title: EOMES KO, iPSC, MS102Y38

description:
Sample 19
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#5 line, harvested at iPSC, non-sorted

value: iPSC

value: EOMES-/-


title: tt2MO_st34_frogE

status: Public on Feb 21 2018

type: SRA

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description: injected 18 ng t/t2 donor splice- and translation-blocking morpholino (t/t2 MO) into 1-cell stage embryos from frog E

library_source: transcriptomic

data_processing:
Bases were called using Casava version 1.8.2
Paired-end reads were aligned to a revised version of X. tropicalis gene models 7.2 and known off-genome EST assemblies including ribosomal and mitochondrial RNA by running Bowtie2 (version 2.1.0) with the following constraints: -k 200 -X 800 --rdg 6,5 --rfg 6,5 --score-main L,-.6,-.4 --no-discordant --no-mixed.
Only read pairs that uniquely align to one gene were counted. Differential expression analysis was performed with raw fragment counts excluding those belonging to ribosomal and mitochondrial RNA using DESeq2 (Love et al., 2014)
For genome browser visualisation, paired-end reads were mapped to the X. tropicalis genome assembly 7.1 and known off-genome EST assemblies using Tophat (version 2.0.10) with the following parameters: -r 77 --mate-std-dev 110 -G v7.2 (gene models of version 7.2 as used above) -g 200 --report-secondary-alignments. genome_v71.gff3.gz (genome annotation file in GFF3 format) and GO_terms_v71.txt.gz (GO term annotation file) are linked on the Series record.
Genome_build: X. tropicalis v7.1

molecule: polyA RNA

organism: Xenopus tropicalis

source_name: embryo

growth_protocol: Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.

extract_protocol:
Single embryos were homogenised in 200 µl TRIzol (Thermo Fisher Scientific) by vortexing. For phase separation, 40 µl of chloroform was added to the homogenate, shaken vigorously for 15 secs before spinning for 5 mins at 16,000 g at 4ºC. The aqueous phase containing total RNA was snap-frozen in liquid nitrogen and stored at -80ºC while the interphase-organic layer was processed to extract genomic DNA for genotyping. The aqueous phases from 5 to 10 sibling embryos of shared genotype or treatment were then combined. Total RNA was precipitated with one volume of 100% ethanol and cleaned using the RNA Clean and Concentrator 5 or 25 (Zymo Research) with in-column 3 U Turbo DNase (Thermo Fisher Scientific) treatment according to the manufacturer’s instructions.
Libraries were made from ~1 µg total RNA by following version 2 of the TruSeq RNA low sample protocol (Illumina) with the following modifications. After second strand synthesis 1 µl of the remaining eluate was used to measure the cDNA concentration using the Qubit fluorometer and Qubit dsDNA high sensitivity reagents (Thermo Fisher Scientific). The resultant cDNA yield was used to estimate the number of requisite PCR cycles to generate high complexity libraries without chimera fragments. We routinely used ten PCR cycles for 10 ng cDNA and adjusted the number of PCR cycles accordingly.

treatment_protocol: Embryos were injected as indicated at 1-cell stage with 18 ng morpholino antisense oligonucleotide.

tag: strain

value: wild-type (out-bred Nigerian)

tag: developmental stage

value: mid-tailbud (stage 34)

tag: treatment

value: morpholino


title: Ctrl_SOX17/EOMES, iMeLC, MS082Y20

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description:
Sample 60
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iMeLC, non-sorted

data_processing:
Samples were sequenced by four separate runs with different conditions, 3 runs on NextSeq 500 and 1 run on HiSeq 2500 with length between 76 and 134 bases (detail available on GEO records). For equal comparison between these samples, all bases longer than 76 bases from read data were trimmed from 3'-end by trimmomatic v0.35 (Bolger et.al., 2014).
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the human genome hg19 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and hg19 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

molecule: total RNA

organism: Homo sapiens

source_name: iMeLC, from 585B1 hiPSC line

growth_protocol: 585B1 hiPSCs (XY) was cultured with AK03N medium on iMatrix coated plate as reported previously (Sasaki and Yokobayashi et al., 2015).

extract_protocol:
The cells were pelleted down and snap frozen until use.  RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For 3'-seq analysis, cDNA synthesis / amplification from RNA samples and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

treatment_protocol:
The iMeLC induction was induced from iPSC cultured in above condition, passaged to fibronectin coated plate with Activin A (50 ng/ml), CHIR99021 (3µM) and Y27632 (10µM) in GMEM containing 15% KSR, and cultured for 44 to 48 hours.
Above iMeLCs were then dissociated and replated to low-adherent V-bottom plates to form aggregates with BMP4 (200 ng/ml), SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), and Y27632 (10µM) in GMEM containing 15% KSR, until the harvest day.

tag: sampled time point

value: iMeLC

tag: cell line

tag: transgenes

value: Blimp1-tdTomato, TFAP2C-EGFP

tag: genotype/variation

value: WT control

tag: differentiation series

value: Series 1, SOX17 KO and EOMES KO


title: SOX17 KO, iPSC, MS082Y38

description:
Sample 18
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iPSC, non-sorted

source_name: iPSC, from 585B1 hiPSC line


title: ∆ribN RF+ rep1

city: Cuernavaca

first: Luis

middle: Fernando

last: Lozano

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

description: RF+ riboflavin present

data_processing:
Quality control visualization and analysis (adapter and quality trimming) was performed using FastQC version 0.11.2 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and Trim_galore version 0.4.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), respectively.
Reads were mapped to the genome of Vibrio cholerae 01 biovar El Tor str. N16961 (RefSeq, NCBI) using Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012). In all the samples the alignment percentage of reads were above 98%.
Differential expression analysis between samples was performed with the Bioconductor package edgeR version 3.18.1 (Robinson et al., 2010) using negative binomial model and exact test based on quantile-adjusted conditional maximum likelihood method (qCML). Genes with a statistically significant change in expression (P<0.05) were selected for further analysis.
Analyses of enrichment of Gene Ontology (GO) terms of biological processes in the indicated subsets of genes were performed on the online platform of the Gene Ontology Consortium (www.geneontology.org), and statistically significant (P<0.05) functional terms were retrieved.
Genome_build: Vibrio cholerae 01 biovar El Tor str. N16961 (RefSeq, NCBI)
Supplementary_files_format_and_content: tab-delimited text files include read counts of every gene for each Sample

organism: Vibrio cholerae

source_name: Bacteria Strain

growth_protocol: V. cholerae N16961 strain and its ∆ribD and ∆ribN derivatives were grown overnight in LB plates at 37 °C. 5 ml of LB broth were inoculated with a colony of the plate cultures and incubated at 37 °C in an orbital shaker at 150 rpm until they reached an OD600 nm of 1.0.

extract_protocol:
RNA extraction was performed with the Thermo Scientific Genejet RNA purification kit according to manufacturer´s instructions. RNA extracts were digested with Turbo DNA-free DNAase at 37 °C for 1 hour.
rRNA removal, cDNA libraries generation and RNAseq were performed at Genoma Mayor (Santiago, Chile)

tag: genotype

value: RF+ (riboflavin present)


title: tt2MO_st34_frogD

description: injected 18 ng t/t2 donor splice- and translation-blocking morpholino (t/t2 MO) into 1-cell stage embryos from frog D


title: SOX17 KO, iPSC, MS082Y13

description:
Sample 17
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iPSC, non-sorted


title: tt2_het_st26_cross1

value: te1.2D/+ t2e3.7D/+ (out-bred Nigerian)

value: mid-tailbud (stage 26)

tag: origin

value: t/t2 heterozygotes (t/t2 het) from natural pairing of te1.2D/+ t2e3.7D/+ (out-bred Nigerian) frogs (cross 1)


title: ∆ribD RF+ rep2

description: RF+ riboflavin present


title: cMO_st34_frogF

description: injected 18 ng standard control morpholino (cMO) into 1-cell stage embryos from frog F


title: SOX17 KO, iPSC, MS082Y37

description:
Sample 14
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iPSC, non-sorted


title: SOX17 KO, iPSC, MS082Y09

description:
Sample 16
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#33 line, harvested at iPSC, non-sorted


title: cMO_st34_frogE

description: injected 18 ng standard control morpholino (cMO) into 1-cell stage embryos from frog E


title: ∆ribD RF+ rep1

description: RF+ riboflavin present


title: cMO_st34_frogD

description: injected 18 ng standard control morpholino (cMO) into 1-cell stage embryos from frog D


title: SOX17 KO, iPSC, MS082Y16

description:
Sample 13
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iPSC, non-sorted


title: SOX17 KO, iPSC, MS082Y10

description:
Sample 12
Transcriptome of amplified cDNA from PGCLC induction of SOX17-/-#26 line, harvested at iPSC, non-sorted


title: WT RF+ rep3

description: RF+ riboflavin present

value: Wild Type


title: uni_st34_frogE

description: uninjected embryos from frog E


title: Ctrl_SOX17/EOMES, iPSC, MS102Y40

description:
Sample 10
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iPSC, non-sorted


title: WT RF+ rep1

description: RF+ riboflavin present


title: uni_st34_frogD

description: uninjected embryos from frog D


title: Ctrl_SOX17/EOMES, iPSC, MS082Y39

description:
Sample 9
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iPSC, non-sorted


title: tt2MO_st26_frogF

description: injected 18 ng t/t2 donor splice- and translation-blocking morpholino (t/t2 MO) into 1-cell stage embryos from frog F


title: Ctrl_SOX17/EOMES, iPSC, MS082Y17

description:
Sample 8
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iPSC, non-sorted


title: tt2MO_st26_frogE


title: ∆ribD RF+ rep3

description: RF+ riboflavin present


title: tt2MO_st26_frogD


title: Ctrl_SOX17/EOMES, iPSC, MS082Y08

description:
Sample 7
Transcriptome of amplified cDNA from PGCLC induction of control for SOX17 KO and EOMES KO lines, harvested at iPSC, non-sorted


title: cMO_st26_frogF


title: uni_st26_frogF

description: uninjected (uni) embryos from frog F


title: uni_st34_frogF

description: uninjected embryos from frog F


title: Ag_M4

city: Guangzhou, P. R. China

first: Xiangcheng

last: Yuan

address: 164 West Xingang Road, Guangzhou, 510301, P. R. China

country: China

institute: South China Sea Institute of Oceanology

description: Middle CO2

data_processing:
Base-calling were performed using RTA and CASAVA.
The quality of sequencing data was estimated using FastQC (v0.11.3). Then adaptors and low quality bases were removed using Trimmomatic (v0.33).
De novo transcriptome sequencing is the method of creating a transcriptome profiling of organisms or species based on the high-throughput technologies without the aid of a reference genome, including 3 parts of library construction, sequencing and bioinformatics analysis.
Genome_build: The FASTA file of assembled transcripts is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all unigenes in each treatment

organism: Acropora gemmifera

source_name: coral tissue

growth_protocol: Larvae were cultivated and settled under ambient conditions (pH NBS 8.16 ± 0.01, 27.5 oC, total alkalinity (TA) 2250.8 ± 5μM, salinity 33 psu). After fertilization, settlement was induced by the introduction.

extract_protocol:
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (foreukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp).
Then the first strand of cDNA is synthesized by using random hexamer-primer.  Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The doublestrand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to thefragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify andquantify of the sample library. The library products are ready for sequencing via Illumina HiSeq TM 2000 or other sequencer when necessary.

treatment_protocol: After induction of settlement, tiles on which A. gemmifera primary polyps settled were transferred to 90 L flow-through tanks, where they were exposed to seawater that had been equilibrated with air containing 380 ppm (pH=8.1), middle level of ~750 ppm (pH=7.8)  and high level of 1000 ppm CO2 (pH=7.5)

value: polyp

tag: co2 treatment

value: Middle


title: Ag_M1

description: Middle CO2


title: WT RF+ rep2

description: RF+ riboflavin present


title: Ag_M6

description: Middle CO2


title: Ag_M5

description: Middle CO2


title: Ag_M3

description: Middle CO2


title: Ag_M2

description: Middle CO2


title: uni_st26_frogD

description: uninjected (uni) embryos from frog D


title: uni_st26_frogE

description: uninjected (uni) embryos from frog E


title: cMO_st26_frogD


title: Ag_H8

description: High CO2

value: High


title: Ag_H4

description: High CO2


title: Ag_H1

description: High CO2


title: Ag_H5

description: High CO2


title: Ag_H3

description: High CO2


title: Ag_H2

description: High CO2


title: Ag_C5

description: Control

value: Control


title: Ag_C6

description: Control


title: Ag_C4

description: Control


title: Ag_C3

description: Control


title: cMO_st26_frogE


title: EOMES KO, iPSC, MS102Y60

description:
Sample 21
Transcriptome of amplified cDNA from PGCLC induction of EOMES-/-#18 line, harvested at iPSC, non-sorted

value: iPSC

value: EOMES-/-


title: Ag_C1

description: Control


title: NHBE_repop_P74_35d

status: Public on Feb 20 2018

city: Mölndal

first: Lisa

last: Öberg

address: Pepparedleden 1

department: Translational Science and Experimental Medicine

country: Sweden

institute: Research and Early Development, Respiratory Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden

description: Repopulation sample 36

data_processing:
Base calling were done by bcl2fastq from Illumina
RNA-Seq fastq files were processed using bcbio-nextgen (version 1.0.1)
Reads were mapped with hisat2 (version 2.0.5)
Counts were generated with featurecounts (version 1.4.4)
Genome_build: hg38 (GRCh38.79)
Supplementary_files_format_and_content: combined.counts (A text file with all combined counts for all genes as obtained from the pipeline specified above.)

source_name: Primary human bronchial epithelial cells

growth_protocol: Primary normal human bronchial epithelial (NHBE) cells were purchased from Lonza and cultured in bronchial epithelial growth medium (BEGM) (Lonza) to passage 3. The cells were harvested and seeded on decellularized bronchial scaffolds where they were allowed to attach and grow for 4 days in BEGM. Differentiation was induced after 4 days by exchanging the BEGM with a differentiation medium (50 % BEGM, 50% Dulbecco's Modified Eagle's Medium and 0.05 µM retinoic acid) and differentiation proceeded during 35 days.

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen). RNA integrity was assessed using Bioanalyzer 2100 (Agilent Technologies) and RIN (RNA Integrity Number) values >8 were obtained for all samples except for sample NHBE_repop_P115_28d (RIN=7.5). RNA was quantified using the Quant-iT RiboGreen RNA Assay kit (Thermo Fisher).
560 ng total RNA/sample was used as input to create cDNA libraries using the TruSeq Stranded mRNA kit (Illumina) with dual indexing following standard instructions. Libraries were validated on the Fragment Analyzer platform (Advanced Analytical) using the Standard Sensitivity NGS Fragment Analysis kit. Sample libraries were pooled in equimolar concentrations and the concentration of the pool was verified using the Qubit fluorometer and the Quant-iT dsDNA High Sensitivity assay kit (Thermo Fisher). The library pool was diluted and denatured according to Illumina guidelines and sequencing was performed using a High Output 1 x 76 bp kit (Illumina) on an Illumina NextSeq500 platform.

treatment_protocol: The treatment consisted of exposing the cells to the native three-dimensional extracellular matrix environment of the bronchial scaffolds derived from COPD patients and healthy donors.

tag: disease state

value: COPD

tag: bronchial scaffold type

tag: bronchial scaffold donor id

tag: cell type

value: Primary bronchial epithelial cells

tag: time (days of differentiation)


title: NHBE_repop_P74_7d

description: Repopulation sample 32


title: NHBE_repop_P74_21d

description: Repopulation sample 34


title: NHBE_repop_P74_14d

description: Repopulation sample 33


title: NHBE_repop_P73_28d

description: Repopulation sample 29


title: NHBE_repop_P74_28d

description: Repopulation sample 35


title: NHBE_repop_P74_0d

description: Repopulation sample 31


title: NHBE_repop_P73_14d

description: Repopulation sample 27


title: NHBE_repop_P73_21d

description: Repopulation sample 28


title: NHBE_repop_P73_7d

description: Repopulation sample 26


title: NHBE_repop_P73_0d

description: Repopulation sample 25


title: NHBE_repop_P68_35d

description: Repopulation sample 24


title: NHBE_repop_P68_21d

description: Repopulation sample 22


title: Ag_C2

description: Control


title: NHBE_repop_P68_28d

description: Repopulation sample 23


title: NHBE_repop_P68_7d

description: Repopulation sample 20


title: NHBE_repop_P118_35d

description: Repopulation sample 18

value: healthy control

value: Normal


title: NHBE_repop_P68_14d

description: Repopulation sample 21


title: NHBE_repop_P68_0d

description: Repopulation sample 19


title: NHBE_repop_P118_21d

description: Repopulation sample 16


title: NHBE_repop_P118_14d

description: Repopulation sample 15


title: NHBE_repop_P118_7d

description: Repopulation sample 14


title: NHBE_repop_P73_35d

description: Repopulation sample 30


title: NHBE_repop_P118_0d

description: Repopulation sample 13


title: NHBE_repop_P115_21d

description: Repopulation sample 10


title: NHBE_repop_P115_7d

description: Repopulation sample 8


title: NHBE_repop_P115_35d

description: Repopulation sample 12


title: PTC9

city: Buenos Aires

first: Natalia

middle: Anahí

last: Juiz

address: 2490, Vuelta de Obligado

country: Argentina

institute: INGEBI-CONICET

data_processing:
Raw reads were subjected to quality test with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).   Finally,
Sequences were mapped implementing STAR
Picard tools were applied to calculate the gene expression level
Differentially expressed genes (DEGs) were identified using edgeR

source_name: middle section placenta

extract_protocol: Trizol

tag: blood test

value: Chagas seropositive mother

tag: pcr test

value: PCR negative


title: NHBE_repop_P115_14d

description: Repopulation sample 9


title: PTC8


title: PTC6

value: PCR positive


title: NHBE_repop_P114_35d

description: Repopulation sample 6


title: PTC5


title: NHBE_repop_P114_28d

description: Repopulation sample 5


title: PTC4


title: NHBE_repop_P114_21d

description: Repopulation sample 4


title: PC3

value: Chagas seronegative mother


title: PC2


title: PC1


title: NHBE_repop_P114_14d

description: Repopulation sample 3


title: NHBE_repop_P114_7d

description: Repopulation sample 2


title: JQ1+PD901-combination treated M93-047, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

data_processing:
Raw reads were trimmed from poly-A tails and aligned using bowtie 2 algorithm against hg19 genome, and Ensembl transcriptome information was used along with RSEM software in order to calculate raw read counts for each gene.
DESeq2 software was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed file contains raw counts for Ensemble gene IDs

source_name: M93-047 NRAS mutant tumor cells

growth_protocol: M93-047 cells were propagated in RPMI-1640 medium (Thermo Scientific, Logan, UT) supplemented with heat inactivated 5% fetal bovine serum (FBS) (Thermo Scientific) and maintained at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit (Life Technology, Grand Island, NY)
Poly-A library was prepared using Lexogen QuantSeq 3’mRNA-Seq library prep kit at the Wistar Institute Genomic Core.

treatment_protocol: Cells were treated  with vehicle (DMSO), JQ-1, PD901, or the combination of both drugs (JQ-1 + PD901) for 48 hours

tag: replicate


title: NHBE_repop_P114_0d

description: Repopulation sample 1


title: iTreg_72_rep3

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

data_processing:
Paired-end reads were aligned with Tophat (version 2.0.8b) and Bowtie2 (version 2.1.0) to human reference genome (hg19) and Gencode transcriptome (v19).  Based on calculation for one million reads, we set the mean insert size and standard deviation for each sample separately.
Read counts were determined using HTSeq-count (version 0.6.1) with parameters “--stranded no --order name”
Bioconductor package edgeR was used for differential expression calling. Genes with RPKM <3 in at least two samples in both conditions were filtered out before differential expression calling.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: Cord blood CD4+ cells 72h after activation and polarization towards iTreg

growth_protocol: Human CD4 positive T cells were isolated from cord blood using CD4 positive isolation kit from Dynal.  Cells were activated with plate bound anti-CD3 and soluble anti-CD28 in presence (iTreg) or absence (Th0) of IL2, TGF beta and ATRA. The cells were harvested at 0, 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 hours.

extract_protocol:
RNA was isolated with RNeasy mini kit (QIAGEN).
Library was prepared following illumina Truseq protocol and were sequenced by HiSeq2500.

tag: tissue

value: Cord blood

tag: biological replicate

value: human biological replicate:3


title: PTC7


title: Th0_72_rep3

source_name: Cord blood CD4+ cells 72h after activation


title: iTreg_48_rep3

source_name: Cord blood CD4+ cells 48h after activation and polarization towards iTreg


title: JQ1+PD901-combination treated M93-047, replicate 1

tag: treatment


title: PD901-treated M93-047, replicate 3

description: PD901-treated M93-047, replicate 3

value: PD901 (MEK inhibitor)


title: Th0_48_rep3

source_name: Cord blood CD4+ cells 48h after activation


title: Bone marrow, basal

city: Worcester

first: Merav

last: Socolovsky

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description:
bBM
The barcode reads are: SRR5010979 SRR5010981 SRR5010983 SRR5010985
The cDNA reads are: SRR5010980 SRR5010982 SRR5010984 SRR5010986

data_processing:
The barcode read was first filtered based on presence of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015).
The cDNA read was then trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.  All files were submitted to SRA.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols in press)
Genome_build: GRCm38
Supplementary_files_format_and_content: The raw_umifm_counts files include raw unique molecular identifier (UMI)-filtered counts for all transcriptomes (prior to filtering). The filtered_normalized_counts files have normalized counts for transcriptomes passing all filtering steps. In both cases, columns = genes (with exception of first 5 columns), rows = cells. Column 1 contains cell identifier. Column 2 contains matching cell barcode. Column 3 contains library ID. Column 4 contains sequencing run ID (cells with same run ID were run on same flow cell). Column 5 contains flag for cell pass filtering (0=fail, 1=pass). Columns 6+ contain counts for each gene.

organism: Mus musculus

source_name: Bone marrow Kit+ cells, basal

extract_protocol:
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nature Protocols (in press), with the exception of the first round of libraries, for which the final PCR step was carried out as in Klein et al., Cell 2015.

treatment_protocol: For bone-marrow preparation, femurs and tibiae were harvested immediately following euthanasia and placed in cold (4°C) ‘staining buffer’ (phosphate- buffered saline (PBS) containing 0.2% Bovine Serum Albumin (BSA) and 0.08% Glucose). Bones were flushed using a 2 mL syringe with a 26-gauge needle and then crushed with a pestle and mortar to obtain all cells. Harvested bone marrow cells were filtered through a 40 μm strainer and washed in cold ‘Easy Sep’ buffer (PBS; 2% fetal bovine serum (FBS); 1mM EDTA). Fetal livers were prepared by mechanical dissociation in staining buffer and a wash in ‘Easy-Sep’ buffer. Bone marrow and fetal liver cell samples were each enriched for Kit expressing cells using magnetic beads, with the Mouse Biotin Selection Kit (STEMCELL technologies [Cat # 18556]) and Biotin Rat Anti-Mouse CD117 antibody (clone 2B8 , BD Bioscience), following the manufacturer’s protocol. Dead cells and debris were removed from the bone marrow and fetal liver samples using density centrifugation in OptiPrep (Sigma, Cat # D1556). Briefly, cells were re-suspended in 0.5ml staining buffer, mixed with 1mL of 40% of Optiprep in PBS, and placed in a 5 mL tube. The cell suspension was carefully over-layered with 2 mL of 20% OptiPrep solution, and 1mL of 5% OptiPrep solution, and centrifuged at 800g for 15 min (Centrifuge break OFF). The top visible cell band that formed during centrifugation contained the live, Kit+ single cells, confirmed by flow cytometric analysis. This layer was carefully aspirated and used directly in the inDrops platform.

tag: strain

value: BALB/cJ

tag: age

value: 8-week old adult

value: bone marrow

value: Kit+ hematopoietic progenitors

value: basal


title: iTreg_24_rep3

source_name: Cord blood CD4+ cells 24h after activation and polarization towards iTreg


title: JQ1+PD901-combination treated M93-047, replicate 2


title: PD901-treated M93-047, replicate 2

description: PD901-treated M93-047, replicate 2


title: PD901-treated M93-047, replicate 1

description: PD901-treated M93-047, replicate 1


title: NHBE_repop_P118_28d

description: Repopulation sample 17


title: JQ1-treated M93-047, replicate 3

description: JQ1-treated M93-047, replicate 3

value: JQ-1 (BET inhibitor)


title: Th0_24_rep3

source_name: Cord blood CD4+ cells 24h after activation


title: iTreg_12_rep3

source_name: Cord blood CD4+ cells 12h after activation and polarization towards iTreg


title: Th0_12_rep3

source_name: Cord blood CD4+ cells 12h after activation


title: JQ1-treated M93-047, replicate 2

description: JQ1-treated M93-047, replicate 2


title: DMSO-treated M93-047, replicate 3

description: DMSO-treated M93-047, replicate 3

value: DMSO


title: iTreg_6_rep3

source_name: Cord blood CD4+ cells 6h after activation and polarization towards iTreg


title: DMSO-treated M93-047, replicate 2

description: DMSO-treated M93-047, replicate 2


title: Th0_4_rep3

source_name: Cord blood CD4+ cells 4h after activation


title: JQ1-treated M93-047, replicate 1

description: JQ1-treated M93-047, replicate 1


title: untreated M93-047, replicate 3

description: untreated M93-047, replicate 3

value: untreated


title: iTreg_2_rep3

source_name: Cord blood CD4+ cells 2h after activation and polarization towards iTreg


title: untreated M93-047, replicate 2

description: untreated M93-047, replicate 2


title: Th0_2_rep3

source_name: Cord blood CD4+ cells 2h after activation


title: Th0_1_rep3

source_name: Cord blood CD4+ cells 1h after activation


title: NHBE_repop_P115_28d

description: Repopulation sample 11

source_name: Primary human bronchial epithelial cells

value: healthy control

value: Primary bronchial epithelial cells


title: iTreg_0.5_rep3

source_name: Cord blood CD4+ cells 0.5h after activation and polarization towards iTreg


title: iTreg_1_rep3

source_name: Cord blood CD4+ cells 1h after activation and polarization towards iTreg


title: LMPP

city: Yokohama

first: Tomokatsu

last: Ikawa

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

data_processing:
Illumina Casava1.8 software used for basecalling.
The Cell Ranger Single-Cell Software was used to perform sample demultiplexing, barcode processing, single-cell 3’ gene counting, and combining libraries.
For secondary analysis including t-SNE projection and clustering, Cell Ranger R Kit was used.
Genome_build: mm10
Supplementary_files_format_and_content: barcode, gene and matrix files per sample

source_name: bone marrow

growth_protocol: Id3-ERT2-induced hematopoietic multipotent progenitors (induced leukocyte stem, or iLS cells) were co-cultured with TSt-4 feeder cells in IMDM medium supplemented with 20 ng/mL IL-7, 10 ng/mL SCF, 10 ng/mL Flt-3L and 40 nM 4-OHT.

extract_protocol:
iLS cells at day 0 and day 8 of B cell induction or LMPP, CLP and pro-B cells in BM were sorted and ~3000 cells were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel bead in EMulsion (GEMs).
Single cell RNA-seq libraries were prepared using GemCode Single cell 3’ Gel Bead and Library Kit (10x Genomics).

treatment_protocol: To induce B cell differentiation of iLS cells, the cells were co-cultured with TSt-4 cells in IMDM medium supplemented with 5 ng/ml IL-7 in the absence of 4-OHT.

value: LMPP (cKit+Sca1+Flt3+IL7Ra-B220-)

tag: version of chromium chemistry

value: Single Cell 3' v2


title: pro-B

value: pro-B (cKit+Sca1-Flt3-IL7Ra+B220+)


title: Th0_6_rep3

source_name: Cord blood CD4+ cells 6h after activation


title: CLP

value: CLP (cKit+Sca1+Flt3+/-IL7Ra+B220-)


title: iLS_d8

source_name: induced leukocyte stem cells

value: B cells (CD19+)

value: Single Cell 3' v1


title: iTreg_4_rep3

source_name: Cord blood CD4+ cells 4h after activation and polarization towards iTreg

value: Cord blood

value: human biological replicate:3


title: Th0_72_rep2

source_name: Cord blood CD4+ cells 72h after activation

value: human biological replicate:2


title: iTreg_72_rep2

source_name: Cord blood CD4+ cells 72h after activation and polarization towards iTreg


title: iTreg_48_rep2

source_name: Cord blood CD4+ cells 48h after activation and polarization towards iTreg


title: iLS_d0

value: hematopoietic multipotent cells (CD19-Mac1-NK1.1-)


title: Th0_48_rep2

source_name: Cord blood CD4+ cells 48h after activation


title: NO16_24 [Bisulfite-Seq-Cre]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

library_source: genomic

data_processing:
base calling: HiSeq Analysis Software
trimming: reads were adapter-, quality- and end- trimmed using TrimGalore version 0.3.7 using --paired –phred 33 -q 20 -e 0.15 --clip-R1 14 --clip-R2 15 --retain-unpaired --fastqc --three-prime-clip-R1 20 --three-prime-clip-R2 -a  <index-specific adapter> -a2 <index-specific adapter>
alignment: bismark version 0.16.3 to bisulfite-converted and unconverted mm9 genomes
CpG methylation extraction and coverage generation: bismark_methylation_extractor
Low-methylated and unmethylated region detection: MethylSeekR
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format

molecule: genomic DNA

source_name: Ebf1-deficient B cell progenitors_24 hours

growth_protocol: To isolate c-Kit+ progenitor cells, Ebf1-/-RERTCre fetal liver cells were stained with biotinylated c-Kit antibody (BD Biosciences) and purified by streptavidin beads-mediated magnetic-activated cell sorting (MACS, Miltenyi Biotec). OP9 feeder cells were used to maintain the progenitors in OptiMEM medium supplemented with 4% FCS, 1% PSG, 50µM β-mercaptoethanol, 10ng/mL SCF, 10ng/mL Flt3L, and 5ng/mL IL-7.

extract_protocol:
Genomic DNA was prepared using DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer's instructions.
Libraries were prepared via theEpiTect Bisulfite and Illumina Truseq PCRFree DNA library preparation protocol according to manufacturer's instructions

treatment_protocol: Ebf1-/- RERTCre B cell progenitors were transduced with a Cre-based inducible EBF1 expression retroviral construct. The transduced cells were treated with 2μM 4-hydroxy-tamoxifen (4-OHT) to initiate EBF1 expression. Cells were harvested at different time points after 4-OHT treatment for analysis.

value: Ebf1-deficient B cell progenitors

tag: stage post 4-oht treatment

value: 24 hours

value: bisulfite-treated genomic DNA


title: NO16_72 [Bisulfite-Seq-Cre]

source_name: Ebf1-deficient B cell progenitors_72 hours

value: 72 hours


title: DMSO-treated M93-047, replicate 1

description: DMSO-treated M93-047, replicate 1

source_name: M93-047 NRAS mutant tumor cells

value: DMSO


title: iTreg_24_rep2

source_name: Cord blood CD4+ cells 24h after activation and polarization towards iTreg


title: Th0_24_rep2

source_name: Cord blood CD4+ cells 24h after activation


title: iTreg_12_rep2

source_name: Cord blood CD4+ cells 12h after activation and polarization towards iTreg


title: untreated M93-047, replicate 1

description: untreated M93-047, replicate 1

value: untreated


title: NO15_72 [Bisulfite-Seq-Cre]


title: NO15_CD19 [Bisulfite-Seq-Cre]

source_name: Ebf1-deficient B cell progenitors_CD19+


title: NO15_24 [Bisulfite-Seq-Cre]


title: iTreg_6_rep2

source_name: Cord blood CD4+ cells 6h after activation and polarization towards iTreg


title: NO16_CD19 [Bisulfite-Seq-Cre]


title: Thp_rep3

source_name: Cord blood CD4+ cells without any treatments


title: NO15_0  [Bisulfite-Seq-Cre]

source_name: Ebf1-deficient B cell progenitors_0 hours

value: 0 hours


title: RNAseq_72hrs_rep2 [RNA-Seq-Cre]

data_processing:
base calling: HiSeq Analysis Software
alignment:tophat2 (2.0.14)
transcript assembly: cufflinks (2.2.1)
FPKM generation: cufflinks (2.2.1)
coverage generation: bedtools genomecov (2.19.0)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format

extract_protocol:
Total RNA was prepared using RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. Then mRNA was enriched using Oligo dT magnetic beads for library preparation.
Libraries were prepared via the TruSeq® Stranded mRNA library preparation protocol according to manufacturer's instructions

tag: cell type source


title: Th0_6_rep2

source_name: Cord blood CD4+ cells 6h after activation


title: RNAseq_proB_rep2 [RNA-Seq-Cre]


title: Th0_4_rep2

source_name: Cord blood CD4+ cells 4h after activation


title: Th0_0.5_rep3

source_name: Cord blood CD4+ cells 0.5h after activation


title: RNAseq_24hrs_rep2 [RNA-Seq-Cre]


title: iTreg_4_rep2

source_name: Cord blood CD4+ cells 4h after activation and polarization towards iTreg


title: iTreg_1_rep2

source_name: Cord blood CD4+ cells 1h after activation and polarization towards iTreg


title: iTreg_2_rep2

source_name: Cord blood CD4+ cells 2h after activation and polarization towards iTreg


title: RNAseq_proB_rep1 [RNA-Seq-Cre]


title: Th0_2_rep2

source_name: Cord blood CD4+ cells 2h after activation


title: NO16_0 [Bisulfite-Seq-Cre]


title: NHBE_repop_P115_0d

description: Repopulation sample 7

source_name: Primary human bronchial epithelial cells

value: healthy control

value: Normal

value: Primary bronchial epithelial cells


title: RNAseq_72hrs_rep1 [RNA-Seq-Cre]


title: Th0_1_rep2

source_name: Cord blood CD4+ cells 1h after activation


title: RNAseq_0hrs_rep2 [RNA-Seq-Cre]


title: RNAseq_24hrs_rep1 [RNA-Seq-Cre]


title: iTreg_0.5_rep2

source_name: Cord blood CD4+ cells 0.5h after activation and polarization towards iTreg


title: ∆ribN RF+ rep3

description: RF+ riboflavin present

source_name: Bacteria Strain

tag: genotype

value: RF+ (riboflavin present)


title: RNAseq_0hrs_rep1 [RNA-Seq-Cre]


title: ∆ribN RF+ rep2

description: RF+ riboflavin present


title: Thp_rep2


title: input_proB  [Pax5-ChIP-Seq-Tet-On]

data_processing:
base calling: HiSeq Analysis Software
alignment: bowtie2 (2.3.2)
duplicated reads and low mapping quality read removal: samtools 1.3.1
peak calling and depth coverage generation (bedGraph): macs2 2.1.0
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format

growth_protocol: To isolate c-Kit+ progenitor cells, Ebf1-/- fetal liver cells were stained with biotinylated c-Kit antibody (BD Biosciences) and purified by streptavidin beads-mediated magnetic-activated cell sorting (MACS, Miltenyi Biotec). OP9 feeder cells were used to maintain the progenitors in OptiMEM medium supplemented with 4% FCS, 1% PSG, 50µM β-mercaptoethanol, 10ng/mL SCF, 10ng/mL Flt3L, and 5ng/mL IL-7.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Then they were washed with PBS and lysed for sonication. Chromatin was precipitated with a specific antibody (anti-Pax5, Santa Cruz, sc-1974X, 4µg/sample) and protein A or G-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified using MinElute PCR Purification Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared via the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® library preparation protocol according to manufacturer's instructions

treatment_protocol: Ebf1-/- B cell progenitors were transduced with a Tet-on Pax5 inducible expression retroviral construct. The transduced cells were treated with 1ug/ml doxycycline to initate Pax5 expression. Cells were harvested 6 hours after treatment for analysis. Ebf1-/- RERTCre B cell progenitors were transduced with a Cre-based inducible EBF1 expression retroviral construct. The transduced cells were treated with 2μM 4-hydroxy-tamoxifen (4-OHT) to initiate EBF1 expression. After 5days, CD19+ pro-B cells were sorted for analysis.

tag: stage post dox treatment

value: 6 hrs

tag: antibody


title: iTreg_72_rep1

source_name: Cord blood CD4+ cells 72h after activation and polarization towards iTreg

value: human biological replicate:1


title: Pax5_ChIP_6hrs  [Pax5-ChIP-Seq-Tet-On]


title: input_6hrs [Pax5-ChIP-Seq-Tet-On]


title: iTreg_48_rep1

source_name: Cord blood CD4+ cells 48h after activation and polarization towards iTreg

value: Cord blood


title: Th0_72_rep1

source_name: Cord blood CD4+ cells 72h after activation


title: H3K27ac_ChIP_proB  [Histone-ChIP-Seq-Cre]

data_processing:
base calling: HiSeq Analysis Software
alignment: bowtie2 (2.3.2)
duplicated reads and low mapping quality read removal: samtools 1.3.1
peak calling and depth coverage generation (bedGraph): macs2 2.1.0
Genome_build: mm9
Supplementary_files_format_and_content: bigWig format

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Then they were washed with PBS and lysed for sonication. Chromatin was precipitated with a specific antibody (anti-H3K4me2, Millipore, 07-030, 2µg/sample; anti-H3K27me3, Millipore, 07-449, 4µg/sample; anti-H3K27ac, Abcam, ab4729, 2µg/sample) and protein A or G-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified using MinElute PCR Purification Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared via the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® library preparation protocol according to manufacturer's instructions

value: Abcam, ab4729


title: Th0_48_rep1

source_name: Cord blood CD4+ cells 48h after activation


title: iTreg_12_rep1

source_name: Cord blood CD4+ cells 12h after activation and polarization towards iTreg


title: Th0_12_rep1

source_name: Cord blood CD4+ cells 12h after activation


title: iTreg_24_rep1

source_name: Cord blood CD4+ cells 24h after activation and polarization towards iTreg


title: H3K27me3_ChIP_proB  [Histone-ChIP-Seq-Cre]

value: Millipore, 07-449


title: H3K27ac_ChIP_72hrs  [Histone-ChIP-Seq-Cre]


title: Th0_24_rep1

source_name: Cord blood CD4+ cells 24h after activation


title: H3K27ac_ChIP_24hrs  [Histone-ChIP-Seq-Cre]


title: iTreg_6_rep1

source_name: Cord blood CD4+ cells 6h after activation and polarization towards iTreg


title: H3K27me3_ChIP_72hrs  [Histone-ChIP-Seq-Cre]


title: H3K27ac_ChIP_0hrs  [Histone-ChIP-Seq-Cre]


title: H3K27me3_ChIP_24hrs  [Histone-ChIP-Seq-Cre]


title: iTreg_4_rep1

source_name: Cord blood CD4+ cells 4h after activation and polarization towards iTreg


title: Th0_6_rep1

source_name: Cord blood CD4+ cells 6h after activation


title: Th0_0.5_rep2

source_name: Cord blood CD4+ cells 0.5h after activation

value: human biological replicate:2


title: Th0_4_rep1

source_name: Cord blood CD4+ cells 4h after activation


title: H3K4me2_ChIP_72hrs  [Histone-ChIP-Seq-Cre]

value: Ebf1-deficient B cell progenitors

value: Millipore, 07-030


title: iTreg_2_rep1

source_name: Cord blood CD4+ cells 2h after activation and polarization towards iTreg


title: Th0_2_rep1

source_name: Cord blood CD4+ cells 2h after activation


title: iTreg_1_rep1

source_name: Cord blood CD4+ cells 1h after activation and polarization towards iTreg


title: Th0_1_rep1

source_name: Cord blood CD4+ cells 1h after activation


title: input_72hrs  [Histone-ChIP-Seq-Cre]


title: input_proB  [Histone-ChIP-Seq-Cre]


title: iTreg_0.5_rep1

source_name: Cord blood CD4+ cells 0.5h after activation and polarization towards iTreg


title: H3K4me2_ChIP_24hrs  [Histone-ChIP-Seq-Cre]

value: 24 hours


title: input_24hrs  [Histone-ChIP-Seq-Cre]


title: Th0_0.5_rep1


title: input_0hrs  [Histone-ChIP-Seq-Cre]


title: Thp_rep1

source_name: Cord blood CD4+ cells without any treatments


title: EBF1_ChIP_6hrs_rep1 [EBF1-ChIP-Seq-Tet-On]

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Then they were washed with PBS and lysed for sonication. Chromatin was precipitated with a specific antibody (anti-EBF1, BioGenes, 4µg/sample) and protein A or G-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified using MinElute PCR Purification Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared via the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® library preparation protocol according to manufacturer's instructions

treatment_protocol: Ebf1-/- B cell progenitors were transduced with a Tet-on EBF1 inducible expression retroviral construct. The transduced cells were treated with 1ug/ml doxycycline to initate EBF1 expression. Cells were harvested 6 hours after treatment or without treatment for analysis.

value: BioGenes 1C


title: HeLa cell wild type

city: Houston

first: Hyun Jung

last: Park

state: TX

address: One Baylor Plaza

department: Dan L. Duncan Cancer Center

institute: Baylor College of Medicine

description: microRNA

data_processing:
Small RNA libraries were generated from one control and one CFIm25 depletion sample using the Illumina TruseqTM Small RNA Preparation kit.
The libraries are sequenced on Illumina GAIIx.
Raw sequencing reads (40 nts) were obtained using Illumina's Sequencing Control Studio software following image analysis and base-calling by Illumina's Real-Time Analysis (v 1.8.70).
Then a script ACGT101-miR v 4.2 (LC Sciences) was used for data analysis, where reads are mapped to the reference database (miRbase).
The script also normalizes the counts by a library size parameter for comparison.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized values for each Sample

source_name: HeLa cell

growth_protocol: HeLa cells were routinely grown on tissue culture tretaed plastic plates in DMEM media with GlutaMAX(ThermoFisher Scientific) supplemented with 10% FBS and 1% Pen/Strep. antibiotics

extract_protocol: Total RNA was extracted from the cells using Trizol reagent. SYBRGreen based qRT-PCR was perfomed in triplicate to validate 3'UTR shortening of select known gene targets. The CFIm25 depleted RNA sample with the highest shortening was used for library construction together with a control.

treatment_protocol: Cells were transfected with control or CFIm25 specific siRNA using Lipofectamine 2000 (ThermoFisher Scientific) in quadruplicate. CFIm25 knockdown was validated using western blot.

value: control

tag: cell line

value: HeLa


title: H3K27me3_ChIP_0hrs  [Histone-ChIP-Seq-Cre]

value: 0 hours


title: EBF1_ChIP_proB_rep2 [EBF1-ChIP-Seq-Cre]

tag: cell type


title: H3K4me2_ChIP_proB  [Histone-ChIP-Seq-Cre]


title: 10C_MG+PMA_t60

city: Athens

first: Stephen

middle: Patrick

last: LaVoie

state: Ga

address: 527 Biological Sciences Bldg.

department: Microbiology

institute: University of Georgia

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t60 (biological rep. 3)

data_processing:
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20.
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format.
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode.
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control.
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf )
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli

growth_protocol: For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm.

extract_protocol:
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions.
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations.

treatment_protocol: When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection.

value: MG1655 + 3µM PMA at t60


title: EBF1_ChIP_72hrs_rep2 [EBF1-ChIP-Seq-Cre]

value: 72 hours


title: 8C_MG+PMA_t10

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t10 (biological rep. 3)

value: MG1655 + 3µM PMA at t10


title: 7C_MG+Hg_t60

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t60 (biological rep. 3)

value: MG1655 + 3µM HgCl2 at t60


title: 9C_MG+PMA_t30

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t30 (biological rep. 3)

value: MG1655 + 3µM PMA at t30


title: H3K4me2_ChIP_0hrs  [Histone-ChIP-Seq-Cre]


title: Th0_12_rep2


title: 6C_MG+Hg_t30

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t30 (biological rep. 3)

value: MG1655 + 3µM HgCl2 at t30


title: 5C_MG+Hg_t10

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t10 (biological rep. 3)

value: MG1655 + 3µM HgCl2 at t10


title: EBF1_ChIP_proB_rep1 [EBF1-ChIP-Seq-Cre]


title: EBF1_ChIP_24hrs_rep2 [EBF1-ChIP-Seq-Cre]


title: input_proB_rep2 [EBF1-ChIP-Seq-Cre]


title: input_72hrs_rep2 [EBF1-ChIP-Seq-Cre]


title: HeLa cell CFIm25 knockdown

description: microRNA

value: CFIm25 knockdown


title: 2C_MG_t10

description:
rRNA-depleted total RNA
MG1655 - unexposed at t10 (biological rep. 3)

value: MG1655 - unexposed at t10


title: 4C_MG_t60

description:
rRNA-depleted total RNA
MG1655 - unexposed at t60 (biological rep. 3)

value: MG1655 - unexposed at t60


title: 3C_MG_t30

description:
rRNA-depleted total RNA
MG1655 - unexposed at t30 (biological rep. 3)

value: MG1655 - unexposed at t30


title: input_proB_rep1 [EBF1-ChIP-Seq-Cre]

value: Ebf1-deficient B cell progenitors


title: 10B_MG+PMA_t60

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t60 (biological rep. 2)


title: 1C_MG_t0

description:
rRNA-depleted total RNA
MG1655 - unexposed at t0 (biological rep. 3)

value: MG1655 - unexposed at t0


title: input_24hrs_rep2 [EBF1-ChIP-Seq-Cre]

value: 24 hours


title: EBF1_ChIP_6hrs_rep2 [EBF1-ChIP-Seq-Tet-On]

value: 6 hrs

value: BioGenes 1C


title: 9B_MG+PMA_t30

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t30 (biological rep. 2)


title: input_24hrs_rep1 [EBF1-ChIP-Seq-Cre]


title: 8B_MG+PMA_t10

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t10 (biological rep. 2)


title: ATAC_6hrs_rep2 [ATAC-Seq-Tet-On]

extract_protocol:
ATAC-seq library was prepared using Nextera DNA Library Prep Kit (Illumina). Briefly, 100,000 cells were resuspended in 50µl of cold lysis buffer (10mM Tris·Cl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) Igepal CA-630) and incubated on ice for 15 min. Immediately after lysis, nuclei were collected and re-suspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (TDE1) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 minutes at 37 °C and immediately put on ice. Then the sample was purified using MinElute PCR Purification Kit (Qiagen). Following purification, the library was amplified using indexed Nextera PCR primers and NEBNext High-Fidelity 2× PCR Master Mix. Finally the library was purified using MinElute PCR Purification Kit.
Libraries were prepared via the Nextera® DNA Sample Preparation library preparation protocol according to manufacturer's instructions


title: ATAC_0hrs_rep2 [ATAC-Seq-Tet-On]

value: 0 hrs


title: 7B_MG+Hg_t60

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t60 (biological rep. 2)


title: 6B_MG+Hg_t30

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t30 (biological rep. 2)


title: ATAC_6hrs_rep1 [ATAC-Seq-Tet-On]


title: 5B_MG+Hg_t10

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t10 (biological rep. 2)


title: ATAC_proB_rep2  [ATAC-Seq-Cre]


title: ATAC_0hrs_rep1 [ATAC-Seq-Tet-On]


title: Footprints WT fibroblasts replicate2

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
Library strategy: Ribo-Seq
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to mouse rRNA sequences were discarded.
All remaining reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the mouse genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *wig: Wiggle files contain aligned reads following the described pre-processing steps.

source_name: MEF derived from C57BL/6 background

extract_protocol:
Cells were lysed with 0.5% Triton, and the lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. RNA was then isolated from cells using the acid:phenol extraction method.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

tag: strain/background

tag: genotype/variation

value: WT

value: mouse embryonic fibroblasts (MEFs)


title: Footprints 4EHP KO fibroblasts replicate2

value: 4EHP KO


title: 4B_MG_t60

description:
rRNA-depleted total RNA
MG1655 - unexposed at t60 (biological rep. 2)


title: mRNA 4EHP KO fibroblasts replicate2

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to mouse rRNA sequences were discarded.
All remaining reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the mouse genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *wig: Wiggle files contain aligned reads following the described pre-processing steps.


title: ATAC_72hrs_rep2  [ATAC-Seq-Cre]

value: 72 hrs


title: 3B_MG_t30

description:
rRNA-depleted total RNA
MG1655 - unexposed at t30 (biological rep. 2)


title: Footprints 4EHP KO fibroblasts replicate1


title: mRNA 4EHP KO fibroblasts replicate1


title: ATAC_24hrs_rep2  [ATAC-Seq-Cre]

value: 24 hrs


title: 2B_MG_t10

description:
rRNA-depleted total RNA
MG1655 - unexposed at t10 (biological rep. 2)


title: ATAC_proB_rep1  [ATAC-Seq-Cre]


title: mRNA WT fibroblasts replicate1


title: 10A_MG+PMA_t60

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t60 (biological rep. 1)

value: MG1655 + 3µM PMA at t60


title: 1B_MG_t0

description:
rRNA-depleted total RNA
MG1655 - unexposed at t0 (biological rep. 2)


title: ATAC_72hrs_rep1  [ATAC-Seq-Cre]


title: HiC_DN4_1

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description:
KZ620
DN3_DP_HiC.bin1Kmin5Kmax2M.III.bed
DN4_PCA20k.PC1.txt

data_processing:
Basecalls performed using CASAVA 1.8.4
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (v2-2.0.2; default parameters; PMID 3322381). Only pair-end tags (PETs) mapped with high quality score (MAPQ > 10) were include for the analysis of chromatin interaction. For ChIP-Seq and scDNase-Seq analysis, if multipe reads were mapped to the same genomic site, only one read  was kept.
The HOMER (PMID 20513432) package was employed to partition the genome into A and B compartment, at a resolution of 20K bps, with compartment signal across the genome corresponding to the cooridantes of the first principal obtained from PCA analysis on the normalized interaction matrix. Interaction matrices at a resolution of 20Kb were normalized by ICE (PMID 22941365). The  gross intearcion of a gene is measured by the PETs with at least one end originated from the gene. PETs with distance less than 4K and longer than 2M were excluded. Also, FitHi-C (PMID: 24501021) was used to filtered PETs potentially orignated from background; potential interactions between any pairs of 2Kb bins were called under p<0.05 and an minimal of 2PETs. Potential HSs from DNase-Seq data were called by SICER (PMID 19505939), with a window size of 100 bps, E-value = 0.001 and no gap. Bcl11b binding sites from ChIP-Seq data were also called by SICER (PMID 19505939) with a window size of 200 bps, E-value = 1, and gap = 400 bps. Gene expression from RNA-Seq was quantified by RPKM with in-house script and RefSeq gene annotation. Nucleosome positioning was called by Danpos (v2.2.1, -m 1, quantile normalization, others default; PMID 23193179).
genome build: mm9
processed data files format and content: file name ending with "rpkm.txt": plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
processed data files format and content: file name ending with "scoreisland": plan text output from SICER. Columns from right to left are for chr, start, end, score.
processed data files format and content: file name ending with "positions.xls": plan text file; prediction of nucleosome position from Danpos. Columns from left to right denote chr, start, end, sumit_pos, sumit_value_quantile_normalized, and fuzziness_score.
processed data files format and content: file name ending with "PC1.bedGraph.sort" or "PCA.bedgraph.sort": plan text file; compartment score output from HOMER (PMID 20513432). Columns from left to right include: "chr     start   end  PC1". The file was sorted into the "bedgraph" format acceptable by WahsU epigenome browser (PMID 23629413).
processed data files format and content: file name ending with "mtx.normICE.washU.sort": plain text file recording the number of interacting PETs between pairs of 20K bins, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).
processed data files format and content: file name ending with "sbsmp.iii.genWashU.sort": plain text file recording the number of gross interacting PETs of genes, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).

extract_protocol:
For Hi-C, five thousands to millions cells were stained with Biotin anti-CD45.2 antibody. Cells were bound to biotin binder (Dynabeads Biotin Binder, Cat#11047, Invitrogen) and cross-link with 1% formaldehyde.  Biotin binders were blocked by 0.5mM biotin solution. Cells were lysed and digested with CviQ I + CviA II + Bfa I for 20min. For DNase-Seq, 1000 purified cells were lysed in 32ul of lysis buffer (10mM Tris-Cl, pH7.5, 10mM NaCl, 3mM MgCl2) and digested with 8ul of DNase I for 5 min at 37°C. The reaction was stopped by adding 40ul of stop buffer containing 10mM Tris-Cl, pH7.5, 10mM NaCl, 10mM EDTA, 2% SDS, 0.5mg/ml Proteinase K, and 1ng/ul of circular carrier DNA), followed by incubation at 65°C for 1 hour. For MNase-Seq, 100 purified cells were lysed in 32ul of lysis buffer (10mM Tris-Cl, pH7.5, 10mM NaCl, 2mM CaCl2) and digested with 8ul of MNase I for 5 min at 37°C. The reaction was stopped by adding 40ul of stop buffer containing 10mM Tris-Cl, pH7.5, 10mM NaCl, 10mM EGTA, 2% SDS, 0.5mg/ml Proteinase K, and 1ng/ul of circular carrier DNA), followed by incubation at 65°C for 1 hour. For RNA-Seq, 2ng of total RNA were extracted miRNeasy Micro Kit (50) from Qiagen (Cat # 217084).
The Hi-C samples were processed following the Hi-C protocol (PMID 19815776) with modifications briefly described as follows: DNA end were marked by biotin-14-dATP with Klenow(larg) for 1hrs at 37°C. Blunt-end DNA were ligated with T4 DNA Ligase for overnight at 16°C. DNA were reverse cross-linked and purified by phenol/chloroform extraction. Biotin were removed from unligated DNA-ends by T4 DNA polymerase for 2hrs at 12°C. DNA were purified by phenol/chloroform. DNA were sheared to 300-500bps by sonication and flowed by DNA-end repair and add”A”34. Biotin labeled DNA were pull-downed by streptavidin beads and then flowed by illumine adapter ligation and PCR amplification. Library construction protocals for DNase-Seq, MNase-Seq and RNA-Seq follow that described in (PMID 26605532), (PMID 18329373) and (PMID 24056875), respectively.

value: Thymus

tag: dilution setting


title: 9A_MG+PMA_t30

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t30 (biological rep. 1)

value: MG1655 + 3µM PMA at t30


title: HiC_DP_1

description:
KZ621
DN3_DP_HiC.bin1Kmin5Kmax2M.III.bed
DP_PCA20k.PC1.txt

source_name: DP


title: HiC_DN3_1

description:
KZ619
DN3_DP_HiC.bin1Kmin5Kmax2M.III.bed
DN3_PCA20k.PC1.txt


title: HiC_ETP_1

description:
KZ617
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
ETP_PCA20k.PC1.txt

source_name: ETP


title: HiC_DN2_1

description:
KZ618
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
DN2_PCA20k.PC1.txt


title: HiC_CLP_1

description:
KZ616
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
CLP_PCA20k.PC1.txt

source_name: CLP

value: Bone marrow


title: HiC_MPP_1

description:
KZ615
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
MPP_PCA20k.PC1.txt

source_name: MPP


title: ATAC_0hrs_rep1  [ATAC-Seq-Cre]


title: 7A_MG+Hg_t60

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t60 (biological rep. 1)

value: MG1655 + 3µM HgCl2 at t60


title: Footprints WT fibroblasts replicate1


title: HiC_HSC_1

description:
KZ614
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
HSC_PCA20k.PC1.txt

source_name: HSC


title: RNASeq_DP


title: ATAC_0hrs_rep2  [ATAC-Seq-Cre]


title: EBF1_ChIP_24hrs_rep1 [EBF1-ChIP-Seq-Cre]


title: 6A_MG+Hg_t30

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t30 (biological rep. 1)

value: MG1655 + 3µM HgCl2 at t30


title: RNASeq_DN4


title: RNASeq_DN3


title: mRNA WT fibroblasts replicate2


title: Neg_d5

city: Minneapolis

first: Nobuaki

last: Kikyo

state: Minnesota

department: Stem Cell Institute

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using HISAT 2 v2.0.2.
Read assignments were performed by SUBREAD featureCounts v1.4.6.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include SUBREAD assigned raw reads for each sample.

source_name: Mouse myoblast

growth_protocol: C2C12 Cells were maintained in 10% fetal bovine serum (FBS) supplemented Dulbecco’s Modified Eagle’s Medium (DMEM) in an incubator at 37°C with 5% CO2.

extract_protocol:
Cells were collected at day 0, day 3 and day 5. Total RNA were extracted using RNeasy Plus Mini Kit (Qiagen, Catalog: 74136), according to manufacturer’s protocol.
Library construction were performed by University of Minneosta Genomic Center using TruSeq RNA v2 library preparation kits (Illumina; Catalog: RS-122-2001) according to manufacturer’s protocol.

treatment_protocol: Differentiation for C2C12 was induced as follows. On day -2, cells were seeded at 1x105 cells/well in a 12-well plate. On day 0 cells were rinsed twice with phosphate buffered saline (PBS) and cultured with 1% Insulin-Transferrin-Selenium and 5% horse serum (HS) in DMEM. Medium was changed with fresh DMEM with HS every two days.’

value: Control

value: Mouse myoblast


title: Neg_d3


title: Neg_d0


title: ATAC_24hrs_rep1  [ATAC-Seq-Cre]

value: Ebf1-deficient B cell progenitors


title: 5A_MG+Hg_t10

description:
rRNA-depleted total RNA
MG1655 + 3µM HgCl2 at t10 (biological rep. 1)

value: MG1655 + 3µM HgCl2 at t10


title: RNASeq_CLP


title: RNASeq_MPP


title: RNASeq_HSC


title: 3A_MG_t30

description:
rRNA-depleted total RNA
MG1655 - unexposed at t30 (biological rep. 1)

value: MG1655 - unexposed at t30


title: Cry2_d3_kd

value: Cry2 knockdown


title: Cry2_d5_kd


title: 2A_MG_t10

description:
rRNA-depleted total RNA
MG1655 - unexposed at t10 (biological rep. 1)

value: MG1655 - unexposed at t10


title: Mnase_DN2

value: Mnase 1:3000 dilution


title: Dnase_DP_2

value: Dnase 1:20 dilution


title: Dnase_DN4_2


title: Cry2_d0_kd


title: Dnase_DN3_2


title: RNASeq_ETP


title: 1A_MG_t0

description:
rRNA-depleted total RNA
MG1655 - unexposed at t0 (biological rep. 1)

value: MG1655 - unexposed at t0


title: Cry1_d5_kd

value: Cry1 knockdown


title: 4A_MG_t60

description:
rRNA-depleted total RNA
MG1655 - unexposed at t60 (biological rep. 1)

value: MG1655 - unexposed at t60


title: Dnase_ETP_2

value: Thymus


title: Cry1_d0_kd


title: Cry1_d3_kd


title: FRT82B_3 [reanalysis]

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

institute: CECAD Research Center  Cologne

description:
control
GSM1591023

data_processing:
Data were processed using a high-throughput Next-Generation Sequencing analysis pipeline (Wagle et al, 2015)
Basic read quality check was performed with FastQC (v0.10.1)
Read statistics were acquired with SAMtools v0.1.19 (Li et al, 2009).
Reads were mapped to the Drosophila reference assembly (version BDGP R5/dm3, April 2006) using Tophat v2.0.10 (Trapnell et al, 2009),
Gene quantification was carried out using a combination of Cufflinks v2.1.1 (Trapnell et al, 2010), and the DESeq2 package v1.10.1 (Anders & Huber, 2010), with genomic annotation from the Ensembl database, version 84.
The results were uploaded into an in-house MySQL database and joined with BiomaRt v2.26.1 (Durinck et al, 2005) annotations from Ensembl, version 84. Lists of differentially expressed genes were defined by a final database export using 5 and 0.01 as cutoffs for DESeq2-based FCs and p-values, respectively.
Genome_build: version BDGP R5/dm3, April 2006
Supplementary_files_format_and_content: tab-delimited text file contains FPKM values for each FRT82B control (GSM1591021, GSM1591022, GSM1591023, GSM1591024) and FRT82B atf3 samples (FV1, FV2, FV3, FV4)

organism: Drosophila melanogaster

source_name: Drosophila eye antenna imaginal disc

growth_protocol: Fly crosses were carried out at 25°C on standard media in large bottles

extract_protocol:
RNA was isolated from FRT82B atf3 mosaic EAD 7 days AEL as described (Mundorf & Uhlirova, 2016)
Libraries were prepared according to Illumina's instructions

value: Eye antenna imaginal disc

tag: developmental stage

value: third larval instar


title: FRT82B_4 [reanalysis]

description:
control
GSM1591024

tag: tissue


title: Dnase_CLP_2

value: Bone marrow


title: Dnase_MPP_2


title: FRT82B_2 [reanalysis]

description:
control
GSM1591022


title: Dnase_HSC_2


title: Mnase_DN3


title: FRT82B_1 [reanalysis]

description:
control
GSM1591021


title: H3K27Ac ChIP on thymoctes fixed with formaldehyde #2

city: Pasadena

first: Satoshi

last: Hirose

state: CA

address: 1200 E. California

department: Biology and Bioengineering

institute: California Institute of Technology

description: ChIP-Seq

data_processing:
Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4.
DNA sequence reads from each ChIP-seq library (single-read) were mapped onto NCBI37/mm9 using Bowtie (bowtie-1.1.1, https://sourceforge.net/projects/bowtie-bio/files/bowtie/) with three or fewer mismatches. Data from multiple lanes of the same biological sample were combined. Uniquely mapped reads were used for further analysis. The obtained data were processed by the Homer v4.7.2 to obtain tag directory followed by conversion to BED files.
Genome_build: mm9
Supplementary_files_format_and_content: tag directory bed

source_name: whole thymocyte, fixed with formaldehyde

growth_protocol: Mice were sacrificed, their thymi were removed, and single-cell suspensions were made.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E6240) following manufacturer’s instructions. Briefly, ChIP DNA was purified and end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3’ 'A' base for ligation of NEBNext Multiplex Oligos for Illumina (NEB #E7335) which have a single 3' overhanging 'T' base and a hairpin structure. After ligation, adapters were converted to the ‘Y’ shape by treating with USER enzyme and DNA fragments were size selected using Agencourt AMPure XP beads (Beckman Coulter #A63880) to generate fragment sizes between 250 and 350 bp. Adaptor-ligated DNA was PCR amplified for 18 cycles followed by AMPure XP bead clean up. Libraries were quantified with Qubit dsDNA HS Kit (ThermoFisher Scientific #Q32854) and the size distribution was confirmed with High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies #5067). Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions.

value: thymocyte

value: adult (8.1 weeks)

tag: Sex

value: male

value: wild type

value: Abcam (Cat# ab4729)


title: Dnase_DN2_1

value: Dnase 1:30 dilution


title: Dnase_CLP_1


title: Bcl11b ChIP on thymoctes fixed with formaldehyde #2

description: ChIP-Seq

value: Bethyl (Cat# A300-383A)


title: atf3 CHIP 3

data_processing:
Base calling and sequence alignment were performed with Illumina HiSeq software
BAM files were converted to BED files using bedtools
BED files were submitted to the Comparative Profile Analyzer (CoPrA) workflow for peak calling and significance testing (Donohoe et al, 2015)
Regions differentially bound in Atf3 samples were tested for significance by a two-sided Kolmogorov-Smirnov test of the discretized region values of Atf3 and control and multiple testing corrected by Benjamini-Hochberg.
Genomic coordinates marking the boundaries of differential regions differntially bound in Atf3 samples with a q-value < 0.05 were exported as a TXT file
Genome_build: dm3
Supplementary_files_format_and_content: TXT. Genomic coordinates of regions differentially bound by Atf3

source_name: Adult male fly

extract_protocol:
Lysates were clarified from sonicated nuclei and Atf3-DNA complexes were isolated with agarose beads coupled to anti-GFP antibody
Libraries were prepared according to Illumina's instructions

value: Whole Body

value: adult

tag: genetic background

value: atf3 mutant

tag: transfection

value: Atf3::GFP fusion protein

tag: chip antibody

value: GFP-Trap_A (gta-20, Chromotek, Germany)


title: atf3 CHIP 2


title: input DNA for ChIP on thymoctes fixed with formaldehyde#1

description: ChIP-Seq

tag: strain

tag: age

value: adult (11 weeks)


title: Dnase_MPP_1


title: Dnase_HSC_1


title: H3K27Ac ChIP on thymoctes fixed with formaldehyde #1

description: ChIP-Seq


title: control CHIP 3


title: input DNA for Bcl11b ChIP on thymoctes fixed with EGS and formaldehyde

description: ChIP-Seq

source_name: whole thymocyte, fixed with EGS and formaldehyde


title: Dnase_DN4_1

value: Thymus


title: Bcl11b ChIP on thymoctes fixed with formaldehyde #1

description: ChIP-Seq


title: Dnase_DP_1


title: input DNA for ChIP on thymoctes fixed with formaldehyde#2

description: ChIP-Seq


title: Dnase_DN3_1


title: atf3 CHIP 1


title: HiC_DP_2

description:
KZ761
DN3_DP_HiC.bin1Kmin5Kmax2M.III.bed
DP_PCA20k.PC1.txt


title: control CHIP 2


title: control INPUT


title: HiC_DN4_2

description:
KZ827
DN3_DP_HiC.bin1Kmin5Kmax2M.III.bed
DN4_PCA20k.PC1.txt


title: Bcl11b ChIP on thymoctes fixed with EGS and formaldehyde

description: ChIP-Seq


title: control CHIP 1


title: HiC_DN3_2

description:
KZ826
DN3_DP_HiC.bin1Kmin5Kmax2M.III.bed
DN3_PCA20k.PC1.txt


title: HiC_ETP_2

description:
KZ759
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
ETP_PCA20k.PC1.txt


title: HiC_HSC_2

description:
KZ757
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
HSC_PCA20k.PC1.txt


title: HiC_NIV_ko_1

description: NIVBCLKO_20k_Reg.chrAll.mtx.normICE.washU.sort

data_processing:
Library strategy: Hi-C
Basecalls performed using CASAVA 1.8.4
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (v2-2.0.2; default parameters; PMID 3322381). Only pair-end tags (PETs) mapped with high quality score (MAPQ > 10) were include for the analysis of chromatin interaction. For ChIP-Seq and scDNase-Seq analysis, if multipe reads were mapped to the same genomic site, only one read  was kept.
The HOMER (PMID 20513432) package was employed to partition the genome into A and B compartment, at a resolution of 20K bps, with compartment signal across the genome corresponding to the cooridantes of the first principal obtained from PCA analysis on the normalized interaction matrix. Interaction matrices at a resolution of 20Kb were normalized by ICE (PMID 22941365). The  gross intearcion of a gene is measured by the PETs with at least one end originated from the gene. PETs with distance less than 4K and longer than 2M were excluded. Also, FitHi-C (PMID: 24501021) was used to filtered PETs potentially orignated from background; potential interactions between any pairs of 2Kb bins were called under p<0.05 and an minimal of 2PETs. Potential HSs from DNase-Seq data were called by SICER (PMID 19505939), with a window size of 100 bps, E-value = 0.001 and no gap. Bcl11b binding sites from ChIP-Seq data were also called by SICER (PMID 19505939) with a window size of 200 bps, E-value = 1, and gap = 400 bps. Gene expression from RNA-Seq was quantified by RPKM with in-house script and RefSeq gene annotation. Nucleosome positioning was called by Danpos (v2.2.1, -m 1, quantile normalization, others default; PMID 23193179).
Genome_build: mm9
Supplementary_files_format_and_content: file name ending with "rpkm.txt": plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
Supplementary_files_format_and_content: file name ending with "scoreisland": plan text output from SICER. Columns from right to left are for chr, start, end, score.
Supplementary_files_format_and_content: file name ending with "positions.xls": plan text file; prediction of nucleosome position from Danpos. Columns from left to right denote chr, start, end, sumit_pos, sumit_value_quantile_normalized, and fuzziness_score.
Supplementary_files_format_and_content: file name ending with "PC1.bedGraph.sort" or "PCA.bedgraph.sort": plan text file; compartment score output from HOMER (PMID 20513432). Columns from left to right include: "chr     start   end  PC1". The file was sorted into the "bedgraph" format acceptable by WahsU epigenome browser (PMID 23629413).
Supplementary_files_format_and_content: file name ending with "mtx.normICE.washU.sort": plain text file recording the number of interacting PETs between pairs of 20K bins, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).
Supplementary_files_format_and_content: file name ending with "sbsmp.iii.genWashU.sort": plain text file recording the number of gross interacting PETs of genes, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).

value: C57BL/6 BCL11B deficient

value: Peripheral lymph node


title: HiC_NIV_ko_2


title: Bcl11b_NIV_1

data_processing:
Basecalls performed using CASAVA 1.8.4
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (v2-2.0.2; default parameters; PMID 3322381). Only pair-end tags (PETs) mapped with high quality score (MAPQ > 10) were include for the analysis of chromatin interaction. For ChIP-Seq and scDNase-Seq analysis, if multipe reads were mapped to the same genomic site, only one read  was kept.
The HOMER (PMID 20513432) package was employed to partition the genome into A and B compartment, at a resolution of 20K bps, with compartment signal across the genome corresponding to the cooridantes of the first principal obtained from PCA analysis on the normalized interaction matrix. Interaction matrices at a resolution of 20Kb were normalized by ICE (PMID 22941365). The  gross intearcion of a gene is measured by the PETs with at least one end originated from the gene. PETs with distance less than 4K and longer than 2M were excluded. Also, FitHi-C (PMID: 24501021) was used to filtered PETs potentially orignated from background; potential interactions between any pairs of 2Kb bins were called under p<0.05 and an minimal of 2PETs. Potential HSs from DNase-Seq data were called by SICER (PMID 19505939), with a window size of 100 bps, E-value = 0.001 and no gap. Bcl11b binding sites from ChIP-Seq data were also called by SICER (PMID 19505939) with a window size of 200 bps, E-value = 1, and gap = 400 bps. Gene expression from RNA-Seq was quantified by RPKM with in-house script and RefSeq gene annotation. Nucleosome positioning was called by Danpos (v2.2.1, -m 1, quantile normalization, others default; PMID 23193179).
Genome_build: mm9
Supplementary_files_format_and_content: file name ending with "rpkm.txt": plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
Supplementary_files_format_and_content: file name ending with "scoreisland": plan text output from SICER. Columns from right to left are for chr, start, end, score.
Supplementary_files_format_and_content: file name ending with "positions.xls": plan text file; prediction of nucleosome position from Danpos. Columns from left to right denote chr, start, end, sumit_pos, sumit_value_quantile_normalized, and fuzziness_score.
Supplementary_files_format_and_content: file name ending with "PC1.bedGraph.sort" or "PCA.bedgraph.sort": plan text file; compartment score output from HOMER (PMID 20513432). Columns from left to right include: "chr     start   end  PC1". The file was sorted into the "bedgraph" format acceptable by WahsU epigenome browser (PMID 23629413).
Supplementary_files_format_and_content: file name ending with "mtx.normICE.washU.sort": plain text file recording the number of interacting PETs between pairs of 20K bins, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).
Supplementary_files_format_and_content: file name ending with "sbsmp.iii.genWashU.sort": plain text file recording the number of gross interacting PETs of genes, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).

value: againt BCL11B, Bethyl (Cat# A300-385A)


title: Bcl11b_NIV_2


title: HiC_NIV_ctrl_2

description: NIVBCLWT_20k_Reg.chrAll.mtx.normICE.washU.sort


title: atf3 INPUT


title: HiC_NIV_ctrl_1


title: Dnase_NIV_ko_3


title: Dnase_NIV_ko_2


title: Dnase_NIV_ko_1


title: iTreg_NT_48h_rep3

data_processing:
Paired-end reads were aligned with Tophat (version 2.1.1) and Bowtie2 (version 2.2.5) to human reference genome (hg19) and Gencode transcriptome (v19).  Based on calculation for one million reads, we set the mean insert size and standard deviation for each sample separately.
Read counts were determined using HTSeq-count (version 0.6.1) with parameters “--stranded no --order name”
Bioconductor package edgeR was used for differential expression calling. Genes with RPKM <3 in at least two samples in both conditions were filtered out before differential expression calling.
Genome_build: hg19
Supplementary_files_format_and_content: Estimated RPKM values (txt)

source_name: Cord blood CD4+ cells 48h after activation and polarization towards iTreg with control siRNA

growth_protocol: Human CD4 positive T cells were isolated from cord blood using dynal CD4 positive T cell isolation kit.  Control (NT) or HIC1 (HicSi) targeting siRNA transfections were performed with Amaxa nucleofector device. After 24h, resting cells were activated with plate bound anti-CD3 and soluble anti-CD28 in presence of IL2, TGF beta and ATRA for 48/72 hours.

extract_protocol:
RNA was isolated with RNeasy mini kit (QIAGEN).
Library was prepared following illumina Truseq protocol and were sequenced by HiSeq3000.

value: Cord blood

value: CD4+ T cell

tag: biological replicate

value: control siRNA

tag: time


title: RNASeq_NIV_KO_2


title: iTreg_NT_48h_rep2


title: iTreg_HicSi_72h_rep2

source_name: Cord blood CD4+ cells 72h after activation and polarization towards iTreg with HIC1 siRNA

value: HIC1 siRNA


title: iTreg_HicSi_48h_rep3

source_name: Cord blood CD4+ cells 48h after activation and polarization towards iTreg with HIC1 siRNA


title: RNASeq_NIV_KO_1


title: iTreg_NT_72h_rep3

source_name: Cord blood CD4+ cells 72h after activation and polarization towards iTreg with control siRNA


title: iTreg_HicSi_72h_rep3


title: Dnase_NIV_ctrl_2


title: Dnase_NIV_ctrl_3


title: HiC_CLP_2

description:
KZ758
HSC_DN2_HiC.bin1Kmin5Kmax2M.III.bed
CLP_PCA20k.PC1.txt

value: Bone marrow


title: iTreg_NT_72h_rep2


title: Dnase_NIV_ctrl_1

value: Dnase 1:30 dilution


title: iTreg_HicSi_48h_rep2


title: iTreg_NT_72h_rep1


title: RNASeq_NIV_ctrl_2


title: RNASeq_NIV_ctrl_1


title: iTreg_NT_48h_rep1


title: Dnase_ETP_1


title: RNASeq_DP_KO_2


title: Ctrl_amanitin rep2

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

institute: West China Second Hospital, Sichuan University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA seq reads were adaptor-trimmed and mapped to human genome(hg19) by bowtie2 software with default parameters.
Genome_build: hg19

source_name: ovarian cancer cell

extract_protocol:
RNA extracted using Trizol by following manufacturer’s instruction (Invitrogen).
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

tag: group

value: alpha amanitin-treated control group


title: iTreg_HicSi_72h_rep1


title: iTreg_HicSi_48h_rep1


title: RNASeq_DP_KO_1

tag: antibody


title: SORBS2_amanitin rep2

value: alpha amanitin-treated SORBS2-knockdown group


title: RNASeq_DN2


title: Ctrl rep2

value: control group


title: SORBS2_amanitin rep1


title: Ctrl_amanitin rep1


title: RNASeq_DP_ctrl_1


title: Ctrl rep1


title: HiC_HSC_3

description:
HSCv2_20k_Reg.chrA.mtx.norm.washu.sort
HSC_KZ614KZ757GA9757.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort


title: SORBS2 rep2

value: SORBS2-knockdown group


title: SORBS2 rep1


title: HiC_MPP_2

description:
MPPv2_20k_Reg.chrA.mtx.norm.washu.sort
MPP_KZ615GA9758.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort


title: RNASeq_DP_ctrl_2


title: Eyedisc_tubGal4_Dam_2

city: London

first: Gabriel

last: Aughey

address: Imperial college road

institute: Imperial College London

description: E.Coli Dam methylase expressed in antennal-eye discs for detection of open chromatin regions - second replicate

data_processing:
Library strategy: DamID-seq / CATaDa
The forward sequencing reads were mapped to release 6 of the Drosophila genome using Bowtie2 _see PMID: 26112292 for details of the damidseq_pipeline_
Reads were extended to adjacent GATC sites and binned for each GATC fragment
GATC fragments without any reads were excluded.
Data was rpm normalised.
Genome_build: BDGP6
Supplementary_files_format_and_content: GFF files for rpm normalised reads mapped to GATC fragments

source_name: Imaginal antennal/eye disc

growth_protocol: Flies were maintained on standard fly media.

extract_protocol:
Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors _Marshall et al., 2016_.
Libraries were generated using the Illumina Truseq Library Kit

treatment_protocol: Animals were raised at 18 degrees, then shifted to 29 degrees 24 h before DNA extraction

value: All antennal/eye cell types

tag: enzyme

value: Dam methylase


title: HiC_ETP_4

description:
ETPv2_20k_Reg.chrA.mtx.norm.washu.sort
ETP_KZ617KZ759GA9760GA9925.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort


title: Eyedisc_tubGal4_Dam_1

description: E.Coli Dam methylase expressed in antennal-eye discs for detection of open chromatin regions - first replicate

tag: cell type


title: FV3

description: experimental sample

value: Eye antenna imaginal disc

value: third larval instar

tag: genotype

value: FRT82B atf3[wt]


title: HiC_CLP_3

description:
CLPv2_20k_Reg.chrA.mtx.norm.washu.sort
CLP_KZ616KZ758KZ1150.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort

value: Thymus


title: IGG_RIPseq

data_processing:
Basecalls performed using CASAVA version 1.8
RIP-seq reads were adaptor-trimmed and mapped to human genome(hg19) by bowtie2 software with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peak

extract_protocol:
RNA extraction protocol
library construction protocol

value: control IP group


title: SORBS2_RIPseq

value: SORBS2 IP group


title: FV2

description: experimental sample


title: HiC_DN2_3

description:
DN2v2_20k_Reg.chrA.mtx.norm.washu.sort
DN2_KZ618GA9761GA9926.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort


title: FV4

description: experimental sample


title: NP1Gal4_Dam_2

description: E.Coli Dam methylase expressed in enterocytes for detection of open chromatin regions - second replicate

source_name: Adult midgut

value: Enterocytes


title: NP1Gal4_Dam_1

description: E.Coli Dam methylase expressed in enterocytes for detection of open chromatin regions - first replicate


title: su_H_Gal4_Dam_2

description: E.Coli Dam methylase expressed in enteroblasts for detection of open chromatin regions - second replicate

value: Enteroblasts


title: FV1

description: experimental sample


title: HiC_DN3_6

description:
DN3v2_20k_Reg.chrA.mtx.norm.washu.sort
DN3_KZ619KZ826GA9762GA9764GA9927GA9931.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort


title: HiC_DN4_4

description:
DN4v2_20k_Reg.chrA.mtx.norm.washu.sort
DN4_KZ620KZ827GA9928GA9763.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort


title: esgGal4_su_H_Gal80_Dam_1

description: E.Coli Dam methylase expressed in intestinal stem cells for detection of open chromatin regions - first replicate

value: Intestinal stem cells


title: HiC_DN3_3


title: Larval_nsybGal4_Dam_2

description: E.Coli Dam methylase expressed in third instar larval neurons for detection of open chromatin regions -second replicate

source_name: Larval CNS

value: Neurons


title: Adult_nsybGal4_Dam_2

description: E.Coli Dam methylase expressed in adult neurons for detection of open chromatin regions - second replicate

source_name: Adult CNS


title: HiC_DN2_2


title: HiC_ETP_3

source_name: ETP


title: HiC_DN4_3


title: HiC_DP_r3

description:
DPv2_20k_Reg.chrA.mtx.norm.washu.sort
DP_KZ621KZ761GA9929GA9930GA9932.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort

source_name: DP


title: su_H_Gal4_Dam_1

description: E.Coli Dam methylase expressed in enteroblasts for detection of open chromatin regions - first replicate


title: Larval_nsybGal4_Dam_1

description: E.Coli Dam methylase expressed in third instar larval neurons for detection of open chromatin regions - first replicate


title: HiC_DN3_5


title: HiC_DN3_4


title: HiC_DN3_BM_culture

description:
GA8159
DN3BM.III.bed

value: Bone marrow


title: 71C09Gal4_Dam_2

description: E.Coli Dam methylase expressed in GMCs and newly born neurons for detection of open chromatin regions - second replicate

value: Ganglion mother cells / newly born neurons


title: 71C09Gal4_Dam_3

description: E.Coli Dam methylase expressed in GMCs and newly born neurons for detection of open chromatin regions - third replicate


title: 4O_sRNA-seq

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

description: sRNA-seq

data_processing:
The program trim galore was used with base settings to trim adapter sequences from reads and to filter out low phred score reads (<20).
The reference-based alignments were assembled into transcriptomes using the program stringtie in order to build full-length transcripts, calculate coverage and expression values (TPM). The assembly was guided by a gene annotation file from the H. volcanii DS2 (NCBI refseq taxid 2246) genome to build transcripts and annotate them either as a gene or novel transcript.
gffcompare under default options was used to compare the assembled transcriptomes against the gene annotation file from H. volcanii DS2 (NCBI refseq taxid 2246) to annotate transcripts as genes or non-coding RNA (antisense or intergenic).
The program featureCounts was used to rapidly count reads and was run with strand-specific options on, paired-end mode on, multi-mapping off.
The read counts were then used in the R differential expression software package DESeq2 to calculate differential expression of sRNAs and mRNAs.
Genome_build: ASM2568v1 GCF_000025685.1

organism: Haloferax volcanii DS2

source_name: Replicate 4 Oxidative Stress sRNA-sq

growth_protocol: H. volcanii auxotrophic strain H53 (Δpyre2, ΔtrpA) was used for all experiments. Culturing in liquid and solid media was done in rich medium (Hv-YPC), at 42°C and with shaking at 220 rpm (Amerix Gyromax 737).[31] Uracil and tryptophan were added to a final concentration of 50 µg/mL, each.

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep kit with the following modifications: after addition of RNA lysis buffer to the frozen cell pellets, cells were processed with a 23 G needle and syringe to insure complete cell lysis. H. volcanii liquid culture is slimy and viscous thus to increase cellular lysis a 23 G needle and syringe was used to suck up and break down the cell pellet. Total RNA was then extracted following the standard kit protocol.
Total RNA, for each biological replicate and condition, was size-selected using denaturing polyacrylamide gel electrophoresis. 20 µg of total RNA was loaded onto a 7% denaturing urea polyacrylamide gel (SequaGel, National Diagnostics) in 0.5 x TBE buffer and ran at constant power of 30 W until bromophenol blue bands reached the bottom of the gel. The gel was stained with SYBR Gold, visualized on a blue light box, and bands in the 50-500 nucleotide range, as indicated by the RNA Century Marker plus ladder (ThermoFisher), were excised. Small RNAs (sRNA) were eluted by rotating overnight in 1.2 mL 0.3 M NaCl, ethanol precipitated, and DNase I (NEB) treated (37 °C for 2 hours) as previously described. Strand-specific libraries were prepared using the SMART-seq Ultralow RNA input kit (Takara), insert sizes checked with the Bioanalyzer RNA pico kit (Agilent), and paired-end sequencing (2 x 150 bp) was carried out on the Illumina HiSeq 2500 platform at the Johns Hopkins University Genetic Resources Core Facility (GRCF). Library preparation and sequencing was as described above, omitting the size-selection by denaturing gel electrophoresis.

treatment_protocol: We exposed 5 biological replicates of H. volcanii strain H53 liquid cultures to the oxidative stress agent H2O2. Initially, cultures were grown in 80 mL of Hv-YPC under optimal conditions to an OD of 0.4 (mid exponential phase). To ensure homogeneity, each replicate was subsequently split into two 40 mL cultures, one used for the non-challenged (control) condition and the other for the oxidative stress condition. For the latter condition, 2 mM H2O2  (80% survival rate, previously determined) was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Cultures were then rapidly cooled down, centrifuged at 8000 rpm  for 5 minutes and the pellets resuspended in 18% sea water. The cell suspensions were then transferred to a 1 mL tube and centrifuged at 8000 rpm  for 3 minutes, the pellets were flash frozen and stored at -80 °C until ready for RNA extraction. Control non-challenged culture replicates were processed in the same manner without the addition of H2O2.

tag: strain/background

tag: treatment

value: 2 mM H2O2

tag: target molecule

value: size-selected 50-500 nt


title: 4C_sRNA-seq

description: sRNA-seq

source_name: Replicate 4 Control No challenge sRNA-sq

value: No challenge


title: 71C09Gal4_Dam_1

description: E.Coli Dam methylase expressed in GMCs and newly born neurons for detection of open chromatin regions - First replicate


title: Adult_nsybGal4_Dam_1

description: E.Coli Dam methylase expressed in adult neurons for detection of open chromatin regions - first replicate


title: esgGal4_su_H_Gal80_Dam_2

description: E.Coli Dam methylase expressed in intestinal stem cells for detection of open chromatin regions - second replicate


title: HiC_DN2_BM_culture

description:
GA8157
DN2a.III.bed

tag: tissue

tag: dilution setting


title: 3C_sRNA-seq

description: sRNA-seq

source_name: Replicate 3 Control No challenge sRNA-sq


title: 5C_sRNA-seq

description: sRNA-seq

source_name: Replicate 5 Control No challenge sRNA-sq


title: 5O_sRNA-seq

description: sRNA-seq

source_name: Replicate 5 Oxidative Stress sRNA-sq


title: 3O_sRNA-seq

description: sRNA-seq

source_name: Replicate 3 Oxidative Stress sRNA-sq


title: Bcl11b_DP_1

value: Bethyl (Cat# A300-385A)


title: HiC_DP_r4