title: Satb2 cKO rep6

city: Innsbruck

first: Galina

last: Apostolova

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to mm10 using RNA STAR (default parameters)
Reads were counted using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing gene counts

source_name: cortex

extract_protocol:
Visual cortex was dissected  from 3 month-old Satb2flx/flx and Satb2 cKO mice and snap-frozen in liquid nitrogen. RNA was extracted with Tri reagent (Sigma) and treated with DNAse I (Life Technologies) according to manufacturer's instructions.
Libraries were made according to Illumina standard protocols

value: neocortex

tag: age

value: 3 months


title: Satb2 cKO rep5

status: Public on Feb 19 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype


title: AB2776 (scRNA-Seq)

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: [AB*.txt]  tab-delimited text files include mRNA molecule count values for each Sample
[metadata.txt]  file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: Auricular lymph node

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
[treatment protocol (1)]  Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
[treatment protocol (2)]  mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

value: Lymph node

tag: cell type

value: innate immune cells

tag: selection marker

tag: infection

value: PBS (control)

tag: time point

value: Intradermal injection of inactivated pathogen

tag: replicate id

value: PBS control rep.2

tag: mouse age

value: 8 weeks


title: Case1

type: genomic

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

country: Spain

institute: IDIBAPS

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Samples were hybridized onto  Affymetrix OncoScan FFPE Assay ki arrays and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
CHP files generated by Oncoscan console 1.3.
[Primary data description] Nexus biodiscovery 9.0 edition Software. Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozygosity regions were considered when size was >5Mb.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Laterocervical Lymph Node

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: disease state

value: Burkitt like lymphoma with 11q

tag: gender

value: male

value: Laterocervical Lymph Node

tag: sample type

value: FFPE


title: AB2775 (scRNA-Seq)


title: D11 (Agilent)

city: Houston

first: Hui

last: Yao

state: TX

address: 1515 Holcombe Blvd.

department: Bioinformatics and Computational Biology

country: USA

institute: MD Anderson Cancer Center

description: Genomic DNA extracted from bladder samples was genotyped using a custom aCGH array.

hyb_protocol: Microarray from Agilent Technologies

scan_protocol: Agilent Technologies Scanner G2505B US23502362 using feature extraction 9.5

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and normalization.

source_name: Normal urothelium (NU)

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) Protocol Version 3.0

extract_protocol: DNA from each sample was extracted using Qiagen kit

tag: tumor stage

value: Normal urothelium (NU)

value: Human bladder

source_name: Normal urothelium from ureter (reference)

value: Human ureter


title: NT-input

city: Edison

first: Jiali

last: Li

state: middlesex

address: 65 James ST

department: Neuroscience Intitute

institute: HMH JFK Medical Center

description: hMeDIP seq

library_source: genomic

data_processing:
Base calling were performed using Off-Line Basecaller software (OLB V1.8)
Pass Solexa CHASTITY quality filter
The clean reads were aligned to mouse genome (UCSC mm10) using Bowtie2 software
Aligned reads were used for peak calling, using a q-value threshold of 10 −4 by MACS2 software
mRNA, LncRNA associated hMeDIP enriched regions (peaks) were annotated by the nearest gene using the newest UCSC RefSeq database
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Peak annotation Excel files

source_name: Cortical neurons

extract_protocol: DNA samples were fragmented to a size range of ∼200-800bp with a Diagenode Bioruptor. About 1 μg of fragmented DNA was prepared for Illumina HiSeq 4000 sequencing as the following steps: 1) End repair of DNA samples; 2) A single ‘A’ base was added to the 3’ ends; 3) Ligation of Illumina’s genomic adapters to DNA fragments; 4) hMeDIP to enrich Hydroxymethylated DNA by anti-5-Hydroxymethylcytosine antibody; 5) PCR amplification to enrich precipitated fragments; 6) Size selection of ∼300-900bp DNA fragments using AMPure XP beads. The completed libraries were quantified by Agilent 2100 Bioanalyzer.

value: Cortical neurons

tag: ip antibody


title: OL-2016-1423-13

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

description: Mixture of 10% CD8+ T cells and 90% placental cells.

hyb_protocol: Arrays were hybridized, washed, and stained in GeneChip Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: Arrays were scanned using the GeneChip 3000 7G scanner according to manufacturer's protocols.

data_processing: Data processed using Affymetrix OncoScan Console (v1.3) software.

label: Biotin

label_protocol: MIP probe annealing and hybridization were performed according to manufacturer's protocols.

extract_protocol: Genomic DNAs were extracted according to manufacturer's standard protocols.

tag: disease

value: Normal

value: T mixed

tag: preparation


title: NT3

description: hMeDIP seq


title: B3 (Agilent)


title: OL-2016-1423-12

description: Reactive lymphoid tissue in tonsil sample.

source_name: Reactive lymphoid tissue in tonsil

value: Reactive Tonsil

value: Mixed


title: NT2

description: hMeDIP seq


title: AB2751 (scRNA-Seq)

value: Lymph node

value: innate immune cells

value: Mycobacterium smegmatis

value: Ms day1 rep.3


title: B4 (Agilent)


title: NW3

description: hMeDIP seq

value: Wild type


title: OL-2016-1423-11

description: Plasmablastic lymphoma sample.

source_name: Plasmablastic lymphoma

value: PBL

value: B


title: Satb2 cKO rep3

value: neocortex

tag: age

value: 3 months


title: OL-2016-1423-10

description: Classical Hodgkin lymphoma sample.

source_name: Classical Hodgkin lymphoma

value: CHL

value: FFPE


title: NT1

description: hMeDIP seq


title: Satb2 cKO rep2

tag: strain


title: NW2

description: hMeDIP seq


title: Satb2 cKO rep1

tag: tissue


title: NW1

description: hMeDIP seq

tag: genotype


title: AB2731 (scRNA-Seq)

tag: cell type

value: Intradermal injection of inactivated pathogen

value: 8 weeks


title: OL-2016-1423-09

description: Classical Hodgkin lymphoma sample.


title: Floxed rep6


title: Satb2 cKO rep4


title: Floxed rep5


title: GT3

description: hMeDIP seq

source_name: astrocytes

value: astrocytes


title: AB2729 (scRNA-Seq)

tag: selection marker

value: Nippostrongylus brasiliensis

value: Nb day1 rep.3


title: OL-2016-1423-07

description: Mucosa-associated lymphoid tissue lymphoma sample.

value: MALT


title: AB2728 (scRNA-Seq)

value: Lymph node

tag: infection


title: Floxed rep4


title: OL-2016-1423-08

description: Diffuse large B-cell lymphoma sample.

source_name: Diffuse large B-cell lymphoma

value: DLBCL


title: GT2

description: hMeDIP seq


title: OL-2016-1423-06

description: Nodular lymphocyte-predominant Hodgkin lymphoma sample.

value: NLPHL

value: Mixed


title: AB2727 (scRNA-Seq)

value: innate immune cells

value: Mycobacterium smegmatis

tag: time point

value: Ms day2 rep.4


title: GT1

description: hMeDIP seq


title: Floxed rep3

value: neocortex


title: AB2726 (scRNA-Seq)

tag: replicate id


title: OL-2016-1423-05

description: Peripheral T-cell lymphoma sample.

source_name: Peripheral T-cell lymphoma

value: PTCL

value: T


title: OL-2016-1423-04

description: Peripheral T-cell lymphoma sample.

value: FFPE


title: Floxed rep2

value: 3 months


title: AB2730 (scRNA-Seq)

value: Intradermal injection of inactivated pathogen

tag: mouse age

value: 8 weeks


title: GT-input

description: hMeDIP seq

value: astrocytes


title: GW3

description: hMeDIP seq

value: Wild type


title: Floxed rep1


title: AB2274 (scRNA-Seq)

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Candida albicans

value: Ca day1 rep.3


title: AB2273 (scRNA-Seq)

value: Lymph node


title: Case2

description: Cytoscan HD

hyb_protocol: Samples were hybridized onto Affymetrix CytoScan HD Array arrays and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
CHP files generated by Chas 3.2.
[Primary data description] Nexus biodiscovery 9.0 edition Software.  Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozygosity regions were considered when size was >5Mb. See "Global table of CN and CNN-LOH.xlsx" linked to the SuperSeries record.

source_name: Axilary Lymph Node

label_protocol: CytoScan™ Reagent Kit

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

tag: disease state

value: Burkitt like lymphoma with 11q

value: male

value: Axilary Lymph Node

value: frozen tissue


title: OL-2016-1423-03

description: Peripheral T-cell lymphoma sample.

value: PTCL


title: GW2

description: hMeDIP seq


title: AB2272 (scRNA-Seq)

value: innate immune cells


title: 621 V170M Nutlin-treated

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
621-V170M-Nut
mRNA
processed data file: GeneCounts.txt

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were aligned to the mouse genome by Rsubread version 1.22.2.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Lymphoma cell line

extract_protocol:
Cells were collected in 1 mL Trizol and purification of mRNA was performed using the RNeasy (Qiagen) kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with nutlin-3a (5 μM) for 12 hours in the presence of the broad-spectrum caspase inhibitor, QVD-OPH (25 μM) (MP-Biomedicals Cat# OPH-109), to prevent cell death.

tag: strain/background

value: Em-myc

tag: cell line

tag: trp53 mutation

tag: nutlin treatment

value: nutlin-3a treated


title: OL-2016-1423-02

description: Peripheral T-cell lymphoma sample.

tag: disease

value: T

value: FFPE


title: GW-input

description: hMeDIP seq

value: astrocytes

tag: ip antibody


title: 621 V170M untreated

description:
621-V170M-Con
mRNA
processed data file: GeneCounts.txt

value: untreated


title: GW1

description: hMeDIP seq

value: Wild type


title: AB2271 (scRNA-Seq)

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Mycobacterium smegmatis

value: Intradermal injection of inactivated pathogen

value: Ms day2 rep.3

value: 8 weeks


title: OL-2016-1411-13

description: High grade B-cell lymphoma sample.

source_name: High grade B-cell lymphoma

value: HGBCL

value: B

tag: preparation


title: OL-2016-1423-01

description: Peripheral T-cell lymphoma sample.

value: PTCL


title: 621 R270H Nutlin-treated

description:
621-R270H-Nut
mRNA
processed data file: GeneCounts.txt


title: Case7

description: Cytoscan HD

value: Burkitt like lymphoma with 11q

tag: gender

value: male

value: Laterocervical Lymph Node

tag: sample type

value: frozen tissue


title: AB2270 (scRNA-Seq)

tag: strain

tag: tissue

value: Lymph node


title: OL-2016-1411-12

description: Follicular lymphoma sample.

source_name: Follicular lymphoma

value: FL

tag: cell type

value: FFPE


title: AB2268 (scRNA-Seq)

value: innate immune cells

tag: selection marker

tag: infection

value: Ms day1 rep.2


title: OL-2016-1411-11

source_name: Mucosa-associated lymphoid tissue lymphoma

value: MALT


title: AB2269 (scRNA-Seq)

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Mycobacterium smegmatis

tag: time point

tag: replicate id


title: 621 R270H untreated

description:
621-R270H-Con
mRNA
processed data file: GeneCounts.txt

value: Em-myc

value: untreated


title: OL-2016-1411-10

description: Anaplastic large cell lymphoma sample.

source_name: Anaplastic large cell lymphoma

value: ALCL

value: T


title: OL-2016-1411-08

description: Angioimmunoblastic T-cell lymphoma sample.

source_name: Angioimmunoblastic T-cell lymphoma

value: AITL


title: AB2266 (scRNA-Seq)

source_name: Auricular lymph node

value: Intradermal injection of inactivated pathogen

tag: mouse age

value: 8 weeks


title: 621 negative control Nutlin-treated

description:
621-pMIG-Nut
mRNA
processed data file: GeneCounts.txt

tag: strain/background

value: negative control

value: nutlin-3a treated


title: AB2267 (scRNA-Seq)

value: Lymph node


title: 621 R246Q Nutlin-treated

description:
621-R246Q-Nut
mRNA
processed data file: GeneCounts.txt

tag: cell line


title: AB2750 (scRNA-Seq)

value: Ms day1 rep.3


title: AB2188 (scRNA-Seq)

value: innate immune cells

value: Candida albicans

value: Ca day1 rep.1


title: AB2187 (scRNA-Seq)

value: Nippostrongylus brasiliensis

value: Nb day1 rep.1


title: OL-2016-1411-07

description: Peripheral T-cell lymphoma sample.

value: PTCL

value: FFPE


title: OL-2016-1411-06

description: Normal B cells.

source_name: Normal B cells

value: Normal

value: B

value: Blood


title: 621 I192S Nutlin-treated

description:
621-I192S-Nut
mRNA
processed data file: GeneCounts.txt

value: Em-myc

tag: trp53 mutation


title: 621 G280 Nutlin-treated

description:
621-G280-Nut
mRNA
processed data file: GeneCounts.txt

tag: nutlin treatment


title: OL-2016-1411-05

description: Normal B cells.

tag: disease


title: 621 I192S untreated

description:
621-I192S-Con
mRNA
processed data file: GeneCounts.txt

value: untreated


title: OL-2016-1411-04

description: Normal T cells.

source_name: Normal T cells

value: T


title: HepG2_RNASeq_CsA_Rep2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
RNA-seq was processed using the tuxedo protocol
Differential gene expression determined using cuffdiff v2.2.1 against the hg19 reference genome, (last update of RefGene.gtf july 2018)
processed data files format and content: fpkm_tracking files with 13 columns tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status
Genome_build: hg19

source_name: hepatocarcinoma (HepG2) cell

growth_protocol: HepG2 cells were cultured in DMEM/F12 with 10% fetal calf serum and 1% penicillin-streptomycin.

extract_protocol:
RNA-Seq: Total RNA from 2 replicates of HepG2 treated and untreated cells were extracted using the RNeasy Mini Kit (Qiagen). DNase treatment was performed with RQ1 RNase-Free DNase (M101, Promega).
The ChIP-seq and RNA-seq sequencing libraries were prepared according to  Illumina protocols for the HSeq2500 at the Norwegian Sequencing Center.

treatment_protocol: HepG2 cells were either cultured as above under proliferating conditions, or cultured with 10 µM CsA (Sigma-Aldrich) for 72 h before harvesting for analyses.

value: HepG2 cells

value: hepatocarcinoma

tag: treatment

value: CsA treatment


title: 621 R246Q untreated

description:
621-R246Q-Con
mRNA
processed data file: GeneCounts.txt


title: 621 G280 untreated

description:
621-G280-Con
mRNA
processed data file: GeneCounts.txt


title: OL-2016-1411-03

description: Normal T cells.

tag: preparation


title: AB2186 (scRNA-Seq)

value: Lymph node

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Intradermal injection of inactivated pathogen

value: Nb day1 rep.2

value: 8 weeks


title: HepG2_RNASeq_CsA_Rep1


title: OL-2016-1411-02

description: Normal NK cells.

source_name: Normal NK cells

value: NK cell


title: AB2120 (scRNA-Seq)

value: Nippostrongylus brasiliensis

value: Nb day2 rep.3


title: HepG2_RNASeq_Ctrl_Rep2


title: 287 V170M Nutlin-treated

description:
287-V170M-Nut
mRNA
processed data file: GeneCounts.txt

value: nutlin-3a treated


title: 287 V170M untreated

description:
287-V170M-Con
mRNA
processed data file: GeneCounts.txt


title: HepG2_RNASeq_Ctrl_Rep1


title: AB2114 (scRNA-Seq)

value: Candida albicans

value: Ca day2 rep.2


title: AB2118 (scRNA-Seq)


title: 287 R270H Nutlin-treated

description:
287-R270H-Nut
mRNA
processed data file: GeneCounts.txt

value: Em-myc


title: OL-2016-1405-12

description: Reactive lymphoid tissue in lymph node sample.

source_name: Reactive lymphoid tissue in lymph node

value: Reactive Lymph Node

value: Mixed

value: FFPE


title: 287 R270H untreated

description:
287-R270H-Con
mRNA
processed data file: GeneCounts.txt

value: untreated


title: OL-2016-1411-01

description: Normal NK cells.

value: Normal

value: Blood


title: OL-2016-1405-11

description: Reactive lymphoid tissue in tonsil sample.

source_name: Reactive lymphoid tissue in tonsil

value: Reactive Tonsil


title: AB2121 (scRNA-Seq)

value: Lymph node

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Intradermal injection of inactivated pathogen

value: Nb day2 rep.4


title: AB2048 (scRNA-Seq)

value: 8 weeks


title: HepG2_ChIPSeq_CsA_LMNA

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.25.0
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth for each chromosom individually by downsampling the deeper sequenced experiment using home built python script DownsampleSam
Peak calling was done using EDD version 1.1.15, run 10 times on each samples in order to pptimized binSize and GapPenalty settings
LAD with a length less than the estimated Edd technical replicat resolution were reomove (19 on 951 total LADs, or <2 % of domains )
processed data files format and content: bed files with 3 columns: chromosome, start position, end position, score
processed data files format and content: bedgraph files with 4 columns: chromosome, start position, end position, score
Genome_build: hg19

extract_protocol:
ChipSeq: ChIP was performed as previously described (Rønningen et al., 2015). Untreated and CsA treated HepG2 cells were cross-linked with 1% formaldehyde for 10 min, with 5 x106 cells per condition. The cells were lysed for 10 min in RIPA lysis buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% triton X-100, 1% SDS, 0.1% sodium deoxycholate, 1 mM PMSF, and protease inhibitors). To generate 200-500bp DNA fragments the cells were sonicated 4 times for 10 min in a Bioruptor (Diagenode). The samples were sedimented at 10000g for 10 min and the supernatant was diluted 10 times in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1 mM PMSF, and protease inhibitors). Part of the diluted chromatin were kept for input; the remaining chromatin was incubated overnight at 4°C with primary antibodies coupled to magnetic beads DynaBeads Protein G (Invitrogen). The antibodies used were mouse anti-Lamin A/C (10µg, sc7292x, Santa Cruz Biotechnology) and rabbit anti-LaminB1 (10µg, ab16048, Abcam). The ChIP samples were washed three times in ice-cold-RIPA buffer. The samples were incubated for 6 hours at 68°C in elution buffer (50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 1% SDS) and 40 ng of proteinase K, for crosslink reversal an DNA elution. The DNA was extracted and dissolved in H2O and processed for Illumina library preparation and sedquencing.
The ChIP-seq and RNA-seq sequencing libraries were prepared according to  Illumina protocols for the HSeq2500 at the Norwegian Sequencing Center.

value: HepG2 cells

value: hepatocarcinoma

value: CsA treatment

tag: chip-antibody

value: Santa Cruz mouse monoclonal sc7292x


title: OL-2016-1405-10


title: AB2047 (scRNA-Seq)

value: Candida albicans

value: Ca day2 rep.2


title: 621 negative control untreated

description:
621-pMIG-Con
mRNA
processed data file: GeneCounts.txt

value: Em-myc

value: negative control


title: 287 R246Q Nutlin-treated

description:
287-R246Q-Nut
mRNA
processed data file: GeneCounts.txt

value: nutlin-3a treated


title: HepG2_ChIPSeq_Ctrl_LMNB

value: Abcam rabbit polyclonal Ab16048


title: OL-2016-1405-09

description: Diffuse large B-cell lymphoma sample.

value: DLBCL

value: B

value: FFPE


title: AB2046 (scRNA-Seq)

value: Lymph node

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Ca day1 rep.1


title: HepG2_ChipSeq_Ctrl_LMNA

value: HepG2 cells


title: OL-2016-1405-08

description: Peripheral T-cell lymphoma sample.

value: PTCL

value: T


title: AB2045 (scRNA-Seq)

value: Mycobacterium smegmatis

value: Intradermal injection of inactivated pathogen

value: Ms day2 rep.2

value: 8 weeks


title: AB2111 (scRNA-Seq)

value: Candida albicans

value: Ca day1 rep.2


title: HepG2_ChIPSeq_CsA_LMNB

value: hepatocarcinoma

value: CsA treatment

value: Abcam rabbit polyclonal Ab16048


title: AB2044 (scRNA-Seq)


title: OL-2016-1405-06

description: Follicular lymphoma sample.

value: FL

value: B

value: FFPE


title: AB2043 (scRNA-Seq)

value: Lymph node

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+

value: Ms day1 rep.1


title: Mig_RNA-seq

city: Shanghai

first: Chun-hui

last: Xu

state: Shanghai

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics

country: China

institute: Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were filtered by Seqtk(remove adapters, length less than 25 reads, ribosome RNA, Qual < 20 reads), clean sequenced reads were alignmented to hg38 by TopHat(2.0.9), allow2 mismatches and multihits <=2 per read.(RNA-seq)
Aligned reads were extracted by Htseq(0.9.1) with default parameters and normalized with TMM(trimmed mean of M values) method, FPKM were calculated by perl script.(RNA-seq)
Raw reads were filtered by Seqtk(remove adapters, length less than 25 reads, Qual < 20 reads), clean reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1 -p5.(ChIP-seq)
Peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set. BigWig files were generated by macs2 bdgcmp algorithm with default set.(ChIP-seq)
Genome_build: hg19 for ChIP-seq, hg38 for RNA-seq
Supplementary_files_format_and_content: FPKM files were calculated by definition.(RNA-seq)
Supplementary_files_format_and_content: BigWig files were generated by macs2 bdgcmp algorithm with default set.(ChIP-seq)

source_name: Myeloblast

growth_protocol: Kasumi-1 cells were cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
At 4 days after retrovirus infection of MIGR1 and CEBPa, GFP+ Kasumi-1 cells were harvested by flow sorting and RNA was extracted with TRIzol Reagent (Invitrogen). (RNA-seq)
At 3 days after retrovirus infection of CEBPa, GFP+ Kasumi-1 cells were sorted by BD FACSARIA III through FITC channel. Then they were crosslinked with 1% formaldehyde for 10 mins and then stopped by 125 mM Glycine. After lysis and sonication, 3 μg of HA-Tag (C29F4) Rabbit mAb (CST #3724) was incubated with chromatin sample overnight at 4 ℃, and 20μl protein A/G beads (Smart lifesciences SA032005) were used for immunoprecipitation. Finally, DNA were purified with PCR recovery kit (QIAGEN #28006).(ChIP-seq)
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina #RS-122-2001) and sequenced with Illumina HiSeq2500.(RNA-seq)
Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).(ChIP-seq)

value: leukemic cell line with an 8;21 chromosome translocation

tag: passages

value: 4-5 passages

tag: genotype/variation

value: overexpress MigR1 control vector


title: CEBPa_ChIP-seq

tag: chip antibody

value: HA-Tag (C29F4) Rabbit mAb (CST #3724)


title: OL-2016-1405-05

description: Diffuse large B-cell lymphoma sample.

source_name: Diffuse large B-cell lymphoma

value: DLBCL

tag: cell type


title: CEBPa_RNA-seq

value: overexpress CEBPa


title: AB2042 (scRNA-Seq)

tag: strain

tag: tissue

tag: selection marker

value: Mycobacterium smegmatis

value: Intradermal injection of inactivated pathogen

value: 8 weeks


title: AB2041 (scRNA-Seq)

tag: infection

value: Nippostrongylus brasiliensis

tag: time point

tag: replicate id

value: Nb day2 rep.2


title: AB2040 (scRNA-Seq)

value: Nb day1 rep.1

tag: mouse age


title: OL-2016-1405-04

value: AITL

value: T

value: FFPE


title: OL-2016-1405-02

description: Mantle cell lymphoma sample.

source_name: Mantle cell lymphoma

value: MCL

value: B


title: AB2039 (scRNA-Seq)

value: Lymph node

value: antigen-positive innate cells

value: CD45+, CD19-, CD3-, TCRb-, Antigen+


title: 287 I192S untreated

description:
287-I192S-Con
mRNA
processed data file: GeneCounts.txt

tag: strain/background

value: Em-myc

tag: cell line

tag: trp53 mutation

value: untreated


title: 47A V170M Nutlin-treated

description:
47A-V170M-Nut
mRNA
processed data file: GeneCounts.txt

tag: nutlin treatment

value: nutlin-3a treated


title: CEBPa_ChIP-seq-input

description: ChIP-seq input

value: leukemic cell line with an 8;21 chromosome translocation

value: 4-5 passages


title: 287 negative control untreated

description:
287-pMIG-Con
mRNA
processed data file: GeneCounts.txt

value: negative control


title: 287 G280 untreated

description:
287-G280-Con
mRNA
processed data file: GeneCounts.txt


title: 287 R246Q untreated

description:
287-R246Q-Con
mRNA
processed data file: GeneCounts.txt


title: 287 G280 Nutlin-treated

description:
287-G280-Nut
mRNA
processed data file: GeneCounts.txt


title: 287 I192S Nutlin-treated

description:
287-I192S-Nut
mRNA
processed data file: GeneCounts.txt


title: OL-2016-1405-07

description: Anaplastic large cell lymphoma sample.

tag: disease

value: ALCL

tag: preparation


title: 47A V170M untreated

description:
47A-V170M-Con
mRNA
processed data file: GeneCounts.txt


title: 287 negative control Nutlin-treated

description:
287-pMIG-Nut
mRNA
processed data file: GeneCounts.txt


title: AB2038 (scRNA-Seq)

value: Nippostrongylus brasiliensis

value: Intradermal injection of inactivated pathogen

value: 8 weeks


title: WT_Bleo2

first: Daping

last: Yang

address: No.320 Yueyang Road, Xuhui District

institute: SIBS

description: processed data file: Bleomycin-vs-PBS.FPKM.txt

data_processing:
Bowtie2 was used to map clean reads to reference gene. Bowtie2 parameters for SE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-p16-k 200
HISAT was used to map clean reads to reference genome. HISAT parameters for SE reads:-p8--phred64--sensitive-I1-X 1000
FPKM method is used in calculated expression level.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bleomycin-vs-PBS.FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Lung

growth_protocol: All mice were maintained in specific-pathogen-free (SPF) facility without co-housing.

extract_protocol:
Mice were euthanized and lung tissues were removed for RNA collection.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Four groups of mice were intranasally injected with PBS or Bleomycin for ten days.

value: wild type

value: Lung

tag: age

value: 6-8 weeks

tag: treatment

value: Bleomycin


title: WT_Bleo1

tag: genotype/variation


title: AB1851 (scRNA-Seq)

value: Lymph node

tag: cell type

value: innate immune cells

value: Mycobacterium smegmatis

value: Ms day7 rep.1


title: WT_PBS1

value: PBS


title: AB1850 (scRNA-Seq)

tag: strain

value: total immune cells


title: 47A R246Q Nutlin-treated

description:
47A-R246Q-Nut
mRNA
processed data file: GeneCounts.txt

source_name: Lymphoma cell line

value: Em-myc

value: nutlin-3a treated


title: 47A R270H untreated

description:
47A-R270H-Con
mRNA
processed data file: GeneCounts.txt

value: untreated


title: 47A R246Q untreated

description:
47A-R246Q-Con
mRNA
processed data file: GeneCounts.txt


title: 47A R270H Nutlin-treated

description:
47A-R270H-Nut
mRNA
processed data file: GeneCounts.txt


title: 47A negative control Nutlin-treated

description:
47A-pMIG-Nut
mRNA
processed data file: GeneCounts.txt

value: negative control


title: 47A I192S Nutlin-treated

description:
47A-I192S-Nut
mRNA
processed data file: GeneCounts.txt


title: 47A I192S untreated

description:
47A-I192S-Con
mRNA
processed data file: GeneCounts.txt


title: 47A G280 Nutlin-treated

description:
47A-G280-Nut
mRNA
processed data file: GeneCounts.txt


title: 47A negative control untreated

description:
47A-pMIG-Con
mRNA
processed data file: GeneCounts.txt


title: 47A G280 untreated

description:
47A-G280-Con
mRNA
processed data file: GeneCounts.txt


title: WT_PBS2

tag: tissue


title: AB1842 (scRNA-Seq)

tag: selection marker

value: Candida albicans

value: Ca day5 rep.1


title: AB1849 (scRNA-Seq)

tag: infection

value: Intradermal injection of inactivated pathogen

value: 8 weeks


title: AB1846 (scRNA-Seq)

tag: time point

value: Ms day2 rep.1


title: AB1845 (scRNA-Seq)

tag: replicate id


title: AB1848 (scRNA-Seq)

tag: mouse age


title: AB1847 (scRNA-Seq)


title: AB1841 (scRNA-Seq)


title: AB1843 (scRNA-Seq)


title: OL-2016-1405-03

description: Mucosa-associated lymphoid tissue lymphoma sample.

value: MALT

value: B

value: FFPE


title: NW-input

description: hMeDIP seq

source_name: Cortical neurons

value: Cortical neurons

tag: genotype

value: Wild type

tag: ip antibody


title: AB1835 (scRNA-Seq)

value: Lymph node

value: innate immune cells

value: day0 control rep.1


title: AB1837 (scRNA-Seq)

value: total immune cells

value: Ca day2 rep.1


title: AB1840 (scRNA-Seq)


title: AB1839 (scRNA-Seq)


title: AB1833 (scRNA-Seq)


title: AB1838 (scRNA-Seq)


title: AB1834 (scRNA-Seq)


title: AB1832 (scRNA-Seq)


title: AB1790 (scRNA-Seq)

value: Nippostrongylus brasiliensis

value: Nb day7 rep.1


title: AB1791 (scRNA-Seq)


title: Md-tra-RNAi-treated genotypic male head replicate 1

first: Richard

last: Meisel

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description:
RNAi_head_pub.tsv
tra-SR-H1

data_processing:
Illumina Casava v 1.8 was used for basecalling.
Sequenced reads were mapped to house fly genome assembly v2.0.2 using hisat2 in HISAT2 v0.12.2
The aligned reads were assigned to all annotated genes with htseq-count in HTSeq v0.9.1
The HTSeq output was used as input into DESeq2 v1.16.1 to identify differentially expressed genes with a model (Expression ~ genotypic sex + RNAi treatment + genotypic sex*RNAi treatment). The model allows for pair-wise comparisons between individuals with either the same genotypic sex or RNAi treatment.
Genome_build: house fly genome assembly v2.0.2 and annotation release 102
Supplementary_files_format_and_content: tab-delimited text files include pair-wise comparison, log2FoldChange, and FDR-corrected P value

organism: Musca domestica

source_name: Head

extract_protocol:
Abdomen and head was dissected from individaul flies and frozen in liquid nitrogen. RNA was extracted from the tissue samples from the individual flies with the NucleoSpin RNAII kit following the manufacturer’s protocol including DNA digestion steps. The Illumina TruSeq Stranded mRNA Sample Preparation Kit was used with 1.5ug (1.2ug for GFP-female-H2) of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotypic sex

value: male

tag: phenotypic sex

tag: RNAi treatment

value: Md-tra RNAi


title: GFP-RNAi-treated genotypic female head replicate 1

description:
RNAi_head_pub.tsv
GFP-female-H2

value: female

value: GFP RNAi


title: GFP-RNAi-treated genotypic male head replicate 3

description:
RNAi_head_pub.tsv
GFP-male-H3


title: Md-tra-RNAi-treated genotypic male head replicate 2

description:
RNAi_head_pub.tsv
tra-SR-H2


title: Md-tra-RNAi-treated genotypic male abdomen replicate 2

description:
RNAi_abdomen_pub.tsv
tra-SR-A2

source_name: Abdomen


title: Md-tra-RNAi-treated genotypic female head replicate 2 (sex-reversed males)

description:
RNAi_head_pub.tsv
tra-N-H3


title: GFP-RNAi-treated genotypic male head replicate 1

description:
RNAi_head_pub.tsv
GFP-male-H1


title: Md-tra-RNAi-treated genotypic male abdomen replicate 3

description:
RNAi_abdomen_pub.tsv
tra-SR-A3


title: GFP-RNAi-treated genotypic male head replicate 2

description:
RNAi_head_pub.tsv
GFP-male-H2


title: GFP-RNAi-treated genotypic female head replicate 2

description:
RNAi_head_pub.tsv
GFP-female-H3


title: Md-tra-RNAi-treated genotypic female head replicate 3 (sex-reversed males)

description:
RNAi_head_pub.tsv
tra-N-H4


title: Md-tra-RNAi-treated genotypic female head replicate 1 (sex-reversed males)

description:
RNAi_head_pub.tsv
tra-N-H2


title: GFP-RNAi-treated genotypic female head replicate 3

description:
RNAi_head_pub.tsv
GFP-female-H4


title: Md-tra-RNAi-treated genotypic male head replicate 3

description:
RNAi_head_pub.tsv
tra-SR-H3


title: Md-tra-RNAi-treated genotypic male abdomen replicate 1

description:
RNAi_abdomen_pub.tsv
tra-SR-A1


title: Md-tra-RNAi-treated genotypic female abdomen replicate 2 (sex-reversed males)

description:
RNAi_abdomen_pub.tsv
tra-N-A3


title: Md-tra-RNAi-treated genotypic female abdomen replicate 3 (sex-reversed males)

description:
RNAi_abdomen_pub.tsv
tra-N-A4


title: CC88_48h

city: Cologne

first: Takaki

last: Maekawa

address: Carl-von-Linne Weg 10

country: Germany

institute: Max-Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Blumeria graminis f. sp. hordei DH14 (version 4; ENA PRJEB23502) using tophat v2.0.10 with parameters --read-mismatches 10 --read-gap-length 10 --read-edit-dist 20 --read-realign-edit-dist 0 --mate-inner-dist 260 --mate-std-dev 260 --min-anchor 5 --splice-mismatches 2 --min-intron-length 30 --max-intron-length 10000 --max-insertion-length 20 --max-deletion-length 20 --num-threads 10 --max-multihits 10 --coverage-search --library-type fr-firststrand --segment-mismatches 3 --min-segment-intron 30 --max-segment-intron 10000 --min-coverage-intron 30 --max-coverage-intron 10000 --b2-very-sensitive
Fragment counts per gene per sample were obtained using the Subread function ‘featureCounts’ (version 1.5.0) with options -t CDS -s 2 -M –p
Genome_build: Blumeria graminis fsp. hordeii (Bgh) DH14, genome assembly version 4.0; assembly available at ENA (PRJEB23502) and PhytopathDB (http://fungi.ensembl.org/Blumeria_graminis/Info/Index)
Supplementary_files_format_and_content: tab-delimited text file including raw read counts per gene per sample

organism: Blumeria hordei

source_name: Bgh-infected barley leaf epidermal peels

growth_protocol: For growth of biotrophic Bgh fungus, barley plants were grown at 19 °C, 70% relative humidity, and under a 16-h photoperiod.

extract_protocol:
RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen) according to the manufacurer's instruction and purified by DNase Turbo kit (Thermo Fisher Scientific) and RNA clean up kit (Zymo Research) according to the manufacurer's instruction.
RNA-seq libraries were prepared from total RNA by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).

treatment_protocol: Detached primary leaves from nine day old barley plants were placed on closed agar plates and inoculated with conidiospores of different Bgh isolates.

tag: isolate

tag: time


title: K3_16h


title: YJL_005: N2_mrps-5 RNAi_rep 1

type: RNA

city: Lausanne

first: Yasmine

middle: J

last: Liu

address: Station 19 CH-1015 Lausanne

department: Laboratory of intergrative systems physiology

country: Switzerland

institute: EPFL

description: Gene expression profile

hyb_protocol: hybridized using the Agilent Gene Expression Hybridization Kit (Agilent Technologies)

scan_protocol: An ArrayXS-200108 with WormBase WS241 genome build (OakLabs) was used and fluorescence signals were detected by the SureScan microarray Scanner (Agilent Technologies)

data_processing: Data of all samples were quantile normalized using the ranked median quantiles as described previously in Bolstad 2003 A comparison of normalization methods for high desity oligonucleotide array data based on variance and bias. Bioinformatics. 19, 185-193

organism: Caenorhabditis elegans

source_name: N2_mrps-5 RNAi_replicate 1

label_protocol: RNA was amplified and labeled using a Low Input QuickAmp Labeling Kit (Agilent Technologies)

growth_protocol: C. elegans were routinely grown and maintained on nematode growth media (NGM) at 20ºC. Worms were cultured on plates seeded with E. coli OP50, then eggs were obtained by alkaline hypochlorite treatment of gravid adults and placed onto plates seeded with E. coli OP50. At the L4 stage, worms were transferred to plates seeded with control bacteria HT115 and mrps-5 RNAi bacteria for two days. Then, eggs were synchronized by bleaching these worms and placed onto plates seeded with control bacteria HT115 and mrps-5 RNAi bacteria respectively. At the young adult stage, worms of each condition were collected by washing them off the culture plates with M9 buffer and the worm pellet was washed with dH2O for three times before collection in a 2 mL Eppendorf tube, snap-frozen in liquid N2 and lyophilized overnight. For RNA extraction, 500 worms/tube was collected in four replicates per condition.

extract_protocol: Total RNA was extracted using the standard Trizol method, followed by phenol-chloroform purification and further processing by OakLabs Gmbh (Germany);In short, RNA quality and quantity was assessed after DNase clean-up using a 2100 Bioanalyzer (Agilent Technologies). All samples had a RNA integrity value of ≥7.2

value: N2 (Bristol) treated with siRNA of mitochondrial ribosomal protein-5, mrps-5

value: whole worm

tag: age

value: young adult


title: YJL_008: N2_mrps-5 RNAi_rep 4

description: Gene expression profile

source_name: N2_mrps-5 RNAi_replicate 4

tag: genotype/variation


title: YJL_007: N2_mrps-5 RNAi_rep 3

description: Gene expression profile

source_name: N2_mrps-5 RNAi_replicate 3


title: YJL_006: N2_mrps-5 RNAi_rep 2

description: Gene expression profile

source_name: N2_mrps-5 RNAi_replicate 2


title: YJL_003: N2_HT115_rep 3

description: Gene expression profile

source_name: N2_HT115_replicate 3

value: N2 (Bristol) wild type


title: AB1789 (scRNA-Seq)

source_name: Auricular lymph node

tag: cell type

value: Intradermal injection of inactivated pathogen

value: 8 weeks


title: YJL_001: N2_HT115_rep 1

description: Gene expression profile

source_name: N2_HT115_replicate 1


title: YJL_002: N2_HT115_rep 2

description: Gene expression profile

source_name: N2_HT115_replicate 2


title: S22_16h


title: YJL_004: N2_HT115_rep 4

description: Gene expression profile

source_name: N2_HT115_replicate 4


title: K4_48h


title: S16_48h


title: GFP-RNAi-treated genotypic male abdomen replicate 2

description:
RNAi_abdomen_pub.tsv
GFP-male-A2

tag: strain


title: AB1787 (scRNA-Seq)

tag: tissue

value: Lymph node

value: Nb day4 rep.1


title: GFP-RNAi-treated genotypic male abdomen replicate 3

description:
RNAi_abdomen_pub.tsv
GFP-male-A3


title: S16_16h


title: Md-tra-RNAi-treated genotypic female abdomen replicate 1 (sex-reversed males)

description:
RNAi_abdomen_pub.tsv
tra-N-A2


title: AB1788 (scRNA-Seq)

tag: selection marker


title: K4_16h


title: S22_48h


title: AB1786 (scRNA-Seq)

tag: infection


title: GFP-RNAi-treated genotypic male abdomen replicate 1

description:
RNAi_abdomen_pub.tsv
GFP-male-A1


title: AB1782 (scRNA-Seq)

value: innate immune cells

tag: time point

value: Nb day2 rep.1


title: GFP-RNAi-treated genotypic female abdomen replicate 2

description:
RNAi_abdomen_pub.tsv
GFP-female-A3


title: AB1784 (scRNA-Seq)

tag: replicate id


title: GFP-RNAi-treated genotypic female abdomen replicate 3

description:
RNAi_abdomen_pub.tsv
GFP-female-A4


title: K3_48h


title: AB1780 (scRNA-Seq)

value: total immune cells

tag: mouse age


title: TRE-suspend-adox-36h

city: Guangzhou

first: dongwei

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

extract_protocol:
Total RNA was prepared with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo-dT (Takara), and then analyzed by qPCR with Premix Ex Taq (Takara).
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

treatment_protocol: TRE-ESCs cells  were cultured in N2B27+2i+LIF medium in low adsorption petri dish with or without dox

value: suspend cultured cells

tag: agent

value: dox


title: CC52_48h


title: CC88_16h


title: K2_16h


title: K2_48h


title: female head replicate 1

description:
YM_IIM_head_pub.tsv
IsoCS_female_head_1

data_processing:
Illumina Casava v 1.8 was used for basecalling.
Sequenced reads were mapped to house fly genome assembly v2.0.2 using hisat2 in HISAT2 v0.12.2
The aligned reads were assigned to all annotated genes with htseq-count in HTSeq v0.9.1
The HTSeq output was used as input into DESeq2 v1.16.1 to identify differentially expressed genes with pair-wise comparisons between males of each strain and pair-wise comparisons of males from each strain against females.
Genome_build: house fly genome assembly v2.0.2 and annotation release 102
Supplementary_files_format_and_content: tab-delimited text files include pair-wise comparison, log2FoldChange, and FDR-corrected P value

extract_protocol:
Individual flies were dissected for abdomen and head tissues, frozen at -80˚C, and RNA was extracted from the individual tissues with TRIzol Reagent and the Zymo Direct-zol kit following the manufacturer’s protocol including DNA digestion steps.
The Illumina TruSeq Stranded mRNA Sample Preparation Kit was used with 4 ug of total RNA for the construction of sequencing libraries.

value: female (IsoCS)

tag: genomic background

value: isogenic across females


title: TRE-suspend-36h


title: AB1781 (scRNA-Seq)

value: Nippostrongylus brasiliensis


title: CC52_16h


title: GFP-RNAi-treated genotypic female abdomen replicate 1

description:
RNAi_abdomen_pub.tsv
GFP-female-A2

tag: genotypic sex

value: female

value: GFP RNAi


title: S19_16h


title: E13_cerebella

city: Farmington

first: James

middle: YH

state: CT

address: 263 Farmington Ave

department: Genetics and Genome Sciences

institute: UCHC

data_processing:
The raw reads were processed to molecule counts using the Cell Ranger pipeline with default setting
The raw UMI counts from Cell Ranger was processed by the Seurat R package (version 1.4).
The count matrix without filtering was uploaded.
Genome_build: mm10
Supplementary_files_format_and_content: raw UMI counts in csv format

source_name: Cerebellum

extract_protocol:
The cerebella were dissected from 7 E13.5 mouse embryos in ice-cold phosphate buffered saline. The dissected tissues were pooled and cut into pieces smaller than 1 mm in dimension and digested with Accumax in a 1.5-ml tube at 37˚C for 5-10 min. At the end of digestion, the tissue pieces were dissociated by gentle trituration with a wide-bore pipet tip. The cell suspension was filtered with a 100-µm cell strainer.
After single cell suspension, the 10X Genomics Chromium Single Cell Kit v1 (PN-120233) was used to create libraries.

value: Outbred (CD1)

tag: genotype

value: wild type

value: Embrhonic day 13.5

tag: Sex

value: pooled male and female

value: Cerebellum


title: female head replicate 2

description:
YM_IIM_head_pub.tsv
CSrab_female_head_2

value: female (CSrab)


title: female head replicate 3

description:
YM_IIM_head_pub.tsv
CS_female_head_3

value: female (CS)


title: HMVEC-dLy replicate 3

city: Bethesda

first: Hyun Min

last: Jung

state: MD

address: 6 Center Drive

department: Division of Developmental Biology

institute: National Institutes of Health

data_processing: Data was analyzed using  PartekFlow analysis software. The sequence reads were trimmed to remove  the following adapters: GTTCAGAGTTCTACAGTCCGACGATC (from the 5’ end) and  TGGAATTCTCGGGTGCCAAGG (from the 3’ end). Then, the bases at the end of the  sequences with quality less than 20 were removed. The remaining sequences were  aligned to the human genome browser (hg38) and miRbase mature microRNA version 22  using Bowtie. The data was filtered for the counts smaller than 10 in 50% of samples, and  used CPM (counts per million) for normalization. Differential expression was analyzed  by Partek GSA algorithm.

source_name: dermal lymphatic microvascular endothelial cell

growth_protocol: HMVEC-dLy cells (Lonza) were cultured in EGM-2 MV BulletKit (Lonza, CC-3202)  that contains hEGF, hydrocortisone, GA-1000, FBS, VEGF, hFGF-B, R3-IGF-1, and  ascorbic acid. HUVECs (Lonza) were cultured in bovine hypothalamus extract, 0.01%  Heparin and 20% FBS in M199 base media (Gibco) on 1mg/mL gelatin-coated tissue  culture flasks.

extract_protocol:
RNA was isolated using miRVana kit
Illumina TruSeq Small RNA Sample Preparation Kit

value: HMVEC


title: Y^M male head replicate 2

description:
YM_IIM_head_pub.tsv
IsoCS_male_head_2

value: Y^M (IsoCS)

value: isogenic except for Y^M across males


title: Y^M male head replicate 3

description:
YM_IIM_head_pub.tsv
IsoCS_male_head_3


title: Y^M male head replicate 1

description:
YM_IIM_head_pub.tsv
IsoCS_male_head_1


title: HMVEC-dLy replicate 2


title: S11_16h

tag: isolate


title: HMVEC-dLy replicate 1


title: III^M #2 male head 3

description:
YM_IIM_head_pub.tsv
CSrab_male_head_3

value: III^M (CSrab)

value: isogenic except for III^M across males


title: S25_48h

tag: time


title: S25_16h


title: HUVEC replicate 3

source_name: umbilical vein endothelial cell

value: HUVEC


title: III^M #2 male head replicate 1

description:
YM_IIM_head_pub.tsv
CSrab_male_head_1


title: HUVEC replicate 1


title: III^M #1 male head replicate 3

description:
YM_IIM_head_pub.tsv
CS_male_head_3

value: III^M (CS)


title: S20_48h


title: S20_16h


title: HUVEC replicate 2


title: S19_48h


title: III^M #1 male head replicate 1

description:
YM_IIM_head_pub.tsv
CS_male_head_1


title: S15_48h


title: III^M #1 male head replicate 2

description:
YM_IIM_head_pub.tsv
CS_male_head_2


title: S15_16h


title: Y^M(III) male head replicate 2

description:
YM_IIM_head_pub.tsv
bwbCS_male_head_2

value: Y^M (bwbCS)

value: isogenic except for Y^M and one copy of III chromosome across males


title: III^M #2 male head replicate 2

description:
YM_IIM_head_pub.tsv
CSrab_male_head_2


title: Y^M(III) male head replicate 3

description:
YM_IIM_head_pub.tsv
bwbCS_male_head_3


title: S11_48h


title: Y^M(III) male head replicate 1

description:
YM_IIM_head_pub.tsv
bwbCS_male_head_1


title: D.maur_testis_RNAseq: Ribo-depleted RNA-seq library

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

data_processing:
Adapter sequences in small RNA sequencing and total RNA-seq libraries were removed using cutadapt 1.8.1
For analysis small RNA reads from yw library were passed through quality control and minimal length filter (>18 nt) and finally mapped to genomes of Drosophila melanogaster (dm6 assembly, UCSC Genome Browser, https://genome-euro.ucsc.edu/cgibin/hgGateway?redirect=manual&source=genome.ucsc.edu) without mismatches (0 mm) using bowtie 1.2.2.
For analysis small RNA reads (>15 nt) from interspecies hybrids libraries were mapped to the D. melanogaster dm6 and D. mauritiana (release 1.0 of MS17 strain, http://www.popoolation.at/mauritiana_genome/) genomes using bowtie 0.12.7.
Genome_build: dm6 and D. mauritiana (release 1.0 of MS17 strain, http://www.popoolation.at/mauritiana_genome/)
Supplementary_files_format_and_content: tab-delimited text and excel files include information about mapping individual reads

organism: Drosophila mauritiana

source_name: testes

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and for small RNA libraries preparation were size-fractioned by PAGE (19-29 nt)
Testes were dissected from adult flies (0-5 d) and RNA was isolated with Trizol Reagent (Invitrogene). For small RNA librarires, 19-29 nt RNAs were isolated from total RNA of dissected testes using 12% polyacrylamide gels and cloned as described in previous studies (Aravin et al., 2008; Brennecke et al., 2007). For Ribo-depleted libraries, rRNA was depleted with Ribo-Zero™ rRNA Removal Kit. Standard RNA-seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420) according to the manufacturer's instructions.

value: wt from Centre National de la Recherche Scientifique (CNRS), France

value: testes


title: female abdomen replicate 1

description:
YM_IIM_abdomen_pub.tsv
IsoCS_female_abdomen_1

value: female (IsoCS)

value: isogenic across females


title: ATTATA_D_maur: small RNA library (18-29 nt)

tag: molecule subtype

value: small RNA (19-29 nt)


title: female abdomen replicate 2

description:
YM_IIM_abdomen_pub.tsv
CSrab_female_abdomen_2


title: 2026-4

city: Newark

first: Xin

last: Wang

address: 185 South Orange Avenue

institute: Rutgers University - New Jersey Medical School

data_processing:
CLC Genomics Workbench 10.1 version (http:// www.clcbio.com/products/clc-genomics-workbench/; Qiagen) was used for RNA-seq analysis.
De-multiplexed fastq files from RNA-Seq libraries are imported into the CLC software.
Bases with low quality were trimmed and reads are mapped to reference genome, Mycobacterium tuberculosis H37Rv (NCBI Reference Sequence: NC_000962.3).
The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench.
Differential expression for RNAseq data was carried out using multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM) [Robinson et al., 2010], using RNA-seq tool in CLC Genomic Workbench
Genome_build: M. tuberculosis H37Rv (NCBI Reference sequence: NC_000962.3)
Supplementary_files_format_and_content: RPKM values

organism: Mycobacterium tuberculosis

source_name: mRNA of JSF-2026 treated M. tuberculosis

growth_protocol: M. tuberculosis strain H37Rv was cultured in media 7H9+ADS+tyloxapol to mid log phase (OD = 0.3)

extract_protocol:
M. tuberculosis culture was harvested after centrifugation. Following washing with pre-chilled PBS, the pellet was lysed by TRIzol and total RNA was extracted by addition of chloroform and RNeasy mini kit.
Illumina Ribo-Zero rRNA Removal Kit (Bacteria) was used for the removal of ribosomal RNA according to the manufacturer’s protocol. The Illumina compatible RNAseq library was prepared using NEBNext ultra RNAseq library preparation kit. The cDNA libraries were purified using AmpureXP beads and quantified on an Agilent 2100 Bioanalyzer as well as a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA). An equimolar amount of barcoded libraries were pooled and sequenced on Illumina NextSeq 500 (Illumina, San Diego, CA) with 1x75 configuration

treatment_protocol: Mid-log phase M. tuberculosis was treated with 10x MIC of JSF-2019 and JSF-2026

tag: passage

tag: treatment


title: Y^M male abdomen replicate 3

description:
YM_IIM_abdomen_pub.tsv
IsoCS_male_abdomen_3

tag: strain


title: Y^M male abdomen replicate 2

description:
YM_IIM_abdomen_pub.tsv
IsoCS_male_abdomen_2


title: 2026-3


title: 2026-2


title: 2026-1


title: III^M #2 male abdomen replicate 3

description:
YM_IIM_abdomen_pub.tsv
CSrab_male_abdomen_3


title: D7 (Illumina)

description: Genomic DNA extracted from bladder samples was genotyped using Illumina 1M-Duo V1 SNP array.

hyb_protocol: as per Illumina Human 1M-Duo V1 DNA BeadChip protocol

scan_protocol: scanned on a Illumina BeadArray Reader 500 G

data_processing: The microarray data were imported into SNP genotyping module in the Illumina Genome Studio software to perform CNV analysis. Each mucosa sample was compared to normal blood from the same individual. Somatic copy number altered regions were defined by the normalized log2 ratio of the mucosal samples and normal reference DNA of the same individual.

label: Cy3 and Cy5

source_name: human bladder

extract_protocol: Extraction of genomic DNA from fresh bladder tissue was performed using proteinase K and Qiagen kit

tag: tissue

value: Urothelial carcinoma (UC) Grade 3


title: E2 (Illumina)

label_protocol: as per Illumina Human 1M-Duo V1 DNA BeadChip protocol

value: High-grade intraurothelial neoplasia (HGIN)


title: Y^M male abdomen replicate 1

description:
YM_IIM_abdomen_pub.tsv
IsoCS_male_abdomen_1

source_name: Abdomen


title: C5 (Illumina)


title: D6 (Illumina)


title: C3 (Illumina)


title: C8 (Illumina)

value: Low-grade intraurothelial neoplasia (LGIN)


title: B7 (Illumina)


title: D5 (Illumina)


title: 2019-3

source_name: mRNA of JSF-2019 treated M. tuberculosis


title: III^M #2 male abdomen replicate 1

description:
YM_IIM_abdomen_pub.tsv
CSrab_male_abdomen_1


title: 2019-4


title: 2019-2


title: III^M #2 male abdomen replicate 2

description:
YM_IIM_abdomen_pub.tsv
CSrab_male_abdomen_2


title: III^M #1 male abdomen replicate 3

description:
YM_IIM_abdomen_pub.tsv
CS_male_abdomen_3


title: E3 (Illumina)


title: D9 (Illumina)


title: D8 (Illumina)


title: III^M #1 male abdomen replicate 2

description:
YM_IIM_abdomen_pub.tsv
CS_male_abdomen_2


title: 2019-1


title: DMSO-3

source_name: mRNA of DMSO treated M. tuberculosis

value: DMSO


title: DMSO-4


title: Y^M(III) male abdomen replicate 2

description:
YM_IIM_abdomen_pub.tsv
bwbCS_male_abdomen_2


title: GTAGCC_HmrIxD.maur_hybrid: small RNA library (18-29 nt)

organism: Drosophila melanogaster x Drosophila mauritiana

value: F1 hybrids of P{}Hmr1 D. melanogaster and wt D. mauritiana


title: PB (Illumina)

value: Normal from peripheral blood


title: C6 (Illumina)


title: D3 (Illumina)


title: DMSO-1


title: C2 (Illumina)


title: D4 (Illumina)


title: Y^M(III) male abdomen replicate 1

description:
YM_IIM_abdomen_pub.tsv
bwbCS_male_abdomen_1


title: III^M #1 male abdomen replicate 1

description:
YM_IIM_abdomen_pub.tsv
CS_male_abdomen_1


title: Nor3

status: Public on Feb 18 2019

city: Baltimore

first: Jennifer

last: Elisseeff

address: 5031 Smith Building 400 N. Broadway

institute: Johns Hopkins University

data_processing:
single end sequencing reads were cleaned with quality filter, adapter cutter and length filter, using ACGT101_miR_v4.2g from LC Sciences
Considering that extremely low abundance might lead to false results, the known and new candidate miRs with less than 10 raw reads in the libraries were removed from the analysis. The cleaned reads were mapped to miRBase (miRBase v21) using Bowtie v1.1.1.
The unmapped reads were mapped to multiple databases including mRNA, Rfam11, and genomic DNA, using Bowtie v1.1.1.
Novel miR candidates were identified from genome mapped reads based on the propensity of hairpin formation in corresponding genome positions using ACGT101_miR_v4.2g from LC Sciences
Data were normalized by dividing the sequence counts of individual samples by the corresponding normalization factors which are the median values of the ratios between specific sample counts and geometric mean counts of all samples.
Genome_build: miRBase 21
Supplementary_files_format_and_content: excel file include miRNA name, sequence, raw read counts and normalized values for Nor1~3 and OA1 and 3

source_name: normal_extracellular vesicles isolated from synovial fluid

extract_protocol:
A small RNA was harvested from extracellular vesicles of human synovial fluids of normal and OA patients' joints using miRCURY RNA isolation kit for biofluids.
 A small RNA library was generated from a customer sample using the Illumina Truseq™ Small RNA Preparation kit according to Illumina’s TruSeq™ Small RNA Sample Preparation Guide (Part # 15004197).

tag: subject status

value: normal; control

tag: age

value: 75 years old

value: female

tag: surgery

value: postmortem

value: synovial fluid

tag: sample type

value: extracellular vesicles


title: OA1

source_name: OA_extracellular vesicles isolated from synovial fluid

value: osteoarthritis patient

value: 63 years old

value: total knee replacement


title: OA3

value: 66 years old

value: male


title: Nor2

value: 85 years old


title: B8 (Illumina)


title: Nor1

value: 72 years old


title: E9 (Illumina)

value: Normal urothelium


title: ChIP_H3K27ac_HS895T

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

description: ChIP_H3K27ac_HS895T.nofirst5bp.minMQ4.sorted.bw

data_processing:
Reads obtained from H3K27Ac ChIP-seq were mapped to the genome using Bowtie2 (v2.1.0). The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read. bigWig files were generated from bam files using BEDTools (v2.17.0) and the scores represent the coverage. We used as control the merged control profiles of five cell lines, namely A375, MM011, MM032, MM047 and MM057. We used MACS2 (v2.0.10) with the command 'callpeak -t ChIPseq_file -c  Control_file -g hs --qvalue 0.001 -n name'.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage. Bedfiles supplied with FDR0.001

source_name: Melanoma cell line

growth_protocol: Cells were kept at 37°C, with 5% CO2 and were maintained in Ham's F10 nutrient mix (Thermo Fished Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 µg ml-1 penicillin/streptomycin (Thermo Fished Scientific).

extract_protocol:
Chromatin was extracted using the MagnaChIP-seq kit (millipore). 4 µg of antibody was used on 2 million cells. Sonication was performed for 12 cycles, 30 sec pulses using the biorupter.
Illumina TruSeq

tag: cell line

tag: time point

value: Base line


title: C9 (Illumina)

first: Hui

address: 1515 Holcombe Blvd.

institute: MD Anderson Cancer Center

value: High-grade intraurothelial neoplasia (HGIN)


title: D1 (Illumina)

value: Low-grade intraurothelial neoplasia (LGIN)


title: B9 (Illumina)


title: ATAC-seq mouse E16.5 Cdx2-KO rep2

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
E16_ATAC_Cdx2KO_rep2_NK87
Cdx2-KO midgut epithelial cell chromatin accessibility by ATAC at E16.5 biological rep2

data_processing:
Alignment: ChIP-seq:bowtie2 version 2.2.6. RNA-seq: Tophat, version 2.1.0
peak calling: macs 1.4.1
RNA-seq cxb files: cuffquant v2.2.1
Bigwig: bamCoverage 2.4.2
Genome_build: mm9, hg19
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: cxb file for expression profile and cuffnorm table with normalized gene expression values

source_name: Mouse midgut epithelial cells

extract_protocol:
midguts were dissected and treated in 0.25% Trypsin for 7-10 mins on a vortex station, neutralized with FBS; Epcam+ cells were enriched using magnetic antibody.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs)

tag: developmental stage

value: C57BL6; mixed background

tag: cell type

value: Embryonic epithelial cells from the midgut

value: Cdx2-KO(Shh-cre; Cdx2f/f)

value: NO


title: ATAC-seq mouse E16.5 wt rep1

description:
E16.5MG_ATAC_rep1
Control midgut epithelial cell chromatin accessibility by ATAC at E16.5 biological rep1

tag: genotype

value: Wild-Type


title: C7 (Illumina)


title: ATAC-seq mouse E16.5 wt rep2

description:
E16.5MG_ATAC_rep2
Control midgut epithelial cell chromatin accessibility by ATAC at E16.5 biological rep2


title: RNA-seq E12.5 intestinal epithelium Cdx2-KO rep2

description:
E12.5_Cdx2KO_rep2_KB4.cxb
Cdx2 KO midgut epithelial cell total RNA harvested at E12.5 biological rep2
E12.5_WTvsCdx2KO_cuffnorm_genes.fpkm_table.txt

source_name: Mouse intestinal epithelial cells

extract_protocol:
Gut tubes caudal of stomach were dissected and treated in 0.25% Trypsin for 7-10 mins on a vortex station, neutralized with FBS; Epcam+ cells were enriched using magnetic antibody.
Total RNA was extracted with TRIzol reagent (Life Technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions


title: HMR1xD.maur_testis_RNAseq: Ribo-depleted RNA-seq library

value: F1 hybrids of P{}Hmr1 D. melanogaster and wt D. mauritiana

value: testes


title: E6 (Illumina)


title: E8 (Illumina)


title: ATAC-seq mouse E16.5 Cdx2-KO rep1

description:
E16_ATAC_Cdx2KO_rep1_NK46
Cdx2-KO midgut epithelial cell chromatin accessibility by ATAC at E16.5 biological rep1


title: E4 (Illumina)


title: RNA-seq E12.5 intestinal epithelium wt rep1

description:
E12.5_WT-rep1_NK40
Control midgut epithelial cell total RNA harvested at E12.5 biological rep1
E12.5_WTvsCdx2KO_cuffnorm_genes.fpkm_table.txt

value: Wild-Type (Cdx2 f/f)


title: Cdx2 ChIP-seq mouse Adult rep1

description:
Adult-villus_Cdx2_NK51
midgut harvested at Adult

source_name: Mouse intestinal villus epithelial cells

extract_protocol:
Villus Epithelium was collected and fixed for subsequent chromatin pull down
Whole cell lysates were sonicated and incubated with 6 uL CDX2  antibody overnight for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries

value: adult

value: mixed background

value: Adult villus epithelium

value: Wild type


title: C4 (Illumina)

description: Genomic DNA extracted from bladder samples was genotyped using Illumina 1M-Duo V1 SNP array.


title: DMSO-2

value: DMSO


title: Cdx2 ChIP-seq mouse E16.5 rep1

description:
E16.5_Cdx2_NK21
midgut harvested at E16.5

source_name: Mouse midgut cells

extract_protocol:
midguts were dissected and fixed for subsequent chromatin pull down.
Whole cell lysates were sonicated and incubated with 6 uL CDX2  antibody overnight for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries

value: Embryonic whole tissue from midgut

value: Wild-Type(Cdx2 f/f; vil-Cre-ERT2 X Cdx2 f/f; vil-Cre-ERT2)


title: Cdx2 ChIP-seq mouse E13.5 rep2

description:
E13_Cdx2_NK70
midgut harvested at E13.5 biological rep2

value: CD1 wild type


title: C1 (Illumina)

value: Low-grade intraurothelial neoplasia (LGIN)


title: Cdx2 ChIP-seq mouse E13.5 rep1

description:
E13.5_Cdx2_NK47
midgut harvested at E13.5 biological rep1


title: Y^M(III) male abdomen replicate 3

description:
YM_IIM_abdomen_pub.tsv
bwbCS_male_abdomen_3

value: Y^M (bwbCS)

tag: genomic background

value: isogenic except for Y^M and one copy of III chromosome across males


title: RNA-seq E12.5 intestinal epithelium Cdx2-KO rep1

description:
E12.5_Cdx2KO_rep1_KB3.cxb
Cdx2 KO midgut epithelial cell total RNA harvested at E12.5 biological rep1
E12.5_WTvsCdx2KO_cuffnorm_genes.fpkm_table.txt

value: C57BL6; mixed background

value: Embryonic epithelial cells from the midgut

value: Cdx2-KO(Shh-cre; Cdx2f/f)


title: dKO rep 3

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Sequences were mapped to the mm9 genome with additional ERCC sequences using the STAR aligner (Dobin et al., 2013).
Transcript level data was counted using HTSEQ (Anders et al., 2015). Raw counts were divided into transcript counts and ERCC counts. For quality control purposes, the linearity of the ERCC spike-in controls were considered and two spike-ins that consistently across all samples did not conform to the expected order (which is likely to be a manufacturer’s error) were excluded from the ERCC raw counts.
Genome_build: mm9
Supplementary_files_format_and_content: raw count text files  for each sample which include ERCC counts

extract_protocol:
Telencephalons from E12.5 embryos were dissected, dissociated with StemPro Accutase, and passed through a 40-μm cell strainer to obtain single-cell suspensions. Cells were counted and 1.0 x 106 cells were pelleted by centrifugation. Diluted ERCC spike-in mix (1:20, Thermo Fisher Scientific 4456740) was added to cell pellets and Trizol prior to RNA extraction at a ratio of 1 μl of diluted ERCC spike-in mix per million cells. RNA was purified using a Direct-zol RNA kit (Zymo Research R2052) and eluted in 25 μl of elution buffer.
Library preparation and sequencing were performed by the Genome Sequencing Facility at St. Jude Children’s Research Hospital. RNA quality was checked by a 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) before library generation. Libraries were prepared from 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina 20020597), then quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies). Samples were sequenced on Illumina HiSeq4000, obtaining 100 million 100-bp paired-end reads. RNAs from 5 control and 4 dKO embryos were sequenced.

tag: strain background

value: mixed lineage

tag: genotype/variation

value: Lats1/2 dko

value: Telencephalons


title: Hi-C_PS_bio2

city: Cincinnati

first: Satoshi

middle: H

last: Namekawa

state: Ohio

address: Cincinnati Children's Hospital Medical Center

department: Division of Reproductive Sciences

description:
PS_pooled_validpairs.txt.gz
PS_pooled.mcool

data_processing:
Libraries were sequenced on Illumina HiSeq2500 or HiSeq4000 machines following the manufacturer's instructions. Bases were called using Illumina's HiSeq Control Software.
Paired-end .fastq files of Hi-C libraries were mapped and processed using the cMapping package (https://github.com/dekkerlab/cMapping).
Hi-C reads were iteratively mapped to the Mus musculus mm10 genome via Bowtie2 (version 2.3.3.1), which was called with the following arguments: --very-sensitive --no-head --no-sq --qc-filter --reorder.
Uniquely aligned, paired reads were kept and assigned to the 5’ position of HindIII restriction fragments.
Mapped reads were filtered for fragment ends and uniqueness; PCR duplicates, defined as sequence matches with the exact same start and end, were excluded.
Using the cooler package (version 0.7.10; https://github.com/mirnylab/cooler), valid pairs pooled from biological replicates (in validpairs.txt.gz files) were binned at multiple resolutions (resulting in .mcool files).
To correct for noisy and/or low-signal bins prior to matrix balancing with cooler, bins whose log marginal sum is less than ≤20 genome-wide median absolute deviations below the median log marginal sum of all the bins in the same chromosome were excluded.
Matrices were balanced using Sinkhorn balancing such that the sum of every row and column is equal.
Genome_build: mm10
Supplementary_files_format_and_content: validpairs: Tab-delimited text files listing valid interacting pairs of Hi-C reads; mcool: A file containing chromosome interractions, made from the validPairs files, binned at multiple resolutions (kb) as follows: 1, 2, 5, 8, 10, 15, 20, 30, 40, 64, 100, 128, 250, 256, 512, 1024, 2048, 4096, and 8192.

source_name: Pachytene spermatocytes

extract_protocol:
Pachytene spermatocytes and round spermatids were isolated from adult testes through sedimentation velocity at unit gravity as described (PMID 8231890). At least 12 independent mice, 90-120 days in age, were used for each isolation of germ cells. Wet lab procedures for Hi-C were performed as described (PMID 28435001), and samples were treated with HindIII restriction enzyme.
Hi-C library construction was performed as described (PMID 28435001) with the following detail: For DNA sequencing, NEBNext Oligos for Illumina, Index Primer Set 1, were used.

tag: source tissue

value: Testis

value: Pachytene spermatocytes

tag: number of mice

value: wild type


title: Hi-C_PS_bio1

institute: Cincinnati Children's Hospital Medical Center


title: Control with normal spermatogenesis_2

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

institute: University of Bergen

data_processing:
Reads of murine mRNA were aligned to GRCh38.p10 Gencode release using HISAT2 2.0.5
Aligned reads present within adequate GENCODE gene annotation regions were counted using featureCounts
Count data were analyzed obtained using featureCounts
Data were normalized using DESeq2 in R programming environment
Genome_build: GRCh38.p10 Gencode release
Supplementary_files_format_and_content: We upload one processed data txt file with read counts and one with normalized signals for all samples.

source_name: testis

extract_protocol:
For RNA extraction from frozen tissues, we used the TRI Reagent® (Sigma-Aldrich, St. Louis, MO, USA), and RNA were extracted according to the manufacturer’s protocol. The total RNA was post-purified using the RNeasy Plus Mini Kit to eliminate the DNA contamination (Qiagen, Hilden, Germany).
Sequencing libraries of testis tissues were prepared using the TruSeq RNA Oligo(dT) library preparation kit (Illumina, USA) and sequenced on an Illumina HiSeq4000 platform

value: testis

tag: disease

value: control (normal spermatogenesis)


title: Control with normal spermatogenesis_3


title: Control with normal spermatogenesis_1


title: WT rep 4


title: dKO rep 1


title: dKO rep 2


title: WT rep 5


title: CAIS_2

value: Complete Androgen Insensitivity Syndrome


title: WT rep1


title: WT rep 3


title: dKO rep 4


title: Hi-C_RS_bio2

description:
RS_pooled_validpairs.txt.gz
RS_pooled.mcool

source_name: Round spermatids

tag: strain

value: Round spermatids


title: CAIS_3

tag: tissue


title: CAIS_1


title: ChIP_H3K27ac_MM029

description: ChIP_H3K27ac_MM029.nofirst5bp.minMQ4.sorted.bw

data_processing:
The reads from scATAC-seq samples were first cleaned for adapters using fastq-mcf (as part of ea utils; v1.1.2-686). Read quality was then checked using FastQC (v0.11.5). Paired-end reads were mapped to the human genome (hg19-Gencode v18) using STAR (v2.5.1) applying the parameters --alignIntronMax 1, --aslignIntronMin 2 and --alignMatesGapMax 2000. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Duplicates were removed using Picard (v1.134) MarkDuplicates using OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500. To filter out cell of bad quality, transcription start site aggregation plots were made using a custom script and cell having a noisy profile were removed from further analyses. This lead to a final of 598 good quality cells over 8 Fluidigm C1 runs. Bam files of good quality single cells were aggregated per condition and peaks were called on these aggregated samples using MACS2 (v2.1.1) callpeak using the parameters --nomodel and --call-summits. The peak files per condition were merged (78,661 peaks in total before blacklisting) and a count matrix was generated by using featureCounts (as part of Subread; v1.4.6) of all separate single cell bam files on the merged peak file (after conversion of the merged peak bed file to a gff format using a custom script). To visualise the aggregated cells per sample, normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.23.0) using as scaling parameter (-scale) size factors obtained from DEseq2 (v1.18.1). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs.
The reads from OmniATAC-seq samples were first cleaned for adapters using fastq-mcf (as part of ea utils; v1.1.2-686). Read quality was then checked using FastQC (v0.11.5). The reads were mapped to the human genome (hg19-Gencode v18) using STAR (v2.5.1) applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.1) callpeak using the parameters --nomodel and --call-summits on the 8 conditions separately. A count matrix was generated by using featureCounts (as part of Subread; v1.4.6) of all separate bam files on the merged peak file (after conversion of the merged peak bed file to a gff format using a custom script). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.23.0) using as scaling parameter (-scale) size factors obtained from DEseq2 (v1.18.1). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Reads obtained from H3K27Ac ChIP-seq were mapped to the genome using Bowtie2 (v2.1.0). The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read. bigWig files were generated from bam files using BEDTools (v2.17.0) and the scores represent the coverage.
Genome_build: hg19
Supplementary_files_format_and_content: scATAC-seq abundance measurement is a raw count matrix containing peaks (called from the aggregates per condition) as row and the single cells as columns.
Supplementary_files_format_and_content: OmniATAC-seq abundance measurement is a raw count matrix containing peaks as row and the single cells as columns.
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage

treatment_protocol: SOX10-KD was performed using a SMARTpool of four siRNAs against SOX10 (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00-0005, Dharmacon) at a concentration of 20nM using as medium Opti-MEM (Thermo Fished Scientific) and omitting antibiotics. The cells were incubated for 24, 48 or 72 hours before processing.

tag: time point after sox10 kd

value: Base line


title: ChIP-seq control library mouse

description:
Mouse-Input-ChIP_NK15
background control for transcription factor ChIP-seq

extract_protocol:
midguts were dissected and treated with 3mM EDTA for 20minuites. Floating Epithelial tissue was collected and treated with 0.05% Trypsin, neutralized with FBS, and Epcam+ cells were enriched using magnetic antibody and fixed for subsequent chromatin pull down.
Whole cell lysates were sonicated and incubated without any antibody overnight for determining background chromatin pulldown.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries

value: Epithelial cells from the midgut

value: Wild-Type

tag: treatment

value: NO


title: D11 (Illumina)

city: Houston

last: Yao

value: Normal urothelium


title: RNA-seq E12.5 intestinal epithelium wt rep2

description:
E12.5_WT-rep2_NK41
Control midgut epithelial cell total RNA harvested at E12.5 biological rep2
E12.5_WTvsCdx2KO_cuffnorm_genes.fpkm_table.txt

value: C57BL6; mixed background

value: Embryonic epithelial cells from the midgut


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_84

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM087_Sox10KD_72hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

data_processing:
Library strategy: Tn-Seq
The reads from scATAC-seq samples were first cleaned for adapters using fastq-mcf (as part of ea utils; v1.1.2-686). Read quality was then checked using FastQC (v0.11.5). Paired-end reads were mapped to the human genome (hg19-Gencode v18) using STAR (v2.5.1) applying the parameters --alignIntronMax 1, --aslignIntronMin 2 and --alignMatesGapMax 2000. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Duplicates were removed using Picard (v1.134) MarkDuplicates using OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500. To filter out cell of bad quality, transcription start site aggregation plots were made using a custom script and cell having a noisy profile were removed from further analyses. This lead to a final of 598 good quality cells over 8 Fluidigm C1 runs. Bam files of good quality single cells were aggregated per condition and peaks were called on these aggregated samples using MACS2 (v2.1.1) callpeak using the parameters --nomodel and --call-summits. The peak files per condition were merged (78,661 peaks in total before blacklisting) and a count matrix was generated by using featureCounts (as part of Subread; v1.4.6) of all separate single cell bam files on the merged peak file (after conversion of the merged peak bed file to a gff format using a custom script). To visualise the aggregated cells per sample, normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.23.0) using as scaling parameter (-scale) size factors obtained from DEseq2 (v1.18.1). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs.
The reads from OmniATAC-seq samples were first cleaned for adapters using fastq-mcf (as part of ea utils; v1.1.2-686). Read quality was then checked using FastQC (v0.11.5). The reads were mapped to the human genome (hg19-Gencode v18) using STAR (v2.5.1) applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.1) callpeak using the parameters --nomodel and --call-summits on the 8 conditions separately. A count matrix was generated by using featureCounts (as part of Subread; v1.4.6) of all separate bam files on the merged peak file (after conversion of the merged peak bed file to a gff format using a custom script). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.23.0) using as scaling parameter (-scale) size factors obtained from DEseq2 (v1.18.1). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Reads obtained from H3K27Ac ChIP-seq were mapped to the genome using Bowtie2 (v2.1.0). The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read. bigWig files were generated from bam files using BEDTools (v2.17.0) and the scores represent the coverage.
Genome_build: hg19
Supplementary_files_format_and_content: scATAC-seq abundance measurement is a raw count matrix containing peaks (called from the aggregates per condition) as row and the single cells as columns.
Supplementary_files_format_and_content: OmniATAC-seq abundance measurement is a raw count matrix containing peaks as row and the single cells as columns.
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage

extract_protocol:
Cells were trysinised, spun down (1000 RPM, 5 min), medium was removed and cells were resuspended in fresh medium and passed through a 40 um filter, counted and diluted till 200,000 cells per mL. Cells were loaded (using a 40:60 ratio of RGT:cells) on a primed Open App IFC (10-17 um) and scATAC-seq was performed using the Fluidigm C1 system as described before [Buenrostro et al., 2015] (the protocol for ATAC-seq from the C1 Script Hub was used). After cell loading, the plate was visually checked under a microscope and the number of cells in each of the capture chambers was noted. Next, the “Sample prep” was performed on the Fluidigm C1 during which the cells underwent lysis and ATAC-seq fragments were prepared.
Library prep was performed as described before [Buenrostro et al., 2015]. After the first steps of the library construction by the “Sample prep” on the Fluidigm C1, the libraries were harvested into a 96-well plate and were amplified in a 25 uL PCR reaction. The PCR products were pooled and purified on a single MinElute PCR purification column for a final library volume of 15 uL. Quality checks were performed using the Bioanalyzed high sensitivity chips. Fragments under 150 bp were removed by bead-cleanup using AMPure XP beads (1.2x bead ratio) (Beckman Coulter).

value: 72 hours


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_83


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_85


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_94


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_89


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_95


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_92


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_91


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_86


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_90


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_93


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_96


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_79


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_81


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_80


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_82


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_78


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_77


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_87


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_88


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_76


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_75


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_73


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_74


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_71


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_59


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_65


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_61


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_68


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_60


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_62


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_69


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_70


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_64


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_67


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_58


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_66


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_63


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_57


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_56


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_55


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_72


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_51


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_54


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_52


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_50


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_47


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_44


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_53


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_49


title: WT rep 2

value: mixed lineage


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_45


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_46


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_43


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_41


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_42


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_40


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_39


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_38


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_33


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_37


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_36


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_34


title: Cdx2 ChIP-seq mouse E17.5 rep1

description:
E17.5_Cdx2_NK49
midgut harvested at E17.5

value: CD1 wild type

value: Embryonic whole tissue from midgut


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_35


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_48


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_31


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_32


title: B3 (Illumina)


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_24


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_23


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_29


title: B4 (Illumina)


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_30


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_25


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_26


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_22


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_27


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_21


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_19


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_18


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_17


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_20


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_11


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_15


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_12


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_13


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_16


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_14


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_09


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_10


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_28


title: D10 (Illumina)


title: E7 (Illumina)


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_03


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_04


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_95

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM087_Sox10KD_48hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

value: 48 hours


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_05


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_96


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_02


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_92


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_93


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_89


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_91


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_88


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_08


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_87


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_07


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_84


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_83


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_86


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_82


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_81


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_85


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_80


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_01


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_79


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_94


title: scATAC-seq_MM087_Sox10KD_72hr_Cell_06


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_90


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_78


title: E5 (Illumina)


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_77


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_75


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_76


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_71


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_70


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_73


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_69


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_74


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_66


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_68


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_67


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_65


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_63


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_64


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_62


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_61


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_58


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_60


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_57


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_55


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_54


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_51


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_52


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_56


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_72


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_50


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_49


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_48


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_47


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_59


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_46


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_53


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_45


title: B5 (Illumina)


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_41


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_42


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_44


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_43


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_40


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_39


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_38


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_36


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_37


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_35


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_34


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_32


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_30


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_29


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_25


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_27


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_24


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_28


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_26


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_23


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_22


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_31


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_21


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_20


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_18


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_17


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_16


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_33


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_11


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_14


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_13


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_10


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_09


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_06


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_04


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_02


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_03


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_95

description:
MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts
MM087_Sox10KD_24hr_Aggregate_GoodCells_SizeFactorsNorm.sorted.bw

value: 24 hours


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_93


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_05


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_89


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_96


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_07


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_91


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_94


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_15


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_88


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_90


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_01


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_92


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_86


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_12


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_83


title: scATAC-seq_MM087_Sox10KD_48hr_Cell_08


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_82


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_81


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_84


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_85


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_78


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_77


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_75


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_76


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_71


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_73


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_74


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_72


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_69


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_67


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_70


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_65


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_66


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_68


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_64


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_62


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_59


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_80


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_60


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_87


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_58


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_63


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_79


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_57


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_55


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_53


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_54


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_56


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_61


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_51


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_49


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_50


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_44


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_47


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_43


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_46


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_45


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_48


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_40


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_41


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_38


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_35


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_32


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_42


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_39


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_30


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_34


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_33


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_29


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_52


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_36


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_37


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_26


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_31


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_24


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_28


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_25


title: scATAC-seq_MM087_Sox10KD_24hr_Cell_23