title: [exon] L18MDP aCD3-aCD28 aIL10R diagnosis-CD subject-232 biological rep-5

description:
subject-ID_232
@52084400978708110317428272788059


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-2001 biological rep-38

status: Public on Aug 01 2020

type: RNA

city: Indianapolis

first: Boyd

last: Steere

state: IN

address: Lilly Corporate Center

department: Immunology

country: USA

institute: Lilly

description:
subject-ID_2001
@52084400978711110317428272788251

hyb_protocol: 5 μg of biotin-labeled cDNA per HTA2 platform standard procedure

scan_protocol: Scanning performed with Affymetrix GeneChip station under default settings followed by CEL file derivation from Affymetrix GeneChip Command Console (AGCC)

data_processing:
Background correction and quantile normalization of the gene expression data obtained from the Affymetrix Human Transcriptome Array 2.0 (HTA2) platform were performed by the RMA method while controlling for batch.  Summarization was performed with RLM.  Annotations were defined by the Affymetrix NetAffx(TM) NA35 release, which is based on the GRCh37 human reference genome. Differential expression at the gene-level was performed using the empirical Bayes method implemented in LIMMA{Ritchie:ef}controlling for donor in the model.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Minimum RNA input was 100ng with a concentration range of 10 ng/μl to 50 ng ng/μl.  Label molecule was biotin.  Amplification performed using standard protocol from Affymetrix WT Express Kit.

growth_protocol: Whole blood was collected into EDTA-containing tubes. PBMC were purified using Ficoll-Paque density gradient purification. The absolute number of cells was determined using a haemocytometer (Marienfeld).

extract_protocol: Total RNA was extracted from cultured cells, using the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s protocol. The RNA yield was determined by quantifying the samples on an Agilent Bioanalyzer.  Only samples with a 28S/18S ratio of 0.8 to 3.0 and a RIN Score of >= 6.0 passed QC metrics and were accepted for analysis.

treatment_protocol: For stimulation assays, 0.5×10^6 to 1×10^6 PBMC were cultured in 200 μl medium in duplicates in round bottom 96-well plates and exposed to ultrapure 200 ng/ml LPS (Enzo Life Sciences; Cat.# ALX-581-008), 200 ng/ml L18MDP (Invivogen) 10 μg/ml anti-IL-10R (Biolegend; clone: 3F9), and/or anti-CD3/anti-CD28 beads (Invitrogen) for 16 hours in complete RPMI with L-glutamine (Sigma) supplemented with 10 % human serum (Sigma; Cat.# H4522), non-essential amino acids (Gibco); 1 mM Sodium-Pyruvate (Gibco) and 100 U/ml penicillin and 10 μg/ml streptomycin (Sigma).

tag: stimulation

tag: diagnosis

value: UC

tag: Sex

value: F

tag: batch

tag: tissue

value: peripheral PBMC


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-1014 biological rep-35

description:
subject-ID_1014
@52084400978327102417428100272910


title: WTCHG_388580_207275

type: SRA

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

country: United Kingdom

institute: Newcastle University

library_source: transcriptomic

data_processing:
Trimmed with Trimmomatic v 0.36
Aligned reads with STAR v 2.4.0 - bases with quality scores below Q10 (inferred base cell accuracy below 90%) were trimmed and reads shorter than 60bp were dropped
Counts were obtained with HTSEQ v 0.6.1
Further processing was performed in R 3.3.3. The cells were filtered based on precentage of ERCC counts (<30%), mitochondrial percentage (<25%), total features (>2500), total counts (>50000)
Genome_build: GRCh38.p7 (GENCODE release 25)
Supplementary_files_format_and_content: csv files with HTSEQ counts
Supplementary_files_format_and_content: BM_CD34_flow_channel_values.csv: Channel values produced when sorting the individual cells for scRNA-Seq.

source_name: bone marrow

growth_protocol: primary cells

extract_protocol: Smart-seq2 and Nextera XT

value: LMPP CD117+

tag: passed cell qc

value: YES


title: [exon] L18MDP aCD3-aCD28 aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978711110317428272788244

value: CD


title: [gene] aIL10R diagnosis-UC subject-447 biological rep-30

description:
subject-ID_447
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value: M


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-1338 biological rep-36

description:
subject-ID_1338
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title: [gene] aIL10R diagnosis-UC subject-531 biological rep-31

description:
subject-ID_531
@52084400978710110317428272788166


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-1628 biological rep-37

description:
subject-ID_1628
@52084400980525112917428617727148


title: [gene] aIL10R diagnosis-UC subject-369 biological rep-28

description:
subject-ID_369
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title: WTCHG_388580_207273


title: [gene] aIL10R diagnosis-UC subject-429 biological rep-29

description:
subject-ID_429
@52084400980524112917428617727103


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-554 biological rep-34

description:
subject-ID_554
@52084400978708110317428272788041


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-531 biological rep-33

description:
subject-ID_531
@52084400978710110317428272788181


title: [gene] aIL10R diagnosis-UC subject-113 biological rep-27

description:
subject-ID_113
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title: WTCHG_388580_206274


title: [gene] aIL10R diagnosis-Other subject-464 biological rep-26

description:
subject-ID_464
@52084400978326102417428100272863

value: Other


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-447 biological rep-32

description:
subject-ID_447
@52084400978326102417428100272817


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-429 biological rep-31

description:
subject-ID_429
@52084400980524112917428617727109


title: [exon] L18MDP aCD3-aCD28 diagnosis-Other subject-464 biological rep-28

description:
subject-ID_464
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title: WTCHG_388580_207274


title: WTCHG_388580_206275


title: WTCHG_388580_208274

value: NO


title: [gene] aIL10R diagnosis-IBDu subject-293 biological rep-25

description:
subject-ID_293
@52084400978329102417428100272999

value: IBDu


title: WTCHG_388580_206273


title: [exon] L18MDP aCD3-aCD28 aIL10R diagnosis-CD subject-243 biological rep-6

description:
subject-ID_243
@52084400973515011718428996209109


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1864 biological rep-25

description:
subject-ID_1864
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title: WTCHG_388580_205275


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-369 biological rep-30

description:
subject-ID_369
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title: WTCHG_388580_205274


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1600 biological rep-23

description:
subject-ID_1600
@52084400980522112917428617726971


title: [gene] aIL10R diagnosis-CD subject-1864 biological rep-23

description:
subject-ID_1864
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title: [exon] L18MDP aCD3-aCD28 diagnosis-IBDu subject-104 biological rep-26

description:
subject-ID_104
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title: WTCHG_388580_205273


title: [exon] L18MDP aCD3-aCD28 diagnosis-IBDu subject-293 biological rep-27

description:
subject-ID_293
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title: WTCHG_388580_204275


title: [exon] L18MDP aCD3-aCD28 diagnosis-UC subject-113 biological rep-29

description:
subject-ID_113
@52084400978330102417428100373104


title: [gene] aIL10R diagnosis-CD subject-1600 biological rep-22

description:
subject-ID_1600
@52084400978709110317428272788094


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1016 biological rep-18

description:
subject-ID_1016
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1838 biological rep-24

description:
subject-ID_1838
@52084400978709110317428272788097


title: [gene] aIL10R diagnosis-CD subject-1253 biological rep-21

description:
subject-ID_1253
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title: [gene] aIL10R diagnosis-CD subject-1180 biological rep-20

description:
subject-ID_1180
@52084400978710110317428272788137


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1180 biological rep-21

description:
subject-ID_1180
@52084400978708110317428272788055


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-792 biological rep-16

description:
subject-ID_792
@52084400978711110317428272788249


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
@52084400978326102417428100272852


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1018 biological rep-19

description:
subject-ID_1018
@52084400980525112917428617727152


title: [gene] aIL10R diagnosis-CD subject-1018 biological rep-19

description:
subject-ID_1018
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title: WTCHG_388580_203275


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-670 biological rep-14

description:
subject-ID_670
@52084400978329102417428100273024


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1253 biological rep-22

description:
subject-ID_1253
@52084400980522112917428617726986


title: [gene] aIL10R diagnosis-CD subject-891 biological rep-18

description:
subject-ID_891
@52084400978709110317428272788082


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
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title: WTCHG_388580_203274


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-558 biological rep-11

description:
subject-ID_558
@52084400980524112917428617727089


title: [gene] aIL10R diagnosis-IBDu subject-104 biological rep-24

description:
subject-ID_104
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-528 biological rep-10

description:
subject-ID_528
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-280 biological rep-6

description:
subject-ID_280
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-643 biological rep-12

description:
subject-ID_643
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-423 biological rep-8

description:
subject-ID_423
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title: WTCHG_388580_204274


title: [gene] aIL10R diagnosis-CD subject-792 biological rep-16

description:
subject-ID_792
@52084400978710110317428272788153


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
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title: WTCHG_388580_203273


title: WTCHG_388580_204273


title: WTCHG_388580_202275


title: [gene] aIL10R diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-1045 biological rep-20

description:
subject-ID_1045
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title: [gene] aIL10R diagnosis-CD subject-670 biological rep-14

description:
subject-ID_670
@52084400978327102417428100272893


title: WTCHG_388580_202274


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
@52084400978711110317428272788216


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
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title: WTCHG_388580_201275


title: [exon] L18MDP diagnosis-UC subject-2031 biological rep-36

description:
subject-ID_2031
@52084400980524112917428617727065


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
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title: [gene] aIL10R diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
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title: WTCHG_388580_202273


title: [gene] aIL10R diagnosis-CD subject-643 biological rep-12

description:
subject-ID_643
@52084400978710110317428272788163


title: [exon] L18MDP diagnosis-UC subject-2001 biological rep-35

description:
subject-ID_2001
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-649 biological rep-13

description:
subject-ID_649
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title: [gene] aIL10R diagnosis-CD subject-558 biological rep-11

description:
subject-ID_558
@52084400978327102417428100272908


title: WTCHG_388580_201273


title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-243 biological rep-5

description:
subject-ID_243
@52084400978708110317428272788063


title: [exon] L18MDP diagnosis-UC subject-554 biological rep-31

description:
subject-ID_554
@52084400980524112917428617727069


title: [gene] aIL10R diagnosis-CD subject-649 biological rep-13

description:
subject-ID_649
@52084400978708110317428272788042


title: [gene] aIL10R diagnosis-CD subject-528 biological rep-10

description:
subject-ID_528
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title: WTCHG_388580_201274


title: [gene] aIL10R diagnosis-CD subject-423 biological rep-8

description:
subject-ID_423
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-232 biological rep-4

description:
subject-ID_232
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title: [exon] L18MDP diagnosis-UC subject-369 biological rep-27

description:
subject-ID_369
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title: [gene] aIL10R diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
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title: [exon] L18MDP diagnosis-UC subject-531 biological rep-30

description:
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title: [exon] L18MDP diagnosis-UC subject-429 biological rep-28

description:
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title: [exon] L18MDP diagnosis-UC subject-113 biological rep-26

description:
subject-ID_113
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title: [gene] aIL10R diagnosis-CD subject-280 biological rep-6

description:
subject-ID_280
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title: [exon] L18MDP diagnosis-UC subject-1628 biological rep-34

description:
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title: [exon] L18MDP diagnosis-UC subject-1338 biological rep-33

description:
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title: [exon] L18MDP diagnosis-UC subject-447 biological rep-29

description:
subject-ID_447
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title: [exon] L18MDP diagnosis-UC subject-1014 biological rep-32

description:
subject-ID_1014
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title: [exon] L18MDP diagnosis-CD subject-1864 biological rep-22

description:
subject-ID_1864
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title: [exon] L18MDP aCD3-aCD28 diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978327102417428100272885


title: [gene] aIL10R diagnosis-CD subject-232 biological rep-4

description:
subject-ID_232
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title: [gene] aIL10R diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
@52084400975431121817428781459716


title: [exon] L18MDP diagnosis-IBDu subject-293 biological rep-24

description:
subject-ID_293
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title: [exon] L18MDP diagnosis-CD subject-1838 biological rep-21

description:
subject-ID_1838
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title: HEK293T transfected with ZCWPW1-HA and chimpPRDM9-V5

city: Oxford

first: Simon

last: Myers

address: Roosevelt Drive

department: Wellcome Center for Human Genetics

institute: University of Oxford

description:
processed data file:
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_ChIPHA_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz

library_source: genomic

data_processing:
For the HEK293T experiments, reads were mapped to either hg38 (NCBI’s GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz) using bwa mem (version 0.7.17-r1188) (Li, 2013).
Duplicates were removed using picard’s markDuplicates (version 2.20.4-SNAPSHOT).
Unmapped, mate unmapped, non primary alignment, failing platform, and low MAPQ reads were removed using samtools with parameters “-q 30 -F 3852 -f 2 -u” (version 1.9 (using htslib 1.9)).
Other unmapped reads and secondary alignments were removed using samtools fixmate.
Fragment position bed files were created using bedtools bamtobed (v2.28.0).
For the DMC1 mouse experimental data, we processed the data following the algorithm provided by (Khil et al., 2012) to map the reads to the mouse mm10 reference genome (Lunter and Goodson, 2011), and obtain type I reads.
We called DMC1 peaks, as described previously (Davies et al., 2016).
For the HEK293T experiments, peaks for ZCWPW1, PRDM9, H3K4me3, and H3K36me3 were called using a peak caller previously described (Davies et al., 2016) and available at https://github.com/MyersGroup/PeakCaller.
Single base peaks were called with parameters pthresh 10−6 and peakminsep 250 on 22 autosomes.
Code can be found at github.com/MyersGroup/Zcwpw1 (archived at doi.org/10.5281/zenodo.3559758)
Genome_build: mm10 for SSDS DMC1 ChIP-seq and hg38 for HEK293T cell experiments
Supplementary_files_format_and_content: SingeBasePeaks and ForceCalledPeak files are BED format like files with positions of the peaks in first three columns, followed by fragment coverage of the sample replicates and the input, followed by enrichement value, likelihood, and pvalue
Supplementary_files_format_and_content: Frament Position files are BED format files for the locations of each DNA fragment pulled down in the ChIP (each fragment derived from two paired reads)
Supplementary_files_format_and_content: bigWigs contain the fragment depth in binary format for e.g. IGV visualisation, or creating a average profiles using bwtools
Supplementary_files_format_and_content: bedgraphs contain coverage for the single stranded DNA type 1 reads for 5 prime and 3 prime reads for DMC1 SSDS in ZCWPW1 KO mice

molecule: genomic DNA

growth_protocol: HEK293T cells were cultured in DMEM medium supplemented with 10% FBS, 2 mM L-Glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
Libraries were prepared using the Apollo Prep System (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following the manufacturer’s protocol up to pre-PCR amplification
Protein-DNA immunocomplexes were isolated from sonicates using antibodies against the relevant proteins

treatment_protocol: Cells were transfected for 24h with the relevant plasmid DNA using Fugene HD

tag: cell line

tag: genotype/variation

value: HA-tagged ZCWPW1

tag: passages

tag: chip antibody

value: anti-HA (Abcam ab9110)


title: [exon] L18MDP diagnosis-CD subject-1253 biological rep-19

description:
subject-ID_1253
@52084400978708110317428272788043


title: [gene] aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
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title: HEK293T transfected with ZCWPW1-HA and humanPRDM9-V5 [input]

description:
processed data file:
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz


title: [exon] L18MDP diagnosis-CD subject-843 biological rep-16

description:
subject-ID_843
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title: [gene] aIL10R diagnosis-CD subject-243 biological rep-5

description:
subject-ID_243
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title: [exon] L18MDP diagnosis-CD subject-701 biological rep-14

description:
subject-ID_701
@52084400978327102417428100272889


title: [exon] L18MDP diagnosis-CD subject-1018 biological rep-17

description:
subject-ID_1018
@52084400978327102417428100272890


title: [exon] L18MDP diagnosis-IBDu subject-104 biological rep-23

description:
subject-ID_104
@52084400978709110317428272788077


title: HEK293T transfected with ZCWPW1-HA and humanPRDM9-V5

description:
processed data file:
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_NA15-ChIPHA_humanPRDM9-HA_AND_NA15-ChIPV5_humanPRDM9-V5_vs_NA15-Input_humanPRDM9-HA.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz


title: [exon] L18MDP diagnosis-CD subject-1600 biological rep-20

description:
subject-ID_1600
@52084400978327102417428100272895


title: [gene] aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400978711110317428272788210


title: [exon] L18MDP diagnosis-CD subject-1180 biological rep-18

description:
subject-ID_1180
@52084400978327102417428100272901


title: [exon] L18MDP diagnosis-CD subject-792 biological rep-15

description:
subject-ID_792
@52084400980525112917428617727125


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-2031 biological rep-38

description:
subject-ID_2031
@52084400980525112917428617727137


title: [exon] L18MDP diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
@52084400980524112917428617727098


title: HEK293T transfected with ZCWPW1-HA [input]

description:
processed data file:
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz


title: [exon] L18MDP diagnosis-CD subject-649 biological rep-12

description:
subject-ID_649
@52084400978329102417428100273013


title: HEK293T transfected with ZCWPW1-HA

description:
processed data file:
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_100bpWindows.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA_AT_NA15-ChIPHA_humanPRDM9-HA_AND_NA15-ChIPV5_humanPRDM9-V5_vs_NA15-Input_humanPRDM9-HA.bed.gz
ForceCalledPeaks_ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5_AT_100bpWindows.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+chimpPRDM9-V5_vs_ChIPHA_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA+humanPRDM9-V5_vs_ChIPHA_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA.p0.000001.sep250.ALL.bed.gz
SingleBasePeaks.ChIPHA_ZCWPW1-HA_vs_Input_ZCWPW1-HA_AND_Input_ZCWPW1-HA+humanPRDM9-V5.p0.000001.sep250.ALL.bed.gz


title: [exon] L18MDP diagnosis-CD subject-423 biological rep-8

description:
subject-ID_423
@52084400978708110317428272788024


title: Sample 5: Photoreceptor precursors

city: Bangalore

first: Rajarshi

last: Pal

address: CCAMP, NCBS

country: India

institute: Eyestem research

data_processing:
Illumia HiSeq4000 machine was used for sequencing
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 genome using HISAT2 v2.1.0 with parameters --dta-cufflinks -p 32
Raw read counts were calculated using featureCounts with parameters -Q 10 -s 0 -T 8
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for samples

source_name: Induced pluripotent stem cell

extract_protocol:
The cell pellets were washed and RNA was extracted using Qiagen Rneasy mini kit
TruSeq RNA Library Prep Kit V2 was used for mRNA library preparation

treatment_protocol: Specific combinatorial cocktail used to generate cells at different stages

value: Induced pluripotent stem cell

tag: day point


title: [exon] L18MDP diagnosis-CD subject-670 biological rep-13

description:
subject-ID_670
@52084400978327102417428100272896


title: [exon] L18MDP diagnosis-CD subject-528 biological rep-10

description:
subject-ID_528
@52084400978708110317428272788049


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-1628 biological rep-36

description:
subject-ID_1628
@52084400975431121817428781459666


title: Sample 4: Retinal Pigment Epithelium


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-1338 biological rep-35

description:
subject-ID_1338
@52084400980522112917428617726952


title: [exon] L18MDP diagnosis-CD subject-243 biological rep-5

description:
subject-ID_243
@52084400980525112917428617727126


title: Sample 3: RPE progenitors


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-1014 biological rep-34

description:
subject-ID_1014
@52084400978326102417428100272839


title: [exon] L18MDP diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
@52084400975431121817428781459705


title: [exon] L18MDP diagnosis-CD subject-280 biological rep-6

description:
subject-ID_280
@52084400978709110317428272788074


title: [exon] L18MDP diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400978708110317428272788066


title: [gene] aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978711110317428272788219


title: [exon] L18MDP diagnosis-CD subject-643 biological rep-11

description:
subject-ID_643
@52084400980525112917428617727149


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-531 biological rep-32

description:
subject-ID_531
@52084400978329102417428100273050


title: [exon] L18MDP diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978326102417428100272821


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-554 biological rep-33

description:
subject-ID_554
@52084400980522112917428617726956


title: Sample 1: Induced pluripotent stem cell


title: [exon] L18MDP diagnosis-CD subject-232 biological rep-4

description:
subject-ID_232
@52084400978711110317428272788222


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-2001 biological rep-37

description:
subject-ID_2001
@52084400978710110317428272788135


title: d2_aIL10R

first: Stephen

last: Sansom

state: Oxfordshire

department: NDORMS

institute: Kennedy Institute of Rheumatology

data_processing:
Read mapping, quantitation and aggregation of sample count matrices was performed with the "cellranger count" and "cellranger aggr" (--normalize=none) tools as provided by the 10x Genomics Cell Ranger pipeline (version 2.1.1) and reference sequences (version 1.2.0).
Cells with barcodes common to multiple samples sequenced on the same lane(s) were removed from the analysis to avoid issues associated with index hopping.
Genome_build: GRCh38
Supplementary_files_format_and_content: The "matrix.mtx" MEX file contains the aggregated count matrix (cells in columns, genes in rows). The "barcodes.tsv" TSV file contains the cell barcodes (donor and stimulation codition is indicated in the cell barcode  with the suffixes "-d1_unstim", "-d1_stim", "-d1_aIL10R" or "-d2_aIL10R"). The "genes.tsv" file contains the Ensembl gene identifiers and names. These files can be read with the "Read10X" function from the Seurat R package.

molecule: polyA RNA

source_name: peripheral blood

growth_protocol: For these experiments 0.5x10^6 MACS-purified CD14+ monocytes (Mitenyi Biotec) were cultured in round bottom 96-well plates.

extract_protocol:
Libraries were generated using 10x Genomics Single Cell 3’ Solution (version 2) kit.
Cells were captured with a 10x Genomics Chromium Controller
Libraries were generated using 10x Genomics Single Cell 3’ Solution (version 2) kit and subjected to Illumina sequencing (HiSeq 4000).

treatment_protocol: Cells were unstimulated or exposed to ultrapure 200 ng/ml LPS (Enzo Life Sciences; Cat.# ALX-581-008) with or without 10 ug/ml anti-IL-10R (Biolegend; clone: 3F9) for 16 hours in complete RPMI with L-glutamine (Sigma) supplemented with 10% human serum (Sigma; Cat. H4522), non-essential amino acids (Gibco); 1 mM Sodium-Pyruvate (Gibco) and 100 U/ml penicillin and 10 ug/ml streptomycin (Sigma).

tag: individual

value: donor 2

value: LPS + anti-IL10R antibody


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-447 biological rep-31

description:
subject-ID_447
@52084400978329102417428100272997


title: d1_aIL10R

value: donor 1


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-429 biological rep-30

description:
subject-ID_429
@52084400978709110317428272788120


title: Sample 2: Retinal progenitors


title: [exon] aIL10R diagnosis-UC subject-2031 biological rep-37

description:
subject-ID_2031
@52084400980524112917428617727099


title: [exon] aIL10R diagnosis-UC subject-1338 biological rep-34

description:
subject-ID_1338
@52084400978709110317428272788118


title: [exon] L18MDP diagnosis-Other subject-464 biological rep-25

description:
subject-ID_464
@52084400978327102417428100272881


title: [exon] aIL10R diagnosis-UC subject-2001 biological rep-36

description:
subject-ID_2001
@52084400978708110317428272788022


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-369 biological rep-29

description:
subject-ID_369
@52084400978329102417428100272996


title: [exon] aIL10R diagnosis-UC subject-1014 biological rep-33

description:
subject-ID_1014
@52084400980523112917428617727024


title: [exon] aIL10R diagnosis-UC subject-531 biological rep-31

description:
subject-ID_531
@52084400978710110317428272788166


title: [exon] aIL10R diagnosis-UC subject-1628 biological rep-35

description:
subject-ID_1628
@52084400980524112917428617727068


title: d1_unstim

value: None.


title: [exon] aIL10R diagnosis-UC subject-554 biological rep-32

description:
subject-ID_554
@52084400978708110317428272788040

value: UC


title: [exon] aIL10R diagnosis-UC subject-429 biological rep-29

description:
subject-ID_429
@52084400980524112917428617727103


title: d1_stim

value: LPS alone


title: [exon] aIL10R diagnosis-Other subject-464 biological rep-26

description:
subject-ID_464
@52084400978326102417428100272863

value: peripheral PBMC


title: HOK SC5314 replicate 1

city: Singapore

first: Jaya

last: Seneviratne

address: 20 College Road

country: Singapore

institute: National Dental Centre

data_processing:
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina)
The library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the reference genome was built and paired- end clean reads were aligned to the reference genome using TopHat v2.0.12.
Genome_build: hg38
Supplementary_files_format_and_content: excel file for gene expression quantification table, calculation of all genes' FPKM

source_name: Primary oral keratinocytes

growth_protocol: Co-cultures were incubated at 37 degrees, 5% Carbon dioxide in a humidifed incubator.

extract_protocol:
RNA was extracted using Ribopure RNA purification kit, yeast. 1 μg RNA per sample was used for sample prep.  Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection

value: 3 to 5


title: [gene] aCD3-aCD28 aIL10R diagnosis-Other subject-464 biological rep-27

description:
subject-ID_464
@52084400978329102417428100273042


title: [exon] aIL10R diagnosis-IBDu subject-293 biological rep-25

description:
subject-ID_293
@52084400978329102417428100272999

value: F


title: HOK SC5314 replicate 2


title: [gene] aCD3-aCD28 aIL10R diagnosis-IBDu subject-293 biological rep-26

description:
subject-ID_293
@52084400978327102417428100272886


title: HOK GZY903 replicate 2


title: [gene] aCD3-aCD28 aIL10R diagnosis-IBDu subject-104 biological rep-25

description:
subject-ID_104
@52084400978329102417428100273008


title: [gene] aCD3-aCD28 aIL10R diagnosis-UC subject-113 biological rep-28

description:
subject-ID_113
@52084400978327102417428100272887


title: [exon] aIL10R diagnosis-IBDu subject-104 biological rep-24

description:
subject-ID_104
@52084400980522112917428617726947


title: HOK GZY903 replicate 1


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-1864 biological rep-24

description:
subject-ID_1864
@52084400978327102417428100272875

value: CD


title: [exon] aIL10R diagnosis-CD subject-1864 biological rep-23

description:
subject-ID_1864
@52084400978328102417428100272946


title: [exon] aIL10R diagnosis-UC subject-369 biological rep-28

description:
subject-ID_369
@52084400978328102417428100272947


title: [exon] aIL10R diagnosis-UC subject-113 biological rep-27

description:
subject-ID_113
@52084400978710110317428272788180


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-1600 biological rep-23

description:
subject-ID_1600
@52084400978327102417428100272878


title: [exon] aIL10R diagnosis-CD subject-1600 biological rep-22

description:
subject-ID_1600
@52084400978709110317428272788094


title: [exon] L18MDP diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978708110317428272788029


title: HOK control replicate 2


title: [exon] aIL10R diagnosis-CD subject-1180 biological rep-20

description:
subject-ID_1180
@52084400978710110317428272788137


title: HOK control replicate 1


title: [exon] aIL10R diagnosis-CD subject-1018 biological rep-19

description:
subject-ID_1018
@52084400980522112917428617726957

value: M


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-1180 biological rep-21

description:
subject-ID_1180
@52084400978709110317428272788107


title: [exon] aIL10R diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
@52084400978328102417428100272962


title: [exon] aIL10R diagnosis-CD subject-891 biological rep-18

description:
subject-ID_891
@52084400978709110317428272788082


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-1253 biological rep-22

description:
subject-ID_1253
@52084400978708110317428272788036


title: [exon] aIL10R diagnosis-CD subject-792 biological rep-16

description:
subject-ID_792
@52084400978710110317428272788153


title: [exon] aIL10R diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
@52084400978708110317428272788045


title: GR R2

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

country: China

institute: Chinese Academy of Sciences

description: G.hic

data_processing:
Sequence adapters were remove by cutadapt (version 2.6).
HiC-Pro (version 2.7.9) was used to process Hi-C and tagHi-C data.
The contact matrix was normalized by ICE method.
hicpro2juicbox was used to transform valid contacts to “.hic” files, and these files were imported to juicebox for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: hic

organism: Mus musculus

source_name: granulocytes

growth_protocol: C57BL/6J mice were maintained under specific pathogen free conditions in individually ventilated cages at the State Key Laboratory of Experimental Hematology (SKLEH). Females were used for experiments. All animal procedures were performed in compliance with the animal care guidelines approved by the Institutional Animal Care and Use Committees of the SKLEH and the Institute of Hematology.  Cells were FACS sorted according to stablished markers.

extract_protocol:
After crosslinking reversal, DNA was extracted with Phenol:Chloroform, pH 6.7/8.0 and quantified with Qubit.
DNA libraries were prepared for sequencing using standard Illumina protocols
tagHi-C

tag: cell type

value: granulocytes

value: In vivo FACS purified cell

tag: strain


title: GR R1

description: G.hic


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-1018 biological rep-20

description:
subject-ID_1018
@52084400978711110317428272788229


title: [exon] aIL10R diagnosis-CD subject-643 biological rep-12

description:
subject-ID_643
@52084400978710110317428272788163


title: [exon] aIL10R diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
@52084400978711110317428272788238


title: [exon] aIL10R diagnosis-UC subject-447 biological rep-30

description:
subject-ID_447
@52084400980524112917428617727064


title: [exon] aIL10R diagnosis-CD subject-528 biological rep-10

description:
subject-ID_528
@52084400980522112917428617726959


title: [exon] aIL10R diagnosis-CD subject-670 biological rep-14

description:
subject-ID_670
@52084400978327102417428100272893


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-891 biological rep-19

description:
subject-ID_891
@52084400978709110317428272788110


title: MK R1

description: MK.hic

source_name: megakaryocytes

value: megakaryocytes


title: [exon] aIL10R diagnosis-CD subject-649 biological rep-13

description:
subject-ID_649
@52084400978708110317428272788042


title: [exon] aIL10R diagnosis-CD subject-558 biological rep-11

description:
subject-ID_558
@52084400978327102417428100272908


title: MKP R2

description: MKP.hic

source_name: Megakaryocyte progenitors

value: Megakaryocyte progenitors


title: [exon] aIL10R diagnosis-CD subject-1253 biological rep-21

description:
subject-ID_1253
@52084400978327102417428100272897


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-792 biological rep-17

description:
subject-ID_792
@52084400980524112917428617727061


title: [exon] aIL10R diagnosis-CD subject-423 biological rep-8

description:
subject-ID_423
@52084400978708110317428272788037


title: MKP R1

description: MKP.hic


title: [exon] aIL10R diagnosis-CD subject-280 biological rep-6

description:
subject-ID_280
@52084400980524112917428617727075


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-701 biological rep-16

description:
subject-ID_701
@52084400975431121817428781459717


title: MK R2

description: MK.hic


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-843 biological rep-18

description:
subject-ID_843
@52084400978326102417428100272856


title: [exon] aIL10R diagnosis-CD subject-243 biological rep-5

description:
subject-ID_243
@52084400975431121817428781459696


title: [exon] aIL10R diagnosis-CD subject-232 biological rep-4

description:
subject-ID_232
@52084400978711110317428272788250


title: MEP R1

description: MEP.hic

source_name: megakaryocyte-erythrocyte progenitor

value: megakaryocyte-erythrocyte progenitor


title: MEP R2

description: MEP.hic


title: [exon] aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400978711110317428272788210


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-649 biological rep-14

description:
subject-ID_649
@52084400978328102417428100272982


title: GMP R2

description: GMP.hic

source_name: granulocyte-macrophage progenitor

value: granulocyte-macrophage progenitor


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-643 biological rep-13

description:
subject-ID_643
@52084400978708110317428272788053


title: GMP R1

description: GMP.hic


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-558 biological rep-12

description:
subject-ID_558
@52084400980522112917428617726942


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-528 biological rep-11

description:
subject-ID_528
@52084400978710110317428272788161


title: CMP R2

description: GMP.hic

source_name: common myeloid progenitor

value: common myeloid progenitor


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-1338 biological rep-35

description:
subject-ID_1338
@52084400980522112917428617726952


title: [exon] aIL10R diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
@52084400975431121817428781459716


title: [exon] aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978328102417428100272945


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-2001 biological rep-37

description:
subject-ID_2001
@52084400978710110317428272788135


title: CMP R1

description: GMP.hic


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-508 biological rep-10

description:
subject-ID_508
@52084400978708110317428272788034


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-531 biological rep-32

description:
subject-ID_531
@52084400978329102417428100273050


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-670 biological rep-15

description:
subject-ID_670
@52084400980525112917428617727127


title: CLP R2

description: CLP.hic

source_name: common lymphoid progenitor

value: common lymphoid progenitor


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-554 biological rep-33

description:
subject-ID_554
@52084400980522112917428617726956


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-429 biological rep-30

description:
subject-ID_429
@52084400978709110317428272788120


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-423 biological rep-9

description:
subject-ID_423
@52084400978708110317428272788051


title: [exon] aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978711110317428272788219


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-113 biological rep-28

description:
subject-ID_113
@52084400978327102417428100272887


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-1628 biological rep-36

description:
subject-ID_1628
@52084400975431121817428781459666


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-1014 biological rep-34

description:
subject-ID_1014
@52084400978326102417428100272839


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-447 biological rep-31

description:
subject-ID_447
@52084400978329102417428100272997


title: CLP R1

description: CLP.hic


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-372 biological rep-8

description:
subject-ID_372
@52084400980525112917428617727124


title: MPP R1

description: MPP.hic

source_name: multipotent progenitor

value: multipotent progenitor


title: [exon] aCD3-aCD28 aIL10R diagnosis-Other subject-464 biological rep-27

description:
subject-ID_464
@52084400978329102417428100273042

value: Other


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-1864 biological rep-24

description:
subject-ID_1864
@52084400978327102417428100272875


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-280 biological rep-7

description:
subject-ID_280
@52084400978710110317428272788152


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-243 biological rep-6

description:
subject-ID_243
@52084400978708110317428272788023


title: ST-HSC R2

description: ST.hic

source_name: short term HSC

value: short term HSC


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-2031 biological rep-38

description:
subject-ID_2031
@52084400980525112917428617727137

value: UC


title: ST-HSC R1

description: ST.hic


title: [exon] aCD3-aCD28 aIL10R diagnosis-IBDu subject-104 biological rep-25

description:
subject-ID_104
@52084400978329102417428100273008

value: IBDu

value: peripheral PBMC


title: [exon] aCD3-aCD28 aIL10R diagnosis-IBDu subject-293 biological rep-26

description:
subject-ID_293
@52084400978327102417428100272886

value: F


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-232 biological rep-5

description:
subject-ID_232
@52084400978711110317428272788231

value: CD


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-1253 biological rep-22

description:
subject-ID_1253
@52084400978708110317428272788036


title: [exon] aCD3-aCD28 aIL10R diagnosis-UC subject-369 biological rep-29

description:
subject-ID_369
@52084400978329102417428100272996


title: LT-HSC R2

description: LT.hic

source_name: long term-HSC

value: long term-HSC


title: LT-HSC R1

description: LT.hic


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-1180 biological rep-21

description:
subject-ID_1180
@52084400978709110317428272788107


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-891 biological rep-19

description:
subject-ID_891
@52084400978709110317428272788110


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-843 biological rep-18

description:
subject-ID_843
@52084400978326102417428100272856


title: KO_RW_3

city: San Francisco

first: Jeroen

middle: P.

last: Roose

state: CA

address: 513 Parnassus Ave.

department: Anatomy

institute: University of California, San Francisco

data_processing:
STAR (PMID: 23104886) version 2.7.0f was used to align reads to the Mouse genome, version GRCm38.96, no adapter clipping or filtering was performed before alignment.
Reads uniquely mapped to the mouse genome were used to assess expression changes between genes using DESeq2 (PMID: 25516281).
Variance-stabilized counts were used for creating the heatmap, while blind-stabilized counts were used for PCA.
PCA was generated using the prcomp() function from the stats package in R.
Plotly R package was used for making 3D PCA plots.
Genome_build: Mus Musculus GRCm38 primary assembly with ensembl v96 annotations
Supplementary_files_format_and_content: Genomic read counts were generated by STAR, and were aggregated to make a tab-delimited counts matrix for all samples.  Normalized reads were calculated with DESeq2's counts() function, with normalized=TRUE.

source_name: Mammary organoids

growth_protocol: Mammary organoids were generated from 6-7 wk old WT and RasGRP1-/- C57BL/6 mammary glands, plated in matrigel pellets and were grown in  media containing DMEM/F12, Insulin-Trasnferrin-Selenium, and supplemented with combinations of growth factors.

extract_protocol:
Organoids were dissociated using Tryp-LE and RNA was extracted using the Qiagen Rneasy kit (cat# 74104)
Organoids were dissociated to single cells using TrypLE Select (Life Technologies 12563011). Organoids were incubated with TrypLE for 5 minutes at 37°C, and washed in PBS. RNA was isolated from organoids using the RNeasy Mini Kit (Qiagen 74104). RNA purity and quantitation was assessed using the Nanodrop ND-800 (Nanodrp Technologies, Inc, Wilmington, D) and RNA integrity was assessed using the 5200 Fragment Analyzer System and the RNA high-sensitivity chip (Agilent, Santa Clara, CA, USA). Sequencing libraries were generated using 100 ng of total RNA and the Universal RNA-Seq library preparation Kit with multiplexing primers, according the manufacturer’s protocol (Nugen technologies, Inc, San Carlos, CA, USA). Library size distribution and concentration were assessed using the Fragment Analyzer System and the DNA high-sensitivity chip. Libraries were multiplexed at a density of 8 per flow-cell lane and sequenced on the HiSeq 4000 to generate single end 50bp reads per the manufacturer’s instructions (Illumina, San Diego, CA, USA).

treatment_protocol: WT and RasGRP1-/- mammary organoids were supplemented with either 2.5 nM EGF, 2.5 nM EGF + 0.1 nM NGS-Wnt + 8.3 nM Rspo2, or 0.1 nM NGS-Wnt + 8.3 nM Rspo2.

value: Mammary epithelial cells

tag: genotype

tag: treatment

value: NGS-Wnt + Rspo2

tag: treatment time

value: 5 days


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-701 biological rep-16

description:
subject-ID_701
@52084400975431121817428781459717

tag: stimulation

tag: diagnosis

value: M


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-792 biological rep-17

description:
subject-ID_792
@52084400980524112917428617727061

tag: Sex

tag: batch


title: KO_ERW_3

value: EGF+NGS-Wnt + Rspo2


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978330102417428100373068

tag: tissue


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-670 biological rep-15

description:
subject-ID_670
@52084400980525112917428617727127


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978710110317428272788142


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-225 biological rep-4

description:
subject-ID_225
@52084400978710110317428272788144


title: [gene] aCD3-aCD28 aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400975431121817428781459721


title: KO_EGF_3

value: EGF


title: [gene] aCD3-aCD28 diagnosis-UC subject-2031 biological rep-39

description:
subject-ID_2031
@52084400980523112917428617727026


title: WT_RW_3

value: Wild type


title: [gene] aCD3-aCD28 diagnosis-UC subject-2001 biological rep-38

description:
subject-ID_2001
@52084400978711110317428272788257


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-1018 biological rep-20

description:
subject-ID_1018
@52084400978711110317428272788229


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-643 biological rep-13

description:
subject-ID_643
@52084400978708110317428272788053


title: KYSE510-shLOXL2_rep3

city: Shantou

first: Xiu-Hui

last: Zhan

address: 22, Xinling Road

institute: Shantou University

data_processing:
Zebra software (developed for BGISEQ-500) used for base calling
We define "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. Filtering steps are as follows: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Sequencing reads after filtering were mapped to reference genome using the HISAT software and to reference gene by Bowtie2 tool, followed by strict quality control for each sample from several aspects.
Gene expression was quantified by RSEM software and differentially-expressed genes between samples were analyzed by screening using the NOISeq method.
Genome_build: GRCh37
Supplementary_files_format_and_content: xls files include FPKM values for each sample

source_name: esophageal squamous cell carcinoma cells

extract_protocol:
Total RNA was directly extracted from cells cultured in 6-cm plates using TRIzol reagent, and these samples were then prepared according to GBI's instructions.
RNA libraries were prepared for sequencing using standard BGISEQ-500 RNA-sequencing protocols.

value: stable LOXL2-silenced KYSE510 cells

tag: shRNA

value: specific shRNA against LOXL2


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-372 biological rep-8

description:
subject-ID_372
@52084400980525112917428617727124


title: WT_ERW_3


title: [gene] aCD3-aCD28 diagnosis-UC subject-1628 biological rep-37

description:
subject-ID_1628
@52084400973515011718428996209110


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-1600 biological rep-23

description:
subject-ID_1600
@52084400978327102417428100272878


title: KYSE510-shLOXL2_rep2


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-243 biological rep-6

description:
subject-ID_243
@52084400978708110317428272788023


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-649 biological rep-14

description:
subject-ID_649
@52084400978328102417428100272982


title: WT_EGF_3


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-528 biological rep-11

description:
subject-ID_528
@52084400978710110317428272788161


title: KYSE510-shLOXL2_rep1


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-232 biological rep-5

description:
subject-ID_232
@52084400978711110317428272788231


title: KO_RW_2


title: [gene] aCD3-aCD28 diagnosis-UC subject-1014 biological rep-35

description:
subject-ID_1014
@52084400980522112917428617726953


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-558 biological rep-12

description:
subject-ID_558
@52084400980522112917428617726942


title: KYSE510-shNC_rep3

value: stable KYSE510 control cells

value: scrambled shRNA lentivirus


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-508 biological rep-10

description:
subject-ID_508
@52084400978708110317428272788034


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-423 biological rep-9

description:
subject-ID_423
@52084400978708110317428272788051


title: KO_EGF_2


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-225 biological rep-4

description:
subject-ID_225
@52084400978710110317428272788144


title: [gene] aCD3-aCD28 diagnosis-UC subject-1338 biological rep-36

description:
subject-ID_1338
@52084400978710110317428272788136

value: UC


title: KYSE510-shNC_rep2


title: [gene] aCD3-aCD28 diagnosis-UC subject-531 biological rep-33

description:
subject-ID_531
@52084400980523112917428617727010


title: [exon] aCD3-aCD28 diagnosis-UC subject-2001 biological rep-38

description:
subject-ID_2001
@52084400978711110317428272788257


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400975431121817428781459721


title: KO_ERW_2


title: WT_RW_2


title: KYSE510-shNC_rep1


title: [gene] aCD3-aCD28 diagnosis-UC subject-447 biological rep-32

description:
subject-ID_447
@52084400978332102417428100373196


title: [gene] aCD3-aCD28 diagnosis-UC subject-554 biological rep-34

description:
subject-ID_554
@52084400978709110317428272788080


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-280 biological rep-7

description:
subject-ID_280
@52084400978710110317428272788152


title: [gene] aCD3-aCD28 diagnosis-UC subject-429 biological rep-31

description:
subject-ID_429
@52084400980522112917428617726951


title: [gene] aCD3-aCD28 diagnosis-UC subject-369 biological rep-30

description:
subject-ID_369
@52084400978328102417428100272936


title: [exon] aCD3-aCD28 diagnosis-UC subject-1338 biological rep-36


title: [exon] aCD3-aCD28 diagnosis-UC subject-554 biological rep-34


title: Small RNA library from Trichuris muris EVs treated with Dnase

city: Edinburgh

first: Amy

last: Buck

address: Ashworth Labs, Charlotte Auerbach Road

department: IIIR

institute: The University of Edinburgh

description:
small RNAs
Tm_EvD_Un

data_processing:
Sequence quality using FastQC
Adapters were removed using cutadapt
Genome alignments of sequences using bowtie to the host genome mus musculus (version GRCm38, with additional RefSeq rRNA, as all mouse rRNA genes are not present in the genome) and  T. muris (GCA_000612645.2) requiring perfect matches.
miRNAs were predicted using miDeep2 v2.0.0.8 utilizing sequences from miRBase v22 and additional nematode miRNA sequences from Brugia pahangi.
RNA biotypes were identified using the genome version PRJEB126 TMUE3.0  downloaded from WormBase ParaSite, miRNA identified as above, rRNA using cmsearch from the infernal [v1.1.2], (Friedländer et al., 2012); rRNAs using cmsearch from the infernal [v1.1.2] (Nawrocki et al., 2013) suite to search for eukaryotic rRNAs using covariance models from Rfam [version 14.1], tRNAs using tRNA-scan-SE [v1.1.1], snRNA, protein-coding exons, and protein-coding introns were extracted from publicly available GFF3 annotation on WormBase ParaSite genome PREJEB126.

organism: Trichuris muris

source_name: Secretion product

growth_protocol: T. muris were cultured for 22 hr in RPMI supplemented with 500 U/ml penicillin and 500 μg/ml, conditioned media was collected at 4 hr, discarded and replaced. Conditioned media from 4-22hr was collected, spun at 720 x g for 15 minutes and filtered through a 0.2μm filter. EVs were isolated using ultracentrifugation at 100,000 x g for 2 hr, and washed twice using PBS. EV pellets were re-suspendedin 6 ml of PBS and stored frozen until required. EVs concentrated to 185 μl using a 5kDa MWCO vivapspin and RNA extracted using Qiagen miRNeasy mini kit. Some samples were treated with either polyphosphatase, DNase or both. Small RNA libraries were prepared using CleanTag small RNA library preparation kit from Trilink using 18 PCR cycles. For H.bakeri EVs, the filtered HES were concentrated in a Vivaspin 20 MWCO 3kDa concentrator (Sartorius, Göttingen, Germany). 400 μL of HES (concentration 5mg/mL) was separated into 1 ml fractions by size exclusion chromatography using a Superdex 200 10/300 GL column (GE Healthcare) in PBS with an AKTA basic FPLC system (GE Healthcare). Libraries were prepared using the CleanTag small RNA Library prep kit (Trilink) following manufacturer’s instructions.  Adapters were diluted 1:12 and 18 PCR cycles used. Quantification and size analysis of H. bakeri EVs was performed using the qNano Gold platform (Izon Science).

extract_protocol:
Qiagen miRNeasy mini kit
CleanTag small RNA library prep kit, 18 PCR cycles

tag: product type

value: Extracellular vesicle

tag: developmental stage

value: Adult parasites


title: [exon] aCD3-aCD28 diagnosis-UC subject-1628 biological rep-37

description:
subject-ID_1628
@52084400973515011718428996209110

value: peripheral PBMC


title: Small RNA library from Trichuris muris EVs treated with Dnase + polyphosphatase

description:
small RNAs
Tm_EvD_Pp


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978710110317428272788142

value: CD

value: F


title: Small RNA library from Trichuris muris EVs treated with polyphosphatase

description:
small RNAs
Tm_Ev_Pp


title: [exon] aCD3-aCD28 diagnosis-UC subject-369 biological rep-30


title: KO_ERW_1

value: Mammary epithelial cells


title: mESC_EPZ_ATAC_rep3

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: ATAC-Seq

data_processing:
raw sequencing data were processed with snakePipes  for DNA-mapping and ATAC-seq analysis (Bhardwaj et al., 2019)
ATAC-Seq BW were normalized using Deseq2 scaling factors computed on the locally enriched locy (identified using MACS2)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig, normalized coverage

source_name: mouse embryionic stem cells

growth_protocol: mESC were cultured on inactivated MEFs up to p3, and in feeder-free condition from p4 onwards, in ESC complete medium + LIF (leukemia inhibitor factor) (1/1000) + beta-Mercapto-EtOH (1/500). Cells were splitted every 2-3 days upon reach of ~ 70% confluence.

extract_protocol:
ATAC-seq was performed following the protocol of Buerostro et al. 2015.
Libraries were sequenced on NovaSeq 6000 following manufacturer's protocols.

treatment_protocol: mESC growing in feeder-free plates were treated with either DMSO or EPZ5676 for 48 hours.

tag: cell-type

value: Dot1l-HA-FLAG C57BL/6 mouse embryonic stem cells

tag: passage


title: WT_EGF_2

value: 5 days


title: [exon] aCD3-aCD28 aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978330102417428100373068

value: M


title: WT_ERW_2

value: EGF+NGS-Wnt + Rspo2


title: [exon] aCD3-aCD28 diagnosis-UC subject-1014 biological rep-35

description:
subject-ID_1014
@52084400980522112917428617726953


title: KO_EGF_1

value: EGF


title: [gene] aCD3-aCD28 diagnosis-Other subject-464 biological rep-28

description:
subject-ID_464
@52084400978710110317428272788167

value: Other


title: [gene] aCD3-aCD28 diagnosis-UC subject-113 biological rep-29

description:
subject-ID_113
@52084400978328102417428100272971


title: WT_RW_1

value: Wild type

value: NGS-Wnt + Rspo2


title: [exon] aCD3-aCD28 diagnosis-UC subject-531 biological rep-33


title: [gene] aCD3-aCD28 diagnosis-IBDu subject-104 biological rep-26

description:
subject-ID_104
@52084400980524112917428617727084

value: IBDu


title: mESC_EPZ_ATAC_rep1

description: ATAC-Seq


title: [exon] aCD3-aCD28 diagnosis-UC subject-447 biological rep-32


title: KO_RW_1


title: WT_ERW_1


title: mESC_DMSO_ATAC_rep3

description: ATAC-Seq

value: DMSO


title: [gene] aCD3-aCD28 diagnosis-CD subject-1864 biological rep-25

description:
subject-ID_1864
@52084400978709110317428272788078


title: WT_EGF_1


title: HomIP_Vest3

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads counts were calculated for each sample.
Differential expression of genes were computed between wild type and mutant samples
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include counts per million reads (CPM) for each sample

growth_protocol: Room temperature 18-23°C, 12 hour light/dark cylce

extract_protocol:
The hair cell translatome was enriched for by ribosome immunoprecipitation using an HA antibody (see protocol outlined in Sanz et al., 2009)
Gfi1Cre;RiboTag IP RNA-seq libraries were prepared in biological triplicates from cochlear tissues using the Ovation® Ultralow Library Preparation Kit (NuGEN), and vestibular tissues using the NEBNext® Ultra™ Directional RNA Library Prep Kit (New England BioLabs) per manufacturers instructions.

tag: age

value: vestibular cells (enriched)

tag: antibody

value: HA


title: mESC_DMSO_ATAC_rep1

description: ATAC-Seq


title: [gene] aCD3-aCD28 diagnosis-CD subject-1600 biological rep-23

description:
subject-ID_1600
@52084400978328102417428100272970


title: [exon] aCD3-aCD28 diagnosis-UC subject-429 biological rep-31

value: UC


title: mESC_EPZ_ATAC_rep2

description: ATAC-Seq


title: [exon] aCD3-aCD28 diagnosis-IBDu subject-104 biological rep-26

value: peripheral PBMC


title: Small RNA library from Trichuris muris EVs

description:
small RNAs
Tm_Ev_Un

value: Extracellular vesicle

value: Adult parasites


title: [exon] aCD3-aCD28 diagnosis-UC subject-2031 biological rep-39

description:
subject-ID_2031
@52084400980523112917428617727026


title: Pdyn-lineage nuclei pooled from 8 adult mice of either sex with prior neonatal (P3) hindpaw incision

city: Cincinnati

first: Mark

middle: L

last: Baccei

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

description:
Injured
10X-UC-Baccei-I-20190305-3v3hg_S4

data_processing:
Basecalling: CellRanger v3.0.2 mkfastq
Alignment: Cellranger v3.0.2 count
Seurat v3.0-3.1
Genome_build: mm10
Supplementary_files_format_and_content: raw or normalized counts from all cells or only cells from naïve or neonatally incised animals

source_name: Lumbar (L3-L5) dorsal spinal cord

extract_protocol:
Intact nuclei were liberated from dorsal spinal cord using dounce-type homogenization and filtering/centrifugation steps. Nuclei were sorted on FACSAria on the basis of GFP fluoresence to selectively isolate dynorphin-lineage nuclei.
Prepared according to 10x Genomics and Illumina protocols

treatment_protocol: Injured: surgical incision to left plantar hindpaw occurring at postnatal day (P) 3; Naïve: P3 isoflurane exposure littermate controls.

tag: injury

value: Injured (hindpaw incision at postnatal day 3)

value: Lumbar (L3-L5) dorsal spinal cord

tag: molecule subtype

value: nuclear RNA


title: [gene] aCD3-aCD28 diagnosis-CD subject-1253 biological rep-22

description:
subject-ID_1253
@52084400980524112917428617727078

value: CD

value: F


title: [exon] aCD3-aCD28 diagnosis-IBDu subject-293 biological rep-27

description:
subject-ID_293
@52084400978328102417428100272963


title: [exon] aCD3-aCD28 diagnosis-Other subject-464 biological rep-28

value: M


title: [exon] aCD3-aCD28 diagnosis-CD subject-1838 biological rep-24

description:
subject-ID_1838
@52084400978710110317428272788146


title: [exon] aCD3-aCD28 diagnosis-CD subject-1864 biological rep-25


title: HetIP_Vest3

tag: cell type


title: [gene] aCD3-aCD28 diagnosis-CD subject-1045 biological rep-20

description:
subject-ID_1045
@52084400978329102417428100273016


title: [exon] aCD3-aCD28 diagnosis-UC subject-113 biological rep-29


title: mESC_DMSO_ATAC_rep2

description: ATAC-Seq

value: Dot1l-HA-FLAG C57BL/6 mouse embryonic stem cells

tag: treatment


title: [gene] aCD3-aCD28 diagnosis-CD subject-1838 biological rep-24


title: Pdyn-lineage nuclei pooled from 8 naïve adult mice of either sex

description:
Naïve
10X-UC-Baccei-N-20190305-3v3hg_S3

tag: strain

value: Naïve


title: HomIP_Vest1


title: ASD 67

type: genomic

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

country: Japan

institute: Hirosaki University Graduate School of Medicine

description: Genome-Wide Human SNP Array 6.0

hyb_protocol: Hybridization were carried out using the SNP 6 Core Reagent Kit and a GeneAmp® PCR System 9700 in accordance with manufacture's instructions. Samples were loaded onto  the arrays to rotate in the hybridization oven (GeneChip® Hybridization Oven 645) for 18 hours at 50℃ and 60 rpm. After hybridization, the arrays were washed and stained using GenomeWideSNP6_450 protocol for the Fluidics Station 450.

scan_protocol: GeneChips® were scanned using the GeneChip® Scanner 3000 7G controlled by Affymetrix GeneChip® Command Console® software.

data_processing:
Generated CEL files were conducted to normalize signal intensities using Genotyping Console. Copy number states were derived from a Hidden Markov Model based algorithm implemented Birdseed v2.
Copy number state: 0, 1, 2, 3, 4

source_name: genomic DNA from peripheral blood

label_protocol: Fragmented DNA were subjected to 3' terminal labeling with TdT enzyme.

extract_protocol: Genomic DNA from peripheral blood were extracted using QIAamp DNA Blood Mini kit (QIAGEN, Hilden, Germany) in accordance with manufacturer's instructions. 500 ng of genomic DNA was carried out to digestion by Sty and Nsp.

tag: disease

value: Autism spectrum disorder (ASD)

tag: race

value: Japanese

tag: gender

value: male


title: HetIP_Vest2

value: vestibular cells (enriched)


title: HetIP_Vest1

value: HA


title: HomIP_Vest2


title: ASD 66

description: Genome-Wide Human SNP Array 6.0


title: [gene] aCD3-aCD28 diagnosis-CD subject-1018 biological rep-19

description:
subject-ID_1018
@52084400978326102417428100272823

tag: stimulation

tag: diagnosis

tag: Sex

tag: batch


title: [gene] aCD3-aCD28 diagnosis-IBDu subject-293 biological rep-27

value: IBDu

tag: tissue


title: MDSC-2

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
Demultiplexing and FASTQ conversion was performed uisng bcl2fastqv2.16.
Trimmomatic was used to trim the raw reads to filter out the contaminated adapter sequence and low-quality reads.
Bismark software (version 0.12.5; Krueger F, 2011) was used to perform alignments of  bisulfite-treated reads to a reference genome with the default parameters.adapter sequence and low-quality reads
To estimate methylation levels, we employed a sliding-window approach, which is conceptually similar to approaches that have been used for bulk BS-Seq (http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html).
Differentially methylated regions (DMRs) were identified using the swDMR software (http://122.228.158.106/swDMR/), which uses a sliding-window approach.The window is set to 1000bp and step length is 100bp. Fisher test is implemented to detect the DMRs.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Myeloid-derived suppressor cells from AT3 tumor-bearing mice

growth_protocol: CD11b+Gr1+ MDSCs were purified from spleens of AT3 tumor-bearing mice using CD11b MicroBeads and MACS separation column according to the manufacturer’s instructions (Miltenyi Biotec Inc. San Diego, CA).

extract_protocol:
Genomic DNA was extracted from the purified MDSCs using Quick-DNA Miniprep Plus Kit (Zymo Research, Irvine, CA).
A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research). And the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was checked on Agilent Bioanalyzer 2100 system.

value: Spleen


title: [gene] aCD3-aCD28 diagnosis-CD subject-1016 biological rep-18

description:
subject-ID_1016
@52084400978708110317428272788046

value: peripheral PBMC


title: ASD 65

description: Genome-Wide Human SNP Array 6.0


title: [gene] aCD3-aCD28 diagnosis-CD subject-1180 biological rep-21

description:
subject-ID_1180
@52084400978709110317428272788093


title: MDSC-1


title: [gene] aCD3-aCD28 diagnosis-CD subject-792 biological rep-16

description:
subject-ID_792
@52084400980524112917428617727072


title: [gene] aCD3-aCD28 diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
@52084400978708110317428272788033


title: ASD 64

description: Genome-Wide Human SNP Array 6.0


title: Bswitch_ATACSeq

city: Monrovia

first: Meiling

last: Jin

address: 1218 South Fifth Ave.

institute: City of Hope

data_processing:
Illumina Casava software used for basecalling.
Adaptors were first removed from ATAC-seq reads using Trimmomatic  and then the paired-end reads were mapped to the human reference genome (GRCm38/mm10) using Bowtie2 with the parameter setting as “--very-sensitive -k 10 -X 2000”. Mitochondrial DNA were filtered using SAMTools and duplicated reads were removed using Picard tools MarkDuplicates. The properly mapped paired reads with MAPQ score>30 were remained for downstream analyses.
ATAC-seq peak regions were called using MACS2 with parameter “-B –f BAMPE –g mm –keep-dup all –cutoff-analysis”. ENCODE blacklist regions were removed for downstream analysis (https://www.encodeproject.org/annotations/ENCSR064IDX/).
To generate consensus peaks between Bswitch and TriBMZP cells, we used BEDTools merge and quantified the fragments in each peak using featureCounts. We further normalized fragments (CR) using library size(SL) by formula CN=log2(CR/SL*1000000+1).Peak annotation were performed using ChIPseeker package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includs peak information with quantitative data for each sample

source_name: Myeloid cells converted from TriB MZPs

extract_protocol: Sort-purified cells were lysed in 10mM Tris-HCL (pH7.5), 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.01% Digitonin. Transposition reaction was performed using Nextera DNA Library Prep Kit and DNA was isolated using Qiagen MinElute Reaction Cleanup Kit. Library was generated using PCR reaction using primer pairs of Ad1_noMX + Ad2.5_GGACTCCT and Ad1_noMX + Ad2.6_TAGGCATG, respectively. The library was purified using Ampure beads and submitted for sequencing.

value: Myeloid cells


title: ASD 63

description: Genome-Wide Human SNP Array 6.0


title: ASD 68

description: Genome-Wide Human SNP Array 6.0

value: female


title: TriB MZP_ATACSeq

source_name: sorted MZPs from TriB spleen

value: marginal zone precursor (MZP) B cells


title: [exon] aCD3-aCD28 diagnosis-CD subject-1600 biological rep-23


title: [exon] aCD3-aCD28 diagnosis-CD subject-1018 biological rep-19


title: [exon] aCD3-aCD28 diagnosis-CD subject-1253 biological rep-22


title: ASD 62

description: Genome-Wide Human SNP Array 6.0


title: Coch-P2

data_processing:
10x matrices were input to Seurat R package and normalized.
We filtered cells with <50 or >20,000 unique molecular identifiers (UMIs) and with >20% of UMIs coming from mitochondrial genes.
Highly variable genes were identified using the FindVariableGenes function with the following parameters: dispersion formula = LogVMR, minimum = 0.0123, maximum = 3, y cutoff = 0.5.
Counts from variable genes were scaled, and we regressed out effects of cell cycle, percent of mitochondrial genes, and number of unique molecular identifiers.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: P2_Cochlea.raw_gene_bc_matrices_h5.h5: HDF5 format raw gene expression matrix.

source_name: Cochlea

extract_protocol:
Cochlear ducts were harvested and pooled into Thermolysin (Sigma-Aldrich) for 20 min at 37oC. The Thermolysin was then replaced with Accutase (Sigma-Aldrich) and the tissue incubated for 3 min at 37oC followed by mechanical dissociation, repeating this step 3 times. After inactivation of the Accutase with 5% fetal bovine serum, the cell suspension was filtered through a 35µm nylon mesh to remove cell clumps.
Library were prepared using the Chromium Single Cell Gene Expression Solution from 10x Genomics.
75bp pair-end

value: Post-natal day 2

value: Cochlea


title: [gene] aCD3-aCD28 diagnosis-CD subject-670 biological rep-14

description:
subject-ID_670
@52084400978329102417428100273006

data_processing:
Background correction and quantile normalization of the gene expression data obtained from the Affymetrix Human Transcriptome Array 2.0 (HTA2) platform were performed by the RMA method while controlling for batch.  Summarization was performed with RLM.  Annotations were defined by the Affymetrix NetAffx(TM) NA35 release, which is based on the GRCh37 human reference genome. Differential expression at the gene-level was performed using the empirical Bayes method implemented in LIMMA{Ritchie:ef}controlling for donor in the model.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

extract_protocol: Total RNA was extracted from cultured cells, using the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s protocol. The RNA yield was determined by quantifying the samples on an Agilent Bioanalyzer.  Only samples with a 28S/18S ratio of 0.8 to 3.0 and a RIN Score of >= 6.0 passed QC metrics and were accepted for analysis.

value: CD

value: F


title: ASD 61

description: Genome-Wide Human SNP Array 6.0


title: [gene] aCD3-aCD28 diagnosis-CD subject-649 biological rep-13

description:
subject-ID_649
@52084400978709110317428272788091


title: [gene] aCD3-aCD28 diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
@52084400980523112917428617727004

value: M


title: DTR 4 IP

data_processing:
Base calls were performed using the built-in Illumina basecaller.
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner (2.0.8).
Reads Count per Million mapped reads (CPM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples.
Genome_build: M. musculus GRCm38
Supplementary_files_format_and_content: *.cpm.txt: Tab-delimited text files include CPM values for each sample.

extract_protocol:
Cochleae were isolated and immediately flash-frozen using liquid nitrogen prior to RNA isolation. Cochleae were homogenized, 5% of the homogenate was kept for direct RNA extraction (input) and the 95% remaining was processed for ribosome immunoprecipitation followed by RNA extraction (IP).
Libraries were prepared with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA, Inc.)

value: RiboTag

value: Glast-Cre+ cells

value: DTR treated

tag: sample type

value: IP


title: ASD 60

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)

value: Japanese


title: [exon] aCD3-aCD28 diagnosis-CD subject-1016 biological rep-18


title: DTR 4 input

value: Input


title: [gene] aCD3-aCD28 diagnosis-CD subject-643 biological rep-12

description:
subject-ID_643
@52084400978709110317428272788122


title: [gene] aCD3-aCD28 diagnosis-CD subject-558 biological rep-11

description:
subject-ID_558
@52084400980522112917428617726954


title: ASD 58

description: Genome-Wide Human SNP Array 6.0

value: male


title: Control 4 input

value: No treatment


title: Control 4 IP


title: EEC_MUT_3

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
Sequences were trimmed in order to remove adaptors and low quality bases
Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b (Dobin et al., 2013) and gene expression was measured from the mapped reads by using built-in STAR module (--quantMode GeneCounts).
Genome_build: GRCz11 - release 92 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for annotations for each Sample

organism: Danio rerio

source_name: Enteroendocrine cells (EECs)

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols and staged according to Kimmel (Kimmel et al., 1995).

extract_protocol:
Enteroendocrine cells (EECs) were isolated by dissecting the gut from about 200 Tg(pax6b:GFP)ulg515 larvae at 4 dpf, taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase (Life Technologies) for 10 minutes. Cells were washed in HBSS (Mg2+ and Ca2+ free) containing  1% BSA and GFP-expressing EECs were selected by two consecutive FACS purifications, the first in the “yield mode” and the second in “the purity mode”, using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells (PECs) were also obtained from the Tg(pax6b:GFP)ulg515 line (Delporte et al., 2008b) by dissecting the dorsal pancreatic bud from about 200 27-hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X ( Gibco) supplemented with 100 U/ml collagenase IV (Life Technologies) for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos, the pax6sa0086 line  (Verbruggen et al., 2010) was first crossed with the Tg(pax6b:GFP)ulg515 line; heterozygous pax6bsa0086 fish harboring the transgene (pax6b:GFP) were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygotes were performed in triplicates following the same procedure than for the wild-type larvae. The accuracy of pax6bsa0086 homozygotes selection was verified after the RNA-seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples.
Each EEC or PEC sample obtained after FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer, lysed by freezing in liquid nitrogen and stored at -80°C according the the Smart-seq2 protocol (Picelli et al., 2014). cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay (Agilent technologies). 1 ng cDNA was used for preparing each cDNA library using Nextera-XT kit (Illumina) and sequenced on Hi-seq 2000 to obtain around 60 millions of reads (100 base paired-ends).

treatment_protocol: The following zebrafish transgenic and mutant lines were used: Tg(pax6b:GFP)ulg515 (Delporte et al., 2008b), TgBAC(pdx1:EGFP)bns13 (Helker et al., 2019), TG(-8.5nkx2.2a:GFP)ia2 (Pauls et al., 2007), pax6bsa0086 and pax6bsunrise (Verbruggen et al., 2010).

value: AB

value: Enteroendocrine cells

value: 4 dpf

tag: genotype


title: ASD 57

description: Genome-Wide Human SNP Array 6.0

value: female


title: [exon] aCD3-aCD28 diagnosis-CD subject-843 biological rep-17

first: Boyd

last: Steere

institute: Lilly

value: peripheral PBMC


title: DTR 3 IP

tag: age

value: Cochlea


title: EEC_MUT_2


title: [gene] aCD3-aCD28 diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
@52084400980523112917428617727025

value: CD

value: F


title: ASD 56

description: Genome-Wide Human SNP Array 6.0


title: [exon] aCD3-aCD28 diagnosis-CD subject-1045 biological rep-20


title: DTR 3 input

value: RiboTag


title: [gene] aCD3-aCD28 diagnosis-CD subject-528 biological rep-10

description:
subject-ID_528
@52084400978327102417428100272877

value: M


title: EEC_MUT_1


title: ASD 55

description: Genome-Wide Human SNP Array 6.0


title: Control 3 IP

value: Glast-Cre+ cells


title: [exon] aCD3-aCD28 diagnosis-CD subject-701 biological rep-15


title: EEC_WT_4

value: Wild type


title: ASD 54

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)


title: EEC_WT_3


title: Control 3 input


title: [gene] aCD3-aCD28 diagnosis-CD subject-280 biological rep-7

description:
subject-ID_280
@52084400980524112917428617727079


title: ASD 53

description: Genome-Wide Human SNP Array 6.0

value: Japanese


title: [gene] aCD3-aCD28 diagnosis-CD subject-243 biological rep-6

description:
subject-ID_243
@52084400978711110317428272788209


title: DTR 2 IP

value: DTR treated

value: IP


title: [exon] aCD3-aCD28 diagnosis-CD subject-1180 biological rep-21


title: [gene] aCD3-aCD28 diagnosis-CD subject-232 biological rep-5

description:
subject-ID_232
@52084400978711110317428272788234


title: ASD 52

description: Genome-Wide Human SNP Array 6.0

value: male


title: EEC_WT_2

value: AB


title: DTR 2 input

value: Input


title: [gene] aCD3-aCD28 diagnosis-CD subject-225 biological rep-4

description:
subject-ID_225
@52084400978711110317428272788215


title: [exon] aCD3-aCD28 diagnosis-CD subject-670 biological rep-14


title: EEC_WT_1

value: Enteroendocrine cells

value: 4 dpf


title: Control 2 IP

value: No treatment


title: [exon] aCD3-aCD28 diagnosis-CD subject-792 biological rep-16

value: peripheral PBMC


title: [gene] aCD3-aCD28 diagnosis-CD subject-372 biological rep-8

description:
subject-ID_372
@52084400978327102417428100272912

value: CD


title: [gene] aCD3-aCD28 diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400980525112917428617727144


title: Control 2 input

value: Cochlea


title: ASD 49

description: Genome-Wide Human SNP Array 6.0


title: PEC_MUT_2

source_name: Pancreatic endocrine cells (PECs)

value: Endocrine pancreas

value: 27 hpf


title: DTR 1 IP

value: RiboTag

value: Glast-Cre+ cells


title: [gene] aCD3-aCD28 diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978708110317428272788018

value: M


title: ASD 59

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)

value: Japanese


title: [exon] aCD3-aCD28 diagnosis-CD subject-649 biological rep-13

value: F


title: PEC_MUT_1


title: [exon] aCD3-aCD28 diagnosis-CD subject-558 biological rep-11


title: ASD 48

description: Genome-Wide Human SNP Array 6.0

value: male


title: PEC_MUT_3

value: AB


title: DTR 1 input

value: DTR treated

value: Input


title: [gene] aCD3-aCD28 diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978708110317428272788044


title: PEC_WT_3

value: Wild type


title: ASD 47

description: Genome-Wide Human SNP Array 6.0

value: female


title: PEC_WT_2


title: ASD 46

description: Genome-Wide Human SNP Array 6.0


title: ASD 51

description: Genome-Wide Human SNP Array 6.0


title: ASD 50

description: Genome-Wide Human SNP Array 6.0


title: ASD 45

description: Genome-Wide Human SNP Array 6.0


title: Control 1 IP

value: No treatment

value: IP


title: [exon] aCD3-aCD28 diagnosis-CD subject-643 biological rep-12

value: CD

value: peripheral PBMC


title: Control 1 input

value: Cochlea


title: [exon] aCD3-aCD28 diagnosis-CD subject-372 biological rep-8


title: SHSY5Y CYC065 T4

city: Belmont

first: Evon

last: Poon

state: Surrey

address: 15, Cotswold Road, Godstone Road

department: Clinical Studies

institute: Institute of Cancer Research

description: SH-SY-5Y cells treated with 1 µM CYC065 for 1 hr

hyb_protocol: Following fragmentation, 5.5 ug of ss c-DNA were hybridized for 16 hr at 45C on Gene Chip® human or mouse transcriptome expression array. GeneChips were washed and stained in the Gene Chip®  Fluidics station 450

scan_protocol: GeneChips were scanned using the Gene Chip® Scanner

data_processing:
Samples were RMA normalized using the “limma” package from R and differentially expressed genes were called using a linear model and empirical Bayes statistics from the “affy” package
The file GSE89197_DE_BE2C_and_SHSY5Y.xls contains fold changes and statistics for the BE(2)C and SHSY5Y cell line data.

label: biotin and DNA Labeling Reagent

source_name: 1 µM CYC065 for 1 hr

label_protocol: cRNA were prepared according to the standard Affymetrix GeneChip® WT PLUS Reagent Kit protocol from 100 ng total RNA and labeled (Gene Chip® human or mouse transcriptome expression array)

growth_protocol: Kelly, SKNAS, BE(2)C AND SH-SY-5Y cell lines were maintained in DMEM as recommended by the suppliers, supplemented with 10% fetal calf serum (FCS) (Gibco), and were maintained at 37°C under 5% CO2 in air.

extract_protocol: Cells or tissue were harvested using Qiagen mRNeasy Plus Kit

treatment_protocol: Kelly, BE(2)C AND SH-SY-5Y were treated with 1 µM CYC065 for 1 hour and SKNAS was treated with 5 µM CYC065 for 1 hour.  Mice were treated with CYC065 50 mg/kg or vehicle for 6 hours.

tag: cell line

value: SH-SY-5Y neuroblastoma cell line

value: 1 µM CYC065 for 1 hr


title: PEC_WT_1

value: Endocrine pancreas

value: 27 hpf


title: SHSY5Y CYC065 T6


title: SHSY5Y CYC065 T5


title: G&T_G1

city: København Ø

first: Victoria

last: Probst

address: Genomic Medicine, Blegdamsvej 9

country: Denmark

institute: Rigshospitalet, state hospital

description:
GT_G1
single cell RNA-seq
GT_merged_counts.txt

data_processing:
Fastq files were processed on a bash shell. Two rounds of trimming was performed using TrimGalore!. First trimming removed Nextera XT adaptors. Second trimming removed cDNA amplification adaptors.
Quality assessment of sequencing output was performed by two rounds of FastQC after each trim.
Trimmed sequences were aligned using pseudoaligner ’Spliced Transcripts Alignment to a Reference’ (STAR).
Files comprising reads per gene for each sample, which were merged in a single tab-delimited file imported into R studios as a count matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: *counts.txt: Count matrices.

source_name: T47D cell line

growth_protocol: Cells were cultured in 15 ml Complete growth medium in Nunclon Delta coated flasks with 75 cm2 culture area. Cells were grown in an incubator at 37 Cand 5% CO2. Cells had a doubling time of 32 h, and were passaged twice a week at dilution 1 : 4 using TrypLETM Express Enzyme (1 X)(Cat. nr. 12604013, GIBCOTM, NY, USA). Cell line was maintained in cell culture flasks with 75 cm2 culture area.

extract_protocol: NEBNext Single Cell/ Low Input RNA Library Prep Kit (NEB), SMART-seq HT kit (Takara), and non-commercially available protocol Genome & transcriptome sequencing (G&T).

treatment_protocol: T47D single cell suspension was prepared by removal of growth medium and subsequent washing of cell layer using 10 ml PBS. Cells were disaggregated with 2 ml TrypLETM Express Enzyme (1X) (cat nr. 12604013, GibcoTM, USA) for approximately 2 min in an incubator at 37 C. Reaction was stopped adding full growth media (RPMI-1640+GlutaMAXTM (cat nr. 61870-010, GibcoTM, UK) + 10% Fetal Bovine Serum (FBS) + 5% Penicillin/ Streptamycin) in double the amount of TrypLETM. Suspension was spun down 3 min 1200 rpm. Cells were washed once in PBS, resuspended in FACS buffer (PBS + 0.04 % bovine serum albumin (BSA)), and filtered using a 100 μm strainer.

value: Breast cancer cell line

tag: passages


title: G&T_H1

description:
GT_H1
single cell RNA-seq
GT_merged_counts.txt


title: [exon] aCD3-aCD28 diagnosis-CD subject-528 biological rep-10

city: Indianapolis

address: Lilly Corporate Center

value: M


title: ASD 43

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)

value: Japanese


title: SHSY5Y CYC065 C3

description: Untreated SH-SY-5Y cells

source_name: Untreated

value: Untreated


title: G&T_E2

description:
GT_E2
single cell RNA-seq
GT_merged_counts.txt


title: ASD 42

description: Genome-Wide Human SNP Array 6.0

value: male


title: [exon] aCD3-aCD28 diagnosis-CD subject-280 biological rep-7


title: ASD 41

description: Genome-Wide Human SNP Array 6.0


title: ASD 40

description: Genome-Wide Human SNP Array 6.0


title: G&T_E1

description:
GT_E1
single cell RNA-seq
GT_merged_counts.txt


title: SHSY5Y CYC065 C2

description: Untreated SH-SY-5Y cells


title: WT Pellet 1 replicate 3

city: Berlin

first: Benjamin

last: Lenzen

address: Philippstr. 13, House 22

department: Institute of Biology

institute: Humboldt University of Berlin

data_processing:
The samples were adapter trimmed and filtered for reads size between 40 and 60 bp, using TrimGalore (0.6.4)
The 8 bp UMI sequence in the RNA adapter was extracted and reads were deduplicated after mapping using umi_tools (0.5.4)
Mapping was performed using STAR (2.5.3). The Arabdiopsis thaliana genome TAIR 10 was used as reference.
Read counts were calculated using the featureCounts function of Rsubread (2.0.1) for all protein-coding genes in the chloroplast, including intronic sequences and 100 bp of upstream and downstream UTR.
Read counts of all samples were normalized by gene length and library depth using TPM. In order to avoid biased results from stochastic noise, a high pass filter was used to exclude genes from the analysis, which had less than 5 read counts in any sample. The TPM scores for each gene were log2-transformed for the calculation of enrichment values of pulldown samples over input samples and for the calculation of significance of enrichment by a one-sided, paired t-test using the three replicates of input and pulldown samples.
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel sheet with TPM values and enrichment calculations for all samples

organism: Arabidopsis thaliana

source_name: 14 days old seedlings

growth_protocol: Arabidopsis thaliana Columbia-0 were grown on a soil/vermiculite 4:1 mixture with a 16-h-light/8-h-dark cycle at 21°C in a CLF growth cabinet at 120 µmol·m−2·s−1 for 14 days.

extract_protocol:
Arabidopsis thaliana plants were harvested in triplicates after 14 days and flash-frozen in liquid nitrogen. The flash-frozen plant material was ground in liquid nitrogen. Between 250 to 350 mg plant material was suspended in 3 ml RIP-seq lysis buffer containing formaldehyde (50 mM HEPES-KOH pH 8.0, 200 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 0.5% Nonidet P-40, 0.5% Sodium deoxycholate, 1x cOmpleteTM, EDTA-free Protease Inhibitor Cocktail (Roche), 1% formaldehyde) per 1 g plant material. Crosslinking was performed for 10 min at room temperature, while samples were constantly rotated and quenched by the addition of 125 mM glycine with subsequent incubation at room temperature for 5 minutes. The plant extract was centrifuged for 20 min at 20,000xg and 4°C to remove insoluble plant material. An aliqout of the supernatant was used for a BCA assay (Pierce™ BCA™ Protein-Assay), in order to normalize the input amount used for immunoprecipitation according to protein content. The rest of the supernatant was stored at -80°C.
For the RIP 8 µl affinity-purified anti-CP31A antibody (Kupsch et al., 2012) was bound to 50 µl Dynabeads ProteinG (Invitrogen) under rotation (15 rpm). The plant extract was thawed and centrifuged for 10 min at 20,000xg and 4°C. A volume representing approximately 2 mg of protein of each sample was filled up to 790 µl using CO-IP buffer  (150 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 0.5% Nonidet P-40, 5µg/ml Aprotinin). 10 µl RNaseI (0.5U/µl) were added to each sample, as well as the antibody-coated magnetic beads resuspended in 200 µl CO-IP buffer. The samples were then incubated for 60 min at 15 rpm and 4°C. 190 µl of the antibody-bead solution was taken as the input sample. After the IP the beads were washed four times in CoIP buffer and resuspended in Proteinase K buffer (100 mM NaCl, 10 mM Tris-HCl pH 7.0, 1 mM EDTA, 0.5% SDS). 10 µl SDS (10%) were added to the input samples.
The crosslink was reversed with 0.1 mg/ml Proteinase K (ThermoFisher Scientific) at 50°C for 1 h and RNA was extracted from input and pellet fractions using TRIzol and RNA Clean and Concentrator Columns (Zymo Research) according to the manufacturer’s instructions.

value: seedlings

tag: cultivar

value: WT

value: 14 days

tag: light regime

value: long-day

tag: temperature

value: 21 degrees C

tag: rip antibody


title: G&T_D1

description:
GT_D1
single cell RNA-seq
GT_merged_counts.txt

tag: cell type


title: b-2M-SPa-6+c-kit+ differentiating spermatogonia sample 2

city: Fontenay aux roses

first: Pierre

last: Fouchet

address: 10, route du panorama

country: France

institute: CEA

hyb_protocol: Following fragmentation, 3,6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip MouseGene2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 Scanner.

data_processing: Data were normalized using RMA and statistical analysis was realized on R usin CDF file V19.

source_name: flow sorted adult germinal cells

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation PicoV2 protocol from 500 pg total RNA.

growth_protocol: Adult mouse testis biopsies

extract_protocol: Cell suspension was analysed and cell populations were sorted by flow cytometry. Sorted  cells were retrieved in the lysis buffer from the RNeasy micro kit from Qiagen and RNA repared  according to the manufacturer's instructions.

treatment_protocol: Murine testicular single-cell suspensions were prepared from 2- to 3-month-old FVB/N mice. The immunomagnetic selection of α6+ cells was performed using anti-α6 integrin-PE (GoH3) (BD Pharmingen) and anti-PE (Miltenyi Biotec) microbeads according to the manufacturers’ protocols. Hoechst staining (5 μg/ml) of the cell suspensions was performed. The cells were then labeled with β2m-FITC (Santa Cruz) and anti-CD117-APC (2B8) antibodies (BD Pharmingen).

value: testis


title: [exon] aCD3-aCD28 diagnosis-CD subject-508 biological rep-9

value: CD

value: F

value: peripheral PBMC


title: b-2M-SPa-6+c-kit- undifferentiated spermatogonia sample 1


title: ASD 38

description: Genome-Wide Human SNP Array 6.0

tag: disease

tag: race


title: SHSY5Y CYC065 C1

description: Untreated SH-SY-5Y cells

value: SH-SY-5Y neuroblastoma cell line

tag: treatment


title: G&T_D2

description:
GT_D2
single cell RNA-seq
GT_merged_counts.txt


title: b-2M-SPa-6+c-kit+ differentiating spermatogonia sample 1


title: BE2C in vitro CYC065 C2

description: Untreated BE(2)C cells

value: BE(2)C neuroblastoma cell line


title: [exon] aCD3-aCD28 diagnosis-CD subject-225 biological rep-4

tag: stimulation

tag: diagnosis


title: b-2M-SPa-6+c-kit- undifferentiated spermatogonia sample 3


title: b-2M-SPa-6+c-kit+ differentiating  spermatogonia sample 3


title: BE2C in vitro CYC065 T4

description: BE(2)C cells treated with 1 µM CYC065 for 1 hr

value: 1 µM CYC065 for 1 hr


title: BE2C in vitro CYC065 T6


title: BE2C in vitro CYC065 T5


title: WT Pellet 1 replicate 2


title: WT Pellet 1 replicate 1


title: ASD 37

description: Genome-Wide Human SNP Array 6.0

tag: gender


title: [exon] aCD3-aCD28 diagnosis-CD subject-138 biological rep-2

tag: Sex

value: M

tag: batch

tag: tissue


title: G&T_C1

description:
GT_C1
single cell RNA-seq
GT_merged_counts.txt

value: Breast cancer cell line


title: BE2C in vitro CYC065 C3

description: Untreated BE(2)C cells


title: [exon] aCD3-aCD28 diagnosis-CD subject-232 biological rep-5


title: WT Input 1 replicate 3

tag: genotype

tag: age

value: none (input)


title: G&T_B2

description:
GT_B2
single cell RNA-seq
GT_merged_counts.txt

tag: cell line

tag: passages


title: ASD 35

description: Genome-Wide Human SNP Array 6.0

value: Autism spectrum disorder (ASD)

value: Japanese


title: WT Input 1 replicate 2

value: seedlings

tag: cultivar

tag: light regime


title: ASD 34

description: Genome-Wide Human SNP Array 6.0

value: male


title: G&T_B1

description:
GT_B1
single cell RNA-seq
GT_merged_counts.txt


title: WT Input 1 replicate 1

value: WT

value: 14 days

tag: temperature

tag: rip antibody


title: [exon] aCD3-aCD28 diagnosis-CD subject-186 biological rep-3


title: G&T_A2

description:
GT_A2
single cell RNA-seq
GT_merged_counts.txt

tag: cell type


title: ASD 33

description: Genome-Wide Human SNP Array 6.0

tag: disease

tag: race


title: G&T_A1

description:
GT_A1
single cell RNA-seq
GT_merged_counts.txt


title: b-2M-SPa-6+c-kit- undifferentiated spermatogonia sample 2