DD_4_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: 7787539026_R03C01


title: Time series in DD conditions [DD_0_C]

description:
DD_0_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: Time series in DD conditions [DD_-4_C]

description:
DD_-4_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: Time series in DD conditions [DD_8_C]

description:
DD_8_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: Library NK87

description: snDrop-seq data

tag: ppid

tag: region


title: Time series in DD conditions [DD_-8_C]

description:
DD_-8_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: DD_C.xlsx


title: Library NK86

description: snDrop-seq data

tag: tissue collection

tag: tissue processing


title: 7787539026_R02C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: 7787539026_R02C01


title: Time series in DD conditions [DD_20_B]

description:
DD_20_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Time series in DD conditions [DD_24_B]

description:
DD_24_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Time series in DD conditions [DD_16_B]

description:
DD_16_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Library NK80

description: snDrop-seq data

value: Dry-ice frozen, 7x40uM Sections

tag: Sex

tag: source


title: 7787539026_R01C02

tag: gender

tag: tissue


title: Library NK81

description: snDrop-seq data

tag: cell type


title: Time series in DD conditions [DD_4_B]

description:
DD_4_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Time series in DD conditions [DD_12_B]

description:
DD_12_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Library NK79

description: snDrop-seq data


title: 7787539026_R01C01

tag: disease state


title: Time series in DD conditions [DD_0_B]

description:
DD_0_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Time series in DD conditions [DD_-8_B]

description:
DD_-8_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Time series in DD conditions [DD_24_A]

description:
DD_24_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: 7785461042_R06C02


title: Time series in DD conditions [DD_20_A]

description:
DD_20_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: Time series in DD conditions [DD_-4_B]

description:
DD_-4_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Library NK71

description: snDrop-seq data


title: 7785461042_R06C01


title: Library NK60

description: snDrop-seq data

value: partial nephrectomy


title: 7785461042_R05C02


title: Time series in DD conditions [DD_12_A]

description:
DD_12_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: Time series in DD conditions [DD_16_A]

description:
DD_16_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: 7785461042_R05C01


title: Library NK59

description: snDrop-seq data

value: Cortex


title: 7785461042_R04C02


title: Library NK58

description: snDrop-seq data


title: Time series in DD conditions [DD_8_B]

description:
DD_8_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: DD_B.xlsx


title: Library NK55

description: snDrop-seq data

value: Cortex-Medulla

value: radical nephrectomy

value: M


title: Library NK56

description: snDrop-seq data

value: Dry-ice frozen, 7x40uM Sections - RNAlater

value: Washington University


title: Library NK72

description: snDrop-seq data

value: mixed sample (non-demultiplexed)


title: Time series in DD conditions [DD_4_A]

description:
DD_4_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: Time series in DD conditions [DD_0_A]

description:
DD_0_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: 7785461042_R04C01

value: Unknown

value: Whole blood


title: 7785461042_R03C02

value: Chronic inflammatory skin disease


title: Time series in DD conditions [DD_-4_A]

description:
DD_-4_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: 7785461042_R03C01

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).


title: 7785461042_R02C02


title: Time series in DD conditions [DD_-8_A]

description:
DD_-8_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: Time series in DD conditions [DD_8_A]

description:
DD_8_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: DD_A.xlsx


title: Time series in LD conditions [LD_24_C]

description:
LD_24_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx

value: Normal 16L:8D cycles


title: 7785461042_R01C02


title: Time series in LD conditions [LD_20_C]

description:
LD_20_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx

value: Wild type


title: Library NK44

description: snDrop-seq data

value: donor kidney from MAT

value: Dry-ice frozen, 10x40uM Sections - RNAlater


title: Library NK45

description: snDrop-seq data

value: Medulla


title: Library NK42

description: snDrop-seq data

value: Dry-ice frozen, 10x40uM Sections - Wisc Soln


title: 7785461042_R01C01


title: Time series in LD conditions [LD_16_C]

description:
LD_16_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx

value: Culture


title: Library NK46

description: snDrop-seq data


title: Library NK41

description: snDrop-seq data


title: Time series in LD conditions [LD_12_C]

description:
LD_12_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx


title: Library NK49

description: snDrop-seq data

value: Cortex

value: robotic partial nephrectomy


title: 7785445057_R06C02


title: Time series in LD conditions [LD_8_C]

description:
LD_8_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx


title: Library NK38

description: snDrop-seq data

value: Dry-ice frozen, 10x40uM Sections


title: 7785445057_R06C01


title: 7785445057_R05C02


title: Library NK37

description: snDrop-seq data

value: M


title: scML1_S2

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
For both bull-cell RNA-seq and single-cell RNA-seq data, the quality of bulk-cell RNA-seq data was evaluated by FastQC software (version 0.11.3) and sequencing adaptors were trimmed by Cutadapt software (version 1.8.1)
For bulk-cell RNA-seq, processed reads were aligned to reference genome (version UCSC sacCer3) by Hisat2 software (version 2.0.0-beta) with default parameters. Cufflinks (version 2.2.1) with default settings were separately used for quantifying gene expression, normalizing gene expression and analyzing differential gene expression. The cutoff of statistical significance of differential gene expression was q-value < 0.01.
For single-cell RNA-seq, Cellranger software (version 2.1.1) with default parameters was used to generate gene-cell matrix. For quality control of single-cell RNA-seq data, we excluded the cells with >10,000 UMI (unique molecular identifier) counts as they were potentially from artificial cell or cell duplets. DESeq2 package was used to normalize UMI count data across all cells.
Genome_build: sacCer3
Supplementary_files_format_and_content: For bulk-cell RNA-seq, the processed data files were derived the output (expression value, FPKM) of Cufflinks with 2 columns splitted by Tab (gene ID, and FPKM). For single-cell RNA-seq, the processed data files were derived the output (UMI of gene in each cell) of Cellranger with many columns: the first column is the gene ID and the remaing columns are UMI.

organism: Saccharomyces cerevisiae

source_name: Living cell

growth_protocol: Yeast cells (BY4741 strain) were separately grown at 30℃ in the media including 1% yeast extract, 2% peptone and different carbon sources.

extract_protocol:
For bulk-cell RNA-seq, total RNA was extracted using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research).
For bulk-cell RNA-seq, sequencing library was prepared using TruSeq Stranded mRNA Library Prep Kit. For single-cell RNA-seq, considering the fragility of spheroplasts, we modified the loading strategy of buffer before running the 10X ChromiumTM Controler (10X Genomics): Firstly, Single Cell Master Mix (10X Single Cell 3’ Reagent Kit v2) was prepared and added into Single Cell A Chip; Next, instead of nuclease-free water, sorbitol was added (final conc. = 1 M) and mixed well; Finally, spheroplasts suspended in 1 M sorbitol were added.

treatment_protocol: Yeast cells were collected in the mid-log phase (OD600 of 0.3-0.6) and subjected to bulk-cell RNA-seq and single-cell RNA-seq experiments. For single-cell RNA-seq, spheroplasts were prepared before loading to 10X ChromiumTM Controler (10X Genomics). Cell viability was measured using Trypan blue exclusion method and cell number was counted by hemocytometer.

tag: strain

tag: carbon source

value: 2% glucose


title: Library NK36

description: snDrop-seq data

value: lap nephrectomy

value: Washington University


title: 7785445057_R05C01

value: Unknown


title: Time series in LD conditions [LD_0_C]

description:
LD_0_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx

tag: strain/background

tag: genotype/variation


title: scML1_S4


title: Library NK35

description: snDrop-seq data

value: mixed sample (non-demultiplexed)


title: Time series in LD conditions [LD_-4_C]

description:
LD_-4_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx

tag: light-dark cycle

tag: time point


title: Time series in LD conditions [LD_4_C]

description:
LD_4_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx


title: MR_replicate3

value: 2% raffinose


title: scML1_S1


title: Library NK34

description: snDrop-seq data

tag: experiment

tag: barcode

value: 30 minutes Papain-Collagenase - RNAlater


title: 7785445057_R04C02

value: Whole blood

value: Chronic inflammatory skin disease


title: MR_replicate2


title: 7785445057_R04C01


title: MSC_Donor1_Day0_4

city: Newcastle upon Tyne

first: David

last: Young

address: Institute of Genetic Medicine

country: United Kingdom

institute: Newcastle University

hyb_protocol: DNA methylation profiling of the samples was carried out by Cambridge Genomic Services (Cambridge, UK), using the Illumina Infinium HumanMethylation450 Beadchip array (Illumina, Inc., San Diego, USA).

scan_protocol: standard illumina scanner

data_processing: Minfi Bioconductor Package

label: Cy5 and Cy3

source_name: human bone-marrow-derived mesenchymal stem cells

label_protocol: 1µg of genomic DNA was bisulphite converted using the EpiTect Bisulfite Kit (Qiagen).

growth_protocol: Human bone marrow mesenchymal stem cells (MSC) (from four donors, 18-25 years of age) were isolated from human bone marrow mononuclear cells (Lonza Biosciences, Berkshire, UK) by adherence over 24 hours to tissue culture plastic and were expanded in monolayer culture in Mesenchymal Stem Cell Growth Medium (Lonza) supplemented with 5ng/ml fibroblast growth factor-2 (R&D Systems, Abingdon, UK).

extract_protocol: Genomic DNA was extracted from cells prior to the induction of chondrogenesis (Day0) and from Day14 cartilagenous discs by disruption in Genomic Digestion Buffer using a small disposable plastic pestle and an aliquot of Molecular Grinding Resin (G-Biosciences, St. Louis,MO) followed by proteinase K digestion for 1 hour at 37°C then nuclei acid purification with Invitrogen PureLink Genomic DNA Kit according to manufacturer’s instructions (Life Technologies, Paisley, UK).

treatment_protocol: MSC were resuspended in chondrogenic culture medium consisting of high glucose DMEM containing 100 µg/ml sodium pyruvate (Lonza), 10 ng/ml TGF-β3 (PeproTech, London, UK), 100 nM dexamethasone, 1x ITS-1 premix, 40 µg/ml proline, and 25 µg/ml ascorbate-2-phosphate (all from Sigma-Aldrich, Poole, UK). 5x105 MSC in 100µl medium were pipetted onto 6.5mm diameter, 0.4-µm pore size polycarbonate Transwell filters (Merck Millipore, Watford, UK), centrifuged in a 24-well plate (200g, 5 minutes), then 0.5 ml of chondrogenic culture medium added to the lower well

tag: donor

value: F

tag: age

tag: treatment

value: undifferentiated


title: MSC_Donor2_Day0_2

value: human bone-marrow-derived mesenchymal stem cells

tag: Sex


title: MSC_Donor2_Day14_1

value: chondrogenic


title: Library NK33

description: snDrop-seq data

tag: ppid

tag: region

value: Medulla

tag: tissue collection

tag: tissue processing

tag: source


title: 7785445057_R03C02

tag: gender

tag: tissue

tag: disease state


title: Time series in LD conditions [LD_24_B]

description:
LD_24_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

tag: strain/background

tag: genotype/variation

value: Wild type

tag: cell type

value: Culture

value: Normal 16L:8D cycles


title: MR_replicate1

tag: strain

tag: carbon source


title: MSC_Donor4_Day14_1

tag: donor

value: M

tag: time point


title: MSC_Donor1_Day14_3

tag: age

tag: treatment


title: MSC_Donor1_Day0_1

tag: Sex


title: Time series in LD conditions [LD_20_B]

description:
LD_20_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

tag: light-dark cycle


title: Library NK32

description: snDrop-seq data

tag: experiment

tag: barcode

tag: ppid

tag: region

value: Cortex

tag: tissue collection

value: robotic partial nephrectomy


title: ML5_replicate3

value: 0.125% glucose + 1.875% galactose


title: MSC_Donor3_Day0_4


title: MSC_Donor2_Day0_1


title: ML5_replicate2


title: MSC_Donor1_Day0_3


title: Time series in LD conditions [LD_-8_C]

description:
LD_-8_C
Replica 3/3. Time point 0 corresponds to the light onset.
Raw data: LD_C.xlsx


title: 7785445057_R03C01

tag: gender

value: Unknown

tag: tissue

tag: disease state


title: 7785445057_R02C02


title: Library NK31

description: snDrop-seq data

tag: tissue processing

tag: source

value: Washington University

tag: cell type

value: mixed sample (non-demultiplexed)


title: Library NK30

description: snDrop-seq data

value: Dry-ice frozen, 5x40uM Sections - RNAlater


title: ML5_replicate1

tag: strain

tag: carbon source


title: 7785445057_R02C01

value: Whole blood

value: Chronic inflammatory skin disease


title: 7785445057_R01C02


title: ML3_replicate3

value: 0.5% glucose + 1.5% galactose


title: MSC_Donor1_Day14_2

value: human bone-marrow-derived mesenchymal stem cells

tag: donor

value: F

tag: age

tag: time point


title: MSC_Donor1_Day14_1

tag: Sex

tag: treatment

value: chondrogenic


title: Time series in LD conditions [LD_16_B]

description:
LD_16_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

tag: strain/background

tag: genotype/variation

value: Wild type

tag: light-dark cycle


title: Library NK28

description: snDrop-seq data

tag: experiment

tag: barcode

tag: ppid

tag: region

value: Medulla

tag: tissue collection

value: Dry-ice frozen, 5x40uM Sections - Wisc Soln


title: ML3_replicate2


title: Time series in LD conditions [LD_8_B]

description:
LD_8_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

value: Culture

value: Normal 16L:8D cycles


title: 7785445057_R01C01

tag: gender

tag: tissue

tag: disease state


title: Library NK29

description: snDrop-seq data

value: robotic partial nephrectomy

tag: tissue processing

value: M

tag: source

tag: cell type


title: MSC_Donor1_Day0_2

tag: donor

tag: age

tag: time point

value: undifferentiated


title: Time series in LD conditions [LD_0_B]

description:
LD_0_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

tag: strain/background


title: Time series in LD conditions [LD_12_B]

description:
LD_12_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

tag: genotype/variation


title: Library NK27

description: snDrop-seq data

tag: Sex

value: Washington University


title: ML3_replicate1

tag: strain

tag: carbon source


title: Time series in LD conditions [LD_-4_B]

description:
LD_-4_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

tag: light-dark cycle


title: 7785496042_R06C02

description: Genomic DNA extracted from whole blood was genotyped using Illumina Human Exome Asian BeadChip  (Illumina).

value: Unknown


title: 7785461042_R02C01


title: Library NK26

description: snDrop-seq data

tag: experiment

tag: barcode

tag: ppid

tag: region

value: Cortex

value: lap nephrectomy

value: 30 minutes Papain-Collagenase

value: mixed sample (non-demultiplexed)


title: Library NK25

description: snDrop-seq data

tag: tissue collection


title: 7785496042_R06C01

tag: gender

tag: tissue

value: Whole blood

tag: disease state

value: Chronic inflammatory skin disease


title: 7785496042_R05C02


title: 7785496042_R05C01


title: ML2 replicate2

value: 1% glucose + 1% galactose


title: Time series in LD conditions [LD_-8_B]

description:
LD_-8_B
Replica 2/3. Time point 0 corresponds to the light onset.
Raw data: LD_B.xlsx

value: Wild type

tag: cell type


title: ML1 replicate3

value: 2% glucose


title: Time series in LD conditions [LD_20_A]

description:
LD_20_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx


title: Library NK22

description: snDrop-seq data

tag: tissue processing

value: 60 minutes Trypsin-Collagenase

value: F

tag: source


title: Time series in LD conditions [LD_24_A]

description:
LD_24_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx

tag: strain/background

value: Culture

value: Normal 16L:8D cycles

tag: time point


title: ML2 replicate3


title: 7785496042_R04C02


title: ML2 replicate1


title: Library NK14

description: snDrop-seq data

value: Cortex-Medulla

value: radical nephrectomy

value: RNAlater 6 Hours

tag: Sex

value: M


title: Time series in LD conditions [LD_16_A]

description:
LD_16_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx

tag: genotype/variation


title: Library NK13

description: snDrop-seq data

value: Washington University


title: ML1 replicate1

tag: strain

tag: carbon source


title: 7785496042_R04C01

value: Unknown


title: 7785496042_R03C02


title: 7785496042_R03C01


title: Library NK10

description: snDrop-seq data

tag: experiment

value: Flash Frozen, Cryosection (35umx7) OCT embedded


title: MA replicate3

value: 2% galactose


title: 7785496042_R02C02

value: Whole blood


title: MA replicate2


title: Library NK9

description: snDrop-seq data

tag: barcode

value: mixed sample (non-demultiplexed)


title: Time series in LD conditions [LD_0_A]

description:
LD_0_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx

tag: light-dark cycle


title: 7785496042_R02C01

value: Chronic inflammatory skin disease


title: Time series in LD conditions [LD_4_A]

description:
LD_4_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx

value: Wild type


title: Time series in LD conditions [LD_8_A]

description:
LD_8_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx


title: Library NK21

description: snDrop-seq data

tag: ppid

tag: region

value: Cortex

value: lap nephrectomy


title: Time series in LD conditions [LD_-4_A]

description:
LD_-4_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx


title: Library NK5

description: snDrop-seq data

tag: tissue collection


title: Library NK1

description: snDrop-seq data

value: Fresh Frozen (Dry Ice)


title: ML1 replicate2

value: 2% glucose


title: Time series in LD conditions [LD_12_A]

description:
LD_12_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx

value: Culture

value: Normal 16L:8D cycles


title: Time series in LD conditions [LD_-8_A]

description:
LD_-8_A
Replica 1/3. Time point 0 corresponds to the light onset.
Raw data: LD_A.xlsx


title: Cell-miRNA_5% continuous stretched, biological rep2

status: Public on May 23 2019

city: Providence

first: Tanbir

last: Najrana

address: 200 Chestnut street

institute: Brown University

hyb_protocol: Hybridization   1. Bring the reagents listed in Step 3, below, to room temperature.   2. Completely thaw and then heat the 20X Eukaryotic Hybridization Controls (bioB, bioC, bioD, cre from GeneChipTM Eukaryotic Hybridization Control Kit) for 5 minutes at 65°C.   3. Add the following components in Table 3.1 to the 21.5 μL biotin-labeled sample in the order listed, to prepare the array hybridization cocktail:   4. Incubate at 99°C for 5 minutes, then 45°C for 5 minutes.   5. Aspirate 100 μL (400/169 format array) or 130 μL (100 format array) and inject into an array   6. Remove the pipet tip from the upper right septum of the array.   7. Cover both septa with 1/2 Tough-SpotsTM to minimize evaporation and/or prevent leaks.   8. Place the arrays into hybridization oven trays.   9. Load the trays into the hybridization oven.   10. Incubate the arrays at 48°C and 60 rpm for 18 hours     Table 3.1 Hybridization Cocktail (for a single reaction)   Component Volume for a 400/169 Format Array (miRNA 1.0 and 2.0 Arrays)  Volume for a 100 Format Array (miRNA 3.0 and later designs)  Final Concentration   2X Hybridization Mix  50 μL  66 μL  1X   27.5% Formamide (Vial 12)  15 μL  19.2 μL  4%   DMSO  10 μL  12.8 μL  9.7%   20X Hybridization Controls  5 μL  6.6 μL  1X   Control Oligo B2, 3nM  1.7 μL  2.2 μL  50 pM   Nuclease-free Water  N/A  3.7 μL   Total Volume  81.7 μL  110.5 μL     Component  400/169 Format Array 100 Format Array  (miRNA 1.0 and 2.0 Arrays)   (miRNA 3.0 and later designs)   Biotin-labeled Sample  21.5 μL  21.5 μL   Hybridization Master Mix  81.7 μL  110.5 μL

scan_protocol: Fluidics Station 450 Protocol FS450_0003 (400/169 format array,Arrays were scanned with an Affymetrix 3000 7 G scanner

data_processing:
Affymetrix TAC
miRNA-4_0-st-v1.pgf
miRNA-4_0-st-v1.Mm.ps

label: biotin

organism: Mus musculus

source_name: Cell line MLE12

label_protocol: FlashTag™ Biotin HSR Ligation  1. Briefly microfuge the 15 μL of tailed RNA and place on ice.  2. Add 4 μL 5X FlashTag Biotin HSR Ligation Mix (Vial 5) to each sample.  3. After the Ligation Mix has been added, add 2 μL of T4 DNA Ligase (Vial 6) to each sample. Do not make a master mix at this step, as auto-ligation can occur.  4. Mix gently (do not vortex) and microfuge.  5. Incubate at 25°C (room temperature) for 30 minutes.  6. Stop the reaction by adding 2.5 μL HSR Stop Solution (Vial 7). Mix and microfuge the 23.5 μL of ligated sample.  7. Remove 2 μL of the biotin-labeled sample for use with the ELOSA QC Assay (Appendix A). It is acceptable to store the 2 μL of biotin-labeled sample on ice for up to 6 hours or at –20°C for up to 2 weeks, and run the ELOSA QC Assay at a convenient time. If the ELOSA QC Assay is not performed, it is recommended that 2 μL of biotin-labeled sample be saved until the array QC is complete. Retaining this sample will enable one the ability to troubleshoot possible target preparation issues, if needed.  8. The remaining 21.5 μL biotin-labeled sample may be stored on ice for up to 6 hours, or at –20°C for up to 2 weeks, prior to hybridization on GeneChipTM miRNA Arrays or miRNA Array Plates.

growth_protocol: MLE12 cell line was obtained from American Type Culture Collection (ATCC) (Manassas, Virginia). This is a murine cell line that expresses features of type II lung epithelial cells. The cells were cultured in DMEM/F12 supplemented with insulin (0.005 mg/ml), transferrin (0.01 mg/ml), sodium selenite (30 nM), hydrocortisone (10 nM), β-estradiol (10 nM), HEPES (10 mM), L-glutamine (2 mM) and extracellular-depleted 2% bovine serum.

extract_protocol: Total RNA was isolated from 20 µg of EVs using Total Exosome RNA and Protein Isolation Kit (Invitrogen, cat. no. 447845) following the instruction manual. Total RNA from 3.5 x 106 cells was isolated using Quick-RNA Mini Prep (Zymo Research) according to manufacture provided protocol. RNA integrity was tested by agarose gel electrophoresis analysis. RNA quality and concentration was measured by NanoDrop Spectrophotometer.

treatment_protocol: To apply mechanical stretch to the cells, 0.35-0.45 x 106 cells in 2 ml of medium were seeded onto each well of the 6-well Bioflex multiwall Plates (Flexcell International, Hillsborough, NC, USA) precoated with collagen-1. Monolayers were maintained for an additional 24 hour until reached approximately 80% confluency, and after fresh medium was replaced, plates were mounted in a Flexcell FX-4000 Stretch Unit (Flexcell International). Regimens of 5% continuous stretch or 10% cyclical stretch, at intervals of 40 cycles/min for 24 hours, were used. Cells grown on non-stretched membranes were treated in an identical manner and served as controls.

tag: treatment

value: 5% continuous stretch


title: Cell-miRNA_control, biological rep2 (control for 5% continuous stretch assay)

value: control


title: Cell-miRNA_5% continuous stretched, biological rep1


title: EV-miRNA_5% continuous stretched, biological rep2


title: EV-miRNA_5% continuous stretched, biological rep1


title: Cell-miRNA_control, biological rep1 (control for 5% continuous stretch assay)


title: EV-miRNA_control, biological rep2 (control for 5% continuous stretch assay)


title: Cell-miRNA_10% cyclic stretched, biological rep2

value: 10% cylic stretch


title: MA replicate1


title: EV-miRNA_control, biological rep1 (control for 5% continuous stretch assay)


title: Cell-miRNA_10% cyclic stretched, biological rep1


title: Cell-miRNA_control, biological rep2 (control for 10% cyclic stretch assay)


title: EV-miRNA_10% cyclic stretched, biological rep2


title: Cell-miRNA_control, biological rep1 (control for 10% cyclic stretch assay)


title: EV-miRNA_control, biological rep2 (control for 10% cyclic stretch assay)


title: EV-miRNA_10% cyclic stretched, biological rep1


title: EV-miRNA_control, biological rep1 (control for 10% cyclic stretch assay)


title: Input_WT_ Rep1

city: New York

first: Ryan

middle: D

last: Fine

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

library_source: genomic

data_processing:
Biological duplicate fastq files were concatenated together.
Reads were then mapped to the sacCer3 genome using bowtie with the following options; ---best, --stratum, --nomaqround, and --m10.
The resulting bam files were then converted into bigwig files using bedtools.
As part of the pipeline chromosome names were changed from the sacCer3 NCBI values to values readable by genomics viewers e.g. "ref|NC_001133|" to "chrI".
Genome_build: sacCer3
Supplementary_files_format_and_content: Big Wig files were generated which represent the combined mapped reads of 2 biological replicate libraries and can be viewed in a genome vieiwer such as the Broad Institute's Genome Viwer  (IGV)

source_name: Input_WT_ Rep1

growth_protocol: Cells were grown at 30C in YPD medium with 2% Glucose as the Carbon source.

extract_protocol:
Log-phase cultures were cross-linked with 1% formaldehyde for 20 min at 30C.  Cells were pelleted and washed with Tris-buffered saline.  The cells were lysed in 600ul of FA140 lysis buffer with glass beads using a mini-beadbeater.  The lysate was removed from the beads and sonicated for 60 cycles (30s “on” and 30s “off” per cycle) in a Diagenode Bioruptor.  The sonicated lysates were spun for 5 min at 14krpm in a microcentrifuge. The entire supernatant was transferred to a new tube and incubated overnight at 4C with 5 µg of anti-Myc antibody (9E10) and 20 µl of protein G magnetic beads (Millipore). Following IP, the beads were washed once with FA140 buffer, twice with FA500 buffer, and twice with LiCl wash buffer. DNA was eluted from the beads in 1%SDS TE buffer and cross-links were reversed O/N at 65C.  The IP chromatin was then purified using a Qiagen PCR purification kit (Cat. No. 28106).
Libraries were constructed using the Illumina Trueseq ChIP Sample Prep kit ( IP-202-1012) and protocol with 10ng of initial ChIP DNA.

tag: antibody

value: WT


title: 100bpΔ_HiC_2

data_processing:
Library strategy: HiC-Seq
Heatplots appearing in the publication were produced entirely by python scripts from the Mirny Lab hiclib library publicly available at (http://mirnylab.bitbucket.org/hiclib/index.html).
Briefly, reads were mapped using the iterative mapping program, which uses Bowtie2 to map reads and iteratively trims unmapped reads to increase the total number of mapped reads.
Reads were then parsed into an hdf5 python data dictionary for storage and further analysis.  Mapped reads of the same strains were concatenated using the hiclib library's "Merge" function.
Mapped reads were then run through the fragment filtering program using the default parameters as follows: filterRsiteStart(offset=5), filterDuplicates, filterLarge, filterExtreme (cutH=0.005, cutL=0).
Finally, raw heat maps were futher filtered to remove diagonal reads and iteratively corrected using the heat map processing program.
Genome_build: sacCer3
Supplementary_files_format_and_content: All processed data files are mapped reads stored in .hdf5 format.  This is a highly compressed python data dictionary format that can be analyzed with the Mirnylab hiclib library available at (http://mirnylab.bitbucket.org/hiclib/index.html).

growth_protocol: Cells were grown at 30C in YEP medium with 2% Glucose as the Carbon source.

extract_protocol:
DNA was extracted by pestle and mortar liquid Nitrogen grinding and SDS solubilization.  Triton X-100 was used to quench the SDS before O/N digestion with HindIII.  Digested DNA ends were then biotinylated and blunt-end ligated under dilute conditions.  Unligated biotinylated ends were removed with T4 DNA Polymerase and crosslinks were reversed.  The DNA was concentrated using a Zymogen Clean and Concentrate Kit-5 and sonicated in a Diagenode Bioruptor.
Biotinylated ligation junctions were capture by Streptavidin coupled Dynabeads and libraries were constructed on the beads using Nextera Mate Pair Reagents (Illumina).

treatment_protocol: Log-Phase cultures were cross-linked with 3% formaldehyde for 20 mins.  Cross-linking was quenched with a 2X formaldehyde volume of 2.5M Glycine.

tag: re

value: HindIII


title: GFP-RPL25NLS_WT_Rep1

value: Anti-GFP antibody (Abcam)


title: GFP-RPL25NLS_Sir2deletion_Rep1

value: SIR2 deletion


title: GFP-RPL25NLS_Sir2deletion_Rep2


title: Input_WT_ Rep2

source_name: Input_WT_ Rep2


title: Sir2Δ_HiC_2


title: GFP-RPL25NLS_WT_Rep2


title: WT12_HiC_1


title: Sir2Δ_HiC_1


title: Sir2Δ_HiC_3


title: WT6_HiC_1


title: Smc4-13xMyc_Sir2deletion_Rep1

value: Anti-myc (9E10)


title: Smc4-13xMyc _WT_Rep1

source_name: Smc4-13xMyc _WT_Rep1


title: Smc4-13xMyc _WT_Rep2

source_name: Smc4-13xMyc _WT_Rep2


title: Smc4-13xMyc_Sir2deletion_Rep2


title: scML1_S3


title: Follicular lymphoma 64

city: Madrid

first: Inmaculada

last: Rapado

address: Avenida Cordoba s/n

country: Spain

institute: Hospital Universitario 12 de Octubre

description: Genomic DNA extracted from follicular lymphoma patients was genotyped using Illumina Human1M-Duov3 DNA Analysis BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Te-Flow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a iScan System (Illumina).

data_processing: Genomic DNA extracted from peripheral blood or bone marrow was genotyped using Illumina Human1M-Duov3 DNA Analysis BeadChip (Illumina).

label: C-Bio and A-DNP

source_name: Follicular lymphoma

label_protocol: 400 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37ºC using amplification master mix (AMM) and primer/neutralization mix (MP1). After incubation the amplified DNA was fragmented with fragmentation mix (FRG), precipitated with 2-propanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted from follicular lymphoma samples using MagNA pure LC DNA Isolation Kit - Large Volume and the automatic system MagNA Pure LC Nucleic Acid Extractor (Roche Applied Science, Penzberg, Germany)

tag: gender

value: Male

tag: tissue

value: Peripheral blood

tag: disease state

value: Diagnosis


title: Follicular lymphoma 66

value: Female


title: Follicular lymphoma 76

value: Bone marrow


title: Follicular lymphoma 61


title: Follicular lymphoma 75


title: Follicular lymphoma 74


title: Follicular lymphoma 78


title: Follicular lymphoma 69


title: Follicular lymphoma 57


title: Follicular lymphoma 67


title: Follicular lymphoma 50


title: Follicular lymphoma 54

value: Follow-up


title: Follicular lymphoma 49


title: Follicular lymphoma 59


title: Follicular lymphoma 68


title: Follicular lymphoma 60


title: Follicular lymphoma 71


title: Follicular lymphoma 63


title: Follicular lymphoma 56


title: Follicular lymphoma 55


title: Follicular lymphoma 79


title: Follicular lymphoma 58


title: Follicular lymphoma 62


title: Follicular lymphoma 80


title: Follicular lymphoma 53


title: Follicular lymphoma 46


title: Follicular lymphoma 77


title: Follicular lymphoma 51


title: Follicular lymphoma 52


title: Follicular lymphoma 72


title: Follicular lymphoma 45


title: Follicular lymphoma 42


title: Follicular lymphoma 43


title: Follicular lymphoma 41


title: Follicular lymphoma 40


title: Follicular lymphoma 38


title: Follicular lymphoma 31


title: Follicular lymphoma 26


title: Follicular lymphoma 44


title: Follicular lymphoma 34


title: Follicular lymphoma 16


title: Follicular lymphoma 25


title: Follicular lymphoma 37


title: Follicular lymphoma 39


title: Follicular lymphoma 35


title: Follicular lymphoma 15


title: Follicular lymphoma 30


title: Follicular lymphoma 20


title: Follicular lymphoma 17


title: Follicular lymphoma 36


title: Follicular lymphoma 18


title: Follicular lymphoma 29


title: Follicular lymphoma 22


title: Follicular lymphoma 19


title: Follicular lymphoma 27


title: WCE_SN1583plusFluc3

city: San Francisco

first: Suzanne

middle: M

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

description: H2A.1/H2A.1, H2A.2/H2A.2-FLAG-FRT, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/MTLα

data_processing:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  genome with bowtie v 1.1.2
Analysis performed using custom scripts
Genome_build: C_albicans_SC5314_version_A21-s02-m09-r10
Supplementary_files_format_and_content: CSV

organism: Candida albicans

source_name: yeast

growth_protocol: Samples were grown in YEPD overnight and seeded the next day at an OD600=0.1 in YEPD. Samples were grown to an OD600=1.0 and harvested.

extract_protocol:
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNA was isolated by antibodies directed to our proteins of interest (10 mg of anti-Histone H3, 10 mg anti-FLAG M2, or 4 mg of anti-Cse4).  DNA was then isolated by incubation with SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
Described in Dumesic et al. Cell 2015

treatment_protocol:
Fluconazole: samples were grown in YEPD overnight and seeded the next day at an OD600=0.1 in YEPD + Fluconazole (10mg/ml). Samples were grown to an OD600=1.0 and harvested.
Pre-spo media: Samples were grown in YEPD overnight and seeded the next day at an OD600=0.1 in pre-spo media. Samples were grown to an OD600=1.0 and harvested.

value: yeast cells

tag: genetic tag

tag: molecule subtype

value: Genomic DNA

value: Fluconazole


title: WCE_SN1583plusFluc2


title: WCE_SN1583_2

value: No treatment


title: WCE_SN1583_1


title: WCE_SN1583plusFluc1


title: Follicular lymphoma 21


title: Follicular lymphoma 24


title: WCE_SN1583_3


title: Follicular lymphoma 32


title: WCE_SN152plusFluc2

description: H2A.1/H2A.1, H2A.2/H2A.2, leu2Δ/leu2Δ, his1Δ/his1Δ, arg4Δ/arg4Δ, ura3Δ/URA3, iro1Δ/IRO1, MTLa/MTLα


title: Follicular lymphoma 28


title: WCE_SN152_3


title: WCE_SN152_2


title: WCE_SN152_1


title: SN1583plusFluc3

value: anti-FLAG

value: Affinity purified DNA


title: Follicular lymphoma 33


title: SN1583_2


title: SN1583_3


title: SN1583plusFluc2


title: SN1583plusFluc1


title: SN152_3


title: SN152plusFluc2


title: SN152plusFluc1


title: WCE_SN152plusFluc3


title: SN152plusFluc3


title: SN1589-FLAG-1

description: H2A.1/H2A.1/H2A.1/H2A.1, H2A.2/H2A.2-FLAG-FRT/H2A.2/H2A.2-FLAG-FRT, leu2Δ/leu2Δ/leu2Δ/leu2Δ,  ura3Δ/URA3/ura3Δ/URA3, his1Δ/his1Δ/his1Δ/his1Δ, arg4Δ/arg4Δ/arg4Δ/arg4Δ, iro1Δ/IRO1/iro1Δ/IRO1, mtlaΔ::C.m.LEU2/MTLα/MTLa/mtlαΔ::C.d.ARG4

data_processing:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  genome with bowtie v 1.1.2
Analysis performed using custom scripts
Genome_build: C_albicans_SC5314_version_A21-s02-m09-r10


title: SN1589-H3-1


title: SN1589-FLAG-2


title: SN1589-H3-2


title: SN1588-WCE

description: H2A.1/H2A.1/H2A.1/H2A.1, H2A.2/H2A.2/H2A.2/H2A.2, leu2Δ/leu2::SAT1/leu2Δ/leu2::SAT1,  his1Δ/his1Δ/his1Δ/his1Δ, arg4Δ/arg4Δ/arg4Δ/arg4Δ, ura3Δ/URA3/ura3Δ/URA3,  iro1Δ/IRO1/iro1Δ/IRO1, MTLa/mtlαΔ::C.d.ARG4/mtlaΔ::C.d.HIS1/MTLα


title: SN1588-H3-2


title: SN1588-FLAG-2


title: SN1588-FLAG-1


title: SN1583-WCE-H3


title: SN1583-WCE-FLAG


title: SN1583-H3-2


title: SN1583-FLAG-1


title: SN1583-H3-1


title: SN152-WCE


title: SN152-H3-2


title: SN152-FLAG-2


title: SN152_1


title: SN152-H3-1


title: Follicular lymphoma 14


title: SN152-FLAG-1


title: 1588_WCE


title: 1588-PreSpoWCE

value: Pre-spo media


title: 1588-PreSpo1-cse4


title: 1588-PreSpo2-cse4


title: 1588-2-cse4


title: SN1583-FLAG-2


title: 1588-1-cse4


title: 152_WCE


title: 152-Fluc2-cse4


title: 152-2-cse4


title: 152-1-cse4


title: ChIPseq.ID4eGFP_Dim_Input_Replicate3

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were aligned to the UCSC mm10 genome assembly using Rsubread or QuarR with the default configurations.
Duplicated reads were removed by Picard (http://broadinstitute.github.io/picard/)
peaks were called using Macs2 with the following setting:broadpeaks,narrow peaks (P<1 ×10-6, FDR<0.01),
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated from BAM files using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10

source_name: Spermatogonia

growth_protocol: Cells were subjected to flow cytometry using BD FACS Aria. Propidium iodide (PI) was added to discriminate dead cells . Positive ID4-eGFP epifluorescence was determined by comparison to testis cells from testes of wild-type mice lacking the P6 Id4-eGfp transgene. The gating area of eGFP positive was subdivided into thirds to define the ID4-eGFP+ subsets as being Dim (lower third) or Bright (upper third) by fluorescent intensity.

extract_protocol:
FACS-sorted cells were pelleted and re-suspended in nuclear isolation buffer (Sigma #NUC101-1KT). Depending on input size, chromatin was fragmented for 5-7.5 min using MNase at 21°C or 37°C
IPed DNA were end-repaired in 1x T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25U T4 DNA polymerase, 0.75U Klenow DNA polymerase and 7.5U T4 polynucleotide kinase for 30 min at 21-25°C, then A-tailed in 1x NEB buffer 2, 0.4 mM dNTPs and 3.75U of Klenow(exo-) for 30 min at 37°C and then ligated in 1x rapid DNA ligation buffer plus 1mM Illumina PE adapters and 1,600U DNA ligase for 1-8h at 21-25°C. Ligated fragments were amplified using dual-indexed primers for Illumina (NEB #E7600S) for 8-10 PCR cycles. DNA was purified with 1.8x volume Ampure XP DNA purification beads (Beckman Coulter #A63881) between each step. Fragment length was again checked by Bioanalyzer (Aglient Technology), and DNA concentration was determined using the Qubit dsDNA HS Assay Kit (Invitrogen #Q32854).

tag: strian

value: testis

tag: age

tag: chip antibody

value: none (input)


title: ChIPseq.ID4eGFP_Bright_Input_Replicate3


title: ChIPseq.ID4eGFP_Dim_Input_Replicate1


title: ChIPseq.ID4eGFP_Dim_Input_Replicate2


title: ChIPseq.ID4eGFP_Bright_Input_Replicate1


title: 152-FlucWCE

tag: strain


title: Follicular lymphoma 11


title: Follicular lymphoma 13


title: ChIPseq.ID4eGFP_Bright_Input_Replicate2


title: Follicular lymphoma 10


title: ChIPseq.ID4eGFP_Dim_H3K27me3_Replicate1

value: H3K27me3 ( Abcam #ab6002)


title: ChIPseq.ID4eGFP_Bright_H3K27me3_Replicate3


title: WCE_SN152plusFluc1


title: ChIPseq.ID4eGFP_Bright_H3K27me3_Replicate2


title: Follicular lymphoma 9


title: SN1583_1


title: Follicular lymphoma 1


title: SN1589-WCE


title: SN152_2


title: ChIPseq.ID4eGFP_Dim_H3K9me3_Replicate3

value: H3K9me3 (Abcam #ab8898)


title: ChIPseq.ID4eGFP_Bright_H3K27ac_Replicate1

value: H3K27ac (Active Motif #39133)


title: ChIPseq.ID4eGFP_Bright_H3K27ac_Replicate2


title: ChIPseq.ID4eGFP_Dim_H3K9me3_Replicate2


title: ChIPseq.ID4eGFP_Bright_H3K9me3_Replicate2


title: ChIPseq.ID4eGFP_Dim_H3K9me3_Replicate1


title: ChIPseq.ID4eGFP_Bright_H3K9me3_Replicate3


title: ChIPseq.ID4eGFP_Bright_H3K27me3_Replicate1


title: SN1588-H3-1


title: ChIPseq.ID4eGFP_Dim_H3K27me3_Replicate2


title: ChIPseq.ID4eGFP_Bright_H3K27ac_Replicate3


title: ChIPseq.ID4eGFP_Dim_H3K27ac_Replicate3


title: ChIPseq.ID4eGFP_Bright_H3K9me3_Replicate1


title: ChIPseq.ID4eGFP_Dim_H3K4me3_Replicate3

value: H3K4me3 ( Abcam #ab8580)


title: Follicular lymphoma 2

value: Peripheral blood

value: Diagnosis


title: ChIPseq.ID4eGFP_Dim_H3K27ac_Replicate1


title: ChIPseq.ID4eGFP_Dim_H3K4me3_Replicate2


title: ChIPseq.ID4eGFP_Dim_H3K4me3_Replicate1


title: Follicular lymphoma 7

value: Female


title: ChIPseq.ID4eGFP_Bright_H3K4me3_Replicate3


title: ChIPseq.ID4eGFP_Bright_H3K4me3_Replicate1


title: ChIPseq.ID4eGFP_Dim_H3K4me2_Replicate2

value: H3K4me2 (Abcam #ab7766)


title: ChIPseq.ID4eGFP_Dim_H3K4me2_Replicate3


title: ChIPseq.ID4eGFP_Bright_H3K4me2_Replicate2


title: ChIPseq.ID4eGFP_Bright_H3K4me3_Replicate2


title: ChIPseq.ID4eGFP_Dim_H3K4me2_Replicate1


title: ChIPseq.ID4eGFP_Dim_H3K4me1_Replicate3

value: H3K4me1 (Abcam #ab8895)


title: Follicular lymphoma 6

value: Bone marrow


title: ChIPseq.ID4eGFP_Bright_H3K4me2_Replicate3


title: Follicular lymphoma 4

value: Male


title: ChIPseq.ID4eGFP_Bright_H3K4me2_Replicate1


title: ChIPseq.ID4eGFP_Bright_H3K4me1_Replicate3


title: ChIPseq.ID4eGFP_Bright_H3K4me1_Replicate2


title: ChIPseq.ID4eGFP_Dim_H3K4me1_Replicate2


title: ChIPseq.ID4eGFP_Bright_H3K4me1_Replicate1


title: ATACseq.ID4eGFP_Dim_Replicate3

data_processing:
Illumina Casava1.8 software used for basecalling.
ATAC-seq reads were aligned to the UCSC mm10 genome assembly using Rsubread or QuarR with the default configurations.
Duplicated reads were removed by Picard (http://broadinstitute.github.io/picard/)
peaks were called using Macs2 with the following setting:-shift -100 --extsize 200 --call-summits -p 1e-6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated from BAM files using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10

extract_protocol:
After FACS sorting, each aliqout of fresh cells (~50,000 cells/aliquot) was pelleted and re-suspended in transposition mix (25µl 2x TD buffer, 2.5 µl Tn5 transposase [100 nM final], 16.5µl PBS, 0.5 µl 1% Digitonin, 0.5µl 10% Tween-20, 5µl H2O) and incubated at 37°C for 30 min in a thermomixer. The mix was then treated with a Zymo DNA Clean and Concentrator-5 Kit (Zymo research #D4014).
DNA were end-repaired in 1x T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25U T4 DNA polymerase, 0.75U Klenow DNA polymerase and 7.5U T4 polynucleotide kinase for 30 min at 21-25°C, then A-tailed in 1x NEB buffer 2, 0.4 mM dNTPs and 3.75U of Klenow(exo-) for 30 min at 37°C and then ligated in 1x rapid DNA ligation buffer plus 1mM Illumina PE adapters and 1,600U DNA ligase for 1-8h at 21-25°C. Ligated fragments were amplified using dual-indexed primers for Illumina (NEB #E7600S) for 8-10 PCR cycles. DNA was purified with 1.8x volume Ampure XP DNA purification beads (Beckman Coulter #A63881) between each step. Fragment length was again checked by Bioanalyzer (Aglient Technology), and DNA concentration was determined using the Qubit dsDNA HS Assay Kit (Invitrogen #Q32854).


title: ATACseq.ID4eGFP_Dim_Replicate2


title: Follicular lymphoma 5

value: Follow-up


title: Follicular lymphoma 8


title: Follicular lymphoma 3


title: ATACseq.ID4eGFP_Bright_Replicate3


title: ATACseq.ID4eGFP_Dim_Replicate1


title: 152-Fluc1-cse4

value: yeast cells

value: Fluconazole


title: ATACseq.ID4eGFP_Bright_Replicate2


title: ATACseq.ID4eGFP_Bright_Replicate1


title: MeDIPseq.ID4eGFP_Dim_Replicate2

data_processing:
Illumina Casava1.8 software used for basecalling.
MeDIP-seq reads were aligned to the UCSC mm10 genome assembly using Rsubread or QuarR with the default configurations.
Duplicated reads were removed by Picard (http://broadinstitute.github.io/picard/)
peaks were called using Macs2 with the following setting:narrow peaks (P<1 ×10-6, FDR<0.01),
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated from BAM files using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10

extract_protocol:
After FACS sorting, each aliqout (~50,000) of fresh cells was pelleted and re-suspended in lysis buffer (50mM Tris pH 8.0, 10 mM EDTA, 100 mM NaCl, 1% SDS, 0.5 mg/ml proteinase K) and incubated at 55°C for 5h. Genomic DNA was isolated using Phenol:Chloroform:Isoamyl Alcohol (Invitrogen #15593031), and sheared using a Bioruptor (Diagenode UCD-200). 10% raw sheared DNA was retained to serve as an input control. Samples were end-repaired in 1x T4 DNA ligase buffer, 0.4mM dNTP mix, 2.25U T4 DNA polymerase, 0.75U Klenow DNA polymerase and 7.5U T4 polynucleotide kinase for 30 min at 21-25°C, then A-tailed in 1x NEB buffer 2, 0.4mM dNTPs and 3.75U of Klenow(exo-) for 30 min at 37°C, and then ligated in 1x rapid DNA ligation buffer, 1mM Illumina PE adapters and 1,600U DNA ligase for 1-8 h at 21-25°C. Samples were denatured at 95°C for 10 min, then transfered immediately to ice to prevent re-annealing. 0.2pM λ-DNA fragments (50% methylated) were used as a spike-in control. MeDIP on purified adapter-ligated DNA with spike-in was performed in 0.1 M Na2HPO4/NaH2PO4, 35μl of 2 M NaCl, 2.5 μl of 10% Triton X-100 and 1μl of anti-methylcytidine antibody (1 mg/ml Diagenode # MAb-081-100) overnight. DNA-IgG complexes were captured by protein A/G agarose beads. DNA was extracted by phenol:chloroform:isoamyl alcohol (25:24:1, v/v).
IPed DNA were end-repaired in 1x T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25U T4 DNA polymerase, 0.75U Klenow DNA polymerase and 7.5U T4 polynucleotide kinase for 30 min at 21-25°C, then A-tailed in 1x NEB buffer 2, 0.4 mM dNTPs and 3.75U of Klenow(exo-) for 30 min at 37°C and then ligated in 1x rapid DNA ligation buffer plus 1mM Illumina PE adapters and 1,600U DNA ligase for 1-8h at 21-25°C. Ligated fragments were amplified using dual-indexed primers for Illumina (NEB #E7600S) for 8-10 PCR cycles. DNA was purified with 1.8x volume Ampure XP DNA purification beads (Beckman Coulter #A63881) between each step. Fragment length was again checked by Bioanalyzer (Aglient Technology), and DNA concentration was determined using the Qubit dsDNA HS Assay Kit (Invitrogen #Q32854).


title: MeDIPseq.ID4eGFP_Dim_Replicate3


title: MeDIPseq.ID4eGFP_Dim_Replicate1


title: MeDip_Input_Bright


title: MeDip_Input_Dim


title: MeDIPseq.ID4eGFP_Bright_Replicate3


title: ChIPseq.ID4eGFP_Dim_H3K4me1_Replicate1


title: ChIPseq.ID4eGFP_Dim_H3K27ac_Replicate2


title: RNAseq.ID4eGFP_Dim_Replicate3

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to the UCSC mm10 genome assembly using Rsubread or QuarR with the default configurations.
DEGs were analyzed by DESeq2.
fpkm was calculated by cufflink.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated from BAM files using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10

extract_protocol:
Populations of at least ≥1000 ID4-eGFPBright or ID4-eGFPDim cells recovered by FACS sorting were counted, pelleted, and subjected to direct cDNA synthesis using the SMART-Seq v4 ultra Low Input RNA Kit for Sequencing (Clontech Laboratories #634888)
Approximately 250pg of cDNA was used for preparation of dual-indexed libraries using the Nextera XT DNA Library Preparation Kit (Illumina # FC-131-1002) following the manufacturer’s procedures.


title: RNAseq.ID4eGFP_Dim_Replicate2


title: Follicular lymphoma 12


title: MeDIPseq.ID4eGFP_Bright_Replicate1


title: RNAseq.ID4eGFP_Dim_Replicate1


title: RNAseq.ID4eGFP_Bright_Replicate3


title: ChIPseq.ID4eGFP_Dim_H3K27me3_Replicate3


title: GA2

city: Grand Rapids

first: Tao

address: 333 Bostwick Ave NE

department: Cancer and Cell Biology

institute: Van Andel Research Institute

data_processing:
Quality control:   Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter,  reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30  and GC content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
Reads mapping to the reference genome:  Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We  selected TopHat as the mapping tool for that TopHat can generate a database of splice  junctions based on the gene model annotation file and thus a better mapping result than  other non-splice mapping tools.
Quantification of gene expression level:  HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM   of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, considers the effect of sequencing depth and gene length  for the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: fpkm

source_name: Bone marrow

growth_protocol: C57BL/6J mice (8 weeks) were euthanized by CO2. Total bone marrow cells were collected from tibia and femur and then cultured in α-MEM with 10% fetal bovine serum (FBS) in an incubator (37 ℃, 5% CO2). After 48 h, the non-adherent cells were removed through three washes with PBS, and the adherent cells were continued in culture and used as a source of BMSCs. The culture medium was replaced every 2 d

extract_protocol:
Total RNA was extracted from cell cultures with TRIzol reagent (Invitrogen), purified with an RNeasy kit (Qiagen) according to manufacturer’s instructions
mRNA is enriched using oligo(dT) beads, and then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: BMSCs were seeded into 24-well plates at 1 x 105/well and cultured in α-MEM. When the cells reached 100% confluence, 50μM GA with 1 μM Dexamethasone or equal volume DMSO with 1μM Dexamethasone were added in to the cells and cultured for 3 days.

tag: cell type

value: Bone marrow stromal cells

tag: passages

tag: genotype

value: wild type


title: GA1


title: DMSO1


title: RNAseq.ID4eGFP_Bright_Replicate2

value: testis


title: DMSO2


title: MeDIPseq.ID4eGFP_Bright_Replicate2


title: RNAseq.ID4eGFP_Bright_Replicate1


title: MtbΔvirSComp at pH6.6 for one hour, replicate 3

city: New Delhi

first: Garima

last: Khare

state: Delhi

address: Benito Juarez Road

department: Biochemistry

country: India

institute: University of Delhi

description:
Gene expression of MtbΔvirSComp cultures in 7H9 medium of pH6.6
MtbΔvirSComp pH 6.6_3

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040).  The purified cRNA (600ng) was fragmented with fragmentation blocking mix by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into the hybridization chamber, samples were placed in thehybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µm using Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer's instructions (G2505-90020). Settings included Agilent HD_GX_1color (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and baseline transformation was done with respect to the control sample using GeneSpring GX  v12.0 from Agilent Technologies

organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

source_name: MtbΔvirSComp at pH6.6 for one hour

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Quick Amplification Labelling kit (Agilent Technologies, G4140-90040) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mtb Erdman, MtbΔvirS and MtbΔvirSComp were grown till  OD600 of 0.3-0.5 in 7H9-ADC-tween medium.

extract_protocol: RNA was isolated from the cultures by using Rneasy kit method (Qiagen). RNA quality was measured using Agilent Bioanalyzer.

treatment_protocol: Early log phase grown cultures of Mtb Erdman, MtbΔvirS and MtbΔvirSComp were exposed to pH of 6.6 and pH 4.5 for one hour at 37 degree at 200rpm.

value: VirS complemented strain of VirS knockout

tag: growth phase

value: early log phase

value: 7H9 medium of pH6.6


title: MtbΔvirS at pH6.6 for one hour, replicate 2

description:
Gene expression of MtbΔvirS cultures in 7H9 medium of pH6.6
MtbΔvirS pH 6.6_2

source_name: MtbΔvirS at pH6.6 for one hour

value: VirS mutant strain of Mtb Erdman


title: MtbΔvirSComp at pH6.6 for one hour, replicate 1

description:
Gene expression of MtbΔvirSComp cultures in 7H9 medium of pH6.6
MtbΔvirSComp pH 6.6_1


title: MtbΔvirSComp at pH4.5 for one hour, replicate 3

description:
Gene expression of MtbΔvirSComp cultures in 7H9 medium of pH4.5
MtbΔvirSComp pH 4.5_3

source_name: MtbΔvirSComp at pH4.5 for one hour

value: 7H9 medium of pH4.5


title: MtbΔvirS at pH6.6 for one hour, replicate 3

description:
Gene expression of MtbΔvirS cultures in 7H9 medium of pH6.6
MtbΔvirS pH 6.6_3


title: MtbΔvirS at pH4.5 for one hour, replicate 3

description:
Gene expression of MtbΔvirS cultures in 7H9 medium of pH4.5
MtbΔvirS pH 4.5_3

source_name: MtbΔvirS at pH4.5 for one hour


title: E. cyaneus, gradual temperature increase, 18 degrees C, sample 2

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_2
differential expression file:
EcyT18annot.csv

data_processing:
Raw reads were mapped onto transcriptome assemblies with salmon v0.9.1.
DESeq2 abundance estimation was performed with an in-house R script, which can be found at https://github.com/drozdovapb/EveEcyGlaDE.
Transcript abundances were merged with transcript annotation for selection of Metazoa-related contigs if necessary.
Genome_build: de novo transcriptome assembly of the corresponding species (FASTA files are available on series record).
Supplementary_files_format_and_content: Salmon output files as TPM (transcript per million counts, *sf.txt files) and DESeq2 output files with custom annotation (*annot.csv)

organism: Eulimnogammarus cyaneus

source_name: whole body

extract_protocol:
Total RNA for RNA sequencing was extracted from either a single individual or from a pool of up to 5 individuals (see individual BioSample description). Amphipods were homogenized in 1 ml of Qiazol Reagent (Qiagen) with MM400 homogenizer (Retsch). RNA isolation from the aqueous phases was performed with a Qiacube (Qiagen) and miRNeasy kit (Qiagen).
mRNA was isolated from the total RNA sample using Oligotex mRNA Mini Kit (Qiagen). The quality of RNA was checked with RNA 6000 Nano Kit on the Agilent Bioanalyzer 2100. mRNA libraries were prepared with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, # SSV21124).

treatment_protocol: Animals were acclimated at 6 degrees C for 3-5 days before the experiment. Please refer to description of individual samples for species- and sample-specific details

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina

tag: depth

value: adult

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina

tag: condition


title: E. cyaneus, gradual temperature increase, 24 degrees C, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_1
differential expression file:
EcyT24annot.csv


title: E. cyaneus, gradual temperature increase, 18 degrees C, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_1
differential expression file:
EcyT18annot.csv


title: E. cyaneus, gradual temperature increase, 18 degrees C, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_4
differential expression file:
EcyT18annot.csv


title: E. cyaneus, gradual temperature increase, 24 degrees C, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_3
differential expression file:
EcyT24annot.csv


title: E. cyaneus, gradual temperature increase, 18 degrees C, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_3
differential expression file:
EcyT18annot.csv


title: E. cyaneus, gradual temperature increase, 24 degrees C, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_2
differential expression file:
EcyT24annot.csv


title: Mtb Erdman at pH4.5 for one hour, replicate 3

description:
Gene expression of Mtb Erdman cultures in 7H9 medium of pH4.5
Mtb Erdman pH 4.5_3

source_name: Mtb Erdman at pH4.5 for one hour

value: Wild type strain of Mtb Erdman

tag: treatment


title: MtbΔvirS at pH4.5 for one hour, replicate 1

description:
Gene expression of MtbΔvirS cultures in 7H9 medium of pH4.5
MtbΔvirS pH 4.5_1


title: Mtb Erdman at pH4.5 for one hour, replicate 2

description:
Gene expression of Mtb Erdman cultures in 7H9 medium of pH4.5
Mtb Erdman pH 4.5_2


title: Mtb Erdman at pH6.6 for one hour, replicate 3

description:
Gene expression of Mtb Erdman cultures in 7H9 medium of pH6.6
Mtb Erdman pH 6.6_3

source_name: Mtb Erdman at pH6.6 for one hour


title: Mtb Erdman at pH4.5 for one hour, replicate 1

description:
Gene expression of Mtb Erdman cultures in 7H9 medium of pH4.5
Mtb Erdman pH 4.5_1


title: MtbΔvirS at pH6.6 for one hour, replicate 1

description:
Gene expression of MtbΔvirS cultures in 7H9 medium of pH6.6
MtbΔvirS pH 6.6_1


title: E. cyaneus, gradual temperature increase, 24 degrees C, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_4
differential expression file:
EcyT24annot.csv


title: MtbΔvirS at pH4.5 for one hour, replicate 2

description:
Gene expression of MtbΔvirS cultures in 7H9 medium of pH4.5
MtbΔvirS pH 4.5_2


title: E. cyaneus, gradual temperature increase, 12 degrees C, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EcyT12_2
differential expression file:
EcyT12annot.csv


title: E. cyaneus, gradual temperature increase, 12 degrees C, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EcyT12_3
differential expression file:
EcyT12annot.csv


title: MtbΔvirSComp at pH4.5 for one hour, replicate 1

description:
Gene expression of MtbΔvirSComp cultures in 7H9 medium of pH4.5
MtbΔvirSComp pH 4.5_1


title: E. cyaneus, parallel control for EcyT24, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB247
differential expression file:
EcyT24annot.csv


title: E. cyaneus, parallel control for EcyT24, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB24_4_7
differential expression file:
EcyT24annot.csv


title: E. cyaneus, parallel control for EcyT24, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB24_2_6
differential expression file:
EcyT24annot.csv


title: Mtb Erdman at pH6.6 for one hour, replicate 1

description:
Gene expression of Mtb Erdman cultures in 7H9 medium of pH6.6
Mtb Erdman pH 6.6_1


title: E. cyaneus, parallel control for EcyT24, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB24_1_6
differential expression file:
EcyT24annot.csv


title: Mtb Erdman at pH6.6 for one hour, replicate 2

description:
Gene expression of Mtb Erdman cultures in 7H9 medium of pH6.6
Mtb Erdman pH 6.6_2


title: E. cyaneus, parallel control for EcyT18, sample 1b

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_1b
differential expression file:
EcyT18annot.csv


title: E. cyaneus, parallel control for EcyT12, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_3
differential expression file:
EcyT12annot.csv


title: E. cyaneus, parallel control for EcyT12, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_2
differential expression file:
EcyT12annot.csv


title: E. cyaneus, parallel control for EcyT12, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_1
differential expression file:
EcyT12annot.csv


title: E. cyaneus, parallel control for EcyT18, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_1a
differential expression file:
EcyT18annot.csv


title: E. cyaneus, parallel control for EcyT18, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_2
differential expression file:
EcyT18annot.csv


title: E. cyaneus, parallel control for EcyT12, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_4
differential expression file:
EcyT12annot.csv


title: E. cyaneus, parallel control for EcyT18, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_4
differential expression file:
EcyT18annot.csv


title: E. cyaneus, initial control for EcyT, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_1
differential expression file:


title: E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_3
differential expression file:
EcyPh24_annot.csv


title: E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_1
differential expression file:
EcyPh24_annot.csv


title: WT DY125F

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description:
WT
Ribosome-protected RNA 25-34 nt

data_processing:
Base calling and demultiplexing was performed at the NIDDK Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina Truseq Stranded ribo-zero kit.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.


title: E. cyaneus, initial control for EcyT, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_2
differential expression file:


title: E. cyaneus, gradual temperature increase, 12 degrees C, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EcyT12_1
differential expression file:
EcyT12annot.csv


title: E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_2
differential expression file:
EcyPh24_annot.csv


title: E. cyaneus, initial control for EcyT, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_4
differential expression file:


title: E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_4
differential expression file:
EcyPh3_annot.csv


title: E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_3
differential expression file:
EcyPh3_annot.csv


title: E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_4
differential expression file:
EcyPh24_annot.csv


title: hcr1-delta hcHCR1 DY119F

description:
hcr1-delta hcHCR1
Ribosome-protected RNA 25-34 nt

value: hcr1-delta hcHCR1


title: E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_2
differential expression file:
EcyPh3_annot.csv


title: hcr1-delta hcRLI1 DY120F

description:
hcr1-delta hcRLI1
Ribosome-protected RNA 25-34 nt

value: hcr1-delta hcRLI1


title: E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_1
differential expression file:
EcyPh3_annot.csv


title: hcr1-delta YEplac195 DY118F

description:
hcr1-delta YEplac195
Ribosome-protected RNA 25-34 nt

value: hcr1-delta YEplac195


title: E. cyaneus, initial control for EcyT, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_3
differential expression file:


title: E. cyaneus, 0.1% acetone, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EcyPB24_2
differential expression file:
EcyPB24_annot.csv


title: E. cyaneus, 0.1% acetone, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EcyPB24_1
differential expression file:
EcyPB24_annot.csv


title: WT6_HiC_2

tag: re

value: HindIII

tag: genotype/variation

value: WT


title: Sir2Δ_HiC_4


title: E. cyaneus, 0.1% acetone, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EcyPB3_2
differential expression file:
EcyPB3_annot.csv

tag: tissue


title: 100bpΔ_HiC_1


title: E. cyaneus, 0.1% acetone, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EcyPB3_1
differential expression file:
EcyPB3_annot.csv


title: WT12_HiC_2


title: E. cyaneus, LT10, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_4
differential expression file:
Ecy10LT24_annot.csv


title: E. cyaneus, LT10, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_1
differential expression file:
Ecy10LT24_annot.csv


title: E. cyaneus, LT10, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_2
differential expression file:
Ecy10LT24_annot.csv


title: ED19_4

city: Mississippi State

first: Gregory

middle: Todd

last: Pharr

state: MS

address: 240 Wise Center Drive

department: College of Veterinary Medicine

institute: Mississippi State University

data_processing:
Base quality and Phred score relationship determined with Illumina CASAVA v1.8 software.
Clean reads were obtained using in-house perl scripts to remove low quality reads.
The HTSeq v0.601 software was used to calculate the fragments per kilobase of transcript sequence per million of reads mapped.
Differential expression analysis was conducted with the DESeq v1.10.1 software.
Genome_build: The galGal4 chicken genome was used for alignments with paired-end clean reads using TopHat v2.0.12.
Supplementary_files_format_and_content: tables include read counts and RPKM values for each transcript, and a list of differentially expressed genes.

organism: Gallus gallus

source_name: Bursa of Fabricius

extract_protocol:
Bursas were pooled (52 - 55 for each biological replicate) and single cell suspensions of B-lymphocytes were prepared. The single cell suspensions were centrifuged on Histopaque gradients to remove dead cells. Total RNA was extracted from 8 x 10e6 to 1 x 10e7 gradient-purified cells per replicate with the RNeasy Mini Kit (QIAGEN), evaluated with a Implen NanoPhotometer and then quantitated using the Qubit RNA Assay Kit (Life Technologies).
The mRNA was selected from 3 ug of total RNA using poly-T oligo-attached mangnetic beads.  The NEBNext Ultra RNA Library Prep Kit was used to prepare cDNA libraries from the mRNA. The library fragments were size-selected for cDNA fragments of 150 - 200 bp.  The index-coded samples were sequenced on an Illumina Hiseq platform to generate 125 bp/150 bp paired-end reads.

tag: line

value: Hy-Line W-36 commercial layer

value: B-lymphocyte

value: Embryonic day 19

value: Bursa of Fabricius


title: ED16_3

value: Embryonic day 16


title: E. cyaneus, LT10, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_3
differential expression file:
Ecy10LT24_annot.csv

value: whole body

value: rocky littoral zone


title: E. cyaneus, 0.1% acetone, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EcyPB24_3
differential expression file:
EcyPB24_annot.csv

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina


title: ED19_5


title: E. cyaneus, LC10 cadmium, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_3
differential expression file:
EcyCd24_annot.csv

value: adult

value: littoral zone


title: E. cyaneus, LC10 cadmium, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_4
differential expression file:
EcyCd24_annot.csv

value: Maxim Timofeyev, Daria Bedulina


title: E. cyaneus, LT10, 3 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_4
differential expression file:
Ecy10LT3_annot.csv


title: ED16_2


title: E. cyaneus, LT10, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_3
differential expression file:
Ecy10LT3_annot.csv


title: E. cyaneus, LC10 cadmium, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_1
differential expression file:
EcyCd24_annot.csv


title: ED16_1


title: E. cyaneus, LT10, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_2
differential expression file:
Ecy10LT3_annot.csv


title: E. cyaneus, LC10 cadmium, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_2
differential expression file:
EcyCd24_annot.csv


title: E. cyaneus, LC10 cadmium, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_3
differential expression file:
EcyCd3_annot.csv


title: E. cyaneus, LC10 cadmium, 3 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_4
differential expression file:
EcyCd3_annot.csv


title: E. cyaneus, LC10 cadmium, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_2
differential expression file:
EcyCd3_annot.csv


title: E. cyaneus, 0.1% acetone, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EcyPB3_3
differential expression file:
EcyPB3_annot.csv


title: ED19_6


title: E. cyaneus, control, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_4
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv


title: E. cyaneus, LT10, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_1
differential expression file:
Ecy10LT3_annot.csv


title: E. cyaneus, control, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_2
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv


title: E. cyaneus, control, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_3
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv


title: E. cyaneus, control, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_1
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv