title: Mmus_shZfr_1

city: Stanford

first: Jin

middle: Billy

last: Li

address: 300 Pasteur Dr, Alway M341

department: Genetics

institute: Stanford University

data_processing:
Paired-end, 76-base-pair reads were trimmed using Trim Galore 0.4.5 to remove adapter sequences.
Trimmed reads were mapped to the mm9 genome using STAR 2.5.4b with the parameters --outFilterScoreMin 10 --alignEndsType EndToEnd.
To call editing levels, samtools (v1.4) mpileup function was used to extract base calls from uniquely mapped reads at known editing sites. Editing levels were detemined as the number of G reads out of all A and G reads at a site.
To determine gene expression levels, RSEM 1.2.30 was used to count the number of reads mapping to each gene. RSEM calculated expected counts were rounded down to the nearest integer and used as input to DESeq2 v1.20.0
Genome_build: mm9
Supplementary_files_format_and_content: For RNA editing analysis: A and G counts and editing levels at known editing sites. Tab-delimited filtes are formatted as: chr, pos, A counts, G counts, editing level.
Supplementary_files_format_and_content: For expression analysis: genes.results output files from RSEM. Tab-delimited files are formatted as: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM, posterior_mean_count, posterior_standard_deviation_of_count, pme_TPM, pme_FPKM, TPM_ci_lower_bound, TPM_ci_upper_bound, FPKM_ci_lower_bound, FPKM_ci_upper_bound.

growth_protocol: Primary mouse cortical neurons were dissociated into single cell suspensions from E16.5 mouse cortices using a papain dissociation system. Neurons were seeded onto poly-L-lysine coated plates (0.1% w/v) and grown in Neurobasal media supplemented with B-27 serum-free supplement, GlutaMAX, and Penicillin-Streptomycin in a humidified incubator at 37°C, with 5% CO2.

extract_protocol:
Neurons were harvested 7 days after dissection from E16.5 brains. RNA was extracted using the PARIS kit (Ambion) followed by TURBO DNase treatment (Thermo Fisher).
250 ng of RNA was mixed with an equal amount of pooled DNA oligos designed antisense to human rRNAs in 50 bp sections in an 8 ul reaction with 2ul of 5X Hybridization buffer (500 mM Tris-HCl pH 7.4, 1  M NaCl). rRNA antisense oligos were annealed to total RNA samples for 2 minutes at 95°C, the temperature was slowly reduced to 65°C and 2U of Thermostable Hybridase H (Epicentre) and 1 ul of 10X Digestion buffer (500 mM Tris-HCl, 1 M NaCl, 200mM MgCl2) were added to make 10 ul total and reactions were incubated for 30 minutes at 65°C. rRNA-depleted RNA was then purified using Agencourt RNAClean XP beads, treated with TURBO DNase (Ambion) and then purified with RNAClean XP beads again. rRNA-depleted RNA was used as input to the KAPA RNA HyperPrep Kit (KK8540) to make RNA-seq libraries.

treatment_protocol: Neurons were infected the day after seeding with a 6-well pellet worth of concentrated frozen virus. shRNAs were cloned into the pGreenPuro backbone (System Biosciences) and this construct was used to produce lentivirus according to standard protocols in 293T cells using the third-generation system and concentrated 1:100 with lenti-X. Media was changed 12-16 hours later and after 4 days.

tag: strain background

value: shZfr

tag: cell type

value: primary cortical neuron culture

tag: developmental stage

value: Neurons were harvested 7 days after dissection.

tag: molecule subtype

value: rRNA-depleted RNA


title: 75B BrTuB07 vs. 75R BrTuB07

status: Public on May 08 2019

type: RNA

city: Santa Monica

first: HSIAOWANG

last: CHEN

state: CA

address: 2825 Santa Monica Blvd

department: Medicine

country: USA

institute: UCLA

hyb_protocol: In comparison of expression between each breast tumor baseline sample prior to any treatment and to the same patient sample taken after 2-weeks of treatment with HER2-targeted therapy(run-in). 825 ng each of labeled individual Breast tumor baseline sample(cy3 label) and treatment run-in sample from the same patient were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent Microarray scanner (G2565CA) with extended dynamic range applied. Images were quantified using Agilent Feature Extraction Software version A.10.7 or version 11.0 refer to raw data file column.

data_processing:
Agilent Feature Extraction Software was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used  to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extracted data was imported into Rosetta Resolver version 7.2  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging.
In Rosetta analysis, setting for cluster Algoritm is list here and applies to both sample experiment and sequence.  Algorithm=Agglomerative, Algorithm parameters: Heuristic criteria=Average link, Similarity measure metric type=Cosine correlation.
In Rosetta analysis, setting for statistical cuts is list here to generate the cluster.  Thresholds=equal or bigger than 2 fold change with P-vaule equal or less than 0.01. Number of experiment cut is not applied.

molecule: total RNA

organism: Homo sapiens

source_name: 75B BrTuB07

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions.

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol.

tag: sample type

value: Breast tumor baseline

source_name: 75R BrTuB07

value: after 2-weeks of treatments with HER2-targeted therapy

tag: er status (ihc staining results)

value: Pos

tag: pr_status (ihc staining results)

tag: treatment group

value: TCHTy

tag: drug response

value: PCR


title: Mmus_shZfr_2

type: SRA

library_source: transcriptomic

organism: Mus musculus

tag: genotype/variation


title: Influenza_Control [8784170101_B]

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
raw data file: MRC06.txt
Control samples from Influenza A virus infection model

hyb_protocol: 1.5 µg cRNA was then hybridized to Mouse WG-6 v2.0 bead chips (Illumina) according to the manufacturer’s protocols.

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray data was processed in GeneSpring GX v14.8 (Agilent Technologies). Flags were used to filter out the probe sets that did not result in a ‘present’ call in at least 10% of the samples, with the ‘present’ lower cut-off of 0.99. Signal values were then set to a threshold level of 10, log2 transformed, and per-chip normalised using 75th percentile shift algorithm. Next, per-gene normalisation was applied by dividing each messenger RNA transcript by the median intensity of all the samples. Next, transcripts were filtered to select the most variable probes: those that had a minimum of 1.5-fold expression change compared with the median intensity across all samples, in greater than 10% of all samples.

label: biotin

label_protocol: cRNA was prepared from 200 ng globin-reduced blood RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). Quality was checked using an RNA 6000 Nano kit (Agilent) using a BioAnalyzer 2100 (Agilent). Biotinylated cRNA samples were randomized.

extract_protocol: Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Ambion).

tag: mouse strain

tag: mouse model

value: Influenza A virus

tag: condition

value: Control

tag: infection protocol

value: Influenza A/X-31 (H3N2) strain (a kind gift from Dr J. Skehel, MRC NIMR) was grown in the allantoic cavity of 10 day-embryonated hen’s eggs, stored at -80 °C and titrated on MDCK cells prior to infection. Female C57BL/6/J mice were infected intranasally with 8x103 TCID50 in 30 ml of PBS. Control uninfected mice received PBS only. Lung samples were collected from individual infected and control treated mice on day 6 post infection.

tag: tissue

value: whole blood


title: 76B BrTuB07 vs. 76R BrTuB07

source_name: 76B BrTuB07

source_name: 76R BrTuB07

value: Neg


title: 74B BrTuB07 vs. 74R BrTuB07

source_name: 74B BrTuB07

source_name: 74R BrTuB07

value: TCTy


title: Influenza_Control [8784170097_D]


title: Mmus_shAdar2_1-3


title: Mmus_shAdar2_2


title: 70B BrTuB07 vs. 70R BrTuB07

source_name: 70B BrTuB07

source_name: 70R BrTuB07


title: 71B BrTuB07 vs. 71R BrTuB07

source_name: 71B BrTuB07

source_name: 71R BrTuB07

value: RD


title: 69B BrTuB07 vs. 69R BrTuB07

source_name: 69B BrTuB07

source_name: 69R BrTuB07

value: TCH


title: Influenza_Disease [8784170097_E]

description:
raw data file: MRC06.txt
Disease samples from Influenza A virus infection model

value: Disease


title: Mmus_shAdar2_1-1

value: primary cortical neuron culture


title: Mmus_shAdar2_1-2

value: Neurons were harvested 7 days after dissection.


title: 82B BrTuB07 vs. 82R BrTuB07

source_name: 82B BrTuB07

source_name: 82R BrTuB07


title: Influenza_Disease [8762536147_C]


title: Mmus_shAdar1_2

value: rRNA-depleted RNA


title: 73B BrTuB07 vs. 73R BrTuB07

source_name: 73B BrTuB07

value: Breast tumor baseline

source_name: 73R BrTuB07


title: Influenza_Control [8762536147_A]


title: Mmus_shAdar1_1


title: 67B BrTuB07 vs. 67R BrTuB07

source_name: 67B BrTuB07

source_name: 67R BrTuB07

value: after 2-weeks of treatments with HER2-targeted therapy


title: Influenza_Disease [8762536122_D]


title: 59B BrTuB07 vs. 59R BrTuB07

source_name: 59B BrTuB07

source_name: 59R BrTuB07

value: Pos


title: 68B BrTuB07 vs. 68R BrTuB07

source_name: 68B BrTuB07

source_name: 68R BrTuB07


title: 58B BrTuB07 vs. 58R BrTuB07

source_name: 58B BrTuB07

source_name: 58R BrTuB07


title: Influenza_Disease [8762536122_A]


title: 65B BrTuB07 vs. 65R BrTuB07

source_name: 65B BrTuB07

source_name: 65R BrTuB07

value: TCHTy


title: 61B BrTuB07 vs. 61R BrTuB07

source_name: 61B BrTuB07

source_name: 61R BrTuB07


title: Mmus_shControl2_2


title: 60B BrTuB07 vs. 60R BrTuB07

source_name: 60B BrTuB07

source_name: 60R BrTuB07

value: PCR


title: Mmus_shControl2_1


title: 62B BrTuB07 vs. 62R BrTuB07

source_name: 62B BrTuB07

source_name: 62R BrTuB07


title: 57B BrTuB07 vs. 57R BrTuB07

source_name: 57B BrTuB07

source_name: 57R BrTuB07


title: 52B BrTuB07 vs. 52R BrTuB07

source_name: 52B BrTuB07

source_name: 52R BrTuB07


title: Influenza_Control [8762536087_E]

value: Influenza A virus


title: 53B BrTuB07 vs. 53R BrTuB07

source_name: 53B BrTuB07

source_name: 53R BrTuB07


title: Influenza_Control [8762536122_F]

value: Control


title: Mmus_shControl1_1

value: Neurons were harvested 7 days after dissection from E16.5 brains.


title: Mmus_shControl1_2


title: 51B BrTuB07 vs. 51R BrTuB07

source_name: 51B BrTuB07

source_name: 51R BrTuB07


title: 47B BrTuB07 vs. 47R BrTuB07

source_name: 47B BrTuB07

source_name: 47R BrTuB07


title: 43B BrTuB07 vs. 43R BrTuB07

source_name: 43B BrTuB07

source_name: 43R BrTuB07


title: pooled_input.SMC1a_ChIPseq

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

library_source: genomic

data_processing:
ChIP-seq reads were filtered to retain only read pairs with mean base quality score >20.  ERa ChIP-seq samples were hard-clipped to 36nt.  SMC1a ChIP-seq samples were submitted to cutadapt v1.2.1 with parameters "-a AGATCGGAAGAG -O 5 q 0" to trim adapter, then filtered to retain only reads at least 30nt in length.
Trimmed & filtered ChIP-seq reads were mapped to mm10 via Bowtie allowing only uniquely-mapped hits (parameter "-m 1"), then coordinate-sorted and deduplicated via the Picard tool suite.
Normalized depth tracks for ChIP-seq data were generated by BEDTools genomeCoverageBed after extending all uniquely-mapped non-duplicate reads to average fragment size (150nt for ERa, 200nt for all others), then normalized to 15M (for ERa) or 20M (all others) and converted to bigWig format with UCSC utility bedGraphToBigWig.
genome build: mm10
processed data files format and content: ChIP-seq and RNA-seq normalized depth track in bigWig format

molecule: genomic DNA

source_name: uterus

extract_protocol:
ChIP-seq: Frozen mouse tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
ChIP-seq: Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: Mice were either used at 21 days old or were ovariectomized at 10 weeks old, held for 10-14 days to allow endogenous hormones to clear. Mice were given a single intraperitoneal injection of 250 ng E2  dissolved in 0.1 ml of normal saline or 1 mg P4 dissolved in sesame oil. Control vehicle (V) animals were injected with 0.1 ml normal saline. Tissue samples  were collected 1, 2, 6, 8 12 or 24 hours after the injections.

value: uterus

tag: strain

tag: antibody

value: none (input)


title: E2-1h.SMC1a_ChIPseq

value: Active Motif #61067


title: 41B BrTuB07 vs. 41R BrTuB07

source_name: 41B BrTuB07

source_name: 41R BrTuB07

value: Neg

value: RD


title: 44B BrTuB07 vs. 44R BrTuB07

source_name: 44B BrTuB07

source_name: 44R BrTuB07


title: 38B BrTuB07 vs. 38R BrTuB07

source_name: 38B BrTuB07

source_name: 38R BrTuB07

value: TCTy


title: Influenza_Control [8762536085_C]

value: Influenza A/X-31 (H3N2) strain (a kind gift from Dr J. Skehel, MRC NIMR) was grown in the allantoic cavity of 10 day-embryonated hen’s eggs, stored at -80 °C and titrated on MDCK cells prior to infection. Female C57BL/6/J mice were infected intranasally with 8x103 TCID50 in 30 ml of PBS. Control uninfected mice received PBS only. Lung samples were collected from individual infected and control treated mice on day 6 post infection.

value: whole blood


title: 39B BrTuB07 vs. 39R BrTuB07

source_name: 39B BrTuB07

source_name: 39R BrTuB07


title: Veh.SMC1a_ChIPseq


title: Influenza_Control [8762536059_A]


title: Influenza_Control [8762536044_C]


title: Influenza_Disease [8762536059_B]

value: Disease


title: Influenza_Disease [8762536085_F]


title: Influenza_Disease [8762536087_B]


title: 34B BrTuB07 vs. 34R BrTuB07

source_name: 34B BrTuB07

value: Breast tumor baseline

source_name: 34R BrTuB07


title: 21d_input.hmod_ChIPseq


title: P4-1h.SMC1a_ChIPseq


title: 40B BrTuB07 vs. 40R BrTuB07

source_name: 40B BrTuB07

source_name: 40R BrTuB07

value: after 2-weeks of treatments with HER2-targeted therapy

value: TCH


title: 35B BrTuB07 vs. 35R BrTuB07

source_name: 35B BrTuB07

source_name: 35R BrTuB07

value: Pos


title: 30B BrTuB07 vs. 30R BrTuB07

source_name: 30B BrTuB07

source_name: 30R BrTuB07

value: PCR


title: 27B BrTuB07 vs. 27R BrTuB07

source_name: 27B BrTuB07

source_name: 27R BrTuB07


title: 32B BrTuB07 vs. 32R BrTuB07

source_name: 32B BrTuB07

source_name: 32R BrTuB07

value: TCHTy


title: 37B BrTuB07 vs. 37R BrTuB07

source_name: 37B BrTuB07

source_name: 37R BrTuB07


title: 31B BrTuB07 vs. 31R BrTuB07

source_name: 31B BrTuB07

source_name: 31R BrTuB07


title: Influenza_Disease [8762536044_A]

value: Influenza A virus


title: 29B BrTuB07 vs. 29R BrTuB07

source_name: 29B BrTuB07

source_name: 29R BrTuB07


title: adult_input.hmod_ChIPseq

source_name: uterus


title: 21d_E2-1h.H3K27ac_ChIPseq

value: Active Motif #39133


title: 21d_Veh.H3K27ac_ChIPseq

value: uterus


title: adult_E2-1h.H3K27ac_ChIPseq


title: adult_Veh.H3K27ac_ChIPseq


title: COLO205_PIWIL1_KO2_2

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

institute: Henry M Jackson Foundation

description: GeneQuantitationTPM; TEQuantificationCOUNTS

data_processing:
When applicable, raw data with multiple sequencing runs for the same sample were concatenated in termianl using 'cat' command
Trimming 5' (GTTCAGAGTTCTACAGTCCGACGATC) and 3' Adapters and barcode splitting for small RNA was performed with Cutadapt v1.16
Mapping to tRNA and rRNA (UCSC) for removal of contaminating fragemnts in small RNA was performed using STAR v2.5.2b
Genome mapping to hg38 for transposon quantitation and small RNA analysis was performed using STAR v2.5.2b
Genome mapping to hg38 for differential gene expression was performed using Hisat  v2.2.1.0
Gene quantiation was performed using Stringtie v1.3.4d
Transposon quantitation was performed using Tetoolkit v2.0.3
Immunoprecipitated RNAs (RIP) and small RNAs (sRNA) were further processed and normalized in R environment with custom scripts provided upon request.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files: (1) GeneQuantificationTPM, (2) TEQuantificationCOUNTS, (3) SizeDistributionAllCOUNTS, (4) ReadAnnotationNormCOUNTS

growth_protocol: COLO205 cells were grown according to the standard procedures outlined on ATCC website

extract_protocol:
total RNA: extracted RNA was used to prepare libraries using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
Extraction was performed using Zymo Direct-Zol RNA Miniprep Kit and associated procedures

treatment_protocol: No treatements of cells were performed

value: colon adenocarcinoma

tag: genotype

value: CRISPR PIWIL1 knock-out

tag: cell line


title: Influenza_Control [8762536019_F]

value: Control


title: COLO205_PIWIL1_KO2_3

tag: cell type


title: Influenza_Disease [8762536019_D]


title: COLO205_PIWIL1_KO2_1


title: 21d_E2-1h.H3K4me3_ChIPseq

value: Active Motif #39159


title: COLO205_PIWIL1_KO1_3


title: 21d_Veh.H3K4me3_ChIPseq


title: 22B BrTuB07 vs. 22R BrTuB07

source_name: 22B BrTuB07

source_name: 22R BrTuB07

value: Neg

value: RD


title: 24B BrTuB07 vs. 24R BrTuB07

source_name: 24B BrTuB07

source_name: 24R BrTuB07


title: Bps_acute_Control [8784129070_D]

description:
raw data file: MRC02.txt
Control samples from Burkholderia pseudomallei - acute infection model

value: Burkholderia pseudomallei - acute

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 2,500 colony forming units (acute model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Lung samples were collected from individual infected and control treated mice on day 3 post infection.

value: whole blood


title: 16B BrTuB07 vs. 16R BrTuB07

source_name: 16B BrTuB07

value: Breast tumor baseline

source_name: 16R BrTuB07

value: after 2-weeks of treatments with HER2-targeted therapy


title: 26B BrTuB07 vs. 26R BrTuB07

source_name: 26B BrTuB07

source_name: 26R BrTuB07

value: TCH


title: 18B BrTuB07 vs. 18R BrTuB07

source_name: 18B BrTuB07

source_name: 18R BrTuB07

value: Pos

value: PCR


title: COLO205_PIWIL1_KO1_2


title: Bps_acute_Control [8697771097_E]


title: 25B BrTuB07 vs. 25R BrTuB07

source_name: 25B BrTuB07

source_name: 25R BrTuB07

value: TCHTy


title: 21B BrTuB07 vs. 21R BrTuB07

source_name: 21B BrTuB07

source_name: 21R BrTuB07


title: 14B BrTuB07 vs. 14R BrTuB07

source_name: 14B BrTuB07

source_name: 14R BrTuB07


title: 19B BrTuB07 vs. 19R BrTuB07

source_name: 19B BrTuB07

source_name: 19R BrTuB07


title: Bps_acute_Control [8784129070_F]


title: Bps_acute_Control [8697771097_B]


title: 20B BrTuB07 vs. 20R BrTuB07

source_name: 20B BrTuB07

source_name: 20R BrTuB07


title: adult_E2-1h.H3K4me3_ChIPseq

source_name: uterus


title: 13B BrTuB07 vs. 13R BrTuB07

source_name: 13B BrTuB07

source_name: 13R BrTuB07


title: 12B BrTuB07 vs. 12R BrTuB07

source_name: 12B BrTuB07

source_name: 12R BrTuB07


title: Bps_acute_Control [8697771071_A]


title: Bps_acute_Control [8697771067_C]


title: 21d_E2-1h.H3K4me1_ChIPseq

value: Active Motif #39297


title: COLO205_PIWIL1_TAG_3

value: CRISPR tagged exon1 of PIWIL1


title: COLO205_PIWIL1_KO1_1

value: colon adenocarcinoma


title: Bps_acute_Control [8615616102_B]


title: COLO205_PIWIL1_TAG_2


title: 21d_Veh.H3K4me1_ChIPseq

value: uterus


title: COLO205_PIWIL1_TAG_1


title: Bps_acute_Control [8615616101_C]

value: Control


title: adult_E2-1h.H3K4me1_ChIPseq


title: COLO205_PIWIL1_WT_2

value: wild type


title: COLO205_PIWIL1_WT_3


title: 8B BrTuB07 vs. 8R BrTuB07

source_name: 8B BrTuB07

source_name: 8R BrTuB07

value: Neg


title: COLO205_PIWIL1_WT_1


title: 21d_E2.ERa_ChIPseq

value: Santa Cruz SC-542


title: 9B BrTuB07 vs. 9R BrTuB07

source_name: 9B BrTuB07

source_name: 9R BrTuB07

value: RD


title: 21d_Veh.ERa_ChIPseq


title: 11B BrTuB07 vs. 11R BrTuB07

source_name: 11B BrTuB07

source_name: 11R BrTuB07


title: Bps_acute_Control [7988314090_D]

value: Burkholderia pseudomallei - acute

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 2,500 colony forming units (acute model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Lung samples were collected from individual infected and control treated mice on day 3 post infection.


title: adult_Veh.H3K4me1_ChIPseq


title: Bps_acute_Control [7988314090_E]

value: whole blood


title: Bps_acute_Disease [8697771071_D]

description:
raw data file: MRC02.txt
Disease samples from Burkholderia pseudomallei - acute infection model

value: Disease


title: Bps_acute_Disease [8697771097_D]


title: Bps_acute_Disease [8697771081_D]


title: S4_KO1

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institue

data_processing:
Raw sequence reads were processed using Trimmomatic-0.33 with the following parameters: TRAILING:25 MINLEN:35. Sequences were aligned using STAR aligner. Gene counts were determined using FeatureCounts.
Genome_build: Mus musculus 10

source_name: biliary cells from mouse treated with Doxycycline 1mg/ml in drinking water for 7 days, isolated 14 days after start with Doxycycline

extract_protocol:
RNA was isolated from FACs sorted EpCAM+CD45-CD11b-TER119- cells using the NucleoSpin® RNA XS Kit (Macherey-Nagel) according to the manufacturer’s instructions.
Libraries were prepared on the same day using Illumina TruSeq RNA Library Preparation Kit v2, Set B. Quantitative PCR and TapeStation to assess library concentration was run by the Biopolymers facility at Harvard Medical School.
Illumina TruSeq adapaters

tag: experiment

value: Yap flox/flox, tetO-Cre, CAGs-rtTA3 female

tag: protocol

value: bulk RNA-sequencing


title: S5_KO2

treatment_protocol: Doxycycline 1mg/ml in drinking water for 7 days


title: S6_KO3


title: 5B BrTuB07 vs. 5R BrTuB07

source_name: 5B BrTuB07

tag: sample type

value: Breast tumor baseline

source_name: 5R BrTuB07

value: after 2-weeks of treatments with HER2-targeted therapy

tag: er status (ihc staining results)

value: Pos


title: 2B BrTuB07 vs. 2R BrTuB07

source_name: 2B BrTuB07

source_name: 2R BrTuB07

tag: pr_status (ihc staining results)

tag: treatment group

value: TCHTy


title: Bps_acute_Disease [8784129070_B]


title: S3_Ctl2

value: Yap flox/flox, tetO-Cre, female


title: S2_Ctl2


title: 4B BrTuB07 vs. 4R BrTuB07

source_name: 4B BrTuB07

source_name: 4R BrTuB07

tag: drug response

value: PCR


title: MDA-MB-231: Ctl_1

city: Baltimore

first: Konstantinos

last: Konstantopoulos

address: 3400 N Charles St

department: Chemical and Biomolecular Engineering

institute: Johns Hopkins University

description: Each sample was split and run on four lanes, creating four read files

data_processing:
Quality control using Illumina pipeline
RNA-seq reads were mapped to hg38 reference genome using HISAT2 aligner
Htseq-count command from the HTSeq framework was used to quantify read counts per gene from aligned reads using human ENSEMBL 86 (GRCh38.p7) gene models
The Bioconductor/R package DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: human ENSEMBL 86 (GRCh38.p7) gene models
Supplementary_files_format_and_content: Gene symbols and normalized reads contains a list of genes recognized by the sequencing data and the normalized reads associated with each gene.

source_name: Breast cancer cells

growth_protocol: Cells were maintained at 37C and 5% CO2 in Dulbecco's Modified Eagle Media (DMEM) supplemented with 10% v/v heat inactivated Fetal Bovine Serum (FBS) and 1% v/v penicllin streptomycin (P/S).

extract_protocol:
RNA was isolated from samples of 1000 migratory or unsorted cells in triplicate using the Nucleospin RNA XS kit (Macherey-Nagel).
RNA was isolated from samples of 1000 migratory or unsorted cells in triplicate using the Nucleospin RNA XS kit (Macherey-Nagel). cDNA libraries were amplified using the SMART-seq ultra low input RNA kit (Takara) and then tagmented and barcoded by indexing primers using Nextera XT DNA library prep kit (Illumina). Samples were pooled and paired-end sequenced on an Illumina NextSeq 500 using the NextSeq 500/550 Mid Output v2 kit with 150 cycles and an output of up to 130 million reads.

treatment_protocol: Prior to RNA isolation, cells were passed from tissue culture flasks and seeded in microfluidic devices as described in Yankaskas, CL et al Nature Biomedical Engineering 2019. Highly motile (migratory) cells were isolated and compared to the unsorted (ctl) population.

value: Breast cancer


title: Bps_acute_Disease [8697771067_A]

tag: mouse strain


title: Bps_acute_Control [8697771081_B]

tag: mouse model

value: Control


title: MDA-MB-231: Ctl_2


title: MDA-MB-231: Mig_3


title: Bps_acute_Disease [8697771071_B]

tag: condition


title: S1_Ctl2


title: Bps_acute_Disease [8615616102_F]

tag: infection protocol


title: KO insulin treatment rep4

city: Shanghai

first: Qinglei

last: Yin

address: Ruijin Second Road No.197

country: China

institute: Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
We used Hisat v2.0.4 to map the cleaned reads to the mouse mm10 reference genome.
After genome mapping, Stringtie v1.3.0  and TMM were used to caculate FPKM values.
Differentially expressed genes were identified using edgeR. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: beta cells

extract_protocol:
Islets were isolated, digested into single cells and FACS. RNA was harvested using RNeasy micro kit and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 8 weeks

value: BetaRapKOGFP-/- with insulin pellet


title: MDA-MB-231: Mig_1

tag: tissue


title: Bps_acute_Disease [7988314090_B]


title: KO insulin treatment rep3

tag: strain


title: Toxoplasma_Disease [5871841153_E]

description:
raw data file: Benaroya.txt
Disease samples from Toxoplasma gondii infection model

value: Toxoplasma gondii

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.


title: KO insulin treatment rep2

tag: genotype


title: HEP_ctr1

data_processing:
Reads were mapped using bwa mem-0.7.10 with default parameters to the reference transcriptome (Mus musculus 10) after extraction of the corresponding cell-specific barcode and unique molecular identifier (UMI). The number of unique transcripts per gene for each cell-specific barcode was extracted from the UMI count as previously described in Grün et al.(Grün et al., 2016). We hence refer to transcripts as unique molecules based on UMI correction.
Genome_build: Mus musculus 10
Supplementary_files_format_and_content: Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell.

source_name: hepatocytes from 1 healty adult mouse

extract_protocol:
Optimal isolation of single biliary epithelial cells was obtained by modifying previously established, two-step liver perfusion protocols(Dorrell et al., 2008; Li et al., 2010). Mice were euthanized, the heart and liver were surgically exposed, and a cannula was immediately inserted through an incision in the right atrium through the suprahepatic vena cava. Mice livers were then perfused by a pre-warmed (37°C) perfusion buffer (50 mM EDTA, 10 mM HEPES in 1X HBSS [Gibco, #14185-052]) at an initial flow rate of 3 ml/min for 2.5 minutes, followed by an increase in flow rate to 4 ml/min for an additional 2.5 minutes. This was then followed by perfusion with a pre-warmed (37°C) Collagenase Type IV (150 U/mL; Invitrogen, #17104019) digestion buffer solution (1.25 mM CaCl2, 4 mM MgCl2, 10 mM HEPES in 1x HBSS) for 8-10 minutes at a flow rate of 4 ml/min. For the duration of the two-step liver perfusion, the infrapatic vena cava was digitally occluded every 30 seconds for 10 seconds. After isolating the liver and surgically removing the gallbladder, the capsule was disrupted and the liver was gently and mechanically agitated to release dissociated single cells. The remaining liver was than subjected to serial digestions in Collagenase Type IV (150 U/mL), Accutase (EMD Millipore), and trypsin (0.25%) for 30 minutes, 30 minutes, and 20 minutes, respectively, at 37°C. Dissociated cells were collected after each step and filtered through a 100 μm cell strainer, washed, and re-suspended in ice-cold resuspension buffer (2% FBS, 1.25 mM CaCl2, 4 mM MgCl2, 10mM HEPES, 5 mM glucose in 1X HBSS). Hepatocytes were pelleted and removed by a 30xg spin and the remaining cells were spun at 300xg to isolate biliary cells. After treatment in red blood cell lysis buffer (eBioscience) on ice for 7 mins, the cells were re-suspended in cold resuspension buffer. For hepatocyte isolation, a similar perfusion protocol as described for BEC isolation was used with adaptation of the digestion step, by using liver digest medium (Thermo Fisher, #17703034) and increasing the digestion time to 16-20 minutes while maintaining identical flow rates increasing the digestion time to 16-20 minutes. The liver was then excised, the liver capsule removed, and the liver gently swirled in resuspension buffer to yield a cell suspension. After filtration through a 100 µm cell strainer, the hepatocytes were selectively pelleted by centrifugation with 30xg for 5 minutes, which removes the non-parenchymal cell fraction. The resuspended hepatocytes were then mixed 1:2.2 with 40% iodixanol (Optiprep, Axis-Shield, #1114542) solution (diluted in resuspension buffer) for a volume of 4.8ml, overlayered with 3 ml 18% iodixanol and 0.5 ml resuspension buffer and spun at 500xg for 25 minutes at 4°C with reduced deceleration. The top cell layer was collected, mixed with resuspension buffer supplemented with 3% BSA and washed once at 30xg for 5 min at 4°C. The cells were then re-suspended in ice-cold resuspension buffer (containing 2% BSA and 9% Optiprep), quantified and assessed for viability by Trypan blue stain. Routinely, viability of over 98% was obtained.
Isolated single cells were encapsulated, and libraries were generated using inDrops(Zilionis et al., 2016). Approximately 1500 cells were encapsulated for each sample
Illumina TruSeq adapaters
For BEC sample raw data - R1: transcript (read with biological content), R2: first 8 nucleotides of cell-specific barcode, R3: Library index; R4: first 8 bases correspond to second half of cell-specific barcode; next 6 bases correspond to the UMI; the rest contains the polyA tail.

tag: strain background

value: control

value: hepatocytes

value: indrops


title: BEC_ctr3

source_name: biliary cells from 1 healty adult mouse

tag: cell type

value: biliary cells


title: KO rep4

value: BetaRapKOGFP-/- without insulin pellet


title: BEC_ctr2

tag: experiment


title: HEP_DDC1

source_name: hepatocytes from 1 adult mouse fed with DDC1 diet

value: DDC

tag: protocol


title: Toxoplasma_Control [5871841153_C]

description:
raw data file: Benaroya.txt
Control samples from Toxoplasma gondii infection model

value: whole blood


title: Bps_acute_Disease [8615616101_A]

value: Burkholderia pseudomallei - acute

value: Disease

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 2,500 colony forming units (acute model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Lung samples were collected from individual infected and control treated mice on day 3 post infection.


title: KO rep3


title: BEC_ctr1


title: KO rep2


title: Toxoplasma_Disease [5871841152_F]


title: Toxoplasma_Control [5871841152_E]


title: KO rep1


title: Acly-/- adipocyte replicate 3

city: Philadelphia

first: Kathryn

last: Wellen

state: PA

address: 421 Curie Blvd, BRB 653

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
bcl2fastq2 was used for basecalling
RNA-seq alignment was performed using BaseSpace Workflow version 1.1.0, including BowTie2 Aligner version 2.2.6
Differential expression was analyzed using Cufflinks 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file includes FKPM per sample

source_name: Acly-/- adipocyte

growth_protocol: Preadipocytes were grown in DMEM + 10% FBS, grown to confluence and induced to differentiate using a standard adipogenic cocktail including rosiglitazone.  Adipocytes were harvested 4 days after induction of differentiation

extract_protocol:
RNA was isolated using Trizol
Illumina TruSeq kitl

value: adipose tissue

value: adipocyte

tag: immortalization

value: Acly-/-

tag: time


title: Acly-/- adipocyte replicate 2


title: 6B BrTuB07 vs. 6R BrTuB07

source_name: 6B BrTuB07

tag: sample type

value: Breast tumor baseline

source_name: 6R BrTuB07

value: after 2-weeks of treatments with HER2-targeted therapy

tag: er status (ihc staining results)

value: Pos

tag: pr_status (ihc staining results)

value: Neg

value: TCHTy

value: RD


title: WT rep3

value: 8 weeks

value: wild type


title: adult_Veh.H3K4me3_ChIPseq

source_name: uterus

value: uterus

tag: antibody

value: Active Motif #39159


title: KO insulin treatment rep1

value: BetaRapKOGFP-/- with insulin pellet


title: WT rep2


title: Acly-/- adipocyte replicate 1


title: Toxoplasma_Disease [5871841148_B]

tag: mouse strain

tag: mouse model

value: Toxoplasma gondii

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.

value: whole blood


title: BEC_DDC1

source_name: biliary cells from 1 adult mouse fed with DDC1 diet

value: DDC

value: biliary cells

value: indrops


title: Toxoplasma_Control [5871841152_A]

tag: condition

value: Control

tag: infection protocol


title: Aclyf/f adipocyte replicate 3

source_name: Aclyf/f adipocyte

tag: tissue

value: adipose tissue

value: adipocyte

value: Aclyf/f


title: WT rep1

tag: strain

tag: age


title: Toxoplasma_Control [5871841152_B]


title: Aclyf/f adipocyte replicate 2

tag: genotype


title: Toxoplasma_Control [5871841148_A]


title: Toxoplasma_Control [5871841144_F]


title: Toxoplasma_Disease [5871841147_C]

value: Disease


title: Aclyf/f adipocyte replicate 1

tag: cell type


title: Acly-/- preadipocyte replicate 3

source_name: Acly-/- preadipocyte

value: preadipocyte

value: Acly-/-


title: Zn72D-GFP_RIP_1

data_processing:
Paired-end, 76-base-pair reads were trimmed using Trim Galore 0.4.5 to remove adapter sequences.
Trimmed reads were mapped to the dm6 genome using STAR 2.5.4b with the parameters --outFilterScoreMin 10 --alignEndsType EndToEnd.
To determine gene expression levels, RSEM 1.2.30 was used to count the number of reads mapping to each gene. RSEM calculated expected counts were rounded down to the nearest integer and used as input to DESeq2 v1.20.0
Genome_build: dm6
Supplementary_files_format_and_content: For expression analysis: genes.results output files from RSEM. Tab-delimited files are formatted as: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM, posterior_mean_count, posterior_standard_deviation_of_count, pme_TPM, pme_FPKM, TPM_ci_lower_bound, TPM_ci_upper_bound, FPKM_ci_lower_bound, FPKM_ci_upper_bound.

organism: Drosophila melanogaster

growth_protocol: Flies were raised at 25C in a 12 hour light/dark cycle on molasses, cornmeal, agar, and yeast media.

extract_protocol:
RNA immunoprecipitation was performed after homogenizing ~500 ul of fly heads in IP Buffer (150 mM NaCl, 20 mM HEPES pH 7.5, 2 mM MgCl2, 0.1% NP40, cOmplete protease inhibitor, RNaseOUT RNase inhibitor 1U/ul (Invitrogen)). Lysates were split in half, and 4% of input was removed for input control libraries. IP lysates were incubated overnight at 4C with Dynabeads Protein G (Invitrogen: 10003D), plus 5 ug of anti-GFP antibody (Abcam: ab290). IPs were washed 8 times in IP buffer. Beads with protein bound and saved inputs were added to 1 mL of TRIzol (Thermo Fisher: 15596026). 200 ul of chloroform was added, and samples were centrifuged at 14000 xg at 4C for 15 minutes. Aqueous phases were collected, mixed with 1 volume of 70% ethanol and then transferred to a RNeasy MinElute column (Qiagen, Hilden, Germany: 74204) for purification following the standard protocol.
RNA was mixed with an equal amount of pooled DNA oligos designed antisense to Drosophila rRNAs in 50 bp sections in an 8 ul reaction with 2ul of 5X Hybridization buffer (500 mM Tris-HCl pH 7.4, 1  M NaCl). rRNA antisense oligos were annealed to total RNA samples for 2 minutes at 95°C, the temperature was slowly reduced to 65°C and 2U of Thermostable Hybridase H (Epicentre) and 1 ul of 10X Digestion buffer (500 mM Tris-HCl, 1 M NaCl, 200mM MgCl2) were added to make 10 ul total and reactions were incubated for 30 minutes at 65°C. rRNA-depleted RNA was then purified using Agencourt RNAClean XP beads, treated with TURBO DNase (Ambion) and then purified with RNAClean XP beads again. rRNA-depleted RNA was used as input to the KAPA HyperPrep RNA-seq Kits (Kapa Biosystems: KK8540) to make RIP-seq libraries for fly samples.

tag: Sex

value: pooled male and female

tag: developmental stage

value: adult

tag: genotype/variation

value: head

tag: replicate

tag: molecule subtype

value: rRNA-depleted anti-GFP immunoprecipitated RNA


title: Zn72D-GFP_input_3

value: rRNA-depleted RNA


title: Toxoplasma_Disease [5871841144_B]

value: Toxoplasma gondii

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.


title: Acly-/- preadipocyte replicate 1

tag: immortalization

tag: time


title: Acly-/- preadipocyte replicate 2


title: Aclyf/f preadipocyte replicate 3

source_name: Aclyf/f preadipocyte


title: Zn72D-GFP_input_2


title: Toxoplasma_Control [5871841143_F]

value: whole blood


title: Zn72D-GFP_input_1


title: Toxoplasma_Disease [5871841143_C]


title: MDA-MB-231: Ctl_3

tag: cell line

value: Breast cancer


title: Dmel_Zn72D_BDSC55635_RNAi_2

data_processing:
Paired-end, 76-base-pair reads were trimmed using Trim Galore 0.4.5 to remove adapter sequences.
Trimmed reads were mapped to the dm6 genome using STAR 2.5.4b with the parameters --outFilterScoreMin 10 --alignEndsType EndToEnd.
To call editing levels, samtools (v1.4) mpileup function was used to extract base calls from uniquely mapped reads at known editing sites. Editing levels were detemined as the number of G reads out of all A and G reads at a site.
To determine gene expression levels, RSEM 1.2.30 was used to count the number of reads mapping to each gene. RSEM calculated expected counts were rounded down to the nearest integer and used as input to DESeq2 v1.20.0
Genome_build: dm6
Supplementary_files_format_and_content: For RNA editing analysis: A and G counts and editing levels at known editing sites. Tab-delimited filtes are formatted as: chr, pos, A counts, G counts, editing level.
Supplementary_files_format_and_content: For expression analysis: genes.results output files from RSEM. Tab-delimited files are formatted as: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM, posterior_mean_count, posterior_standard_deviation_of_count, pme_TPM, pme_FPKM, TPM_ci_lower_bound, TPM_ci_upper_bound, FPKM_ci_lower_bound, FPKM_ci_upper_bound.

source_name: whole brain_Dmel_Zn72D_BDSC55635_RNAi

growth_protocol: Flies were raised at 25C in a 12 hour light/dark cycle on molasses, cornmeal, agar, and yeast media. Brains of 3-5 day old adult females were dissected for RNA extractions.

extract_protocol:
RNA was extracted from ~15 brains using RNAdvanced Tissue Kit (Beckman Coulter) followed by TURBO DNase treatment (Thermo Fisher).
150-250 ng of total RNA was mixed with an equal amount of pooled DNA oligos designed antisense to Drosophila rRNAs in 50 bp sections in an 8 ul reaction with 2ul of 5X Hybridization buffer (500 mM Tris-HCl pH 7.4, 1 M NaCl). rRNA antisense oligos were annealed to total RNA samples for 2 minutes at 95°C, the temperature was slowly reduced to 65°C and 2U of Thermostable Hybridase H (Epicentre) and 1 ul of 10X Digestion buffer (500 mM Tris-HCl, 1 M NaCl, 200mM MgCl2) were added to make 10 ul total and reactions were incubated for 30 minutes at 65°C. rRNA-depleted RNA was then purified using Agencourt RNAClean XP beads, treated with TURBO DNase (Ambion) and then purified with RNAClean XP beads again. rRNA-depleted RNA was used as input to the KAPA Stranded RNA-seq Kit (KK8400) to make RNA-sequencing libraries.

value: female

value: C155-Gal4; UAS-Zn72D_RNAi (BDSC55635)

value: 3-5 day old

value: whole brain


title: Aclyf/f preadipocyte replicate 2

value: adipose tissue

value: Aclyf/f


title: Aclyf/f preadipocyte replicate 1

value: preadipocyte


title: Zn72D-GFP_RIP_3


title: MDA-MB-231: Mig_2


title: Zn72D-GFP_RIP_2


title: Dmel_Zn72D_RNAi_2

source_name: whole brain_Dmel_Zn72D_RNAi

value: C155-Gal4; UAS-Zn72D_RNAi


title: Donor 4 : Lang+ [AH31_3]

city: Westmead

first: J

middle: Dinny

last: Graham

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

country: Australia

institute: University of Sydney

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH31_3

data_processing:
Reads were aligned using STAR v2.5.3 to the GRCh38 genome and were summarized to gene counts as annotated by GENCODE v26.
Gene counts were normalized using TMM and variance stabilized using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file containing read counts for each lane of sequencing data for each sample. Each biological sample has 4 lanes of raw sequence data.

molecule: polyA RNA

source_name: Abdominal skin dermal tissue

extract_protocol:
Primary cell populations isolated by flow cytometry (n=200 cells per population) were captured directly into lysis buffer containing 0.1% triton X-100, 1U RNaseOUT RNase inhibitor, 2.5mM each dNTP mix, 2.5uM anchored oligo-dT primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) in a total volume of 20ul. Full-length mRNA was reverse transcribed and amplified using the Smart-seq2 protocol of Picelli et al (Nature Methods. 2013;10(11):1096-8).
Sequencing libraries were prepared from 1ng cDNA product using Illumina Nextera XT reagents, in accordance with the supplier’s protocol, except that PCR was limited to 8 cycles to minimize read duplicates, and final library elution was performed using 17.5μl elution buffer EB.  All libraries were pooled and sequenced on four lanes of an Illumina HiSeq 2500 sequencer, using a HiSeq Rapid Cluster Kit v2.

value: Abdominal skin dermal tissue

value: Dermal cDC2 (lang+)

tag: biological replicate/donor number

tag: sample number


title: Toxoplasma_Disease [5871841140_D]

tag: mouse strain

tag: mouse model

tag: condition

value: Disease


title: Dmel_Zn72D_RNAi_1

tag: tissue


title: Donor 4 : Lang+ [AH31_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH31_4


title: Donor 4 : Lang+ [AH31_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH31_2


title: Toxoplasma_Control [5871841140_A]

value: Control

tag: infection protocol


title: Dmel_shep_RNAi_2

source_name: whole brain_Dmel_shep_RNAi

tag: genotype

value: C155-Gal4; UAS-shep_RNAi

tag: age

value: rRNA-depleted RNA


title: Dmel_shep_RNAi_1

tag: Sex


title: Toxoplasma_Disease [5871841141_A]

value: Toxoplasma gondii

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.


title: Toxoplasma_Control [5871841139_B]

value: whole blood


title: Toxoplasma_Control [5871841143_B]


title: Donor 4 : CDC1 [AH30_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH30_4

tag: cell type

value: Dermal cDC1


title: Donor 4 : CDC1 [AH30_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH30_3


title: Donor 4 : CDC1 [AH30_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH30_2


title: Toxoplasma_Disease [5871841140_E]


title: 8week-H19KO

city: Farmington

last: Zhang

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
RTA 2.4.11 software was used for basecalling
Alignment was performed by using STAR 2.5.0a, and gene read counts were assessed using Cufflinks 2.2.1. (Both STAR 2.5.0a and Cufflinks 2.2.1 were from RNA-Seq Alignment 1.0.0 embedded in illumina BaseSpace platform).
Relative differential expression of genes between WT and H19 KO samples was determined by using DESeq2 1.0.0 (DESeq2 App embedded in illumina BaseSpace platform).
DESeq2 output of read counts for each gene was used as the processed data.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes read counts for each gene

source_name: Ovary

growth_protocol: Mice were housed at 22ºC–24ºC with a 12 h light/12 h dark cycle with regular chow and water provided ad libitum.

extract_protocol:
Total RNA was extracted from harvested mice ovaries by using PureLink RNA Mini Kit.
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Human/Mouse/Rat, setA (Cat# rs-122-2201) according to the sample preparation protocol. Briefly, 1 ug total RNA was subjected to Ribo-Zero depletion to remove rRNAs. The remaining RNA was purified, fragmented, and primed with random hexamers for cDNA synthesis. After first and second cDNA synthesis, cDNA fragments were adenylated and then ligated to indexing   adapters. The cDNA fragments were enriched by PCR, purified, and then sequenced on an illumina NextSeq500 using paired-end chemistry and 76-bp cycles.

treatment_protocol: No special treatment.

tag: strain

value: 8 weeks old


title: 8week-WT

value: wild type


title: Dmel_Rbp6_RNAi_1

source_name: whole brain_Dmel_Rbp6_RNAi

value: female

value: C155-Gal4; UAS-Rbp6_RNAi

value: 3-5 day old

value: whole brain

tag: replicate


title: Input ChIP-seq

city: Memphis

first: Jinghui

state: TN

address: 262 Danny Thomas PL, Mail stop 1135

institute: St. Jude Children's Research Hospital

description:
The Nalm6 cell line was established from the peripheral blood of a 19-year-old man with acute lymphoblastic leukemia (ALL) in relapse in 1976.
processed data file: Nalm6_H3K27ac.bw

data_processing:
BWA (version 0.7.12-r1039, default parameter) to align the reads to human genome hg19 (GRCh37), Picard (version 1.65(1160)) then have been used for marking duplicated reads.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: B cell precursor leukemia

extract_protocol: A frozen cell pellet containing 10 million cells was sent to Active Motif for ChIP and library preparation. The sample was divided into an aliquot for ChIP using an antibody to H3K27Ac (Active Motif AM, cat# 39133, lot# 8) and an input control. Single-end sequencing was performed using an Illumina NextSeq 500 generating 76 cycles for each sequencing read.

value: B cell precursor leukemia cell line

tag: chip antibody


title: Donor 4 : CD14 MDM [AH29_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH29_3

value: Abdominal skin dermal tissue

value: Dermal CD14 MDM


title: Donor 4 : Lang+ [AH31_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH31_1

value: Dermal cDC2 (lang+)


title: H3K27ac ChIP-seq


title: Donor 4 : CD14 MDM [AH29_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH29_2


title: Dmel_qkr58E-2_RNAi_2

source_name: whole brain_Dmel_qkr58E-2_RNAi

value: C155-Gal4; UAS-qkr58E-2_RNAi

tag: molecule subtype


title: Toxoplasma_Disease [5871841139_F]

value: Disease


title: H3K27Ac HiChip

description: The Nalm6 cell line was established from the peripheral blood of a 19-year-old man with acute lymphoblastic leukemia (ALL) in relapse in 1976.

data_processing:
Library strategy: HiChIP
HiC-Pro was used for H3K27ac HiChIP data analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: hic

growth_protocol: Nalm6 cell line was cultured under recommended conditions to about 80% confluence.

extract_protocol: DNA from ten million cells were crosslinked with 1% formaldehyde for 10 min at room temperature, digested with 375 units of MboI, labeled by biotinylated nucleotides and proximity-ligated. After sheared by Covaris, chromatin immunoprecipitated (ChIP) with H3K27Ac antibody (Active Motif AM, cat# 39133, lot# 8), the ChIP DNA was de-crosslinked and purified by Zymo Genomic GNA Clean & Concentrator kit. Finally, after streptavidin beads pull-down and Illumina library construction by Kapa Hyper Prep Kit, HiChIP library was sequenced paired-end 75 cycles on Illumina NextSeq 500.

tag: antibody


title: Dmel_Rsf1_RNAi_2

source_name: whole brain_Dmel_Rsf1_RNAi

value: C155-Gal4; UAS-Rsf1_RNAi

value: rRNA-depleted RNA


title: Donor 4 : Mac [AH28_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH28_4

value: Dermal macrophage


title: Donor 4 : CD14 MDM [AH29_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH29_1


title: Donor 4 : CD14 MDM [AH29_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH29_4


title: Dmel_pum_RNAi_1

source_name: whole brain_Dmel_pum_RNAi

value: C155-Gal4; UAS-pum_RNAi


title: Dmel_pum_RNAi_2


title: Dmel_Zn72D_BDSC55635_RNAi_1

value: C155-Gal4; UAS-Zn72D_RNAi (BDSC55635)


title: Dmel_ps_RNAi_2

source_name: whole brain_Dmel_ps_RNAi

value: C155-Gal4; UAS-ps_RNAi


title: Dmel_Rbp6_RNAi_2


title: Donor 4 : Mac [AH28_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH28_1


title: Dmel_ps_RNAi_1


title: Donor 4 : Mac [AH28_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH28_2


title: Dmel_mub_RNAi_2

source_name: whole brain_Dmel_mub_RNAi

value: C155-Gal4; UAS-mub_RNAi


title: Dmel_qkr58E-2_RNAi_1

value: female


title: Donor 4 : CDC2 [AH27_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH27_4

value: Dermal cDC2 (lang-)


title: Dmel_mub_RNAi_1

value: 3-5 day old


title: Donor 4 : CDC2 [AH27_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH27_3


title: Dmel_mod_RNAi_2

source_name: whole brain_Dmel_mod_RNAi

value: C155-Gal4; UAS-mod_RNAi

value: whole brain


title: Donor 4 : Mac [AH28_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH28_3

value: Abdominal skin dermal tissue


title: PPD3_OE_1

city: University Park

first: Hardik

last: Kundariya

address: 361 N. Frear

institute: The Pennsylvania State University

description: PPD3 over expression

data_processing:
Illumina for basecalling
Alignments were performed using RUM 2.0.4 (--min-length 70) (Grant et al., 2011) keeping only uniquely mapped reads
The read count data were generated from the SAM files by using QoRTs software package (Hartley and Mullikin, 2015) --singleEnded --minMAPQ 25 --dropChrom Pt,Mt
DESeq2 (Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 2014) was used for gene count normalization and to identify differentially expressed genes (FDR < 0.05, |log2FC| > 0.5. GTF file TAIR10.31
Genome_build: TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with DESeq2

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 16hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
These libraries were sequenced with the 150-bp single read option, in Hi-Seq 2500 analyzer (Illumina, USA) at Gemonics core facility at The Pennsylvania Stete University.

treatment_protocol: Two individual plants of Col-0 wild type and two PPD3 over expression plants were used. Whole plants at at bolting were flash freezed in liquid nitrogen.  Tissues were ground by mortar and pestle in liquid nitrogen

value: biological rep 1

value: whole rosette

tag: genotype/variation

value: PPD3 over expression


title: Col-0_2

description: Wild type

value: biological rep 2

value: wild type


title: Donor 4 : CD33 Low [AH26_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH26_4

source_name: Abdominal skin epidermal tissue

value: Abdominal skin epidermal tissue

value: Epidermal CD33 low

tag: biological replicate/donor number


title: Scramble siRNA, biological rep3

city: San Francisco

first: Francesco

last: Caiazza

address: 600 16th street, Room S-514

department: Pharmaceutical Chemistry

institute: UCSF

hyb_protocol: labeled cDNA targets were hybridized to a GeneChip® Human Transcriptome Array 2.0 (Affymetrix, Thermo Fisher) following manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: CEL files were analysed with the Affymetrix® Expression Console™ Software, using the Affymetrix Human Transcripome Array 2.0 library files and the HTA-2_0.na35.2.hg19 annotation files. An RMA workflow was performed which used a quantile normalization procedure and a general background correction. The resulting normalised CHP files were then imported in the Affymetrix® Transcriptome Analysis Console software to test for differential expression using a paired One-Way Repeated Measure (ANOVA) approach, and the default filter criteria (fold change > |2|, and p-value < 0.05).

source_name: SW480 cells

label_protocol:
Amplified cDNA for gene expression analysis
was prepared with the Ovation® PicoSL WTA System V2 (Nugen, San Carlos, CA, USA); labeled cDNA targets were generated with the Encore® Biotin Module (Nugen)

growth_protocol: maintained in DMEM supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1% Fungizone

extract_protocol: Total RNA was extracted from cells using the RNeasy Plus kit (Qiagen); the integrity and concentration of RNA was confirmed using the RNA 6000 Nano kit on a Bioanalyzer 2100 (Agilent), with reported RNA Integrity Numbers (RIN) > 9.

treatment_protocol: Cells were seeded in 24-well plates to be transfected with 30 pmol KHSRP siRNA (Silencer Select, Thermo Fisher) or non-targeting scramble siRNA using 2 μl Lipofectamine 2000 (Invitrogen) for 48h

value: colon

tag: morphology

value: epithelial

tag: cell line

tag: transfection

value: Scramble siRNA

tag: tumor type

value: Dukes B adenocarcinoma


title: Donor 4 : CDC2 [AH27_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH27_2

tag: tissue

tag: sample number


title: Donor 4 : CDC2 [AH27_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH27_1


title: Dmel_Irp-1A_RNAi_2

source_name: whole brain_Dmel_Irp-1A_RNAi

value: female

tag: genotype

value: C155-Gal4; UAS-Irp-1A_RNAi

value: rRNA-depleted RNA


title: Dmel_mod_RNAi_1

value: C155-Gal4; UAS-mod_RNAi

tag: age

value: 3-5 day old


title: Col-0_1

description: Wild type


title: Scramble siRNA, biological rep2


title: Donor 4 : CD33 Low [AH26_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH26_3


title: adult_E2-6h.ERa_ChIPseq

source_name: uterus

value: uterus

value: Santa Cruz SC-542


title: KHSRP siRNA, biological rep3

value: KHSRP siRNA


title: KHSRP siRNA, biological rep1


title: KHSRP siRNA, biological rep2


title: COLO205_sRNA_3

description:
size selected small RNA
TAGGATCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS

extract_protocol:
size selected small RNA: total RNA was extracted, and small RNA was selected based on size before 5' and 3' adapter ligation, RT-PCR, PCRs, and quality control
Extraction was performed using Zymo Direct-Zol RNA Miniprep Kit and associated procedures

value: colon adenocarcinoma


title: Dmel_Hrb98DE_RNAi_1

source_name: whole brain_Dmel_Hrb98DE_RNAi

tag: Sex

value: C155-Gal4; UAS-Hrb98DE_RNAi

value: whole brain


title: Donor 4 : CD33 Low [AH26_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH26_2

value: Abdominal skin epidermal tissue

tag: cell type


title: Scramble siRNA, biological rep1


title: Dmel_yps_RNAi_1

source_name: whole brain_Dmel_yps_RNAi

value: C155-Gal4; UAS-yps_RNAi


title: PPD3_OE_2

description: PPD3 over expression

value: biological rep 2

value: whole rosette

value: PPD3 over expression


title: Dmel_Hrb87F_RNAi_2

source_name: whole brain_Dmel_Hrb87F_RNAi

value: C155-Gal4; UAS-Hrb87F_RNAi


title: COLO205_sRNA_2

description:
size selected small RNA
TAGAGTCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS

value: wild type


title: Donor 4 : CD11c+ [AH25_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH25_4

value: Epidermal CD11c+


title: Dmel_Irp-1A_RNAi_1

value: female

value: C155-Gal4; UAS-Irp-1A_RNAi

value: rRNA-depleted RNA


title: COLO205_PIWIL1_IP_4

description:
small RNA from IP
TTAAGTCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS; ReadAnnotationNormCOUNTS

extract_protocol:
small RNA from IP: Flag-tagged protein was immunoprecipitated, and associated RNAs were extracted, followed by ligation of 5' and 3' adapters, RT-PCR, PCRs, and quality control
Extraction was performed using Zymo Direct-Zol RNA Miniprep Kit and associated procedures

value: CRISPR tagged exon1 of PIWIL1


title: COLO205_sRNA_1

description:
size selected small RNA
TAATATCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS


title: Donor 4 : CD11c+ [AH25_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH25_2


title: Donor 4 : CD11c+ [AH25_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH25_3


title: Dmel_Hrb98DE_RNAi_2

value: 3-5 day old


title: Dmel_Hrb87F_RNAi_1


title: Dmel_hfp_RNAi_2

source_name: whole brain_Dmel_hfp_RNAi

value: C155-Gal4; UAS-hfp_RNAi


title: COLO205_PIWIL1_IP_3

description:
small RNA from IP
TCTGATCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS; ReadAnnotationNormCOUNTS

value: colon adenocarcinoma


title: Dmel_hfp_RNAi_1


title: COLO205_PIWIL1_IP_2

description:
small RNA from IP
TCTCCTCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS; ReadAnnotationNormCOUNTS


title: Dmel_Fmr1_RNAi_2

source_name: whole brain_Dmel_Fmr1_RNAi

value: C155-Gal4; UAS-Fmr1_RNAi


title: Donor 4 : CD11c+ [AH25_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH25_1


title: Donor 4 : CD33 Low [AH26_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH26_1

value: Epidermal CD33 low


title: Dmel_Fmr1_RNAi_1

value: whole brain


title: COLO205_PIWIL1_IP_1

description:
small RNA from IP
TCTAGTCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS; ReadAnnotationNormCOUNTS


title: Donor 4 : LC [AH24_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH24_3

value: Abdominal skin epidermal tissue

value: Langerhans cell


title: Donor 4 : LC [AH24_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH24_2


title: COLO205_PIWIL1_IP_BCKG

description:
small RNA from IP
TCGCGTCGTATGCCGTCTTCTGCTTG
SizeDistributionAllCOUNTS; ReadAnnotationNormCOUNTS


title: Dmel_eIF4H1_RNAi_2

source_name: whole brain_Dmel_eIF4H1_RNAi

value: C155-Gal4; UAS-eIF4H1_RNAi


title: Donor 4 : LC [AH24_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH24_1


title: Dmel_eIF4H1_RNAi_1


title: Dmel_CG4612_RNAi_2

source_name: whole brain_Dmel_CG4612_RNAi

value: C155-Gal4; UAS-CG4612_RNAi


title: Donor 3 : CDC1 [AH23_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH23_4

source_name: Abdominal skin dermal tissue

value: Abdominal skin dermal tissue

value: Dermal cDC1


title: primary myoblasts, 0.8mM glycine, Lib2-6

city: Tianjin

first: GANG

last: HAN

address: No.22 Qi Xiang Tai Road

institute: Tianjin medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 2.0.5.
The RNA-seq alignments were assembled into transcripts using StringTie 1.3.3.
The differential expression was tested based on the negative binomial distribution model using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

source_name: primary myoblast

extract_protocol:
RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary myoblast cell

tag: passages

tag: strain

tag: treatment

value: 0.8mM glycine


title: Dmel_CG4612_RNAi_1

value: female

tag: replicate

tag: molecule subtype


title: Donor 3 : CDC1 [AH23_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH23_3


title: primary myoblasts, 0.8mM glycine, Lib2-3


title: primary myoblasts, 0.8mM glycine, Lib2-5


title: Dmel_CG1316_RNAi_2

source_name: whole brain_Dmel_CG1316_RNAi

value: C155-Gal4; UAS-CG1316_RNAi

value: rRNA-depleted RNA


title: primary myoblasts, 0.8mM glycine, Lib2-4


title: Dmel_yps_RNAi_2

value: C155-Gal4; UAS-yps_RNAi

value: 3-5 day old


title: primary myoblasts, 0.8mM glycine, Lib2-1


title: Dmel_CG1316_RNAi_1


title: Dmel_caz_RNAi_2

source_name: whole brain_Dmel_caz_RNAi

value: C155-Gal4; UAS-caz_RNAi


title: Donor 3 : Lang+ [AH22_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH22_4

value: Dermal cDC2 (lang+)


title: Donor 3 : CDC1 [AH23_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH23_1


title: Donor 4 : LC [AH24_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH24_4


title: Donor 3 : CDC1 [AH23_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH23_2


title: primary myoblasts, 0.8mM glycine, Lib2-2


title: primary myoblasts, 0.2mM glycine, Lib1-3

value: 0.2mM glycine


title: Dmel_caz_RNAi_1

value: whole brain


title: primary myoblasts, 0.2mM glycine, Lib1-2


title: Donor 3 : Lang+ [AH22_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH22_3


title: Dmel_Adar_VDRC7763_RNAi_2

source_name: whole brain_Dmel_Adar_VDRC7763_RNAi

value: C155-Gal4; UAS-Adar_RNAi (VDRC7763)


title: Dmel_Adar_VDRC7763_RNAi_1


title: Donor 3 : Lang+ [AH22_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH22_2


title: Donor 3 : Lang+ [AH22_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH22_1


title: Dmel_Adar_BDSC28311_RNAi_2

source_name: whole brain_Dmel_Adar_BDSC28311_RNAi

value: C155-Gal4; UAS-Adar_RNAi (BDSC28311)


title: primary myoblasts, 0.2mM glycine, Lib1-1


title: 5E15WTPrdm16Blood

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: 2 μg

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9

source_name: Brain

extract_protocol:
Cerebral cortex was dissected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: Brain


title: Donor 3 : CD14 MDM [AH21_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH21_4

value: Dermal CD14 MDM

tag: biological replicate/donor number


title: Donor 3 : CD14 MDM [AH21_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH21_3

value: Abdominal skin dermal tissue


title: 6E15KOPrdm16Blood

description: 2 μg


title: Dmel_Adar_BDSC28311_RNAi_1


title: 8E15WTPrdm16

description: 2 μg


title: Donor 3 : CD14 MDM [AH21_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH21_2


title: Dmel_GFP_RNAi_4

source_name: whole brain_Dmel_GFP_RNAi

value: C155-Gal4; UAS-GFP_RNAi


title: Dmel_GFP_RNAi_3


title: Donor 3 : CD14 MDM [AH21_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH21_1


title: Donor 3 : Mac [AH20_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH20_4

value: Dermal macrophage


title: Dmel_GFP_RNAi_1


title: ChIP_Foxh1_KL974_shRen_D7_1

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to bigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: AML

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: The cells were selected with puromycin and were then treated with doxycyclin for 7 days.

tag: disease state

value: AML

value: Bone marrow

value: shRen

tag: time

tag: chip antibody

value: Foxh1 Abcam 49133


title: 3E15KOPrdm16

description: 2 μg


title: Donor 3 : Mac [AH20_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH20_3


title: Input_KL974_shRen_D7_2


title: Donor 3 : Mac [AH20_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH20_2


title: KL974_shRen_D7_2

description: KL974_GEPIR_shRen_DAY7_2_IGO_09439_2_S55

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a)
Genome wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

extract_protocol:
Briefly, total RNA from 11B3fl/Trp53fl;shNf1;shMll3;Vav1-cre or Trp53fl/fl;shNf1;shMll3;Vav1-cre leukaemia cells (four lines per cohort), isolated from the bone marrow of moribund mice, was isolated by Trizol extraction (Life Technologies).
After ribogreen quantification (Life Technologies) and quality control on an Agilent BioAnalyzer, 500 ng of total RNA (RNA integrity number > 8) underwent polyA selection and Truseq library preparation according to instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2) with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 in a 50 bp/50 bp pairedend run, using the TruSeq SBS Kit v.3 (Illumina).

tag: developmental stage


title: P4-1h.HiC

data_processing:
The HiC reads were processed with the Juicer platform (v1.5.6) to generate contact matrix files in ~.hic format and to identify chromatin loops.
genome build: mm10
processed data files format and content: HiC contact matrix in ~.hic format
processed data files format and content: HiC loops in tab-delimited text format

source_name: uterus

extract_protocol: HiC: Illumina-compatible sequencing libraries were prepared by first shearing purified Arima-HiC proximally-ligated DNA and then size-selecting DNA fragments from ~200-600bp using solid phase reversible immobilization (SPRI) magnetic beads. The size-selected fragments were then enriched for biotin and converted into Illumina-compatible sequencing libraries using the KAPA Biosystems Hyper Prep kit (Wilmington, MA). After adapter ligation, DNA was PCR amplified and purified using SPRI beads.

tag: tissue

value: uterus


title: E2-1h.HiC


title: KL974_shRen_D7_1

description: KL974_GEPIR_shRen_DAY7_1_IGO_09439_1_S48


title: KL974_shp53_D7_2


title: Donor 3 : Mac [AH20_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH20_1

tag: sample number


title: V.HiC


title: KL974_shp53_D7_1

tag: genotype


title: Hepatocytes_KO_S9009_Rep3

first: Chunjie

last: Jiang

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

data_processing:
RNA-seq reads were aligned to the mouse genome (mm9) using Hisat2, with default parameters. Only unique mapped reads were considered for further analysis. Normalized expression value, fragments per kilobase of exon per million reads mapped (FPKM), was calculated for each gene using StringTie
Genome_build: mm9
Supplementary_files_format_and_content: Normalized abundance measurement was generated using StringTie.

source_name: Hepatocytes

growth_protocol: Mouse hepatocytes were isolated using a two-step collagenase/DNAse digestion protocol (Miller et al, 2011, JCI) and plated on collagen-coated cell culture plates in DMEM (Gibco) supplemented with 10% FBS (Tissue Culture Biologicals) and 1% P/S.

extract_protocol:
Total RNA was extracted by using Qiagen RNeasey Mini kit and enriched for polyadenylated RNA using oligo(dT) beads. rRNA is removed using the Ribo-Zero kit
RNA libraries were prepared for sequencing using the NEBNext Ultra II kit

treatment_protocol: Mouse hepatocytes were treated with DMSO vs 10uM SR9009 for 8 hours.

tag: gender

value: male

value: REV-ERB KO

value: Hepatocytes


title: Donor 3 : CDC2 [AH19_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH19_3

value: Dermal cDC2 (lang-)


title: Donor 3 : CDC2 [AH19_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH19_4


title: Hepatocytes_KO_S9009_Rep2


title: Donor 3 : CDC2 [AH19_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH19_2


title: Dmel_GFP_RNAi_2

city: Stanford

first: Jin

last: Li

address: 300 Pasteur Dr, Alway M341

institute: Stanford University

tag: Sex

value: female

tag: age

value: 3-5 day old

value: whole brain

value: rRNA-depleted RNA


title: KL974_shFoxh1_1072_D7_2

description: KL974_GEPIR_shFoxh1_1072_DAY7_2_IGO_09439_8_S60


title: KL974_shFoxh1_1072_D7_1

description: KL974_GEPIR_shFoxh1_1072_DAY7_1_IGO_09439_7_S59


title: Hepatocytes_KO_DMSO_Rep3

tag: cell type

value: DMSO


title: Hepatocytes_KO_S9009_Rep1


title: Donor 3 : CDC2 [AH19_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH19_1

value: Abdominal skin dermal tissue


title: E24h-3.RNAseq

data_processing:
RNAseq data was filtered to retain only read pairs with mean base quality score >20, then mapped to mm10 via STAR v2.5 with parameters "--outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical").
Normalized depth tracks for RNAseq data were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand Stranded --outWigNorm None", then normalized by size factors reported from DESeq2 and converted to bigWig format with UCSC utility bedGraphToBigWig.
RNA-seq counts per gene were determined via Subread featureCounts v1.5.0-p1 with parameters "-s2 -Sfr -p" for gene models as defined by RefSeq as of Febrary 9 2015.
genome build: mm10
processed data files format and content: ChIP-seq and RNA-seq normalized depth track in bigWig format
processed data files format and content: RNAseq counts-per-gene in tab-delimited text format

extract_protocol:
RNA: Uterine RNA from mice treated with V or with E2 for 2, 6 or 24 hours was isolated using miRNeasy Mini Kit
RNAseq: Stranded RNA-Seq libraries were constructed from 1 µg total RNA after rRNA depletion using Ribo-Zero GOLD.   The Illumina TruSeq Stranded Total RNA Sample Prep Kit was used according to manufacturer’s instructions except where noted. Amplification was performed using 10 cycles which was optimized for the input amount and to minimize the chance of over-amplification.  Unique barcode adapters were applied to each library. Libraries were pooled together for sequencing.

tag: strain


title: Hepatocytes_KO_DMSO_Rep2

tag: treatment


title: Donor 3 : CD33 Low [AH18_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH18_3

source_name: Abdominal skin epidermal tissue

value: Abdominal skin epidermal tissue

value: Epidermal CD33 low


title: Hepatocytes_KO_DMSO_Rep1


title: Donor 3 : CD33 Low [AH18_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH18_4


title: Donor 3 : CD33 Low [AH18_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH18_2


title: E6h-3.RNAseq


title: Hepatocytes_Control_S9009_Rep3

value: control


title: E24h-2.RNAseq


title: Donor 3 : CD33 Low [AH18_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH18_1


title: Hepatocytes_Control_S9009_Rep1


title: Hepatocytes_Control_S9009_Rep2


title: E24h-1.RNAseq


title: Donor 3 : CD11c+ [AH17_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH17_4

value: Epidermal CD11c+


title: E6h-1.RNAseq


title: Donor 3 : CD11c+ [AH17_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH17_3


title: Hepatocytes_Control_DMSO_Rep3


title: Donor 3 : CD11c+ [AH17_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH17_2


title: E2h-3.RNAseq


title: E2h-2.RNAseq


title: Hepatocytes_Control_DMSO_Rep2


title: Donor 3 : CD11c+ [AH17_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH17_1


title: E2h-1.RNAseq


title: Donor 3 : LC [AH16_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH16_4

value: Langerhans cell


title: Hepatocytes_Control_DMSO_Rep1


title: S-2.RNAseq


title: Donor 3 : LC [AH16_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH16_2


title: Donor 3 : LC [AH16_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH16_1


title: Donor 3 : LC [AH16_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH16_3


title: Donor 4 : CDC1 [AH30_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH30_1

value: Dermal cDC1


title: S-1.RNAseq

value: uterus


title: E6h-2.RNAseq


title: Donor 2 : Lang+ [AH15_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH15_3

value: Dermal cDC2 (lang+)


title: Donor 2 : Lang+ [AH15_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH15_4


title: Dmel_Rsf1_RNAi_1

source_name: whole brain_Dmel_Rsf1_RNAi

value: C155-Gal4; UAS-Rsf1_RNAi

tag: replicate


title: tail_DNA-HU-1318.pump

type: genomic

city: Ann Arbor

first: Thomas

middle: E.

last: Wilson

state: MI

address: 2065 BSRB, 109 Zina Pitcher

department: Department of Pathology

institute: University of Michigan

description: test F1 pup from the pump experiment

hyb_protocol: DNA was hybridized to Nimblegen mouse MM9 whole genome tiling UX3 microarrays using manufacturer’s instructions. We used a single female C57BL/6 x C3H/HeJ hybrid animal for reference DNA for all hybridizations.

scan_protocol: Arrays were scanned on a NimbleGen MS 200 scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 data extraction.

source_name: pump HU sample 1318

label_protocol: DNA was labeled for hybridization to Nimblegen mouse MM9 whole genome tiling UX3 microarrays using manufacturer’s instructions.

extract_protocol: DNA was isolated from tail snips of selected pups using the Qiagen Blood & Cell Culture DNA Mini Kit using manufacturer’s protocol (https://www.qiagen.com/us/resources/resourcedetail?id=28375699-647d-4b6b-a6a3-6a2715f7d46f&lang=en).

treatment_protocol: hydroxyurea administered to sire by peristaltic pump

tag: route

value: pump

tag: type

value: HU

value: C57BL/6J (sire) x C3H/HeJ (dam)

tag: sire

tag: dam

value: tail snip genomic DNA from F1 pup

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse

value: Ref

value: C57BL/6J x C3H/HeJ


title: Donor 2 : Lang+ [AH15_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH15_2

tag: biological replicate/donor number


title: p53R172H/-_rep1

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file containing quantified counts

tag: disease state

value: AML

value: Bone marrow


title: p53-/-_rep4


title: Donor 2 : Lang+ [AH15_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH15_1

value: Abdominal skin dermal tissue


title: p53-/-_rep3


title: p53-/-_rep2


title: tail_DNA-HU-1287.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1287


title: Donor 2 : CDC1 [AH14_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH14_4


title: tail_DNA-HU-1306.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1306


title: p53-/-_rep1


title: S-3.RNAseq

address: 111 Alexander Dr


title: Donor 2 : CDC1 [AH14_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH14_3

source_name: Abdominal skin dermal tissue


title: tail_DNA-HU-1326.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1326


title: Donor 2 : CDC1 [AH14_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH14_2


title: tail_DNA-HU-1296B.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1296B


title: LIV-178

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

institute: Michigan State University

data_processing:
[Quality control] FASTQC v0.11.3
[Removal of artifacts] FASTX v0.0.14
[Alignment] TopHat2 v2.1.0
[Conversion to SAM format] SAMTools v1.2
[Abundance measurement] HTSeq v0.6.1
[Count transformation] DESeq
[Normalization and analysis] Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene (raw counts)

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Ambion, Waltham, MA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified using a Nano-drop spectrophotometer (Thermo Scientific, Wilmington, DE) at 260 nm and purity was assessed by calculating the A260/A280 ratio. RNA quality was analyzed using the Caliper LabChip GX (Perkin Elmer, Waltham, MA).
Libraries were were prepared using the Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions.

treatment_protocol: Male C57BL/6 mice were gavaged with sesame oil vehicle or 30 ug/kg TCDD every  4 days for 28 days.

value: Male

value: 9-10 weeks old

value: Liver

value: 30 µg/kg TCDD

tag: duration of treatment

value: 28 Days

tag: frequency of treatment

value: Mice dosed every 4 days for 28 days

tag: timepoint


title: LIV-177

tag: tissue


title: p53R172H/-_rep2

tag: genotype


title: tail_DNA-HU-1260.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1260


title: Donor 2 : CDC1 [AH14_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH14_1

extract_protocol:
Primary cell populations isolated by flow cytometry (n=200 cells per population) were captured directly into lysis buffer containing 0.1% triton X-100, 1U RNaseOUT RNase inhibitor, 2.5mM each dNTP mix, 2.5uM anchored oligo-dT primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) in a total volume of 20ul. Full-length mRNA was reverse transcribed and amplified using the Smart-seq2 protocol of Picelli et al (Nature Methods. 2013;10(11):1096-8).
Sequencing libraries were prepared from 1ng cDNA product using Illumina Nextera XT reagents, in accordance with the supplier’s protocol, except that PCR was limited to 8 cycles to minimize read duplicates, and final library elution was performed using 17.5μl elution buffer EB.  All libraries were pooled and sequenced on four lanes of an Illumina HiSeq 2500 sequencer, using a HiSeq Rapid Cluster Kit v2.

value: Dermal cDC1

tag: sample number


title: LIV-176

tag: Sex

tag: age


title: Donor 2 : CD14 MDM [AH13_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH13_4

tag: cell type

value: Dermal CD14 MDM


title: tail_DNA-HU-1268.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1268

value: pump

tag: strain


title: Donor 2 : CD14 MDM [AH13_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH13_3


title: tail_DNA-HU-1286.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1286

value: HU


title: tail_DNA-HU-1325.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1325

value: C57BL/6J (sire) x C3H/HeJ (dam)


title: LIV-174

tag: treatment

value: Sesame Oil Control


title: LIV-173


title: Donor 2 : CD14 MDM [AH13_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH13_1


title: tail_DNA-HU-1311.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1311

tag: route

value: tail snip genomic DNA from F1 pup

value: Ref


title: Donor 2 : Mac [AH12_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH12_4

value: Dermal macrophage


title: LIV-179


title: LIV-166


title: Donor 2 : Mac [AH12_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH12_3


title: LIV-168


title: tail_DNA-HU-1243.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1243

tag: type

value: C57BL/6J x C3H/HeJ


title: Donor 2 : Mac [AH12_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH12_2

value: Abdominal skin dermal tissue


title: tail_DNA-HU-1273b.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1273b

tag: sire


title: tail_DNA-HU-1310A.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1310A

tag: dam


title: Donor 2 : Mac [AH12_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH12_1

tag: biological replicate/donor number


title: LIV-183

value: Male


title: LIV-182

value: 9-10 weeks old


title: LIV-175

value: Liver


title: Donor 2 : CDC2 [AH11_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH11_4

value: Dermal cDC2 (lang-)


title: tail_DNA-HU-1307.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1307


title: Donor 2 : CDC2 [AH11_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH11_2


title: Donor 2 : CD14 MDM [AH13_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH13_2


title: LIV-159

value: 30 µg/kg TCDD

value: 28 Days


title: Donor 2 : CDC2 [AH11_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH11_3


title: LIV-158

value: Mice dosed every 4 days for 28 days


title: tail_DNA-HU-1293.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1293


title: Donor 2 : CDC2 [AH11_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH11_1


title: tail_DNA-HU-1280b.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1280b

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: LIV-127


title: tail_DNA-HU-1272.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1272


title: Donor 2 : CD33 Low [AH10_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH10_4

source_name: Abdominal skin epidermal tissue

value: Abdominal skin epidermal tissue

value: Epidermal CD33 low


title: tail_DNA-HU-1265.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1265

value: pump

value: HU


title: LIV-155

value: Sesame Oil Control


title: sir2 (i.e. mutant), G1, MNase-seq

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: sir2 (i.e. mutant), G1, MNase-seq

data_processing:
align paired-end fastq files with GSNAP
sort bam files with Picard's SortSam
annotate bam files with Picard's AddOrReplaceReadGroups
count per-base pair read depths with BedTools' genomecov
Genome_build: sacCer3 for all files, except chrXII replaced with chrXIIrDtH.fa for strains with terminator downstream of c-pro (16818, 16851, 16907, 16920) and with chrXII replaced with chrXIIrDHYGdel.fa for "no terminator" control strains (16833, 16849, 16855, 16905)
Supplementary_files_format_and_content: processed_files_for_Foss_et_al_042219_1.txt: text; this file contains read depths for base pairs 458000-460000 on chrXII for all raw fastq files after they have been aligned to the appropriate genomes with the gsnap alignment algorithm
Supplementary_files_format_and_content: chrXIIrDtH.fa: fasta:  this file contains the chrXII sequence for strains with a terminator inserted immediately downstream from c-pro; all other chromosomes are the same as for sacCer3 genome build
Supplementary_files_format_and_content: chrXIIrDHYGdel.fa: fasta:  this file contains the chrXII sequence for "no terminator control" strains, i.e. controls for strains with a terminator inserted immediately downstream from c-pro; all other chromosomes are the same as for sacCer3 genome build

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast experiments were carried out using standard YPD (yeast peptone dextrose) medium [2% (wt/vol) glucose, 1% yeast extract, 2% (wt/vol) peptone].

extract_protocol:
as described:  Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108(45):18318-23. Epub 2011/10/26. doi: 1110731108 [pii]10.1073/pnas.1110731108. PubMed PMID: 22025700; PubMed Central PMCID: PMC3215028.
as described:  Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108(45):18318-23. Epub 2011/10/26. doi: 1110731108 [pii]10.1073/pnas.1110731108. PubMed PMID: 22025700; PubMed Central PMCID: PMC3215028.
paired-end

treatment_protocol: sonication (replication profiling), MNase (MNase-seq), calcium (MCM2-ChEC), details in manuscript

tag: sample type

value: MNase-seq

value: alpha factor-arrested cells


title: tail_DNA-HU-1269.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1269

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup

value: Ref


title: Donor 2 : CD33 Low [AH10_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH10_3

data_processing:
Reads were aligned using STAR v2.5.3 to the GRCh38 genome and were summarized to gene counts as annotated by GENCODE v26.
Gene counts were normalized using TMM and variance stabilized using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file containing read counts for each lane of sequencing data for each sample. Each biological sample has 4 lanes of raw sequence data.


title: Donor 2 : CD33 Low [AH10_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH10_2


title: LIV-184

source_name: Liver

value: Male

tag: duration of treatment


title: SIR2 (i.e. WT), G2, MNase-seq

description: SIR2 (i.e. WT), G2, MNase-seq

value: nocodazole-arrested cells


title: LIV-154

value: 9-10 weeks old

value: Liver

tag: frequency of treatment


title: tail_DNA-HU-1258d.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1258d

value: C57BL/6J x C3H/HeJ


title: tail_DNA-HU-1301.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1301


title: SIR2 (i.e. WT), G1, MNase-seq

description: SIR2 (i.e. WT), G1, MNase-seq


title: Donor 2 : CD33 Low [AH10_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH10_1


title: LIV-153

value: 28 Days

tag: timepoint


title: LIV-149

tag: tissue

value: 30 µg/kg TCDD

value: Mice dosed every 4 days for 28 days


title: Donor 2 : CD11c+ [AH9_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH9_4

value: Abdominal skin epidermal tissue

value: Epidermal CD11c+


title: sir2 (i.e. mutant) strain without terminator, MCM2-ChEC, G1, calcium-treated, replicate

value: calcium-treated DNA (ChEC)