title: WT Minimal+LIV stationary rep1-ChIPseq input

description:
WT_minLIV_stat_I100
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz


title: Ski-WT SLAM Cell40

status: Public on Nov 28 2018

type: SRA

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

country: USA

institute: Cincinnati Childrens Hospital Medical Center

description:
061016_Cell88-G7
Ski-WT SLAM

library_source: transcriptomic

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell RNA-Seq data were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
cDNA Synthesis: Fluidigm C1 protocol
Nextera XT DNA Library Preparation Kit (Illumina)
150bp Paired-End, 150 million reads/96 cell library
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting of Cd45.2+ Lineage- c-Kit+ Sca-1+ Cd48- Cd150+ bone marrow cells. Single cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
cDNA was made with the SMARTer mRNA-Seq Kit (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

tag: strain

tag: cell type

value: Fetal liver derived HSC - transplanted for 6 months

tag: genotype/variation

value: Ski-WT


title: Ski-WT SLAM Cell39

description:
061016_Cell87-F7
Ski-WT SLAM


title: WT_SPI-2_R1

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
Ribo-Zero (Bacteria) + fragmentation + standard cloning protocol
gene_wise_quantifications_combined.csv

data_processing:
Adaptor removal and quality trimming with cutadapt (version 1.13)
Read mapping with READemption (version 0.4.3)  and segemehl (0.2.20)
Feature quantification with READemption (version 0.4.3)
Genome_build: NC_016810.1, NC_017718.1, NC_017720.1
Supplementary_files_format_and_content: reads per feature in csv format (tabular separated)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: S. Typhimurium_in-vitro conditions

growth_protocol: Salmonella enterica serovar Typhimurium strain SL1344 (strain JVS-1574; (Stocker et al., 1983)) and a constitutively GFP-expressing derivative thereof (JVS-3858; (Papenfort et al., 2009)) are considered as wild-type. Chromosomal mutations were generated as previously described (Datsenko and Wanner, 2000), the respective resistance cassettes eliminated using the FLP helper plasmid pCP20 (Datsenko and Wanner, 2000) at 42°C, and the mutated alleles subsequently transduced into one of the wild-type backgrounds (GFP-negative or –positive, respectively) using P22 phage (Sternberg and Maurer, 1991). For plasmid transformation, the respective Salmonella strains were electroporated with ~10 ng of DNA. The complete lists of bacterial strains and plasmids used in this study are provided in Supplementary Tables S5 and S6. Routinely, Salmonella strains were grown in liquid Lennox broth (LB) medium or on solid LB agar medium at 37°C. When appropriate, liquid or solid media were supplemented with 30 μg/mL chloramphenicol (Cm), 100 μg/mL ampicillin (Amp), 50 μg/mL kanamycin (Kan), or 0.02% (w/vol) L-arabinose (final concentrations).

extract_protocol:
TRIzol
TruSeq-based (at Vertis Biotech. AG, Freising, Germany)

treatment_protocol: Infection assays were carried out as previously described (Westermann et al., 2016). To avoid loss of the proQ overexpression plasmid (and the respective empty control vector) during intracellular bacterial growth, we performed HeLa infection assays in the presence or absence of the respective selection marker (ampicillin) in the host cell medium.

value: WT

tag: medium

value: SPI-2 inducing


title: WT_LB_R3

value: LB


title: 2W_STR_injured_rep2

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

data_processing:
Sequenced reads were mapped to mouse genome mm10 using TopHat (version 2.0.11)
After read mapping, ‘featureCounts’ from Rsubread package (version 1.22.2) was used to generate gene-wise read counts.
Genes were filtered from downstream analysis if they did not have a CPM (counts per million mapped fragments) value of at least 2 in at least five libraries
RUVseq was used to normalize the data using 25 housekeeping genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 CPM values for each sample .

source_name: 2W_STR_injured_knee joint

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (QIAGEN Inc, Germantown, MD, USA) according to manufacturer’s protocol.
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq Sample Preparation kit (Illumina Inc, Hayward, CA, USA)  according to manufacturer’s protocol.

treatment_protocol: Right knee joints of 10 weeks old STR/ort, C57BL/6 and MRL/MpJ mice were injured using a compressive load of 10-12N. Injured and uninjured (contralateral) joints were collected at 0-day [before injury], 1-day, 1-week, and 2-weeks post-injury. Subsequently, joints were dissected and cut at the base edges of femoral and tibial joint regions with small traces of soft tissues to preserve the intact knee joint.  Dissected joints were then cut into small pieces and submerged in RNA Later (Qiagen) and stored at 4 ̊C until processing.

value: STR/ort

tag: age

value: 10 Weeks

tag: susceptibility to ptoa

value: highly susceptible

tag: tissue

value: Knee joints

tag: treatment

value: Injured

tag: sample collection

value: 2-weeks post-injury

tag: experimental batch


title: WT Minimal transition point rep1-ChIPseq input

city: Ann Arbor

first: Peter

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

description:
WT_min_mid_I154
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E155_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E164_actual.bedgraph.gz

library_source: genomic

data_processing:
pre-processing RNA-Seq: Sequencing adapters were removed from all sequences using CutAdapt version 1.8.1 (Martin 2011) with parameters --quality-base=33 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -n 3 -m 20 --mask-adapter --match-read-wildcards. Low quality reads were trimmed with Trimmomatic version 0.32 (Bolger et al. 2014) using the parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20. For all samples, remaining ribosomal reads were removed from analysis (details in the publication).
Wald Test RNA-seq: Gene-centric quantification of RNA expression for all samples was performed using kallisto version 0.43.0 (Bray et al. 2016) with the arguments: quant -t 4 -b 100 --rf-stranded. wald_test.csv files represent a Wald test calculated using sleuth (Pimento et al. 2017) performed on the genotype term of a simple model where transcript_abundance ~ genotype for each condition and time point combination seperately. The lrp::kanR genotype is considered the baseline in this model.
TPM estimates RNA-seq: log2(WT/KO) TPM ratios were calculated from the TPM estimates given by kallisto run as described in the Wald Test RNA-seq step above. Percentile-based 95% confidence intervals are estimated from 100 bootstrap replicates of the log2(WT/KO) TPM ratios (details in publication)
pre-processing ChIP-Seq: Sequencing adapters were removed from all sequences using CutAdapt version 1.8.1 (Martin 2011) with parameters -a AGATCGGAAGAGC -A AGATCGGAAGAGC -n 3 -m 20 --mask-adapter --match-read-wildcards. Low quality reads were trimmed with Trimmomatic version 0.32 (Bolger et al.2014)  using the parameters TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20.
Lrp WT - lrp::kanR ChIP-signal: Median-normalized WT log2(Extracted/Input) - KO(Extracted/Input) signal at every 10 bp is reported for each combination of WT and KO replicates for each time and condition. (details in publication)
Robust-Z ChIP summary signal: Each subtracted replicate in the step above was converted to a Robust-Z score and average between replicates for each time and condition combination to give a final summary signal (details in publication)
Lrp ChIP peaks: High-confidence Lrp binding regions were called through the use of three filters: 1. technical reproducibility estimated by bootstrap replicates sampled from raw reads. 2. biological signal estimated from the Lrp WT- lrp::kanR ChIP signal. 3. Biological reproducibility estimated from the IDR (Li et al. 2011)  between biological replicates. (details in publication)
Genome_build: E.coli MG1655 U00096.2 modified to match ATCC47076 strain as reported by Freddolino et al. 2012. All genome annotations were taken from RegulonDB version 9.4 (Gama-Castro S et al. 2016) with genome coordinates converted appropriately
Supplementary_files_format_and_content: Files ending in wald_test.csv: Results of Wald test as described in the Wald Test RNA-seq data processing step for each time and condition combination in the file name. Files are in csv format
Files ending in log2_wt_ko_ratio.tsv: Results of the log2(WT/KO) expression estimates. RNA-seq data processing step for each time and condition combination in the file name. Files are in tab seperated format (tsv). Column 1 is the estimate. Columns 2 and 3 represent a conservative percentile based 95% confidence interval.
Files ending in actual.bedgraph.gz: Results of Lrp WT- lrp::kanR ChIP-signal data processing step for the appropriate combination of WT and lrp::kanR replicates in the file name. Lines include a one 1bp entry for each location reported. Locations resulting in a NaN, inf, or -inf were not included in each .bedgraph
Files ending in robust_z.bedgraph.gz: Results of the Robust-Z ChIP summary signal data processing step for the appropriate combination of time and condition in the file name. Lines include a one 1bp entry for each location reported. Locations resulting in a NaN, inf, or -inf were not included in each .bedgraph
Files ending in peaks.bed.gz: Results of the Lrp ChIP peaks data processing step for each time and condition combination in the file name. Peaks are in .bed6+4 format with ATCC47076 as the chromosome name. The score (fifth) field is the maximum robustZ score found in the peak.The additional 4 fields include: 7. Maximum -log10(qvalue) for the technical filter 8. maximum -log10(qvalue) for the biological filter and 9. maximum -log10(qvalue) for the idr reproducibility filter. 10. peak 0-based offset from start where maximum robustZ score occured. In all cases where -log10(qvalue) resulted in an +infinite value (i.e. when qvalue = 0)  the -log10(qvalue) was truncated to the next highest finite -log10(qvalue) in the dataset for that filter.
Files ending in abundance.tsv: Results of quantification of each individual RNA sample from kallisto

molecule: genomic DNA

organism: Escherichia coli

source_name: Culture lysate

growth_protocol: Cells isolated from a single colony were grown in liquid culture at 37C until harvest.

extract_protocol:
RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
Specific Lrp-DNA complexes were isolated using a monoclonal antibody developed against Lrp, and DNA was isolated by phenol-chloroform extraction.
DNA was preprared for sequencing using the NEBNext DNA Library Prep Kit.  RNA was prepared fro sequencing using the NEBNext Ultra Directionaly RNA Library Prep Kit.

treatment_protocol: Cells were cross-linked by addition of 1% formaldehyde.

tag: genotype

value: wild type

tag: media

value: MOPS minimal media + glycerol

tag: time of harvest

value: transition point

tag: chip antibody


title: Ski-WT SLAM Cell38

description:
061016_Cell86-E7
Ski-WT SLAM


title: 2W_BL6_uninjured_rep5

source_name: 2W_BL6_uninjured_knee joint

value: moderately susceptible

value: Uninjured


title: 2W_STR_injured_rep1


title: Ski-WT SLAM Cell37

description:
061016_Cell85-D7
Ski-WT SLAM


title: Ski-WT SLAM Cell43

description:
061016_Cell91-C8
Ski-WT SLAM


title: WT Minimal+LIV transition point rep1-ChIPseq input

description:
WT_minLIV_mid_I156
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz

value: MOPS minimal media + LIV + glycerol


title: WT_LB_R1


title: WT Minimal logarithmic rep2-ChIPseq input

description:
WT_min_log_I42
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E23_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E25_actual.bedgraph.gz

value: logarithmic phase


title: 2W_BL6_uninjured_rep4


title: dproQ_SPI-2_R3

value: proQ mutant


title: Ski-WT SLAM Cell36

description:
061016_Cell84-C7
Ski-WT SLAM

value: Fetal liver derived HSC - transplanted for 6 months

value: Ski-WT


title: Ski-WT SLAM Cell35

description:
061016_Cell83-A7
Ski-WT SLAM


title: dproQ_SPI-2_R2

value: SPI-2 inducing


title: 2W_BL6_uninjured_rep3


title: Lrp::kanR Rich stationary rep2-ChIPseq extracted

description:
KO_RDM_stat_E123
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E123_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E123_actual.bedgraph.gz

value: MOPS rich defined media + glycerol

value: stationary phase

value: anti-Lrp monoclonal antibody (NeoClone, custom antibody clone# 1G4D9A10, Lot# 2016E25-001)


title: 2W_BL6_uninjured_rep2

value: 10 Weeks

value: Knee joints


title: Ski-WT SLAM Cell34

description:
061016_Cell82-G6
Ski-WT SLAM


title: dproQ_SPI-2_R1


title: WT Minimal transition point rep2-ChIPseq input

description:
WT_min_mid_I167
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E155_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E164_actual.bedgraph.gz


title: 2W_BL6_uninjured_rep1

value: 2-weeks post-injury


title: Ski-WT SLAM Cell33

description:
061016_Cell81-E6
Ski-WT SLAM


title: Lrp::kanR Rich transition point rep2-ChIPseq extracted

description:
KO_RDM_mid_E153
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E153_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E153_actual.bedgraph.gz


title: dproQ_LB_R3

value: LB


title: Ski-WT SLAM Cell32

description:
061016_Cell80-D6
Ski-WT SLAM


title: WT_LB_R2

value: WT


title: 2W_BL6_injured_rep5

source_name: 2W_BL6_injured_knee joint

value: Injured


title: Lrp::kanR Rich transition point rep1-ChIPseq extracted

description:
KO_RDM_mid_E146
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E146_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E146_actual.bedgraph.gz

value: transition point


title: Lrp::kanR Rich logarithmic rep2-ChIPseq extracted

description:
KO_RDM_log_E117
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E117_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E117_actual.bedgraph.gz


title: dproQ_LB_R2


title: Ski-WT SLAM Cell31

description:
061016_Cell79-B6
Ski-WT SLAM


title: 2W_BL6_injured_rep4

value: moderately susceptible


title: Ski-WT SLAM Cell30

description:
061016_Cell78-A6
Ski-WT SLAM


title: 2W_BL6_injured_rep3


title: Lrp::kanR Rich logarithmic rep1-ChIPseq extracted

description:
KO_RDM_log_E113
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E113_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E113_actual.bedgraph.gz


title: 2W_BL6_injured_rep2


title: dhfq_SPI-2_R3

value: hfq mutant


title: WT Minimal logarithmic rep1-ChIPseq input

description:
WT_min_log_I11
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E23_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E25_actual.bedgraph.gz

value: wild type

value: MOPS minimal media + glycerol

value: logarithmic phase


title: Ski-WT SLAM Cell29

description:
061016_Cell77-H5
Ski-WT SLAM

value: Fetal liver derived HSC - transplanted for 6 months

value: Ski-WT


title: Lrp::kanR Minimal+LIV stationary rep2-ChIPseq extracted

description:
KO_minLIV_stat_E122
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz

value: MOPS minimal media + LIV + glycerol


title: Lrp::kanR Rich stationary rep1-ChIPseq extracted

description:
KO_RDM_stat_E115
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E115_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E115_actual.bedgraph.gz

value: MOPS rich defined media + glycerol

value: stationary phase


title: dhfq_SPI-2_R2

value: SPI-2 inducing


title: 2W_BL6_injured_rep1

value: 10 Weeks

value: Knee joints


title: 2W_MRL_uninjured_rep5

source_name: 2W_MRL_uninjured_knee joint

value: MRL/MpJ

value: not susceptible

value: Uninjured

value: 2-weeks post-injury


title: Lrp::kanR Minimal+LIV stationary rep1-ChIPseq extracted

description:
KO_minLIV_stat_E114
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz

value: anti-Lrp monoclonal antibody (NeoClone, custom antibody clone# 1G4D9A10, Lot# 2016E25-001)


title: dhfq_SPI-2_R1

value: hfq mutant


title: Lrp::kanR Minimal+LIV transition point rep2-ChIPseq extracted

description:
KO_minLIV_mid_E165
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz

value: transition point


title: Ski-WT SLAM Cell27

description:
061016_Cell75-F5
Ski-WT SLAM


title: 2W_MRL_uninjured_rep4


title: Lrp::kanR Minimal+LIV transition point rep1-ChIPseq extracted

description:
KO_minLIV_mid_E157
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz


title: Ski-WT SLAM Cell26

description:
061016_Cell74-D5
Ski-WT SLAM


title: dhfq_LB_R2

value: LB


title: 2W_MRL_uninjured_rep3


title: dproQ_LB_R1

value: proQ mutant


title: Ski-WT SLAM Cell24

description:
061016_Cell72-B5
Ski-WT SLAM

value: Fetal liver derived HSC - transplanted for 6 months


title: Lrp::kanR Minimal+LIV logarithmic rep1-ChIPseq extracted

description:
KO_minLIV_log_E112
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E112_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E112_actual.bedgraph.gz

value: logarithmic phase


title: 2W_MRL_uninjured_rep2


title: dhfq_LB_R1

description:
Ribo-Zero (Bacteria) + fragmentation + standard cloning protocol
gene_wise_quantifications_combined.csv


title: Lrp::kanR Minimal+LIV logarithmic rep2-ChIPseq extracted

description:
KO_minLIV_log_E116
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E116_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E116_actual.bedgraph.gz

value: MOPS minimal media + LIV + glycerol


title: Ski-WT SLAM Cell23

description:
061016_Cell71-H4
Ski-WT SLAM

value: Ski-WT


title: 2W_MRL_uninjured_rep1


title: dhfq_dproQ_SPI-2_R3

value: proQ/hfq double mutant


title: 2W_MRL_injured_rep5

source_name: 2W_MRL_injured_knee joint

value: Injured


title: Lrp::kanR Minimal stationary rep2-ChIPseq extracted

description:
KO_min_stat_E98
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E98_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E98_actual.bedgraph.gz

value: MOPS minimal media + glycerol

value: stationary phase


title: Ski-WT SLAM Cell28

description:
061016_Cell76-G5
Ski-WT SLAM


title: dhfq_dproQ_SPI-2_R1

value: SPI-2 inducing


title: Lrp::kanR Minimal stationary rep1-ChIPseq extracted

description:
KO_min_stat_E102
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E102_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E102_actual.bedgraph.gz


title: Ski-WT SLAM Cell22

description:
061016_Cell70-G4
Ski-WT SLAM


title: Ski-WT SLAM Cell21

description:
061016_Cell69-F4
Ski-WT SLAM


title: dhfq_LB_R3


title: Lrp::kanR Minimal transition point rep2-ChIPseq extracted

description:
KO_min_mid_E164
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E164_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E164_actual.bedgraph.gz


title: Ski-WT SLAM Cell20

description:
061016_Cell68-E4
Ski-WT SLAM


title: Ski-WT SLAM Cell19

description:
061016_Cell67-C4
Ski-WT SLAM


title: dhfq_dproQ_LB_R1


title: 2W_MRL_injured_rep1

value: MRL/MpJ

value: 10 Weeks

value: not susceptible

value: Knee joints


title: Ski-WT SLAM Cell25

description:
061016_Cell730-C5
Ski-WT SLAM


title: dhfq_dproQ_SPI-2_R2


title: STnc540-S_R2

description:
RNA fragmentation followed by standard cloning protocol
gene_wise_quantifications_combined.csv

source_name: S. Typhimurium_pulse-expression of STnc540

treatment_protocol: Pulse-expression of the respective isoform of STnc540 was induced from the pBAD promoter by the addition of 0.02% (w/vol) L-arabinose (Sigma) to the respective cultures in minimal SPI-2-inducing media at an OD600 of 0.3. 10 min after the induction, total RNA was extracted using TRIzol LS reagent (Invitrogen), treated with DNase I, and analyzed by RNAseq.

tag: inducer

value: S-arabinose


title: Ski-WT SLAM Cell18

description:
061016_Cell66-A4
Ski-WT SLAM


title: 2W_MRL_injured_rep3

value: 2-weeks post-injury


title: Lrp::kanR Minimal transition point rep1-ChIPseq extracted

description:
KO_min_mid_E155
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E155_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E155_actual.bedgraph.gz

value: transition point

value: anti-Lrp monoclonal antibody (NeoClone, custom antibody clone# 1G4D9A10, Lot# 2016E25-001)


title: dhfq_dproQ_LB_R2

value: LB


title: WT Rich stationary rep2-ChIPseq extracted

description:
WT_RDM_stat_E105
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E115_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E105_Sub_KO_RDM_stat_E123_actual.bedgraph.gz

value: wild type

value: MOPS rich defined media + glycerol


title: Ski-WT SLAM Cell17

description:
061016_Cell65-F3
Ski-WT SLAM

value: Fetal liver derived HSC - transplanted for 6 months

value: Ski-WT


title: 1W_STR_uninjured_rep3

source_name: 1W_STR_uninjured_knee joint

value: STR/ort

value: highly susceptible

value: Uninjured

value: 1-week post-injury


title: Lrp::kanR Minimal logarithmic rep1-ChIPseq extracted

description:
KO_min_log_E23
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E23_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E23_actual.bedgraph.gz

value: MOPS minimal media + glycerol

value: logarithmic phase


title: STnc540-S_R1


title: 1W_STR_uninjured_rep4

value: 10 Weeks


title: Ski-WT SLAM Cell16

description:
061016_Cell64-E3
Ski-WT SLAM


title: WT Rich stationary rep1-ChIPseq extracted

description:
WT_RDM_stat_E101
RDM_stat_called_peaks.bed.gz
RDM_stat_actual_10bp_robust_z.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E115_actual.bedgraph.gz
RDM_stat_actual_10bp_WT_RDM_stat_E101_Sub_KO_RDM_stat_E123_actual.bedgraph.gz

value: stationary phase


title: dhfq_dproQ_LB_R3

value: proQ/hfq double mutant


title: STnc540-L_R2

value: L-arabinose


title: 1W_STR_uninjured_rep2

value: Knee joints


title: Ski-WT SLAM Cell15

description:
061016_Cell63-C3
Ski-WT SLAM


title: WT Rich transition point rep2-ChIPseq extracted

description:
WT_RDM_mid_E152
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E146_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E152_Sub_KO_RDM_mid_E153_actual.bedgraph.gz

value: transition point

value: anti-Lrp monoclonal antibody (NeoClone, custom antibody clone# 1G4D9A10, Lot# 2016E25-001)


title: 2W_MRL_injured_rep4

value: MRL/MpJ

value: not susceptible

value: Injured

value: 2-weeks post-injury


title: STnc540-L_R1


title: Lrp::kanR Minimal logarithmic rep2-ChIPseq extracted

description:
KO_min_log_E25
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E25_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E25_actual.bedgraph.gz


title: 2W_MRL_injured_rep2


title: WT Rich transition point rep1-ChIPseq extracted

description:
WT_RDM_mid_E147
RDM_mid_called_peaks.bed.gz
RDM_mid_actual_10bp_robust_z.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E146_actual.bedgraph.gz
RDM_mid_actual_10bp_WT_RDM_mid_E147_Sub_KO_RDM_mid_E153_actual.bedgraph.gz

value: wild type

value: MOPS rich defined media + glycerol


title: Ski-WT SLAM Cell14

description:
061016_Cell62-B3
Ski-WT SLAM

value: Fetal liver derived HSC - transplanted for 6 months

value: Ski-WT


title: EV_R2


title: 1W_STR_injured_rep5

source_name: 1W_STR_injured_knee joint

value: STR/ort

value: highly susceptible

value: 1-week post-injury


title: Ski-WT SLAM Cell13

description:
061016_Cell61-A3
Ski-WT SLAM


title: Ski-WT SLAM Cell12

description:
061016_Cell60-H2
Ski-WT SLAM


title: WT Rich logarithmic rep1-ChIPseq extracted

description:
WT_RDM_log_E40
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E113_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E40_Sub_KO_RDM_log_E117_actual.bedgraph.gz

value: logarithmic phase


title: WT Rich logarithmic rep2-ChIPseq extracted

description:
WT_RDM_log_E9
RDM_log_called_peaks.bed.gz
RDM_log_actual_10bp_robust_z.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E113_actual.bedgraph.gz
RDM_log_actual_10bp_WT_RDM_log_E9_Sub_KO_RDM_log_E117_actual.bedgraph.gz


title: Ski-WT SLAM Cell11

description:
061016_Cell59-G2
Ski-WT SLAM


title: 1W_STR_injured_rep4

value: 10 Weeks


title: EV_R1


title: RPE1_PCM1_KO_rep2

city: Istanbul

first: seref

last: gul

address: Yalikoy Mh., Beykoz

department: Institute of Life Sciences and Biotechnology

country: Turkey

institute: Bezmialem Vakif University

data_processing:
The fluorescent images were processed into sequences, and base calling and quality value calculations were performed using the Illumina data processing pipeline (v1.5). FastQC (v0.11.5) was utilized to evaluate the initial quality of the reads.
Adaptor sequence and low-quality bases (quality score < Q30) were trimmed from the sequence reads by using Trimmomatic (v0.35).
Clean high quality data were mapped to the reference hg38 genome for human cells, and  to GRCm38.p5 genome for mouse cells via STAR  aligner (v2.5.3) with the following options --outSJfilterReads Unique --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate.
Fragments per kilobases of exons per million mapped read (FPKM) and fold changes were calculated using the Cuffdiff command from the Cufflinks suite. Quartile library normalization and pooled dispersion estimation methods were performed for the differential expression analysis. We used a minimum alignment count of 10, false discovery rate (FDR) < 0.05 and the absolute value of |Fold change| ≥ 2 as the threshold to judge significant differences in gene expression. To identify differentially expressed genes (DEGs) in WT and KO samples, the FPKM values for each gene (in KO samples) were compared to controls (WT sample) of each subject.
DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/) was utilized to test the statistical enrichment of the significantly (p-val < 0.05) differentially expressed genes in KEGG pathways and GO enrichment analysis.
Genome_build: hg38 for human  GRCm38.p5 for mouse cells
Supplementary_files_format_and_content: Tab-delimited text files for all genes having differential expression, p-val and q-val data obtained as a result of comparing WT vs KO cells (RPEI and IMCD3 samples), e.g. RPEI_gene_exp_diff.csv and IMCD3_gene_exp_diff.csv

organism: Homo sapiens

source_name: retinal epithelial cells

extract_protocol:
Total RNA from the fibroblast cell lines was extracted using the RNeasy Mini Kit (Qiagen, USA) protocol according to manufacturer’s instructions including the DNase I treatment.
After checking the quality and quantity of total RNA via 2100 BioAnalyzer, RNA-seq library preparation was performed using TruSeq mRNA Sample Preparation Kit (Illumina, USA) according to the manufacturer’s instructions. Paired-end sequencing was performed for the two cDNA libraries (two biological replicates) for each condition in Illumina HiSeq sequencing platform. All sequence data were PE 2x100 bp. Illumina data processing pipeline (v1.5) was utilized to perform the image processing, base calling, and quality calculation. High quality reads were saved in FASTQ format.

value: retinal epithelial cells

tag: passage


title: 1W_STR_uninjured_rep1

value: Knee joints

value: Uninjured


title: Ski-WT SLAM Cell10

description:
061016_Cell58-C2
Ski-WT SLAM


title: 1W_STR_injured_rep3


title: RPE1_PCM1_KO_rep1


title: 1W_STR_injured_rep2


title: 1W_STR_injured_rep1


title: RPE1_WT_rep1

value: Wild type


title: WT Minimal+LIV stationary rep1-ChIPseq extracted

description:
WT_minLIV_stat_E100
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E100_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz

value: MOPS minimal media + LIV + glycerol

value: stationary phase

value: anti-Lrp monoclonal antibody (NeoClone, custom antibody clone# 1G4D9A10, Lot# 2016E25-001)


title: RPE1_WT_rep2


title: Ski-WT SLAM Cell9

description:
061016_Cell57-B2
Ski-WT SLAM


title: WT Minimal+LIV transition point rep1-ChIPseq extracted

description:
WT_minLIV_mid_E156
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E156_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz

value: transition point


title: TCam-2 transcriptome rep.3

city: Poznan

first: Jadwiga

last: Jaruzelska

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

data_processing:
The pair-end sequence reads obtained from HiSeq4000 platform were trimmed and quality filtered using TRIMMOMATIC V0.35 with following parameters: ILLUMINACLIP:TruSeq2:PE MINLEN:50, SLIDINGWINDOW:10:25MINLEN:50
Paired reads were mapped to the human reference genome (UCSC hg19) using TOPHAT 2.1.0 at the following parameters: mean inner distance between mate pairs:100; st. dev. for distance between mate pairs:20
Mapped reads were counted using CUFFLINKS  2.2.1.0 with default parameters
Files from individual replicates were merged using CUFFMERGE with default parameters
Differential gene expression was calculated with CUFFDIFF 2.2.1.5 using FPKM method
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

molecule: polyA RNA

growth_protocol: TCam-2 cells were grown in 37oC and 5% CO2 in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS (HyClone) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) according to manufacturer protocol
The cDNA libraries were prepared using Illumina Truseq RNA Sample Prep V2 with standard protocol

treatment_protocol: Total RNA isolation from 3 biological replicates followed by RNA-Seq was used to generate TCam-2 transcriptome data

tag: cell line

tag: passages

tag: rip-seq antibody

tag: sirna


title: WT Minimal+LIV stationary rep2-ChIPseq extracted

description:
WT_minLIV_stat_E104
minLIV_stat_called_peaks.bed.gz
minLIV_stat_actual_10bp_robust_z.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E114_actual.bedgraph.gz
minLIV_stat_actual_10bp_WT_minLIV_stat_E104_Sub_KO_minLIV_stat_E122_actual.bedgraph.gz

tag: strain

value: wild type


title: WT Minimal+LIV transition point rep2-ChIPseq extracted

description:
WT_minLIV_mid_E166
minLIV_mid_called_peaks.bed.gz
minLIV_mid_actual_10bp_robust_z.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E157_actual.bedgraph.gz
minLIV_mid_actual_10bp_WT_minLIV_mid_E166_Sub_KO_minLIV_mid_E165_actual.bedgraph.gz


title: Ski-WT SLAM Cell8

description:
061016_Cell56-A2
Ski-WT SLAM

tag: cell type

tag: genotype/variation


title: 1W_BL6_uninjured_rep4

source_name: 1W_BL6_uninjured_knee joint

tag: age

tag: susceptibility to ptoa

value: moderately susceptible

tag: tissue


title: Ski-WT SLAM Cell7

description:
061016_Cell55-H1
Ski-WT SLAM

value: Fetal liver derived HSC - transplanted for 6 months


title: 1W_BL6_uninjured_rep3

tag: treatment

tag: sample collection

tag: experimental batch


title: WT Minimal+LIV logarithmic rep2-ChIPseq extracted

description:
WT_minLIV_log_E21
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E112_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E21_Sub_KO_minLIV_log_E116_actual.bedgraph.gz

tag: genotype

tag: media

tag: time of harvest


title: Ski-WT SLAM Cell6

description:
061016_Cell54-G1
Ski-WT SLAM

value: Ski-WT


title: WT Minimal+LIV logarithmic rep1-ChIPseq extracted

description:
WT_minLIV_log_E13
minLIV_log_called_peaks.bed.gz
minLIV_log_actual_10bp_robust_z.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E112_actual.bedgraph.gz
minLIV_log_actual_10bp_WT_minLIV_log_E13_Sub_KO_minLIV_log_E116_actual.bedgraph.gz

tag: chip antibody


title: TCam-2 transcriptome rep.1

tag: cell line


title: WT Minimal stationary rep2-ChIPseq extracted

description:
WT_min_stat_E99
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E102_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E99_Sub_KO_min_stat_E98_actual.bedgraph.gz

value: MOPS minimal media + glycerol


title: 1W_BL6_uninjured_rep2


title: PUM2 siRNA rep.3

treatment_protocol: TCam-2 cells were transfected with PUM1 siRNA, PUM2 siRNA or control siRNA at the final 40 nM concentration, using NEON transfection/electroporation system (Thermo Fisher Scientific). Transfections were performed in Buffer R using 10µl NEON tips.  Subsequently after transfection cells were cultured in antibiotic-free RPMI 1640 (Gibco) supplemented with 10% FBS (HyClone), at 37 oC and 5 % CO2, for 72 hours. For transcription inhibition, the cells were treated with 5µg/ml  Actinomycin D (A1410 Sigma), 4 h before the cell lysis.

tag: passages

value: PUM2 siRNA (sc-44773 SantaCruz Biotechnology)


title: 1W_BL6_uninjured_rep1

value: 1-week post-injury


title: Ski-WT SLAM Cell4

description:
061016_Cell52-D1
Ski-WT SLAM


title: 1W_BL6_uninjured_rep5


title: 1W_BL6_injured_rep4

source_name: 1W_BL6_injured_knee joint

value: Injured


title: 1W_BL6_injured_rep5

value: 10 Weeks


title: PUM2 siRNA rep.1

tag: rip-seq antibody


title: WT Minimal stationary rep1-ChIPseq extracted

description:
WT_min_stat_E103
min_stat_called_peaks.bed.gz
min_stat_actual_10bp_robust_z.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E102_actual.bedgraph.gz
min_stat_actual_10bp_WT_min_stat_E103_Sub_KO_min_stat_E98_actual.bedgraph.gz


title: PUM2 siRNA rep.2

tag: sirna


title: WT Minimal transition point rep2-ChIPseq extracted

description:
WT_min_mid_E167
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E155_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E167_Sub_KO_min_mid_E164_actual.bedgraph.gz

tag: strain


title: PUM1 siRNA rep.3

value: PUM1 siRNA (sc-62912 SantaCruz Biotechnology)


title: 1W_BL6_injured_rep3

value: Knee joints


title: Ski-WT SLAM Cell1

description:
061016_Cell49-A1
Ski-WT SLAM

tag: cell type


title: Ski-WT SLAM Cell2

description:
061016_Cell50-B1
Ski-WT SLAM

tag: genotype/variation


title: Ski-WT SLAM Cell3

description:
061016_Cell51-C1
Ski-WT SLAM


title: 1W_BL6_injured_rep2

tag: age


title: WT Minimal transition point rep1-ChIPseq extracted

description:
WT_min_mid_E154
min_mid_called_peaks.bed.gz
min_mid_actual_10bp_robust_z.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E155_actual.bedgraph.gz
min_mid_actual_10bp_WT_min_mid_E154_Sub_KO_min_mid_E164_actual.bedgraph.gz


title: Ski-KO SLAM Cell46

description:
051816_Cell48-E3
Ski-KO SLAM

value: Ski-KO


title: WT Minimal logarithmic rep2-ChIPseq extracted

description:
WT_min_log_E42
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E23_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E42_Sub_KO_min_log_E25_actual.bedgraph.gz

value: logarithmic phase


title: PUM1 siRNA rep.2


title: WT Minimal logarithmic rep1-ChIPseq extracted

description:
WT_min_log_E11
min_log_called_peaks.bed.gz
min_log_actual_10bp_robust_z.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E23_actual.bedgraph.gz
min_log_actual_10bp_WT_min_log_E11_Sub_KO_min_log_E25_actual.bedgraph.gz


title: Ski-WT SLAM Cell5

description:
061016_Cell53-E1
Ski-WT SLAM


title: Ski-KO SLAM Cell45

description:
051816_Cell47-D3
Ski-KO SLAM


title: 1W_BL6_injured_rep1

tag: susceptibility to ptoa


title: PUM1 siRNA rep.1


title: TCam-2 transcriptome rep.2


title: control siRNA rep.3

value: control siRNA-A (sc-37007 SantaCruz Biotechnology)


title: 1W_MRL_uninjured_rep4

source_name: 1W_MRL_uninjured_knee joint

value: MRL/MpJ

value: not susceptible

tag: tissue

value: Uninjured


title: control siRNA rep.2


title: Ski-KO SLAM Cell44

description:
051816_Cell46-C3
Ski-KO SLAM


title: 1W_MRL_uninjured_rep3

tag: treatment


title: 1W_MRL_uninjured_rep2

tag: sample collection


title: CRN/PPN1_ctr_r2

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

data_processing:
Adapter sequences were trimmed with Trimmomatic v0.36 (ILLUMINACLIP:../bin/Trimmomatic-0.36/adapt  ers/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:36).
Read mapping and counting was performed with STAR v2.5.3a (default parameters).
Genome_build: Ensembl Saccharomyces_cerevisiae.R64-1-1.90 (genome-build-accession GCA_000146045.2, UCSC sacCer3)
Supplementary_files_format_and_content: the raw read counts as estimated by STAR v2.5.3a with the following columns are provided as sample supplementary files:
1 (relevant to this study): gene ID according to the Ensembl Saccharomyces_cerevisiae.R64-1-1.90 genome annotation
2: read counts ignoring library strand information (unstranded RNA-Seq)
3: counts for the direct read strand aligned with RNA
4 (relevant to this study): counts for the reverse complementary read strand aligned with RNA

organism: Saccharomyces cerevisiae

source_name: CRN/PPN1_ctr_yeast cells

growth_protocol: The cells were cultivated at 29 grad C and 145 rpm/min to logarithmic growth stage. The cells were cultivated for 12 hours in the control medium (both strains), for 40 h in manganese-containing medium (CRN strain), and for 16 h in the manganese containing medium (CRN/PPN1 strain). The control medium: 2% glucose, 2% peptone , 1% yeast extract, 14 mM KH2PO4. The mangenese-containing medium: control medium with 5 mM MnSO4.

extract_protocol:
Total RNA extraction was performed using an RNeasy Plant Kit (Qiagen, Germany) following the manufacturer’s protocol with addition of Plant RNA Isolation aid reagent (Ambion) to lysis buffer RLT.
Illumina cDNA libraries were constructed with the TruSeq RNA Sample Prep Kits v2 (Illumina, USA) following the manufacturer’s protocol.

treatment_protocol: The biomass samples were water-washed in triple and placed in RNALater.

value: CRN/PPN1, MATa ade2 his3 ura3 ppn1delta::CgTRP1  transformed with vector pMB1/PPN1 Sc

tag: growth media


title: Ski-KO SLAM Cell43

description:
051816_Cell45-B3
Ski-KO SLAM


title: control siRNA rep.1


title: Ski-KO SLAM Cell42

description:
051816_Cell44-A3
Ski-KO SLAM


title: CRN/PPN1_Mn_r1

source_name: CRN/PPN1_Mn_yeast cells

value: 2% glucose, 2% peptone , 1% yeast extract, 14 mM KH2PO4, 5 mM MnSO4


title: 1W_MRL_uninjured_rep1

tag: experimental batch


title: Ski-KO SLAM Cell41

description:
051816_Cell43-H2
Ski-KO SLAM

source_name: Bone marrow

value: Fetal liver derived HSC - transplanted for 6 months


title: 1W_MRL_injured_rep5

source_name: 1W_MRL_injured_knee joint


title: CRN/PPN1_Mn_r2


title: RIP-Seq PUM2 rep.2

treatment_protocol: RIP-Seq experiments were performed using Magna RIP RNA-Binding Protein Immunoprecipitation Kit (17-700 Merck). Briefly, 100 µl of Magnetic A/G beads were coated with 12 µg anti-PUM1 antibody, anti-PUM2 antibody or IgG fraction from non-immunized goat serum  for 45 min at RT, in Magna RIP Wash Buffer. Cells were washed twice with ice-cold PBS and subject to UV cross-linking at 254 nm on HEROLAB CL-1 Crosslinker for 30 seconds (0.015 J). For one RIP-Seq reaction 2-3x10^6 cells were lysed in 500 µl Magna RIP Lysis Buffer, for 30 min, at 4oC. Lysates were centrifuged and the supernatant was mixed with antibody pre-coated beads suspended in washing buffer supplemented with protease and RNase inhibitors. RIP reaction was held for 3 h at 4 oC on rotator in the final volume of 1ml. Then magnetic-beads were washed 5x with Magna RIP Washing Buffer followed by a treatment with Proteinase K at  55 oC for 30 minutes and RNA isolation.

value: anti-PUM2 (K-14, sc-31535 Santa Cruz Biotechnology)


title: RIP-Seq PUM2 rep.3


title: CRN/PPN1_ctr_r1

value: 2% glucose, 2% peptone , 1% yeast extract, 14 mM KH2PO4


title: Ski-KO SLAM Cell40

description:
051816_Cell42-G2
Ski-KO SLAM


title: CRN_Mn_r1

source_name: CRN_Mn_yeast cells

value: CRN,MATa ade2 his3 ura3 ppn1delta::CgTRP1

value: WT


title: 1W_MRL_injured_rep4

value: Injured

value: 1-week post-injury


title: RIP-Seq PUM2 rep.1


title: CRN_Mn_r2


title: 1W_MRL_injured_rep3

value: 10 Weeks


title: RIP-Seq PUM1 rep.3

value: anti-PUM1 (S-19, sc-65188 Santa Cruz Biotechnology)


title: CRN_ctr_r2

source_name: CRN_ctr_yeast cells


title: RIP-Seq PUM1 rep.2


title: 1W_MRL_injured_rep2

value: Knee joints


title: Ski-KO SLAM Cell39

description:
051816_Cell41-F2
Ski-KO SLAM

value: Ski-KO


title: Ski-KO SLAM Cell38

description:
051816_Cell40-E2
Ski-KO SLAM


title: Ski-KO SLAM Cell37

description:
051816_Cell39-D2
Ski-KO SLAM


title: Ski-KO SLAM Cell36

description:
051816_Cell38-C2
Ski-KO SLAM


title: RIP-Seq control rep.3

value: IgG fraction from non-immunized goat serum (G9759, Sigma Aldrich)


title: 1D_STR_uninjured_rep5

source_name: 1D_STR_uninjured_knee joint

value: STR/ort

value: highly susceptible

value: 1-day post-injury


title: RIP-Seq PUM1 rep.1


title: Ski-KO SLAM Cell35

description:
051816_Cell37-B2
Ski-KO SLAM


title: 1W_MRL_injured_rep1

value: MRL/MpJ

value: not susceptible


title: CRN_ctr_r1


title: 1D_STR_uninjured_rep4

value: Uninjured


title: RIP-Seq control rep.1


title: RIP-Seq control rep.2


title: Ski-KO SLAM Cell33

description:
051816_Cell35-H1
Ski-KO SLAM

value: Fetal liver derived HSC - transplanted for 6 months


title: 1D_STR_uninjured_rep2


title: Ski-KO SLAM Cell32

description:
051816_Cell34-G1
Ski-KO SLAM


title: Ski-KO SLAM Cell34

description:
051816_Cell36-A2
Ski-KO SLAM


title: 1D_STR_uninjured_rep3


title: 1D_STR_uninjured_rep1


title: Ski-KO SLAM Cell31

description:
051816_Cell33-F1
Ski-KO SLAM


title: 1D_STR_injured_rep5

source_name: 1D_STR_injured_knee joint


title: Ski-KO SLAM Cell30

description:
051816_Cell32-E1
Ski-KO SLAM


title: Ski-KO SLAM Cell29

description:
051816_Cell31-D1
Ski-KO SLAM


title: 1D_STR_injured_rep4


title: Ski-KO SLAM Cell28

description:
051816_Cell30-A1
Ski-KO SLAM


title: 1D_STR_injured_rep3


title: Ski-KO SLAM Cell26

description:
051716_Cell28-D12
Ski-KO SLAM


title: Ski-KO SLAM Cell27

description:
051716_Cell29-G12
Ski-KO SLAM


title: Ski-KO SLAM Cell24

description:
051716_Cell26-A12
Ski-KO SLAM


title: 1D_STR_injured_rep1


title: 1D_BL6_uninjured_rep5

source_name: 1D_BL6_uninjured_knee joint

value: moderately susceptible


title: 1D_STR_injured_rep2


title: Ski-KO SLAM Cell25

description:
051716_Cell27-B12
Ski-KO SLAM


title: 1D_BL6_uninjured_rep2


title: 1D_BL6_uninjured_rep3


title: Ski-KO SLAM Cell23

description:
051716_Cell25-H11
Ski-KO SLAM


title: 1D_BL6_uninjured_rep1


title: Ski-KO SLAM Cell22

description:
051716_Cell24-C11
Ski-KO SLAM


title: UVPAPC_3

type: RNA

city: Vienna

first: Marie-Sophie

last: Narzt

address: Lazarettgasse 14

department: Dermatology

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187

label: Biotin

source_name: human primary keratinocytes exposed to UV-PAPC, 7h

label_protocol: 100ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara, CA)

growth_protocol: human neonatal keratinocytes were grown in KGM-2

extract_protocol: RNA was extracted with TriFast Reagent (VWR International, Radnor, PA) and subsequent RNA cleanup and concentration was performed using the Rneasy MinElure Cleanup Kit (Qiagen, Venlo, Netherlands)

treatment_protocol: human neonatal keratinocytes were treated with 40J/cm² UVA-1, with 40J/cm² UVA-1 plus a UVFilter solved in PBS, with the UVFilter solved in PBS alone, with 25µg/ml UV-PAPC or sham treated. RNA was isolated 7h post stress treatment.

tag: developmental stage

value: neonatal

value: keratinocytes

tag: gender

value: male


title: UVPAPC_2


title: UVA+UVFilter_3

source_name: human primary keratinocytes irradiated with 40J/cm² UVA-1 in the presence of a UVA Filter, 7h


title: 1D_BL6_uninjured_rep4


title: UVFilter_3

source_name: human primary keratinocytes supplemented with a UVA Filter, 7h


title: 1D_BL6_injured_rep5

source_name: 1D_BL6_injured_knee joint

value: Injured


title: UVA+UVFilter_1


title: UVFilter_2


title: UVFilter_1


title: UVA_2

source_name: human primary keratinocytes irradiated with 40J/cm² UVA-1, 7h


title: Ski-KO SLAM Cell20

description:
051716_Cell22-G10
Ski-KO SLAM


title: Ski-KO SLAM Cell21

description:
051716_Cell23-B11
Ski-KO SLAM


title: 1D_BL6_injured_rep4

value: 10 Weeks


title: ctrl_1

source_name: human primary keratinocytes sham treated, 7h


title: UVA+UVFilter_2


title: ctrl_2


title: 1D_BL6_injured_rep3


title: Ski-KO SLAM Cell18

description:
051716_Cell20-D9
Ski-KO SLAM


title: 1D_BL6_injured_rep2


title: ctrl_3


title: UVA_1


title: Ski-KO SLAM Cell17

description:
051716_Cell19-G7
Ski-KO SLAM


title: Ski-KO SLAM Cell19

description:
051716_Cell21-E10
Ski-KO SLAM


title: UVPAPC_1


title: Ski-KO SLAM Cell15

description:
051716_Cell16-H6
Ski-KO SLAM


title: 1D_MRL_uninjured_rep5

source_name: 1D_MRL_uninjured_knee joint


title: 1D_MRL_uninjured_rep4


title: UVA_3


title: 1D_MRL_uninjured_rep3


title: Ski-KO SLAM Cell14

description:
051716_Cell15-F6
Ski-KO SLAM


title: 1D_MRL_uninjured_rep2


title: Ski-KO SLAM Cell12

description:
051716_Cell13-D6
Ski-KO SLAM


title: 1D_MRL_uninjured_rep1


title: MCF-10A/H cells_serum-starved_96 hr_rep1

city: Shanghai

first: Xue-Ling

last: Liu

address: 555 Zuchongzhi Road

department: Shanghai Institute of Materia Medica

country: China

institute: University of Chinese Academy of Sciences

description: Gene expression of MCF-10A/H cells cultured in serum-depleted medium for 96 hours

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was hybridizated at 45°C  overnight in 2x GEx Hyb Buffer and 25% formamide following the manufacturers instructions.  After hybridization, microarrays were washed 5 minutes at 42°C with solution containing 0.2% SDS and 2x SSC and 5 minutes at room temperature with 2x SSC, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting .

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCF-10A cells, 96hr, serum-depleted medium, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 5 ug RNA using the Cy3-dCTP (GE healthcare Cat. No. PA53021) according to the manufacturer's instructions, followed by PCR NucleoSpinExtract (MACHEREY-NAGEL, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The nutrient-sufficient culture was DMEM/F12 (GIBCO, Grand Island, NY, USA) supplemented with 5% horse serum (Invitrogen, Carlsbad, CA, USA), 20 ng/mL epidermal growth factor, 10 μg/mL insulin, 0.5 μg/mL hydrocortisone, 100 ng/mL cholera toxin (Sigma-Aldrich, St. Louis, MO, USA). Cells were cultured at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Cells were homogenized in Trizol (Life Technologies, Gaithersburg, MD, USA) and total RNA was extracted using the NucleoSpin® RNA clean-up Kit (MACHEREY-NAGEL, Germany) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with Formaldehyde modified electrophoresis.

treatment_protocol: Cells were cultured in nutrient-sufficient or serum-depleted medium for 96 hours.

tag: cell lines

value: MCF-10A/H cells

tag: culture medium

value: serum-depleted medium


title: 1D_MRL_injured_rep5

source_name: 1D_MRL_injured_knee joint

value: Knee joints


title: MCF-10A/H cells_serum-starved_96 hr_rep3

source_name: MCF-10A cells, 96hr, serum-depleted medium, replicate 3


title: MCF-10A/H cells_ nutrient-sufficient_96 hr_rep3

description: Gene expression of MCF-10A/H cells cultured in nutrient-sufficient medium for 96 hours

source_name: MCF-10A cells, 96hr, nutrient-sufficient medium, replicate 3

value: nutrient-sufficient medium


title: MCF-10A/H cells_ nutrient-sufficient_96 hr_rep2

source_name: MCF-10A/H cells, 96hr, nutrient-sufficient medium, replicate 2


title: 1D_MRL_injured_rep4


title: Larvae_WT_rep2

city: Tokyo

first: Shigeharu

last: Kinoshita

state: Bunkyo

address: 1-1-1,Yayoi, Bunkyo, Tokyo, 113-8657 Japan room 251

department: Aquatic Bioscience

country: Japan

institute: The University of Tokyo

description:
All_samples_RPKM_values.txt
WT2_embryo_day3

data_processing:
Illumina Casava1.7 software used for basecalling.
HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference (GRCz10) retrieved from Ensembl database together with the annotation file.
The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM).
Genome_build: GRCz10
Supplementary_files_format_and_content: One tab-delimited text file containing all FPKM values for all Samples.

organism: Danio rerio

source_name: Larvae

extract_protocol:
tissues were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep Kit(Cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.

tag: genotype

value: wild type

value: Larvae

value: 3 days post fertilization


title: Ski-KO SLAM Cell9

description:
051716_Cell10-F5
Ski-KO SLAM

source_name: Bone marrow

value: Ski-KO


title: Larvae_WT_rep1

description:
All_samples_RPKM_values.txt
WT1_embryo_day3


title: MCF-10A/H cells_ nutrient-sufficient_96 hr_rep1

source_name: MCF-10A/H cells, 96hr, nutrient-sufficient medium, replicate 1


title: Ski-KO SLAM Cell13

description:
051716_Cell14-E6
Ski-KO SLAM


title: MCF-10A/H cells_serum-starved_96 hr_rep2

source_name: MCF-10A cells, 96hr, serum-depleted medium, replicate 2


title: 1D_MRL_injured_rep3

value: MRL/MpJ

value: not susceptible

value: 1-day post-injury


title: 400-2

city: GuangZhou

first: Youqin

last: Xu

address: No.1023-1063, Shatai Road South, Baiyun District

institute: Southern Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000002985.6_WBcel235  whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCF_000002985.6_WBcel235
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

organism: Caenorhabditis elegans

source_name: C. elegans RNA

growth_protocol: C. elegans were provided by South China Agricultural University, Guangzhou, Guangdong, China. NGM medium containing 0.3% NaCl, 0.25% peptone, 1.7% agar and 1 M KH2PO4-K2HPO4 solution buffer was used to culture C. elegans according to the standard protocol

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

treatment_protocol: Approximately 1000 age-synchronized young adult hermaphrodites (24 h post the L4 larval stage) were irradiated with 0 Gy, 200 Gy and 400 Gy of X-rays using a 600C/D linear accelerator (Varian, USA).

tag: ir treatment


title: Ski-KO SLAM Cell8

description:
051716_Cell9-E5
Ski-KO SLAM

value: Fetal liver derived HSC - transplanted for 6 months


title: Ski-KO SLAM Cell7

description:
051716_Cell8-D5
Ski-KO SLAM


title: Ski-KO SLAM Cell11

description:
051716_Cell12-C6
Ski-KO SLAM


title: 1D_MRL_injured_rep2


title: Larvae_ACRO_rep1

description:
All_samples_RPKM_values.txt
GH1_embryo_day3

value: Acromegaly zebrafish model


title: Ski-KO SLAM Cell10

description:
051716_Cell11-B6
Ski-KO SLAM


title: 400-1


title: MCF-10A cells_serum-starved_96 hr_rep2

description: Gene expression of MCF-10A cells cultured in serum-depleted medium for 96 hours

value: MCF-10A cells


title: MCF-10A cells_serum-starved_96 hr_rep3


title: 1D_MRL_injured_rep1


title: Ski-KO SLAM Cell6

description:
051716_Cell7-G4
Ski-KO SLAM


title: MCF-10A cells_ nutrient-sufficient_96 hr_rep1

description: Gene expression of MCF-10A cells cultured in nutrient-sufficient medium for 96 hours

source_name: MCF-10A cells, 96hr, nutrient-sufficient medium, replicate 1


title: Muscle_WT_rep3

description:
All_samples_RPKM_values.txt
WT_M6_Muscle

source_name: Muscle

value: Muscle

value: 1-year old


title: MCF-10A cells_serum-starved_96 hr_rep1


title: 200-1


title: 0D_STR_rep4

source_name: 0D_STR_knee joint

value: STR/ort

value: 10 Weeks

value: highly susceptible

value: Uninjured

value: 0-day [before injury]


title: MCF-10A cells_ nutrient-sufficient_96 hr_rep2

source_name: MCF-10A cells, 96hr, nutrient-sufficient medium, replicate 2

value: nutrient-sufficient medium


title: 0-2


title: MCF-10A cells_ nutrient-sufficient_96 hr_rep3


title: Larvae_ACRO_rep2

description:
All_samples_RPKM_values.txt
GH2_embryo_day3

value: Larvae


title: 0D_STR_rep3

value: Knee joints


title: Ski-KO SLAM Cell4

description:
051716_Cell5-C4
Ski-KO SLAM

value: Ski-KO


title: Muscle_WT_rep1

description:
All_samples_RPKM_values.txt
WT_M4_Muscle

value: wild type


title: 0-1


title: Ski-KO SLAM Cell3

description:
051716_Cell4-F3
Ski-KO SLAM


title: Muscle_ACRO_rep3

description:
All_samples_RPKM_values.txt
GH_M3_Muscle


title: 0D_STR_rep1


title: 200-2


title: Ski-KO SLAM Cell2

description:
051716_Cell2-C2
Ski-KO SLAM


title: 0D_STR_rep2


title: Muscle_ACRO_rep2

description:
All_samples_RPKM_values.txt
GH_M2_Muscle


title: Ski-KO SLAM Cell1

description:
051716_Cell1-G1
Ski-KO SLAM


title: NRGF-HIS/Fluc_Cohort 2_day0

city: Princeton

first: Alexander

last: Ploss

state: New Jersey

address: Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Raw sequencing reads were filtered by Illumina HiSeq Control Software and only Pass-Filter (PF) reads were used for further analysis.
In the Galaxy platform through Princeton University, single-end short reads were mapped to the human reference (version GRCh38) and the murine reference (version GRCm38) using TopHat and Bowtie 2 with default parameters and read groups specified. Only counts from uniquely mapped reads were used in the DESeq 2 analyses.
Counts were generated by htseq-count version 0.6.1galaxy1 run on a Galaxy installation, downloaded, and read into R version 3.3.1 (2016-06-21) using scripts run in RStudio version 0.99.489. The htseq count data was loaded into R and the DESeq2 (Galaxy Version 2.11.38) utilized, capturing factors for cohort, day, and batch, with the sampling day as the experimental design.
We set up the experimental design for the contrast we were interested in (day 0 versus day 11) and normalized log2 transformed transcript counts within DESeq2. Differential gene expression were determined for each group of mice (NRG-HIS, NRGF-HIS/Flt3LG or NRGF-HIS/Fluc) using the standard DESeq2 filters and nbinomWaldTest.
Genome_build: GRCh38
Supplementary_files_format_and_content: Results were extracted from the DESeq2 analysis as txt file and annotated using Bioconductor’s AnnotationDbi (version 1.32.3) and org.Hs.eg.db packages (version 3.2.3).

source_name: human peripheral blood mononuclear cells

extract_protocol:
Human CD45+ cells were purified from humanized mouse blood using the human CD45+ cells enrichment kit (Stem Cell Technologies, Vancouver, British Columbia, Canada). Total RNA was then extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany).
Sequencing libraries were made from the amplified cDNA samples using the Nextera kit (Illumina, San Diego, CA, USA), assigning a unique barcode to each of the libraries to be sequenced together.

treatment_protocol: NRG-HIS were infected with 1e6 pfu of YFV-17D. NRGF-HIS/Fluc were injected with 10e11 pfu of adenoviral particles expressing the firefly luciferase prior infection with 1e6 pfu of YFV-17D. NRGF-HIS/Ft3LG were injected with 10e10 pfu of adenoviral particles expressing theFlt3LG prior infection with 1e6 pfu of YFV-17D.

tag: mouse strain

value: NRGF

value: blood

tag: human cd45+ purification method

tag: time of extraction post yfv-17d infection

value: day 0


title: NRGF-HIS/Fluc_Cohort 2_day11

value: human CD45+ cells enrichment kit (Stem Cell Technologies, Vancouver, British Columbia, Canada)

value: day 11


title: Ski-KO SLAM Cell5

description:
051716_Cell6-E4
Ski-KO SLAM

tag: strain

tag: cell type

value: Fetal liver derived HSC - transplanted for 6 months

tag: genotype/variation


title: Muscle_ACRO_rep1

description:
All_samples_RPKM_values.txt
GH_M1_Muscle

value: Acromegaly zebrafish model

tag: tissue

value: Muscle

tag: age

value: 1-year old


title: NRGF-HIS/Fluc_Cohort 1_day11


title: Liver_WT_rep3

description:
All_samples_RPKM_values.txt
WT_L6_liver

source_name: Liver

value: Liver


title: 0D_BL6_rep2

source_name: 0D_BL6_knee joint

value: 10 Weeks

tag: susceptibility to ptoa

value: moderately susceptible

tag: treatment

value: Uninjured

tag: sample collection


title: 0D_BL6_rep3

value: 0-day [before injury]

tag: experimental batch


title: Muscle_WT_rep2

description:
All_samples_RPKM_values.txt
WT_M5_Muscle


title: Liver_WT_rep2

description:
All_samples_RPKM_values.txt
WT_L5_liver


title: 0D_BL6_rep1

value: Knee joints


title: Liver_WT_rep1

description:
All_samples_RPKM_values.txt
WT_L4_liver


title: NRGF-HIS/Flt3LG_Cohort 3_day0


title: NRGF-HIS/Flt3LG_Cohort 3_day11


title: 0D_BL6_rep4


title: 0D_MRL_rep3

source_name: 0D_MRL_knee joint

value: MRL/MpJ

value: not susceptible


title: FVB_D300_F1_4

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

data_processing:
Base-calling (HiSeq Control Software 2.2.58, RTA 1.18.64.0, CASAVA-1.8.2)
RA3 clipped and reads > 18 bp from Fastq files using fastx_clipper
mapping to mm10 using TopHat
differential analysis using CuffDiff
analysis using CummeRbund
genes.count_tracking.txt tracks the summed counts of transcripts sharing each gene_id
http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
Genome_build: mm10

source_name: FVB_D300_F1_CASA extracted sperm from cauda epididymis

growth_protocol: animal core facility of Geneva University under conventional accommodation.

extract_protocol:
TRIZOL
RiboZero, fragmentation, Pyrophosphatase, kinase, TruSeq small RNA

treatment_protocol: Prenatal exposure per os to 300 mg/kg/day of bis(2-ethylhexyl)phthalate (D300) or corn oil vehicle (CTL) was administered to pregnant mice during embryonic days 9th to 19th

value: FVB/N

tag: prenatal exposure

value: DEHP 300mg/kg/day

value: 14 weeks

value: sperm from cauda epididymis


title: FVB_D300_F1_5


title: Liver_ACRO_rep2

description:
All_samples_RPKM_values.txt
GH_L2_liver


title: FVB_D300_F1_1


title: Liver_ACRO_rep3

description:
All_samples_RPKM_values.txt
GH_L3_liver


title: FVB_CTL_F1_5

source_name: FVB_CTL_F1_CASA extracted sperm from cauda epididymis

value: CTL


title: 0D_MRL_rep4


title: NRGF-HIS/Fluc_Cohort 1_day0

value: NRGF

value: blood

value: human CD45+ cells enrichment kit (Stem Cell Technologies, Vancouver, British Columbia, Canada)

value: day 0


title: Liver_ACRO_rep1

description:
All_samples_RPKM_values.txt
GH_L1_liver

value: Acromegaly zebrafish model

value: Liver

value: 1-year old


title: NRGF-HIS/Flt3LG_Cohort 2_day0


title: NRGF-HIS/Flt3LG_Cohort 2_day11

value: day 11


title: NRGF-HIS/Flt3LG_Cohort 1_day11


title: FVB_CTL_F1_4


title: FVB_D300_F1_3


title: Kidney_WT_rep2

description:
All_samples_RPKM_values.txt
WT_K6_Kidney

source_name: Kidney

value: wild type

value: Kidney


title: NRGF-HIS/Flt3LG_Cohort 1_day0


title: 0D_MRL_rep2

value: MRL/MpJ

value: 10 Weeks

value: Knee joints

value: Uninjured

value: 0-day [before injury]


title: FVB_CTL_F1_3

value: FVB/N

value: 14 weeks

value: sperm from cauda epididymis


title: Kidney_ACRO_rep3

description:
All_samples_RPKM_values.txt
GH_K3_Kidney


title: NRG-HIS_Cohort 3_day0

value: NRG

value: blood


title: FVB_D300_F1_2

value: DEHP 300mg/kg/day


title: FVB_CTL_F1_2

value: CTL


title: FVB_CTL_F1_1


title: Kidney_ACRO_rep2

description:
All_samples_RPKM_values.txt
GH_K2_Kidney

value: Acromegaly zebrafish model


title: 0D_MRL_rep1

value: not susceptible


title: NRG-HIS_Cohort 2_day11

value: human CD45+ cells enrichment kit (Stem Cell Technologies, Vancouver, British Columbia, Canada)

value: day 11


title: C57_D300_F2_5

source_name: C57_D300_F2_CASA extracted sperm from cauda epididymis

value: second generation after prenatal exposure to DEHP


title: Kidney_ACRO_rep1

description:
All_samples_RPKM_values.txt
GH_K1_Kidney

value: Kidney

value: 1-year old


title: NRG-HIS_Cohort 2_day0

value: day 0


title: Brain_WT_rep2

description:
All_samples_RPKM_values.txt
WT_B5_Brain

source_name: Brain

value: wild type

value: Brain


title: C57_D300_F2_4


title: C57_D300_F2_3


title: NRG-HIS_Cohort 1_day0


title: Brain_WT_rep1

description:
All_samples_RPKM_values.txt
WT_B4_Brain


title: Brain_ACRO_rep3

description:
All_samples_RPKM_values.txt
GH_B3_Brain


title: NRG-HIS_Cohort 1_day11


title: NRG-HIS_Cohort 3_day11


title: C57_D300_F2_1


title: Brain_ACRO_rep2

description:
All_samples_RPKM_values.txt
GH_B2_Brain


title: C57_D300_F2_2


title: Brain_ACRO_rep1

description:
All_samples_RPKM_values.txt
GH_B1_Brain


title: C57_CTL_F1_3 [re-analysis]

source_name: C57_CTL_F1_CASA extracted sperm from cauda epididymis


title: 0503EX_combined

city: Wuhan City

first: Fan

last: Wu

address: Bayi Road No. 299

institute: Wuhan Univwesity

data_processing:
For pull-down data, raw fastq reads were trimmed by cutadapt (v1.14) to remove adapters and mapped to the reference genome GRCm38.p5 and GRCh38.p7 using Bowtie2 (v2.2.9), respectively. Reads with mapping quality less than ten were discarded by SAMtools (v1.3.1), HOMER (v4.9.1) was employed for further process, including peak calling, annotation, and correlation analysis. Tag directories were created and subjected to peak calling in factor mode. Only peaks occuring across replicates were retained for further analysis (fold change cutoff: 5).
Genome_build: GRCm38.p5; GRCh38.p7
Supplementary_files_format_and_content: Peak files contain each peak's coordinate range and correspongding peak score, fold change, etc.

source_name: tissues

extract_protocol: under the instruction of ThruPLEX® DNA-seq Kit (Rubicon). Barcode:GAGATTCC

value: mouse hippocampus


title: C57_CTL_F1_4 [re-analysis]

value: 14 weeks


title: C57_CTL_F1_5 [re-analysis]

value: sperm from cauda epididymis


title: C57_CTL_F1_2 [re-analysis]


title: 0503COn_combined

extract_protocol: under the instruction of ThruPLEX® DNA-seq Kit (Rubicon). Barcode:ATTCAGAA


title: Brain_WT_rep3

description:
All_samples_RPKM_values.txt
WT_B6_Brain


title: C57_CTL_F1_1 [re-analysis]


title: C57_D300_F1_4 [re-analysis]

source_name: C57_D300_F1_CASA extracted sperm from cauda epididymis


title: C57_D300_F1_2 [re-analysis]


title: Human PBMCs treated with PHA (10 μg.ml-1) replicate 3

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

hyb_protocol: The purified total RNA was amplified and labeled, and the microarray analysis was then performed overnight using Agilent Human and Monkey Whole Genome GeneChips (Agilent, Palo Alto, CA).

scan_protocol: the array data were analyzed using Agilent Feature Extraction software.

data_processing: After normalization of the raw data, probes with intensities <400 were removed from the subsequent analysis using Significance Analysis of Microarray (SAM) software. The differentially expressed genes (DEGs) were identified as those having an adjusted q-value of <0.05 and an average fold-change difference of >1.5.

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with PHA ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3

label_protocol: not provided

growth_protocol: Whole heparinized human blood was donated by 3 healthy adult male volunteers of the NIFDC with signed informed consent. The human PBMCs were isolated by Ficoll-Hypaque density centrifugation (Histopaque LTS1119 and LTS1077, Sigma, USA).  A relative centrifugal force of 2000 rpm was used for 30 minutes to separate the PBMCs. The PBMCs were washed twice in Hank’s and re-suspended at a final concentration of 1×10^6 cells/ml in culture medium (RPMI1640, GIBCO, USA) supplemented with 10% fetal calf serum. All experiments using the cultured cells were set up in triplicate.

extract_protocol: The total RNA was extracted from the PBMCs using Trizol reagent (Invitrogen Company) according to the manufacturer’s instructions. The purity of the RNA in each sample was assessed spectrophotometerically at 260 and 280 nm (NanoDrop Technologies), and the RNA integrity was assessed using formaldehyde agarose gel electrophoresis.

treatment_protocol: The PBMCs (1×10^6 cells/ml) obtained from the cynomolgus monkeys or the human donors were treated with PHA (2 μg.ml-1 or 10 μg.ml-1) or LPS (2 μg.ml-1 or 10 μg.ml-1) and incubated at 37 °C for 3 days. Cells cultured under similar conditions without any stimulation served as the negative control.

tag: gender

value: male

value: peripheral blood

value: mononuclear

tag: process

value: test

tag: stimulation

value: PHA

source_name: The PBMCs cultured under similar conditions without any stimulation served as the negative control, replicate 3

value: control


title: Human PBMCs without replicate 3


title: C57_D300_F1_1 [re-analysis]

value: DEHP 300mg/kg/day


title: C57_D300_F1_5 [re-analysis]


title: Ski-KO SLAM Cell16

description:
051716_Cell18-C7
Ski-KO SLAM

source_name: Bone marrow

value: Fetal liver derived HSC - transplanted for 6 months

value: Ski-KO


title: Human PBMCs treated with LPS (2 μg.ml-1) replicate 3

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with LPS ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3

value: LPS


title: C57_D300_F1_3 [re-analysis]


title: Bat5_R6

first: Nancy

last: Ratner

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450:FS450_0004.

scan_protocol: GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)

data_processing: Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R. A custom CDF was used (Brainarray, Mm430_Mm_ENTREZG).

label: biotin

source_name: nerve

label_protocol: We generated biotinylated cDNA probes from a single round of DNA displacement synthesis amplification of 20ng total RNA (Ovation Biotin RNA Amplification and Labelling System; NuGen) for hybridization to the whole-genome Affymetrix GeneChips using the Affymetrix protocol.

growth_protocol: Nf1fl/fl: mixed background, with mainly C57BL/6 and small percent of 129. DhhCre;Nf1fl/fl: Mixed background, with mainly C57BL/6 and small percent of 129 and FVBN. EGFR/EGFR: mixed background, with mainly C57BL/6 and small portion of FVBN.

extract_protocol: Total RNA was extracted by the phenol/chloroform method and purified using the Qiagen microRNA isolation kit (Qiagen, Inc. Valencia, CA).

treatment_protocol: P30: 30 days of age. P60: 60 days of age.

tag: batch

value: batch 5

tag: sample type

value: 2-month nerve

value: nerve

value: Nf1 fl/fl


title: Bat5_1_MouseRef5

value: Mouse reference sample

value: Batch Reference


title: Human PBMCs treated with PHA (2 μg.ml-1) replicate 3

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with PHA ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3


title: Human PBMCs treated with LPS (10 μg.ml-1) replicate 3

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with LPS ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3


title: Bat3_6_I23

value: batch 3

value: 1-month nerve

value: Nf1 fl/fl; DhhCre


title: Bat5_R5


title: Bat3_3_I45

value: EGFR/EGFR


title: Human PBMCs treated with LPS (10 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with LPS ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2

value: male

value: peripheral blood

value: mononuclear

value: test

source_name: The PBMCs cultured under similar conditions without any stimulation served as the negative control, replicate 2


title: Human PBMCs treated with LPS (10 μg.ml-1) replicate 1

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with LPS ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1

source_name: The PBMCs cultured under similar conditions without any stimulation served as the negative control, replicate 1

value: control


title: Human PBMCs treated with PHA (2 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with PHA ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2

value: PHA


title: Human PBMCs treated with PHA (10 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with PHA ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2


title: Human PBMCs cultured without any stimulation replicate 2


title: Bat3_7_I20


title: NRG-HIS_ID788_Day40_CD33+

data_processing:
for each NextSeq sequencing run, raw sequencing data was converted to demultiplexed FASTQ files using bcl2fastq2 (7.17.1.14) based on Nextera N700 indices corresponding to individual samples/arrays.
Reads were then aligned simultaneously to both mm10 and hg19 genomes using the Galaxy portal maintained by the Broad Institute for Drop-Seq alignment using standard settings of the STAR aligner.
Individual reads were tagged according to the 12-bp barcode sequenced and the 8-bp UMI contained in Read 1 of each fragment.
Following alignment, reads were binned onto 12-bp cell barcodes and collapsed by their 8-bp UMI. Digital gene expression matrices for each sample were obtained from quality filtered and mapped reads
Genome_build: mm10 - hg19
Supplementary_files_format_and_content: UMI-collapsed data was utilized as input into R for further analysis. Processed data were extracted as a global, single

source_name: human splenic CD33+ cells

extract_protocol:
Frozen splenocytes from NFA2-HIS/Flt3LG and NRG-HIS mice were thawed and stained with antibodies for anti-human CD33 or CD45. Cell populations that were either anti-human CD33+ or anti-human CD45+ were sorted into RPMI + 10% FBS. Single cells from each sort gate and each animal were loaded onto prepared Seq-Well arrays. Briefly, 10,000 single cells from each sort gate were loaded onto one array containing 86,000 barcoded mRNA capture beads. Cells and beads were co-confined in microwells on the array, and a polycarbonate membrane sealed individual wells to allow for isolated single-cell lysis and transcript hybridization prior to bead recovery for reverse transcription.
each library was treated with Exonuclease I to remove excess primers, and PCR amplification with KAPA Hifi PCR Mastermix (Thermo Scientific, Waltham, MA, USA) to generate final cDNA libraries. Libraries were then constructed using the Nextera XT DNA tagmentation method (Illumina, San Diego, CA, USA). Tagmented and amplified libraries were subsequently purified and sequenced using an Illumina 75 cycle NextSeq500/550v2 kit (paired end reads, custom Read 1 primer, see Gierahn et al Nature Methods 2017, 20bp Cell Barcode and UMI, 50 bp DGE).
scRNA-seq - SeqWell (Gierahn et al. Nature Methods. 2017)

treatment_protocol: NRG-HIS and NFA2-HIS/Flt3LG mice were infected with YFV-17D (1e6 pfu) and total splenocytes were collected and frozen 40 days post infection.

tag: mouse strain

value: NRG

tag: mouse id

value: Spleen

tag: hucell population

value: FACS-sorted human CD33+

value: day 40


title: NFA2-HIS/Flt3LG_ID244_Day40_CD33+

tag: time of extraction post yfv-17d infection


title: Human PBMCs treated with LPS (2 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with LPS ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2

tag: cell type

value: LPS


title: Human PBMCs treated with LPS (2 μg.ml-1) replicate 1

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with LPS ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1

tag: tissue


title: Bo3 [miRNA-Seq]

city: Alar

first: Shaowei

last: Qin

state: Xinjiang

address: Hongqiao Road 705

department: College of Life Sciences

institute: Tarim University

description: small RNA sequencing

data_processing:
The known miRNAs were identified by aligning against miRBase v.21 database (http://www.mirbase.org/,mismatch=0)
Unannotated small RNAs were analyzed by mirdeep2 (-c -j -l 18 -m ) to predict novel miRNAs
miRNAs were quantified and normalized to TPM (transcript per million).
Supplementary_files_format_and_content: tab-delimited text files include TPM values and precursor coordinate of novel miRNAs

organism: Populus euphratica

source_name: juvenile broad-ovate leaf

growth_protocol: The juvenile linear,lanceolate,ovate and broad-ovate leaf groups were respectively sampled from 0-3, 4-6, 8-12 and over 20 years old P. euphratica in Alar (81°17′56.52″ E, 40°32′36.90″ N), Xinjiang province, China at April 2017

extract_protocol:
Total RNA was extracted using the mirVanamiRNA Isolation Kit (Ambion) following the manufacturer’s protocol
The small RNA libraries were constructed using RNA extracted from juvenile linear,lanceolate,ovate and broad-ovate leaves.

tag: leaf shape

value: broad-ovate

tag: tree age

value: over 20 years


title: Bat3_1_MouseRef3

value: batch 3

value: Mouse reference sample

value: nerve

tag: genotype/variation

value: Batch Reference


title: Bat3_10_I29

value: 2-month nerve

value: Nf1 fl/fl; DhhCre


title: Bat2_7_I28

value: batch 2


title: Human PBMCs treated with PHA (10 μg.ml-1) replicate 1

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with PHA ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1

value: male

value: peripheral blood

value: mononuclear

value: test


title: Bat2_8_I32

value: Nf1 fl/fl


title: NFA2-HIS/Flt3LG_ID784_Day40_CD45+

source_name: human splenic CD45+ cells

value: Spleen

value: FACS-sorted human CD45+


title: Bat3_4_I50

value: EGFR/EGFR


title: NRG-HIS_ID305_Day40_CD33+

value: NRG

value: FACS-sorted human CD33+

value: day 40


title: Human PBMCs treated with PHA (2 μg.ml-1) replicate 1

source_name: The PBMCs (1×106 cells/ml) obtained from the human donors were treated with PHA ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1

value: PHA

value: control


title: NFA2-HIS/Flt3LG_ID784_Day40_CD33+


title: Bo1 [miRNA-Seq]

description: small RNA sequencing

value: broad-ovate

value: over 20 years


title: Human PBMCs without stimulation replicate 1


title: NFA2-HIS/Flt3LG_ID244_Day40_CD45+


title: Bat2_6_I22

value: 1-month nerve

value: nerve

value: Nf1 fl/fl; DhhCre


title: NRG-HIS_ID788_Day40_CD45+


title: Ov3 [miRNA-Seq]

description: small RNA sequencing

source_name: juvenile ovate leaf

value: ovate

value: 8-12 years


title: PBMC_HEALTHY_Subject8

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

hyb_protocol: Labeled cRNA was then hybridized for 17 hours at 65°C on Whole Human Genome Microarray 4x44 K slides, (Agilent Technologies, Santa Clara, CA). After hybridization the slides were washed according to manufacturer’s protocols.

scan_protocol: The slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies).

data_processing:
Data extraction was performed using Agilent Feature Extraction software.
A p-value cut-off of 0.05 and a fold-change cut-off of 2,5 were applied to identify differentially expressed genes able to discriminate between the study groups.

source_name: PBMC_healthy subject

label_protocol: Labeled cRNA was generated using the Low Input Quick Amp Labeling (LIQA) kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: Twenty ml of whole blood were harvested from all patients at the time of enrolment. PBMCs were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden). Total RNA was extracted automatically and qualitatively and quantitatively analyzed through Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only samples with good quality characterized by RIN> 8 were used in the microarray experiment.

value: Male

tag: age


title: Bo2 [miRNA-Seq]

description: small RNA sequencing


title: PBMC_HEALTHY_Subject7

value: Female


title: 1D_BL6_injured_rep1

data_processing:
Sequenced reads were mapped to mouse genome mm10 using TopHat (version 2.0.11)
After read mapping, ‘featureCounts’ from Rsubread package (version 1.22.2) was used to generate gene-wise read counts.
Genes were filtered from downstream analysis if they did not have a CPM (counts per million mapped fragments) value of at least 2 in at least five libraries
RUVseq was used to normalize the data using 25 housekeeping genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 CPM values for each sample .

source_name: 1D_BL6_injured_knee joint

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (QIAGEN Inc, Germantown, MD, USA) according to manufacturer’s protocol.
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq Sample Preparation kit (Illumina Inc, Hayward, CA, USA)  according to manufacturer’s protocol.

tag: strain

value: 10 Weeks

tag: susceptibility to ptoa

value: moderately susceptible

value: Knee joints

tag: treatment

value: Injured

tag: sample collection

value: 1-day post-injury

tag: experimental batch


title: NRG-HIS_ID305_Day40_CD45+

value: NRG

value: Spleen

value: FACS-sorted human CD45+

value: day 40


title: Ov1 [miRNA-Seq]

description: small RNA sequencing


title: Bat2_11_I53

city: Cincinnati

source_name: nerve

tag: batch

value: batch 2

value: 2-month nerve

value: EGFR/EGFR


title: La3 [miRNA-Seq]

description: small RNA sequencing

source_name: juvenile lanceolate leaf

value: lanceolate

value: 4-6 years


title: PBMC_HEALTHY_Subject6

tag: gender


title: La2 [miRNA-Seq]

description: small RNA sequencing


title: scID-seq measurement of keratinocytes FACSsorted on ITGB1 levels

city: Nijmegen

first: Jessie

middle: van

last: Buggenum

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

description: Antibody specific DNA-tag

data_processing:
bcl2fastq conversion v2.16.0.10.
Split reads from fastq files using R-package IDseq version 1.0.0.
Remove duplicate reads and count unique barcodes.
Match barcode sequences to antibody and sample.
Supplementary_files_format_and_content: the txt files are the index files used to match DNA-barcode sequences to antibody and samples for that specific experiment; The .tsv files contain the barcode counts with matched antibody and sample specific information.

source_name: primary human keratinocytes

growth_protocol: Epidermal stem cells were cultured in Keratinocyte Serum Free Medium (KSFM) supplemented with 0.2 ng/ml Epidermal Growth Factor (EGF) and 30 μg/ml bovine pituitary extract from Life Technology until 70% confluency

extract_protocol:
Stained cells were sorted single cell with the BD FACSAria SORP flow cytometer (BD biosciences) in 96 well PCR plates containing release buffer (10 mM DTT in 15mM Tris, pH 8.8) and Vapor-lock (Qiagen)
In 96 well plates sorted with cells, a pre-amplification PCR was done to amplify all Antibody-DNA-barcodes per well. Then a overhang PCR was done to add well specific barcodes. All wells per plate were merged and another overhang PCR was done to add Ilumina adaptor and index sequences

tag: cell line

value: KNP

value: primary human keratinocytes

tag: pre-sort antibody

value: ITGB1 (DSHB, P4C10)


title: scID-seq experiments with technical properties of Ab-barcode measurements

description: Antibody specific DNA-tag


title: MQ controls CELseq

description: Two sequencing runs were performed to obtain a larger number of total reads per sample. FASTQ files were generated using CELseq2 demultiplexing approach. Counts from each sequencing run are indicated as replicates in the counts table and can be summed for further analysis.

data_processing:
Read1 and Read2 where swapped to allow compatibility with CELseq2 pipeline
Reads were matched to individual cells using the demultiplexing function of the CELseq2 pipeline
Transcripts were Mapped and UMI corrected using standard settings of the CELseq2 pipeline - Reads were trimmed to 50 bases before mapping to UCSChg38 and hereafter matched to the gencode.v25.basic.annotation transcriptome
Counttable contains merged data from sequencing run 1 and 2 from the same sample
Genome_build: UCSChg38
Supplementary_files_format_and_content: The .csv file contains full count dataset, annotated with gene names and detailed sample information

source_name: Keratinocytes

growth_protocol: Primary human foreskin keratinocytes were cultured on keratinocyte serum free medium (supplemented with 0,2 ng/mL EGF and 30 ug/mL BPE) in a 6-wells plate prior to treatment and grown for 2-3 days

extract_protocol:
RNA was isolated using zymo Quick-RNA purification kit
Libraries were prepared according to slightly modified CEL-seq2 protocol, and sequenced twice (sequencing run 1 and 2)

treatment_protocol: Cells were treated with indicated treatments for 48 (stimulation) or 96 (inhibition) hours

value: Primary human foreskin keratinocytes

tag: hours of treatment

tag: number of biological replicates


title: Kidney_WT_rep1

description:
All_samples_RPKM_values.txt
WT_K4_Kidney

source_name: Kidney

tag: genotype

value: wild type

value: Kidney

value: 1-year old


title: La1 [miRNA-Seq]

description: small RNA sequencing


title: AG1478 + DMHI 96 hours

tag: cell type

tag: treated with

value: AG1478 + DMHI


title: Bat2_5_I19

tag: sample type

value: 1-month nerve

tag: tissue

value: nerve

value: Nf1 fl/fl


title: Li3 [miRNA-Seq]

description: small RNA sequencing

source_name: juvenile linear leaf

tag: leaf shape

value: linear

tag: tree age

value: 0-3 years


title: AG1478 96 hours


title: Bat1_7_I18

value: batch 1

tag: genotype/variation


title: PBMC_HEALTHY_Subject5

value: Male

tag: age


title: Li2 [miRNA-Seq]

description: small RNA sequencing


title: DMHI 96 hours

value: DMHI


title: PBMC_HEALTHY_Subject2

value: Female


title: Cynomolgus monkey PBMCs treated with LPS (10 μg.ml-1) replicate 3

scan_protocol: not provided the array data were analyzed using Agilent Feature Extraction software.

organism: Macaca fascicularis

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with LPS ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3

growth_protocol: Whole heparinized cynomolgus monkey blood was obtained from 3 apparently healthy 2.5-year-old cynomolgus monkeys. The monkey PBMCs were isolated by Ficoll-Hypaque density centrifugation (Histopaque LTS1079, Sigma, USA). All procedures were performed in accordance with the Guide for the Care and Use of Laboratory Animals of NCSED, China. A relative centrifugal force of 2000 rpm was used for 30 minutes to separate the PBMCs. The PBMCs were washed twice in Hank’s and re-suspended at a final concentration of 1×10^6 cells/ml in culture medium (RPMI1640, GIBCO, USA) supplemented with 10% fetal calf serum. All experiments using the cultured cells were set up in triplicate.

value: peripheral blood

value: mononuclear

tag: process

value: test

tag: stimulation

value: LPS

source_name: The PBMCs cultured under similar conditions without any stimulation served as the negative control, replicate 3

value: control


title: Li1 [miRNA-Seq]

description: small RNA sequencing


title: Vehicle 96 hours

value: Primary human foreskin keratinocytes

value: Vehicle


title: Bat1_9_I21

tag: batch

value: Nf1 fl/fl; DhhCre


title: PBMC_MALIGN_Patient 7

tag: gender


title: Bo3

description: strand-specific RNA sequencing

data_processing:
The clean reads obtained from sequencing were compared with P. euphratica genome (GCF_000495115.1_ PopEup_1.0_genomic.fna.gz, https://www.ncbi.nlm.nih.gov/genome/13265) by TopHat2
The clean reads were further compared with P. euphratica transcriptome to calculate the expressive abundance of every transcripts by bowtie2 (-k30 -t) and eXpress (---rf-stranded).
The transcripts were rebuilt based on probabilistic model using cufflinks (--no-update-check--library-type fr-firststrand).
All the transcripts were compared with P. euphratica transcriptome to remove known code transcripts and locus. Then these transcripts shorter than 200 bp or exons less than 2 were also removed. Remainder transcripts were analyzed with CPC (default), CNCI (-m pl), Pfam (-e_seq  0.001) and PLEK (default) to remove code transcripts, and lncRNAs of P. euphratica were obtained at last.
The expressive abundance of mRNA and lncRNA were quantified as FPKM (Fragments Per kb Per Million Reads)
Based on the sequencing results, the circRNAs were predicted De Novo with CIRI (command: CIRI_v2.0.1pl-Ialn-pe.sam-O CircRNA.gtf-S 100000-F genome.fa-M Mt-A reference.gtf)
The expressive abundance of circRNA was quantified as RPM (spliced reads per millon).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and RPM for each Sample

extract_protocol:
Total RNA was extracted using the mirVanamiRNA Isolation Kit (Ambion) following the manufacturer’s protocol
The strand-specific libraries (dUTP) were constructed using TruSeq Stranded Total RNA LT - (with Ribo-Zero Plant) according to the manufacturer’s instructions

value: broad-ovate

value: over 20 years


title: Bat1_4_I49

value: 2-month nerve

value: nerve

value: EGFR/EGFR


title: Bat2_1_MouseRef2

value: batch 2

value: Mouse reference sample

value: Batch Reference


title: PBMC_MALIGN_Patient 8

value: Male


title: PBMC_HEALTHY_Subject3


title: Cynomolgus monkey PBMCs treated with LPS (2 μg.ml-1) replicate 3

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with LPS ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3

value: peripheral blood


title: Bat1_11_I31

value: batch 1

value: Nf1 fl/fl


title: Bat1_3_I43

value: 1-month nerve


title: Cynomolgus monkey PBMCstreated with PHA (10 μg.ml-1) replicate 3

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with PHA ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3

value: mononuclear

value: test

value: PHA

value: control


title: PBMC_MALIGN_Patient 5


title: Bat1_10_I27

value: Nf1 fl/fl; DhhCre


title: PBMC_HEALTHY_Subject4

value: Female


title: AG1478 + BMP27 48 hours

value: Primary human foreskin keratinocytes


title: PBMC_HEALTHY_Subject1


title: Bo2

description: strand-specific RNA sequencing

source_name: juvenile broad-ovate leaf

value: broad-ovate

value: over 20 years


title: AG1478 48 hours


title: Bat1_1_MouseRef1

value: nerve


title: Bo1

description: strand-specific RNA sequencing


title: PBMC_MALIGN_Patient 6


title: BMP27 48 hours


title: PBMC_MALIGN_Patient 4


title: Ov3

description: strand-specific RNA sequencing

value: ovate

value: 8-12 years


title: PBMC_MALIGN_Patient 3

value: Male


title: Vehicle 48 hours

value: Vehicle


title: H3K4me3_ChIPSeq AG1478 treated

data_processing:
fastq files were aligned to hg19 with Burrows-Wheeler Alignment tool (BWA), and processed with SAMtools to generate BAM files.
Peaks were called using MACS14 peak caller (P-value cut-off of 1 × 10−8)
Genome_build: hg19
Supplementary_files_format_and_content: annotated results of differential peak analysis is provided as txt file

growth_protocol: Primary human foreskin keratinocytes were cultured on keratinocyte serum free medium (supplemented with 0,2 ng/mL EGF and 30 ug/mL BPE) in a 15cm dish (4,5*10^6) prior to treatment and grown for 3 days

extract_protocol:
Cells were crosslinked, harvested and stored at -80 degrees. Then nuclei were isolated, DNA sonicated and ChIP was performed. Then DNA was isolated using qiaquick PCR purification kit.
Libraries were prepared according to the standard KAPA Biosystems kit and DNA was size-selected (300-400bp) with E-Gel® iBase™ Power System (Invitrogen)

treatment_protocol: Cells were treated with AG1478 and BMP27 for 6 hours.

tag: hours of culture

tag: passages

tag: treatment

value: AG1478 and BMP27 treatment

tag: chip antibody

value: H3K4me3 (Abcam8580)


title: Ov2

description: strand-specific RNA sequencing


title: Cynomolgus monkey PBMCs without stimulation replicate 3

value: peripheral blood


title: PBMC_MALIGN_Patient 2


title: H3K4me3_ChIPSeq control


title: Cynomolgus monkey PBMCs treated with LPS (10 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with LPS ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2

value: mononuclear

value: LPS

source_name: The PBMCs cultured under similar conditions without any stimulation served as the negative control, replicate 2


title: Ov1

description: strand-specific RNA sequencing


title: PBMC_POST-TX MALIGN_Patient 8

source_name: PBMC_post kidney transplant malignancies

value: Tacrolimus


title: La3

description: strand-specific RNA sequencing

value: lanceolate

value: 4-6 years


title: Cynomolgus monkey PBMCs treated with LPS (2 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with LPS ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2

value: test

value: control


title: La2

description: strand-specific RNA sequencing


title: Cynomolgus monkey PBMCstreated with PHA (10 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with PHA ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2

value: PHA


title: Cynomolgus monkey PBMCs treated with PHA (2 μg.ml-1) replicate 2

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with PHA ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 2


title: PBMC_MALIGN_Patient 1


title: La1

description: strand-specific RNA sequencing


title: PBMC_POST-TX MALIGN_Patient 7

value: Female


title: Cells_coulture medium_3days, replicate 2

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

country: Taiwan

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

description: Gene expression after 3 day in K562 cells

hyb_protocol: Hybridization buffer (Agilent Technologies) was added to the labeled mixture to a final volume of 45 uL. The mixture was heated at 100°C for 5 minutes and immediately cooled to 0°C. Each 45 L sample was hybridized onto an Agilent human miRNA Microarray R21 (Agilent Technologies) at 55°C for 20 hours.

scan_protocol: Microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, model G2505C) at 535 nm for Cy3.

data_processing: Feature Extraction (Agilent Technologies) software version 10.7.3.1 was used for image analysis.

source_name: K562 cells, culture medium only, 3 days, replicate 2

label_protocol: Total RNA (0.1 ug) were dephosphorylated and labeled with pCp-Cy3 by Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies)

growth_protocol: K562 cells culture in RPMI-1640 medium

extract_protocol: The total RNAs of treated K562 cells were isolated by using the QIAamp RNA Blood Mini Kit (QIAGEN GmbH, Germany)

treatment_protocol: K562 cells were cultured in medium with or without the presence of IL-23 (20 ng/mL).

tag: cell line


title: Cells_coulture medium_3days, replicate 3

source_name: K562 cells, culture medium only, 3 days, replicate 3


title: Cynomolgus monkey PBMCs without stimulation replicate 2

tag: cell type


title: PBMC_POST-TX MALIGN_Patient 6

value: Cyclosporin


title: Cynomolgus monkey PBMCs treated with PHA (2 μg.ml-1) replicate 3

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with PHA ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 3


title: Li3

description: strand-specific RNA sequencing

value: linear

value: 0-3 years