title: D100Dn27F04


title: D100Dn27D08

status: Public on Mar 10 2017

type: SRA

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

country: USA

institute: The Allen Institute for Brain Science

library_source: transcriptomic

data_processing:
Read were aligned transcriptome by RSEM to RefSeq gene annotation (April 23, 2013), and unmapped reads were aligned to genome by Bowtie. The remaining reads were aligned to ERCC.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM TPM gene expression matrix

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: hESCs were seeded for a 10-day cortical induction phase in NIMX media with SMAD inhibitors; reseeded for the ventralization phase at D10 in culture media containing Shh and purmorphamine, and finally at D24 for neural differentiation with neurogenic/neurotrophic factors BDNF, GDNF, NT3, and cAMP.  The protocol was ended at D125.

extract_protocol:
To generate single cell suspensions, hESC-derived cultures were dissociated from plates using Accutase  (ThermoFisher)  at  37°C.    Light  trituration  using  a P1000  pipette  was  done  every  5  min  until  nearly  all clumps  had  been  dissociated  (up  to  1  h).    Cell  suspension  was  washed  and  filtered  through  a  40  μm  cell  strainer.  Cells were washed in PBS with 1% FBS and stained with 0.5-1 μg/mL DAPI.  Single-cell suspensions were loaded onto  a  FACSAria  II  SORP  (Becton  Dickinson)  and  sorted  directly  into  PCR  strip  tubes  or  plates  held  in  chilled aluminum  blocks.    Doublets  and  dead  cells  were  excluded  based  on  forward  scatter,  side  scatter  and  DAPI fluorescence. Sorting was done using the 130  μm nozzle with the sort mode set to single cell. Accuracy of single-cell  sorts  was  confirmed  by  sorting  DAPI-stained  fixed  cells  onto  a  dry  well  of  a  96-well  plate  and  analyzing  by fluorescence microscopy.
SmartSeq2 protocol. After  reverse  transcription  and  template  switching,  we amplified  cDNA  with  KAPA  HotStart  HIFI  2×  ReadyMix  (Kapa  Biosystems)  for  22  cycles  for  RNA  from  single primary cortical cells. We purified PCR products using Ampure XP beads (Beckman Coulter). We quantified cDNA using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 or with the Quant-iT PicoGreen dsDNA Assay   Kit  (Thermo  Fisher)  on  an  Enspire  plate  reader  (PerkinElmer).  We  used  1  ng  of  cDNA  to  generate  RNA-Seq libraries using the Nextera XT library prep system (Illumina). We carried out sequencing of human cortical cells the on Illumina HiSeq using 50 base paired-end reads

tag: cell type

value: cultured embryonic stem cells

tag: cre line

value: DCX-

tag: days in culture


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title: D54Dn15A08


title: D54Dn15B08


title: D54Dn15A06


title: D54Dn15A04


title: D54Dn15A03


title: D54Dn15A02


title: D54Dn15A07


title: D54Dn15A01


title: D54Dn15C06


title: D54Dn15A09


title: D54Dn13H09


title: D54Dn15B09


title: D54Dn13H07


title: D54Dn15C04


title: D54Dn13H08


title: D54Dn15B04


title: D54Dn13H06


title: D54Dn13H02


title: D54Dn13H03


title: D54Dn13H11


title: D54Dn15F09


title: D54Dn13G09


title: D54Dn15A05


title: D54Dn13G05


title: D54Dn13G07


title: D54Dn13G10


title: D54Dn13G06


title: D54Dn13G04


title: D54Dn13F11


title: D54Dn13G01


title: D54Dn13H10


title: D54Dn13F09


title: D54Dn13F08


title: D54Dn13F07


title: D54Dn13F06


title: D54Dn13F05


title: D54Dn13H05


title: D54Dn13F02


title: D54Dn13F04


title: D54Dn13E11


title: D54Dn13E10


title: D54Dn13G11


title: D54Dn13F03


title: D54Dn13E09


title: D54Dn13E07


title: D54Dn13E08


title: D54Dn13G08


title: D54Dn13E06


title: D54Dn13E05


title: D54Dn13E02


title: D54Dn13E04


title: D54Dn13D09


title: D54Dn13D11


title: D54Dn13E01


title: D54Dn13D07


title: D54Dn13D04


title: D54Dn13D08


title: D54Dn13D03


title: D54Dn13D02


title: D54Dn13D01


title: D54Dn13C10


title: D54Dn13C11


title: D54Dn13C08


title: D54Dn13C09


title: D54Dn13C05


title: D54Dn13C06


title: D54Dn13C07


title: D54Dn13C03


title: D54Dn13C02


title: D54Dn13B11


title: D54Dn13C01


title: D54Dn13B10


title: D54Dn13B07


title: D54Dn13B06


title: D54Dn13B09


title: D54Dn13F10


title: D54Dn13B05


title: D54Dn13B03


title: D54Dn13A07


title: D54Dn13A06


title: D54Dn13A11


title: D54Dn13A05


title: D54Dn13A03


title: D54Dn13A02


title: D54Dn13A01


title: D54Dp12A11


title: D54Dp12E09


title: D54Dn13C04


title: D54Dp9C08


title: D26Dp28H11


title: D26Dp28H10


title: D26Dp28H08


title: D26Dp28H09


title: D26Dp28H07


title: D26Dp28H06


title: D26Dp28G09


title: D26Dp28H01


title: D26Dp28G10


title: D26Dp28H02


title: D54Dn13B02


title: D26Dp28G08


title: D26Dp28G04


title: D26Dp28G06


title: D26Dp28G07


title: D26Dp28F11


title: D26Dp28G02


title: D26Dp28G01


title: D54Dn13A04


title: D26Dp28F10


title: D54Dn15D07


title: D54Dp12H08


title: D26Dp28F08


title: D26Dp28G03


title: D26Dp28F07


title: D26Dp28F09


title: D26Dp28F06


title: D26Dp28F04


title: D26Dp28F03


title: D26Dp28E11


title: D26Dp28H05


title: D26Dp28H03


title: D26Dp28F02


title: D26Dp28E10


title: D26Dp28F01


title: D26Dp28G11


title: D26Dp28E08


title: D26Dp28E06


title: D26Dp28E09


title: D26Dp28E05


title: D26Dp28E03


title: D26Dp28D08


title: D26Dp28D07


title: D26Dp28D06


title: D26Dp28D05


title: D26Dp28D11


title: D26Dp28D09


title: D26Dp28D04


title: D26Dp28D02


title: D26Dp28D01


title: D26Dp28D03


title: D26Dp28C10


title: D26Dp28C09


title: D26Dp28C07


title: D26Dp28C03


title: D26Dp28C04


title: D26Dp28C05


title: D26Dp28B11


title: D26Dp28C08


title: D26Dp28E01


title: D26Dp28C02


title: D26Dp28C01


title: D26Dp28B06


title: D26Dp28B10


title: D26Dp28D10


title: D26Dp28B09


title: D26Dp28B08


title: D26Dp28B07


title: D26Dp28B05


title: D26Dp28C06


title: D26Dp28B04


title: D26Dp28B02


title: D26Dp28B03


title: D26Dp28C11


title: D26Dp28A11


title: D26Dp28B01


title: D26Dp28A09


title: D26Dp28A08


title: D26Dp28A07


title: D26Dp28A06


title: D26Dp28A04


title: D26Dp28A05


title: D26Dp28A02


title: D26Dp14H11


title: D26Dp14H10


title: D26Dp14H08


title: D26Dp14H07


title: D26Dp14H09


title: D26Dp14H06


title: D26Dp14H04


title: D26Dp14G11


title: D26Dp14G09


title: D26Dp14H05


title: D26Dp14G08


title: D26Dp14H01


title: D26Dp14H02


title: D26Dp14G07


title: D26Dp14G06


title: D26Dp14G05


title: D26Dp14G04


title: D26Dp14F09


title: D26Dp14F08


title: D26Dp14G02


title: D26Dp14G03


title: D26Dp14F11


title: D26Dp14F10


title: D26Dp28A01


title: D26Dp14F04


title: D26Dp14F06


title: D26Dp14F05


title: D26Dp14F02


title: D26Dp14E07


title: D26Dp14E11


title: D26Dp14H03


title: D26Dp14E10


title: D26Dp14F01


title: D26Dp14G10


title: D26Dp14E09


title: D26Dp14E08


title: D26Dp14E01


title: D26Dp14E02


title: D26Dp14D11


title: D26Dp14E06


title: D26Dp14E03


title: D26Dp14D08


title: D26Dp14E04


title: D26Dp14D07


title: D26Dp14D09


title: D26Dp14D10


title: D26Dp14D01


title: D26Dp14D02


title: D26Dp14D03


title: D26Dp14D05


title: D26Dp14D04


title: D26Dp14C10


title: D26Dp14C11


title: D26Dp14C09


title: D26Dp14C07


title: D26Dp14C08


title: D26Dp14C05


title: D26Dp14C01


title: D26Dp14C04


title: D26Dp14B11


title: D26Dp14C02


title: D26Dp14D06


title: D26Dp14B10


title: D26Dp14B06


title: D26Dp14B04


title: D26Dp14B05


title: D26Dp14C03


title: D26Dp14B01


title: D26Dp14B08


title: D26Dp14B09


title: D26Dp14A05


title: D26Dp14A07


title: D26Dp14A09


title: D26Dp14A10


title: D26Dp14A03


title: D26Dp14A02


title: D26Dp14A11


title: D26Dp14A04


title: D26Dp14A01


title: D26Dp4H11


title: D26Dp4H10


title: D26Dp14C06


title: D26Dp4H09


title: D26Dp4H08


title: D26Dp14B02


title: D26Dp4H05


title: D26Dp4H07


title: D26Dp4H01


title: D26Dp14B03


title: D26Dp4H02


title: D26Dp4G08


title: D26Dp4G09


title: D26Dp4G10


title: D26Dp4G07


title: D26Dp4G05


title: D26Dp4G02


title: D26Dp4G04


title: D26Dp4H04


title: D26Dp4G06


title: D26Dp4H03


title: D26Dp4G03


title: D26Dp4F09


title: D26Dp4F11


title: D26Dp4F10


title: D26Dp4F06


title: D26Dp4F02


title: D26Dp4F01


title: D26Dp4F04


title: D26Dp4F05


title: D26Dp4E11


title: D26Dp4F03


title: D26Dp4E10


title: D26Dp4E04


title: D26Dp4E07


title: D26Dp4E09


title: D26Dp4E02


title: D26Dp4G11


title: D26Dp4E05


title: D26Dp4E03


title: D26Dp4E01


title: D26Dp4F08


title: D26Dp4F07


title: D26Dp4D09


title: D26Dp4D11


title: D26Dp4D08


title: D26Dp4D07


title: D26Dp4D10


title: D26Dp4D06


title: D26Dp4G01


title: D26Dp4D04


title: D26Dp4D05


title: D26Dp4D03


title: D26Dp4D02


title: D26Dp4D01


title: D26Dp4C11


title: D26Dp4E08


title: D26Dp4C09


title: D26Dp4C08


title: D26Dp4C07


title: D26Dp4C06


title: D26Dp4C04


title: D26Dp4C03


title: D26Dp4B11


title: D26Dp4C02


title: D26Dp4B08


title: D26Dp4B10


title: D26Dp4C01


title: D26Dp4B07


title: D26Dp4B06


title: D26Dp4A09


title: D26Dp4B03


title: D26Dp4A11


title: D26Dp4A10


title: D26Dp4B05


title: D26Dp4A08


title: D26Dp4B01


title: D26Dp4B02


title: D26Dp4C10


title: D26Dp4A02


title: D26Dp4A01


title: D26Dp4A03


title: D26Dp4A06


title: D26Dn26H09


title: D26Dn26H08


title: D26Dn26H07


title: D26Dp4B09


title: D26Dp4B04


title: D26Dn26H06


title: D26Dn26H03


title: D26Dn26G11


title: D26Dn26G10


title: D26Dn26G08


title: D26Dp4A04


title: D26Dn26G05


title: D26Dn26G01


title: D26Dn26G03


title: D26Dn26G02


title: D26Dn26G04


title: D26Dn26H10


title: D26Dn26F10


title: D26Dn26F09


title: D26Dp4A05


title: D26Dn26H01


title: D26Dn26G06


title: D26Dn26F06


title: D26Dn26F05


title: D26Dn26F04


title: D26Dn26F03


title: D26Dn26F08


title: D26Dn26F07


title: D26Dn26F01


title: D26Dn26E11


title: D26Dn26H02


title: D26Dn26H04


title: D26Dn26E10


title: D26Dn26E09


title: D26Dn26E04


title: D26Dn26E07


title: D26Dn26E06


title: D26Dn26F11


title: D26Dn26E01


title: D26Dn26D11


title: D26Dn26D07


title: D26Dn26D06


title: D26Dn26D08


title: D26Dn26E02


title: D26Dn26D04


title: D26Dn26D05


title: D26Dn26D02


title: D26Dn26C09


title: D26Dn26C10


title: D26Dn26C11


title: D26Dn26D03


title: D26Dn26C07


title: D26Dn26C08


title: D26Dn26B11


title: D26Dn26B08


title: D26Dn26C05


title: D26Dn26C01


title: D26Dn26C06


title: D26Dn26C02


title: D26Dn26B07


title: D26Dn26B09


title: D26Dn26B02


title: D26Dn26B05


title: D26Dn26B06


title: D26Dn26B01


title: D26Dn26B03


title: D26Dn26A11


title: D26Dn26A04


title: D26Dn26A07


title: D26Dn16H10


title: D26Dn16H09


title: D26Dn26A08


title: D26Dn26A05


title: D26Dn26C04


title: D26Dn16H08


title: D26Dn16H11


title: D26Dn16H07


title: D26Dn16H04


title: D26Dn16H02


title: D26Dn16H05


title: D26Dn16G11


title: D26Dn16H06


title: D26Dn16H03


title: D26Dn16G10


title: D26Dn16G08


title: D26Dn16G07


title: D26Dn26A10


title: D26Dn16G03


title: D26Dn16G04


title: D26Dn16G06


title: D26Dn16G05


title: D26Dn26A06


title: D26Dn16G01


title: D26Dn16G02


title: D26Dn26A02


title: D26Dn16F08


title: D26Dn16F11


title: D26Dn16F09


title: D26Dn16E09


title: D26Dn16F01


title: D26Dn16F03


title: D26Dn16E11


title: D26Dn16E08


title: D26Dn16H01


title: D26Dn16E05


title: D26Dn16E04


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title: D26Dn16E01


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title: D26Dn16D09


title: D26Dn16D10


title: D26Dn16D08


title: D26Dn16E07


title: D26Dn16C06


title: D26Dn16C10


title: D26Dn16C09


title: D26Dn16C08


title: D26Dn16C11


title: D26Dn16B11


title: D26Dn16D07


title: D26Dn16C01


title: D26Dn16D06


title: D26Dn16C02


title: D26Dn16D05


title: D26Dn16C03


title: D26Dn16B10


title: D26Dn16C04


title: D26Dn16D01


title: D26Dn16B09


title: D26Dn16B07


title: D26Dn16B04


title: D26Dn16B06


title: D26Dn16B03


title: D26Dn16B08


title: D26Dn16B02


title: D26Dn16D04


title: D26Dn16A11


title: D26Dn16D02


title: D26Dn16C07


title: D26Dn16A10


title: D26Dn16A09


title: D26Dn16A08


title: D26Dn16A06


title: D26Dn6H11


title: D26Dn16B05


title: D26Dn6H04


title: D26Dn6H08


title: D26Dn6H07


title: D26Dn6G09


title: D26Dn16A05


title: D26Dn16A03


title: D26Dn6H09


title: D26Dn6H05


title: D26Dn16A02


title: D26Dn6H01


title: D26Dn16A04


title: D26Dn16A07


title: D26Dn6G08


title: D26Dn6H06


title: D26Dn16A01


title: D26Dn6H03


title: D26Dn6H10


title: D26Dn6G10


title: D26Dn6G02


title: D26Dn6G04


title: D26Dn6G07


title: D26Dn6G06


title: D26Dn6G05


title: D26Dn6G01


title: D26Dn6H02


title: D26Dn6F11


title: D26Dn6F04


title: D26Dn6F08


title: D26Dn6F10


title: D26Dn6F02


title: D26Dn6F09


title: D26Dn6F03


title: D26Dn6F01


title: D26Dn6E10


title: D26Dn6F06


title: D26Dn6E09


title: D26Dn6E08


title: D26Dn6E07


title: Wild Type strain, LB culture, replicate 1

city: Montpellier

first: Sophie

last: Gaudriault

address: case courrier 54, Place Eugène Bataillon

country: France

institute: Université Montpellier 2 - Institut National de la Recherche Agronomique

data_processing:
Libraries were sequenced on an Illumina HiSeq 2000 as 50 pb reads using the Sequence By Synthesis technique at the Montpellier GenomiX facility.
Image analyses and basecalling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
Mapping against reference genome was performed using BWA software (version 0.7.4). Reliable alignments were selected using the samtools software suite (version 0.1.12).
Raw counts of hits on reference annotations were established using the coverageBed software from the Bedtools suite (version 2.10.1).
Genome_build: The Photorhabdus luminescens subsp. laumondii TTO1 genome was used as reference during the mapping process (RefSeq AccNum. NC_005126.1).
Supplementary_files_format_and_content: Processed data files provided are raw counts of hits on reference annotations in csv format (tab delimited).

molecule: total RNA

organism: Photorhabdus laumondii subsp. laumondii TTO1

source_name: Photorhabdus luminescens

growth_protocol: logarithmic culture phase in LB broth or LB broth + polymyxine, M9 low Mg broth, M9 high Mg broth  at 28°C

extract_protocol:
RNEasy QIAGEN kit
The RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit according to the manufacturer's instructions.
Stranded RNA-seq

treatment_protocol: RNA Protect Bacteria reagent 5 min

tag: genotype

value: wild type strain

tag: media

value: LB broth


title: Wild Type strain, Low Mg culture, replicate 2

value: Low Mg broth


title: Wild Type strain, LB culture, replicate 2


title: Wild Type strain, polymyxine condition, replicate 1

value: LB broth + Polymyxine


title: Wild Type strain, High Mg culture, replicate 2

value: High Mg broth


title: D26Dn6E05


title: Wild Type strain, High Mg culture, replicate 1


title: phoP mutant strain, Low Mg culture, replicate 2

value: PhoP mutant


title: D26Dn6E06


title: D26Dn6E04


title: phoP mutant strain, Low Mg culture, replicate 1


title: D26Dn6E03


title: D26Dn26H11


title: D26Dn6E02


title: Wild Type strain, Low Mg culture, replicate 1


title: D26Dn6E01


title: phoP mutant strain, LB culture, replicate 2


title: Wild Type strain, polymyxine condition, replicate 2


title: phoP mutant strain, LB culture , replicate 1


title: D26Dn6D10


title: D26Dn6D11


title: D26Dn6D09


title: D26Dn6D07


title: D26Dn6D08


title: D26Dn6D06


title: D26Dn6D04


title: D26Dn6D05


title: D26Dn6D02


title: D26Dn6C10


title: D26Dn6C07


title: D26Dn6C09


title: D26Dn6C05


title: D26Dn6C06


title: D26Dn6C04


title: D26Dn6C03


title: D26Dn6C01


title: D26Dn6C02


title: D26Dn6B11


title: D26Dn6E11


title: D26Dn6B10


title: D26Dn6B09


title: D26Dn6B06


title: D26Dn6B04


title: D26Dn6B08


title: D26Dn6B07


title: D26Dn6B03


title: D26Dn6B02


title: HB6

city: Clayton

first: Kirill

last: Tsyganov

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Ran RNAsik Ran RNAsik pipleine https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe  which wraps around STAR aligner, featureCounts (subread)
Used Degust http://dna.med.monash.edu:4000/, which is webapp using edgeR or limma-voom for differential gene expression analysis, to get DE genes
Genome_build: Mus Musculus GRC38, Ensembl release 80
Supplementary_files_format_and_content: raw counts file was generated by featureCounts, which than was uploaded to Degust

organism: Mus musculus

source_name: HB

extract_protocol:
Spleens were extracted, and lymphocytes isolated. B cells were separated using negative selection via miltenyi mouse Pan B cell isolation kit and columns. RNA was extacted from the B cells using the qiagen Rneasy mini kit.
Library construction: PolyA RNA seq libraries prepared using Ilumina Stranded Sample prep, Protocol 15031047 RevD Sept 2012.
Cluster generation: c-bot clustering using 2nM of library pool. Illumina Protocol 15006165 v02 Jan 2016.

treatment_protocol: 5 weeks prior to culling, mice were fed treatment diets Gordons, HAMS, HAMSA or HAMSB ad libitum

tag: strain

value: negatively selected Splenic B cells

tag: diet

value: HAMSB Diet


title: HB2


title: D26Dn6D03


title: HB1


title: HA6

source_name: HA

value: HAMSA Diet


title: D26Dn6C08


title: D26Dn6B01


title: D26Dn6D01


title: D26Dn6A11


title: HA2


title: D26Dn6A10


title: HA3


title: H6

source_name: H

value: HAMS Diet


title: D26Dn6A08


title: D26Dn6A09


title: D26Dn6A07


title: H5


title: HA1


title: HB5


title: D26Dn6C11


title: D26Dn6A05


title: H4


title: H1


title: D26Dn6A06


title: D26Dn6A02


title: D26Dn6A03


title: GD3

source_name: GD

value: NP Diet


title: D26Dn6A01


title: GD1


title: GD5


title: WT, 240min 100% nitrogen gas, 2nd replicate

city: Glassboro

first: Mark

last: Hickman

state: NJ

address: 201 Mullica Hill Road

department: Biological Sciences

institute: Rowan University

data_processing:
Each raw file is a de-multiplexed fastq file
FASTQ Quality Trimmer, 5' and 3' ends, window size=1,step size=1,min score=10
Reads aligned to yeast genome using TopHat2
Number of reads per feature was calculating using HTSeq,mode=union
Genome_build: saccharomyces_cerevisiae_R64-1-1_20110208.fasta
Supplementary_files_format_and_content: tab-delimited text files, first column= feature, second column=number of reads that overlap feature

organism: Saccharomyces cerevisiae

source_name: strain yMH914 (S288C background with repaired HAP1)

growth_protocol: A saturated culture was diluted and then placed in 100% nitrogen for the indicated time, with the gas flowing through flasks. Cells were collected in mid-log (1-2x10^cels/ml), filtered and frozen in liquid nitrogen.

extract_protocol:
The Qiagen RNeasy kit, using mechanical lysis with beads, to isolate total RNA. PolyA selection was done through oligo-dT capture
TruSeq RNA Sample Preparation Kit (Illumina)
Multiplex eight samples and then sequence in one sequencing lane

tag: time in 100% n2

value: 240 minutes

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1


title: D26Dn6A04


title: GD4


title: WT, 180min 100% nitrogen gas, 2nd replicate

value: 180 minutes


title: WT, 0min 100% nitrogen gas, 3rd replicate

value: 0 minutes


title: WT, 120min 100% nitrogen gas, 2nd replicate

value: 120 minutes


title: WT, 120min 100% nitrogen gas, 3rd replicate


title: WT, 180min 100% nitrogen gas, 3rd replicate


title: WT, 30min 100% nitrogen gas, 3rd replicate

value: 30 minutes


title: WT, 240min 100% nitrogen gas, 3rd replicate


title: WT, 10min 100% nitrogen gas, 3rd replicate

value: 10 minutes


title: WT, 60min 100% nitrogen gas, 3rd replicate

value: 60 minutes


title: MCF7_FOXA1_ShMEN1

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

description: ChIP-seq of FOXA1 in MEN1 treated cells

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using Bowtie.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

molecule: genomic DNA

source_name: MCF-7 breast cancer cells

growth_protocol: Cells were maintained at 37oC and 5% CO2 in DMEM + 10% FBS and Pen-Strep.

extract_protocol:
Cells were crosslinked, lysed in a buffer containing SDS and sonicated.
ThruPLEX-FD Prep kit, Rubicon Genomics

treatment_protocol: MCF-7 cells that had been lentivirally infected with constructs for inducible expression of small hairpin RNA's directed against the MEN1 mRNA (ShMEN1#1) or a control sequence were synchronized for 72 hrs in phenol red-free medium (DMEM) containing 10% charcoal dextran-treated fetal bovine serum (CDT medium). Expression of small hairpin RNA's was induced by adding 100 ng/ml for 72 hrs.

tag: cell line

tag: chip antibody

value: FOXA1 antibodies mixed ab5089, ab23738

tag: induction


title: WT, 60min 100% nitrogen gas, 2nd replicate


title: MCF7_FOXA1_ShCtrl

description: ChIP-seq of FOXA1 in ShCtrl treated cells

value: ShCtrl


title: WT, 30min 100% nitrogen gas, 2nd replicate


title: ANI_3

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description: Processed data file: Astrocytes_normcount_table.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with FASTX-toolkit, then mapped to mm10 whole genome using TopHat v2.0.9.
Count data are prepared with HTSeq v.0.5.4p3.
Normalization and differential expression analysis performed with R/Bioconductor edgeR package v.3.3.6.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Astrocytes_normcount_table.txt: Tab-delimited text file includes normalized counts for each sample.

source_name: astrocytes, non-injured

extract_protocol:
RNeasy Mini Kit (Qiagen, Maryland, USA), including DNase treatment.
Clontech Smarter Ultra low + Illumina Nextera library protocols.

tag: injury

value: non-injured

tag: time

value: start point

value: astrocytes


title: WT, 10min 100% nitrogen gas, 2nd replicate


title: ANI_2


title: WT, 5min 100% nitrogen gas, 2nd replicate

value: 5 minutes


title: ANI_1


title: AHS2w_2

source_name: astrocytes, hemi-section, 2wk

value: hemi-section

value: 2 weeks after injury


title: WT, 0min 100% nitrogen gas, 2nd replicate


title: MCF-10A_Menin

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using Bowtie.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline at the DFCI

source_name: MCF-10A breast cancer cells

extract_protocol:
Cells were crosslinked, lysed in a buffer containing sarkosyl and sonicated.
ThruPLEX-FD Prep kit, Rubicon Genomics

treatment_protocol: T47D cells were synchronized for 72 hrs in phenol red-free medium (DMEM) containing 10% charcoal dextran-treated fetal bovine serum (CDT medium). MCF-10A cells were not synchronized.

value: anti-Menin(MEN1) (A300-115A,Bethyl)

value: MCF


title: WT, 5min 100% nitrogen gas, 3rd replicate

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1


title: T47D_Menin

source_name: T47D breast cancer cells


title: CME_rep1

city: Novisibirsk

first: Veniamin

last: Fishman

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences

description:
Sample 3
To compute erythrocyte spatial map, bioinformatic analysis require to combine the data from the samples 3 and 4
CME_chr1
CME_chr2
CME_chr3
CME_chr4
CME_chr5
CME_chr6
CME_chr7
CME_chr8
CME_chr9
CME_chr10
CME_chr11
CME_chr12
CME_chr13
CME_chr14
CME_chr15
CME_chr16
CME_chr17
CME_chr18
CME_chr19
CME_chr20
CME_chr21
CME_chr22
CME_chr23
CME_chr24
CME_chr25
CME_chr26
CME_chr27
CME_chr28
CME_chr30
CME_chr31
CME_chr32
CME_chr33
CME_chrLGE64
CME_chrZ
CME_chrW
Barcode: TTAGGC

data_processing:
All unplaced contigs less than 50 KB or containing less than 2 HindIII sites were filtered out, which results in a list of 524 contigs of total lengths 1 022 MB.
Reads were aligned to these contigs as described in Buttulin N. et all Genome Biol. (PMID: 25886366), but using newer version of mirnlib software. This produced a contig-level datasets, used for calculation of dependence of contact probabilities from genomic distance.
For chromosome-level heatmaps, used for domains identification, reads that were aligned to unplaced and unlocalized contigs were discarded. Coordinates of the remaining alignments were converted to coordinate system of assembled chromosomes according to AGP files provided by genome assembly.
Both contig- and chromosome-level datasets were filtered and iteratively corrected as described in Buttulin N. et all Genome Biol. (PMID: 25886366). Heatmaps were generated at different resolutions using mirnlib software. Due to a very high similarity (Pearson R=0.995-0.997 for heatmaps at 1 MB resolution; Supplementary Table 2), corresponding replicas were merged into a single dataset that was used for further analysis.
Genome_build: galGal5
Supplementary_files_format_and_content: Processed data files contain per-chromosome intrachromosomal heatmaps on 40 KB resolution. The data are showed as a matrices. Theirs element i,j represents normalized interactions count between loci i and j within a individual chromosome.

organism: Gallus gallus

source_name: Mature erythrocytes

extract_protocol:
Blood was collected from adult female animal and collected into heparin-containing tube. Blood was centrifuged at 500 g, 4°C for 10 min. Supernatant containing a layer of white cells was discarded, and red pellet was resuspended in 20 ml of cold PBS. The procedure of centrifugation and PBS-wash was repeated 2 more times. Finally, cells were counted, and desired amount of erythrocytes was pelleted and resuspended in fixation solution.
For each sample (red blood cells and fibroblasts) two independent fixations (biological replicas) were performed. All Hi-C libraries were prepared using in situ protocol, as described in Rao S.S. at all Cell (PMID: 25497547). DNA libraries were sequenced from both ends on Illumina HiSeq 2500 platform in 3 runs total. The sequencing was conducted in 2x101 and 2x106 mode with TruSeq Rapid SBS chemistry, and in 2x126 mode using HiSeq® SBS Kit v4

value: Mature erythrocytes


title: AHS1w_2

source_name: astrocytes, hemi-section, 1wk

value: 1 week after injury


title: AHS2w_1


title: AFT2w_1

source_name: astrocytes, full transection, 2wk

value: full transection


title: AHS1w_1


title: AFT2w_2


title: WT rep3

city: Dresden

first: Georg

last: Kretzschmar

address: Zellescher Weg 20b

department: Zoology

country: Germany

institute: Technische Universität Dresden

data_processing:
base calling: Illumina HiSeq instrument control and analysis software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by FASTQ Quality Trimmer 1.0
sequences were then mapped to rn6 whole genome using TopHat 0.9
RPKM values were calculated using Cufflinks 2.2.1
Differentially expressed transcripts were determined by Cuffdiff 2.2.1.3
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include average RPKM values for WT and miR-203 KO cells

organism: Rattus norvegicus

source_name: RUCA-I endometrial adenocarcinoma  cells

growth_protocol: cells were grown to 90% confluence in 25cm² plastic flasks in DMEM/F12 containing 10% FCS.

extract_protocol:
total RNA was isolated using the Macherey Nagel Nucleospin RNA kit.
RNA libraries were prepared for sequencing using a standard stranded Illumina protocol (dUTP method)

treatment_protocol: cells were not treated

value: Lewis

value: wild type


title: S. aureus infected mouse tibia H7

city: Rochester

first: Steven

middle: R.

last: Gill

state: NY

address: 601 Elmwood Avenue

department: Microbiology & Immunology

institute: University of Rochester

data_processing:
Sequences were cleaned using Trimmomatic-0.32  "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Alignment using SHRiMP2.2.3
Differential expression using cuffdiff(cufflinks-2.0.2) - " --FDR 0.05 "
Genome_build: Sequences were aligned to Staphylococcus aureus MRSA252, accession  BX571856.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Staphylococcus aureus

source_name: High fat diet, mouse#3

growth_protocol: TSB O/N, stainless steel pin for 10 minutes prior to infection

extract_protocol:
Infected mouse tibia were transferred to RNAProtect and then RNA extracted by acid phenol/mechanical lysis.
Epicentre ScriptSeq v2 library preparation from RiboZero depleted total RNA

tag: host

value: Mus musculus C57BL6/J

tag: host diet

value: high fat=60% kcal from fat 3 months


title: miR-203 KO rep3


title: miR-203 KO rep1


title: miR-203 KO rep2


title: AFT2w_3


title: AFT1w

source_name: astrocytes, full transection, 1wk


title: S. aureus infected mouse tibia H6

source_name: High fat diet, mouse#2


title: CEF_rep1

description:
Sample 1
To compute fibroblast spatial map, bioinformatic analysis require to combine the data from the samples 1 and 2
CEF_chr1
CEF_chr2
CEF_chr3
CEF_chr4
CEF_chr5
CEF_chr6
CEF_chr7
CEF_chr8
CEF_chr9
CEF_chr10
CEF_chr11
CEF_chr12
CEF_chr13
CEF_chr14
CEF_chr15
CEF_chr16
CEF_chr17
CEF_chr18
CEF_chr19
CEF_chr20
CEF_chr21
CEF_chr22
CEF_chr23
CEF_chr24
CEF_chr25
CEF_chr26
CEF_chr27
CEF_chr28
CEF_chr30
CEF_chr31
CEF_chr32
CEF_chr33
CEF_chrLGE64
CEF_chrZ
CEF_chrW
Barcode: ATCACG

source_name: Embryonic fibroblasts

extract_protocol:
Embryonic fibroblasts were extracted from 14.5-day-old embryos as described elsewhere 77. Each embryo was processed individually. Briefly, embryo was decapitated, chopped into pieces of approximately 1 mm3 and incubated with 0.025% trypsin solution for 20 min. Trypsin was quenched using a medium containing fetal bovine serum (FBS), cells were centrifuged and plated on Petri dishes. Isolated embryonic fibroblasts were cultured in DMEM medium supplemented with 10% FBS at 40°C, 5% CO2.
For each sample (red blood cells and fibroblasts) two independent fixations (biological replicas) were performed. All Hi-C libraries were prepared using in situ protocol, as described in Rao S.S. at all Cell (PMID: 25497547). DNA libraries were sequenced from both ends on Illumina HiSeq 2500 platform in 3 runs total. The sequencing was conducted in 2x101 and 2x106 mode with TruSeq Rapid SBS chemistry, and in 2x126 mode using HiSeq® SBS Kit v4

value: Embryonic fibroblasts


title: WT rep2


title: WT rep1


title: S. aureus infected mouse tibia H5

source_name: High fat diet, mouse#1


title: S. aureus infected mouse tibia L7

source_name: Lean diet, mouse#3

value: lean=10% kcal from fat 3 months


title: S. aureus infected mouse tibia L6

source_name: Lean diet, mouse#2


title: CME_rep2

description:
Sample 4
To compute erythrocyte spatial map, bioinformatic analysis require to combine the data from the samples 3 and 4
CME_chr1
CME_chr2
CME_chr3
CME_chr4
CME_chr5
CME_chr6
CME_chr7
CME_chr8
CME_chr9
CME_chr10
CME_chr11
CME_chr12
CME_chr13
CME_chr14
CME_chr15
CME_chr16
CME_chr17
CME_chr18
CME_chr19
CME_chr20
CME_chr21
CME_chr22
CME_chr23
CME_chr24
CME_chr25
CME_chr26
CME_chr27
CME_chr28
CME_chr30
CME_chr31
CME_chr32
CME_chr33
CME_chrLGE64
CME_chrZ
CME_chrW
Barcode: TGACCA


title: S. aureus infected mouse tibia L5

source_name: Lean diet, mouse#1


title: AHS1w_3


title: CEF_rep2

description:
Sample 2
To compute fibroblast spatial map, bioinformatic analysis require to combine the data from the samples 1 and 2
CEF_chr1
CEF_chr2
CEF_chr3
CEF_chr4
CEF_chr5
CEF_chr6
CEF_chr7
CEF_chr8
CEF_chr9
CEF_chr10
CEF_chr11
CEF_chr12
CEF_chr13
CEF_chr14
CEF_chr15
CEF_chr16
CEF_chr17
CEF_chr18
CEF_chr19
CEF_chr20
CEF_chr21
CEF_chr22
CEF_chr23
CEF_chr24
CEF_chr25
CEF_chr26
CEF_chr27
CEF_chr28
CEF_chr30
CEF_chr31
CEF_chr32
CEF_chr33
CEF_chrLGE64
CEF_chrZ
CEF_chrW
Barcode: CGATGT


title: flower

city: Shenzhen

first: Zhangyan

last: Wu

address: Yantian district, Shenzhen

country: China

institute: Beijing Genomics Institute

data_processing:
Used Dimocarpus longan genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat-v2.0.10 with default parameters except --segment-length 30 , -r 20, -p 16
Genome_build: PRJNA305337
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Dimocarpus longan

source_name: sijimi

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: flower


title: youngfruit

value: young fruit


title: pericarp

value: pericarp


title: leaf

value: leaf


title: flowerbud

value: flower bud


title: seed

value: seed


title: stem

value: stem


title: QLP

city: Zhenjiang

first: Pingyang

last: Wang

state: Jiangsu province

address: Nanxu street

department: School of Biotechnology

institute: Jiangsu University of Science and Technology

description: quail markings

data_processing:
Quality analysis was conducted for the original data obtained using the Illumina HiSeqTM2500 system
Clean reads were screened by filtering out low-quality reads
A second quality analysis for alignment, analysis of the distribution and coverage of the clean reads on the reference sequence was conducted
The sequences were aligned to the silkworm genome database SilkDB.
RPKM (Reads Per Kb per Million reads) was used to calculate the expression level of genes, with RPKM=mapped reads of gene/(the total mapped reads of all genes*the length of this gene)*10^9. The RPKM of a gene ranged up to 5, and difference in expression was considered at P < 0.05; the fold change of q-lp and 932VR RPKMs was greater than 2.
Genome_build: SilkDB (http://silkworm.swu.edu.cn/silkdb/)
Supplementary_files_format_and_content: All files are named with sample name followed by content name using files format of excel. The processed data include the RPKM of two samples wildtype 932VR and q-lp mutant, the differentially expressed genes between 932VR and q-lp with P≤0.05, SNP and Indel of 932VR and q-lp , alternative splicing of 932VR and q-lp respectively, extend gene and novel transcript of 932VR and q-lp.

organism: Bombyx mori

source_name: epidermis

growth_protocol: The silkworm strains 932VR and q-lp were provided by The Sericulture Research Institute, Chinese Academy of Agricultural Sciences (Zhenjiang, China). The silkworms were fed fresh mulberry leaves under standard conditions with alternating 12 hours of illumination and 12 hours of darkness at 25±2 °C. Epidermis samples were collected from every three silkworms after 6 hours of molting in the 4th instar. All samples were frozen and stored at -80 °C.

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa, China) and dissolved in RNase-free water. The concentration of total RNA was determined using a NANODROP1000 microspectrophotometer (Thermo, USA) after treatment with DNase.
Total mRNA was enriched using Oligo (dT) magnetic beads, after which the mRNAs were sheared into short fragments using hybridization-interruption reagents. These short RNA fragments were then synthesized into double-stranded cDNA using six-base random primers, and terminal modification was performed for the purified double-stranded cDNA; a base (A) tail was added, and the fragments were ligated. The quality of the cDNA library constructed was tested using an Agilent 2100 Bioanalyzer; after quality criteria were met, sequencing was executed using an Illumina HiSeqTM2500 system (Illumina, USA).

treatment_protocol: The mutant purple quail-like (q-lp) is a new pigment mutant obtained from the plain silkworm strain 932VR. The characteristics of q-lp are inherited stably after more than 10 generations of inbreeding. Compared with individual exhibiting normal markings, the q-lp mutant has no obvious eye-spots but normal star-spots and semilunar marking. There are dots and lines with longitudinal wave markings on the dorsal sides of the 6th to 7th abdominal segments, which constitute quail markings, in between the star-spots and semilunar markings. The whole-body markings are very similar to those of the quail mutant (q). The larvae of q-lp show light purple skin, eat only small amounts of mulberry leaves, are weak, and develop slowly and unevenly; in addition their larval bodies and cocoons are small.

tag: genotype/variation

value: q-lp mutant

tag: developmental stage

value: 4th instar

value: 6 hours after molting

value: epidermis


title: Log-phase yeast cells

city: Cambridge

first: Richard

last: She

state: Massachusetts

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

description:
Transcribed Genome Array (TGA)
RNA binding targets of Vts1, assayed by a new method called the "Transcribed Genome Array" (TGA)

data_processing:
Trim adapters using Trimmomatic-0.33
Trim low quality sequence with Sickle (-q 30 -l 30)
Align to S. cerevisiae reference genome using bowtie2-2.2.5
Use GATK-3.3.0 FindCoveredIntervals to define intervals with high coverage
Use samtools to filter for reads that fall in high coverage intervals. Turn filtered SAM into an indexed and sorted BAM.
The rows of the mask.txt file are the physical coordinates of individual Vts1 binding events on a MiSeq chip - so in essence, they do map 1-1 to S. cerevisiae transcripts, but that mapping requires parsing the header of the FASTQ file to match locations. The code to do this is provided in our manuscript, and the intermediate processed data are provided as AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_R1_001.fastq,  AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_R2_001.fastq,  AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_control_R1_001.fastq, AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_control_R2_001.fastq.
Genome_build: S288C_reference_sequence_R64-1-1_20110203.fasta
Supplementary_files_format_and_content:
[128nM_SAM_mask.txt] Tab delimited file containing centroids for all foreground objects from a thresholded mask of Vts1 binding events.  Column headers - Area: number of pixels in foreground object. X: X-coordinate of the centroid of the foreground object. Y: Y-coordinate of the centroid of the foreground object. Intensity: Mean intensity of the foreground object. Slice: tile number, corresponding to a physical tile on the MiSeq chip. RNA binding protein targets.  All sequences.
[SupplementaryTable3.xlsx] Excel table containing final mapping between Vts1 binding events and underlying sequences on the MiSeq chip. RNA binding protein targets.  All sequences.
[AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_R1_001.fastq and AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_R2_001.fastq] RNA binding protein target neighborhood. Vts1 binding sequences.
[AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_control_R1_001.fastq and AG1GY_128nM_SAM__offset0_0_NeighborhoodMapping_control_R2_001.fastq] Control RNA binding protein target neighborhood. Control non-specific background.

source_name: Log-phase cells

growth_protocol: S. cerevisiae cells grown to saturation.

extract_protocol:
Phenol chloroform extraction of gDNA
Nextera based library prep with custom barcoding primers that include key RNA polymerase promoter and stall sequences attached

tag: growth phase

value: Log-phase


title: root

value: root


title: 932VR

description: plain silkworm

value: wildtype


title: ChIP-seq from B cell (ENCLB970ANP)

status: Public on Mar 09 2017

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR290YLQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR290YLQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AUW
encode release date: 2017-01-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB970ANP
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens B primary cell female adult (27 years)

extract_protocol: not provided

tag: antibody

value: B cell

value: primary cell

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: 27 year

tag: health state

value: normal

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS836CYW at ENCODE; https://www.encodeproject.org/ENCBS836CYW/

value: Derived from ENCODE donor ENCDO115AAA; https://www.encodeproject.org/ENCDO115AAA/


title: ChIP-seq from B cell (ENCLB269HCT)

description:
https://www.encodeproject.org/experiments/ENCSR290YLQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR290YLQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AUW
encode release date: 2017-01-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB269HCT
size range: 200-600

value: ENCBS400ARI at ENCODE; https://www.encodeproject.org/ENCBS400ARI/


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB598GJQ)

description:
https://www.encodeproject.org/experiments/ENCSR290EHP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR290EHP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR287XMW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB598GJQ
size range: 300-1000

source_name: Homo sapiens mid-neurogenesis radial glial in vitro differentiated cells female embryo (5 days) derived from H9 stably expressing C-terminal eGFP-HES5 fusion protein

value: mid-neurogenesis radial glial cells

value: in vitro differentiated cells

tag: description

value: Mid neurogenesis radial glial cells were collected at day 35 of differentiation (see protocol)

value: embryonic

value: 5 day

value: healthy

tag: passage number

value: ENCBS741FXQ at ENCODE; https://www.encodeproject.org/ENCBS741FXQ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB846ANE)

description:
https://www.encodeproject.org/experiments/ENCSR287XMW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR287XMW
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB846ANE
size range: 300-1000

value: Control


title: ChIP-seq from DOHH2 (ENCLB367RCQ)

description:
https://www.encodeproject.org/experiments/ENCSR279JHU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR279JHU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB367RCQ
size range: 200-600

source_name: Homo sapiens DOHH2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

tag: line

value: immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: adult

value: male

value: ENCBS652PBR at ENCODE; https://www.encodeproject.org/ENCBS652PBR/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from DOHH2 (ENCLB644DEJ)

description:
https://www.encodeproject.org/experiments/ENCSR279JHU/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR279JHU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB644DEJ
size range: 200-600

value: refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma

value: Bradley Bernstein, Broad


title: ChIP-seq from radial glial cell (ENCLB682NTN)

description:
https://www.encodeproject.org/experiments/ENCSR279HKO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR279HKO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR689ICI
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB682NTN
size range: 300-1000

source_name: Homo sapiens radial glial in vitro differentiated cells female embryo (5 days) derived from H9 stably expressing C-terminal eGFP-HES5 fusion protein

value: radial glial cell

value: in vitro differentiated cells

value: Early Radial Glia were collected at day 14 of differentiation (see protocol)

value: female

value: ENCBS772AEX at ENCODE; https://www.encodeproject.org/ENCBS772AEX/


title: ChIP-seq from K562 (ENCLB546EGC)

description:
https://www.encodeproject.org/experiments/ENCSR286PCG/
***************
biological replicate number: 1
technical replicate number: 1
description: ZBED1 ChIP-seq on human K562
experiment encode accession: ENCSR286PCG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR824WND, ENCSR599SPN
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB546EGC

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf

value: K562, myelogenous leukemia

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS601AAA at ENCODE; https://www.encodeproject.org/ENCBS601AAA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from K562 (ENCLB351DFX)

description:
https://www.encodeproject.org/experiments/ENCSR286PCG/
***************
biological replicate number: 2
technical replicate number: 1
description: ZBED1 ChIP-seq on human K562
experiment encode accession: ENCSR286PCG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR824WND, ENCSR599SPN
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB351DFX

value: immortalized cell line

value: adult

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/


title: pulp

value: pulp


title: ChIP-seq from HepG2 (ENCLB850VGI)

description:
https://www.encodeproject.org/experiments/ENCSR269TNX/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR269TNX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR290UXF
encode release date: 2016-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB850VGI

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-GABP fusion protein, C-terminal FLAG-GABP fusion protein

value: FLAG-GABP

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS549TRH at ENCODE; https://www.encodeproject.org/ENCBS549TRH/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ChIP-seq from K562 (ENCLB215JXP)

description:
https://www.encodeproject.org/experiments/ENCSR272JAT/
***************
biological replicate number: 2
technical replicate number: 1
description: CBX5 ChIP-seq on human K562
experiment encode accession: ENCSR272JAT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR599SPN, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB215JXP

value: K562, myelogenous leukemia

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)


title: ChIP-seq from PC-3 (ENCLB485KDR)

description:
https://www.encodeproject.org/experiments/ENCSR275NCH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR275NCH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB485KDR
size range: 300-600
nucleic acid starting quantity: 202.64
nucleic acid starting quantity units: ng
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens PC-3 immortalized cell line

extract_protocol: extraction method: see document

value: prostate cancer cell line

value: 62 year

value: grade IV, adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from HepG2 (ENCLB460TOS)

description:
https://www.encodeproject.org/experiments/ENCSR269TNX/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR269TNX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR290UXF
encode release date: 2016-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB460TOS

value: FLAG-GABP

value: immortalized cell line

value: child

value: male

value: Richard Myers, HAIB

value: ENCBS980ARE at ENCODE; https://www.encodeproject.org/ENCBS980ARE/


title: ChIP-seq from K562 (ENCLB751ZID)

description:
https://www.encodeproject.org/experiments/ENCSR272JAT/
***************
biological replicate number: 1
technical replicate number: 1
description: CBX5 ChIP-seq on human K562
experiment encode accession: ENCSR272JAT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR599SPN, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB751ZID

value: K562, myelogenous leukemia

value: adult

value: 53 year

value: ENCBS602AAA at ENCODE; https://www.encodeproject.org/ENCBS602AAA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from Loucy (ENCLB724MNL)

description:
https://www.encodeproject.org/experiments/ENCSR267UCE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267UCE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2016-11-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB724MNL
size range: 200-600
nucleic acid starting quantity: 10.8
nucleic acid starting quantity units: ng

source_name: Homo sapiens Loucy immortalized cell line

value: Loucy

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

value: female

value: 38 year

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

value: Bradley Bernstein, Broad

value: ENCBS708EFA at ENCODE; https://www.encodeproject.org/ENCBS708EFA/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2629.aspx


title: ChIP-seq from K562 (ENCLB503MAE)

description:
https://www.encodeproject.org/experiments/ENCSR264VDP/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human K562 (fragmentation date 06-19-14)
experiment encode accession: ENCSR264VDP
assay title: ChIP-seq
encode release date: 2016-01-08
lab: Richard Myers, HAIB
library encode accession: ENCLB503MAE

value: Control

value: immortalized cell line

value: K562, myelogenous leukemia

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/


title: ChIP-seq from HepG2 (ENCLB895YHA)

description:
https://www.encodeproject.org/experiments/ENCSR290UXF/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2-human (fragmentation date:Thu Jan 15 2015 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR290UXF
assay title: ChIP-seq
encode release date: 2016-10-11
lab: Richard Myers, HAIB
library encode accession: ENCLB895YHA

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS980ARE at ENCODE; https://www.encodeproject.org/ENCBS980ARE/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ChIP-seq from KOPT-K1 (ENCLB608CDM)

description:
https://www.encodeproject.org/experiments/ENCSR255BOF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR255BOF
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB608CDM
size range: 200-600

source_name: Homo sapiens KOPT-K1 immortalized cell line

value: cells from Birgit; a human T-ALL cell line with a chromosome translocation breakpoint at t(11;14)(p13;q11) affecting the putative oncoprotein

value: unknown

value: not collected

value: Bradley Bernstein, Broad

value: ENCBS345YKN at ENCODE; https://www.encodeproject.org/ENCBS345YKN/

value: Derived from ENCODE donor ENCDO568LPD; https://www.encodeproject.org/ENCDO568LPD/

value: ENCODE dbxrefs Cellosaurus CVCL_4965; http://web.expasy.org/cellosaurus/CVCL_4965


title: ChIP-seq from induced pluripotent stem cell (ENCLB412ASZ)

description:
https://www.encodeproject.org/experiments/ENCSR264RJX/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR264RJX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR447FVP, ENCSR655HDE
encode release date: 2016-06-16
lab: Richard Myers, HAIB
library encode accession: ENCLB412ASZ

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: ChIP-seq from KOPT-K1 (ENCLB081WWJ)

description:
https://www.encodeproject.org/experiments/ENCSR255BOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255BOF
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB081WWJ
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: Control

value: immortalized cell line

value: cells from Birgit; a human T-ALL cell line with a chromosome translocation breakpoint at t(11;14)(p13;q11) affecting the putative oncoprotein

value: ENCBS869LIS at ENCODE; https://www.encodeproject.org/ENCBS869LIS/


title: ChIP-seq from SK-N-MC (ENCLB333UZF)

description:
https://www.encodeproject.org/experiments/ENCSR287VPM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against H3K4me3 using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR287VPM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB333UZF
size range: 200-600
nucleic acid starting quantity: 119.68
nucleic acid starting quantity units: ng

source_name: Homo sapiens SK-N-MC immortalized cell line

value: SK-N-MC

value: Please note:This cell line was previously described as a neuroepithelioma (ATCC HTB-10).  However recent evidence reveals it is Ewing's Sarcoma (http://www.ncbi.nlm.nih.gov/pubmed/15548687, http://www.ncbi.nlm.nih.gov/biosample/3151999, http://www.ncbi.nlm.nih.gov/pubmed/25453903).

value: child

value: female

value: 14 year

value: Ewing's sarcoma

value: Bradley Bernstein, Broad

value: ENCBS203EZT at ENCODE; https://www.encodeproject.org/ENCBS203EZT/

value: Derived from ENCODE donor ENCDO000ABC; https://www.encodeproject.org/ENCDO000ABC/

value: ENCODE dbxrefs Cellosaurus CVCL_0530; http://web.expasy.org/cellosaurus/CVCL_0530


title: ChIP-seq from induced pluripotent stem cell (ENCLB429KAG)

description:
https://www.encodeproject.org/experiments/ENCSR264RJX/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR264RJX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR447FVP, ENCSR655HDE
encode release date: 2016-06-16
lab: Richard Myers, HAIB
library encode accession: ENCLB429KAG

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: ChIP-seq from HepG2 (ENCLB672LUN)

description:
https://www.encodeproject.org/experiments/ENCSR260UJI/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR260UJI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR346XJA
encode release date: 2016-09-28
lab: Richard Myers, HAIB
library encode accession: ENCLB672LUN

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-MBD1_isoform2 fusion protein

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS579HCA at ENCODE; https://www.encodeproject.org/ENCBS579HCA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from HepG2 (ENCLB151EUV)

description:
https://www.encodeproject.org/experiments/ENCSR260UJI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR260UJI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR346XJA
encode release date: 2016-09-28
lab: Richard Myers, HAIB
library encode accession: ENCLB151EUV

value: ENCBS718VVA at ENCODE; https://www.encodeproject.org/ENCBS718VVA/


title: ChIP-seq from DOHH2 (ENCLB393STY)

description:
https://www.encodeproject.org/experiments/ENCSR279JHU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR279JHU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB393STY
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: Bradley Bernstein, Broad

value: ENCBS100ZVH at ENCODE; https://www.encodeproject.org/ENCBS100ZVH/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from HepG2 (ENCLB364AJN)

description:
https://www.encodeproject.org/experiments/ENCSR239QGH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2-human (fragmentation date:2016-06-05
experiment encode accession: ENCSR239QGH
assay title: ChIP-seq
encode release date: 2016-10-11
lab: Richard Myers, HAIB
library encode accession: ENCLB364AJN

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-KDM3A fusion protein

value: Control

value: male

value: ENCBS076HTW at ENCODE; https://www.encodeproject.org/ENCBS076HTW/


title: ChIP-seq from HepG2 (ENCLB254VZC)

description:
https://www.encodeproject.org/experiments/ENCSR240FKS/
***************
biological replicate number: 11
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human HepG2 (fragmentation date 01-30-13)
experiment encode accession: ENCSR240FKS
assay title: ChIP-seq
encode release date: 2016-01-08
lab: Richard Myers, HAIB
library encode accession: ENCLB254VZC
size range: 100-500

source_name: Homo sapiens HepG2 immortalized cell line

value: immortalized cell line

value: HepG2, hepatocellular carcinoma

value: child

value: ENCBS684ULB at ENCODE; https://www.encodeproject.org/ENCBS684ULB/

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: ChIP-seq from KOPT-K1 (ENCLB649EYM)

description:
https://www.encodeproject.org/experiments/ENCSR255BOF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR255BOF
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB649EYM
size range: 200-600

value: cells from Birgit; a human T-ALL cell line with a chromosome translocation breakpoint at t(11;14)(p13;q11) affecting the putative oncoprotein

value: unknown

value: not collected

value: ENCBS345YKN at ENCODE; https://www.encodeproject.org/ENCBS345YKN/

value: Derived from ENCODE donor ENCDO568LPD; https://www.encodeproject.org/ENCDO568LPD/

value: ENCODE dbxrefs Cellosaurus CVCL_4965; http://web.expasy.org/cellosaurus/CVCL_4965


title: ChIP-seq from GM12878 (ENCLB258FSQ)

description:
https://www.encodeproject.org/experiments/ENCSR237VSG/
***************
biological replicate number: 10
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human GM12878 (fragmentation date 08-23-13)
experiment encode accession: ENCSR237VSG
assay title: ChIP-seq
encode release date: 2016-06-13
lab: Richard Myers, HAIB
library encode accession: ENCLB258FSQ

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf

value: GM12878, B-lymphocyte, lymphoblastoid

value: adult

value: female

value: Richard Myers, HAIB

value: ENCBS845TXY at ENCODE; https://www.encodeproject.org/ENCBS845TXY/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878


title: ChIP-seq from HepG2 (ENCLB458EHI)

description:
https://www.encodeproject.org/experiments/ENCSR253OON/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR253OON
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882VRP
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB458EHI

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-ATF1 fusion protein

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS051IBT at ENCODE; https://www.encodeproject.org/ENCBS051IBT/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from HepG2 (ENCLB137PMQ)

description:
https://www.encodeproject.org/experiments/ENCSR237LVA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2-human (fragmentation date:2014-06-18)
experiment encode accession: ENCSR237LVA
assay title: ChIP-seq
encode release date: 2016-06-13
lab: Richard Myers, HAIB
library encode accession: ENCLB137PMQ

value: Control

value: A standard Myers lab growth of HepG2, hepatocellular carcinoma

value: ENCBS515IJA at ENCODE; https://www.encodeproject.org/ENCBS515IJA/

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: ChIP-seq from GM12878 (ENCLB736IVL)

description:
https://www.encodeproject.org/experiments/ENCSR251OVJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on GM12878
experiment encode accession: ENCSR251OVJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR596QDC, ENCSR713ONE
encode release date: 2016-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB736IVL

value: GM12878, B-lymphocyte, lymphoblastoid

value: adult

value: female

value: unknown

value: Richard Myers, HAIB

value: ENCBS460NBS at ENCODE; https://www.encodeproject.org/ENCBS460NBS/

value: Coriell sample source; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from HepG2 (ENCLB350DLA)

description:
https://www.encodeproject.org/experiments/ENCSR253OON/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR253OON
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882VRP
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB350DLA

value: immortalized cell line

value: child

value: male

value: ENCBS949YDI at ENCODE; https://www.encodeproject.org/ENCBS949YDI/


title: ChIP-seq from liver (ENCLB348KKR)

description:
https://www.encodeproject.org/experiments/ENCSR230ZWH/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on RAD21-human
experiment encode accession: ENCSR230ZWH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR443AIH
encode release date: 2016-10-12
lab: Richard Myers, HAIB
library encode accession: ENCLB348KKR

source_name: Homo sapiens liver tissue female child (4 years)

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from HepG2 (ENCLB297LQW)

description:
https://www.encodeproject.org/experiments/ENCSR226ULX/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2-human (fragmentation date:2015-01-27
experiment encode accession: ENCSR226ULX
assay title: ChIP-seq
encode release date: 2016-06-13
lab: Richard Myers, HAIB
library encode accession: ENCLB297LQW

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-RAD21 fusion protein

value: Control

value: 15 year

value: hepatocellular carcinoma

value: ENCBS811PND at ENCODE; https://www.encodeproject.org/ENCBS811PND/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from liver (ENCLB388LGU)

description:
https://www.encodeproject.org/experiments/ENCSR230ZWH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on RAD21-human
experiment encode accession: ENCSR230ZWH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR443AIH
encode release date: 2016-10-12
lab: Richard Myers, HAIB
library encode accession: ENCLB388LGU

value: child

value: female


title: ChIP-seq from HepG2 (ENCLB464JUW)

description:
https://www.encodeproject.org/experiments/ENCSR226QQM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR226QQM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB464JUW

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-NFIA_isoform1 fusion protein, C-terminal FLAG-NFIA_isoform1 fusion protein

value: immortalized cell line

value: male

value: Richard Myers, HAIB

value: ENCBS701FAD at ENCODE; https://www.encodeproject.org/ENCBS701FAD/


title: ChIP-seq from HepG2 (ENCLB937WLY)

description:
https://www.encodeproject.org/experiments/ENCSR226QQM/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR226QQM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB937WLY

value: ENCBS541WDY at ENCODE; https://www.encodeproject.org/ENCBS541WDY/


title: ChIP-seq from K562 (ENCLB890KPJ)

description:
https://www.encodeproject.org/experiments/ENCSR221GAN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562-human
experiment encode accession: ENCSR221GAN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR830KKO, ENCSR599SPN, ENCSR996HUG
encode release date: 2016-06-28
lab: Richard Myers, HAIB
library encode accession: ENCLB890KPJ

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from MCF-7 (ENCLB309TMZ)

description:
https://www.encodeproject.org/experiments/ENCSR204BLL/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on MCF7-human (fragmentation date:2015-03-26
experiment encode accession: ENCSR204BLL
assay title: ChIP-seq
encode release date: 2016-06-13
lab: Richard Myers, HAIB
library encode accession: ENCLB309TMZ

source_name: Homo sapiens MCF-7 immortalized cell line stably expressing C-terminal FLAG-RAD21 fusion protein

value: Control

value: ENCBS974BZV at ENCODE; https://www.encodeproject.org/ENCBS974BZV/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: ChIP-seq from K562 (ENCLB468RPJ)

description:
https://www.encodeproject.org/experiments/ENCSR221GAN/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-Seq on K562-human
experiment encode accession: ENCSR221GAN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR830KKO, ENCSR599SPN, ENCSR996HUG
encode release date: 2016-06-28
lab: Richard Myers, HAIB
library encode accession: ENCLB468RPJ

value: female

value: ENCBS602AAA at ENCODE; https://www.encodeproject.org/ENCBS602AAA/


title: ChIP-seq from liver (ENCLB161XBQ)

description:
https://www.encodeproject.org/experiments/ENCSR205FOW/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on ATF3-human
experiment encode accession: ENCSR205FOW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR443AIH, ENCSR769JUI
encode release date: 2016-03-31
lab: Richard Myers, HAIB
library encode accession: ENCLB161XBQ

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from liver (ENCLB341QAT)

description:
https://www.encodeproject.org/experiments/ENCSR205FOW/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on ATF3-human
experiment encode accession: ENCSR205FOW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR443AIH, ENCSR769JUI
encode release date: 2016-03-31
lab: Richard Myers, HAIB
library encode accession: ENCLB341QAT


title: ChIP-seq from GM12878 (ENCLB385MGI)

description:
https://www.encodeproject.org/experiments/ENCSR207PFI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on GM12878
experiment encode accession: ENCSR207PFI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR785WMC, ENCSR713ONE
encode release date: 2016-02-05
lab: Richard Myers, HAIB
library encode accession: ENCLB385MGI

value: immortalized cell line

value: GM12878, B-lymphocyte, lymphoblastoid

value: adult

value: unknown

value: Richard Myers, HAIB

value: ENCBS845TXY at ENCODE; https://www.encodeproject.org/ENCBS845TXY/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878


title: ChIP-seq from GM12878 (ENCLB395ZVO)

description:
https://www.encodeproject.org/experiments/ENCSR251OVJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on GM12878
experiment encode accession: ENCSR251OVJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR596QDC, ENCSR713ONE
encode release date: 2016-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB395ZVO

value: female


title: ChIP-seq from GM12878 (ENCLB361YAG)

description:
https://www.encodeproject.org/experiments/ENCSR207PFI/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on GM12878
experiment encode accession: ENCSR207PFI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR785WMC, ENCSR713ONE
encode release date: 2016-02-05
lab: Richard Myers, HAIB
library encode accession: ENCLB361YAG

value: A standard Myers lab growth of GM12878, B-lymphocyte, lymphoblastoid

value: ENCBS232JAP at ENCODE; https://www.encodeproject.org/ENCBS232JAP/

value: Coriell sample source; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from GM12878 (ENCLB319YHL)

description:
https://www.encodeproject.org/experiments/ENCSR199WXF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on GM12878-human
experiment encode accession: ENCSR199WXF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR890ZMI, ENCSR136WQZ
encode release date: 2016-03-30
lab: Richard Myers, HAIB
library encode accession: ENCLB319YHL

value: EED

value: ENCBS057BBL at ENCODE; https://www.encodeproject.org/ENCBS057BBL/


title: ChIP-seq from HepG2 (ENCLB348HSQ)

description:
https://www.encodeproject.org/experiments/ENCSR201GGK/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR201GGK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB348HSQ

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-NFIL3 fusion protein, N-terminal FLAG-NFIL3 fusion protein

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS816HNA at ENCODE; https://www.encodeproject.org/ENCBS816HNA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ChIP-seq from A673 (ENCLB845XOY)

description:
https://www.encodeproject.org/experiments/ENCSR196CXJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR196CXJ
assay title: ChIP-seq
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB845XOY
size range: 200-600

source_name: Homo sapiens A673 immortalized cell line

value: Control

value: immortalized cell line

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS385OLC at ENCODE; https://www.encodeproject.org/ENCBS385OLC/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: ChIP-seq from HepG2 (ENCLB523LQM)

description:
https://www.encodeproject.org/experiments/ENCSR201GGK/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR201GGK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB523LQM

value: Richard Myers, HAIB

value: ENCBS332XCN at ENCODE; https://www.encodeproject.org/ENCBS332XCN/


title: ChIP-seq from MCF-7 (ENCLB638NXU)

description:
https://www.encodeproject.org/experiments/ENCSR197XDQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197XDQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB638NXU
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: adult

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: ChIP-seq from PC-3 (ENCLB940VZZ)

description:
https://www.encodeproject.org/experiments/ENCSR197QXT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197QXT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-11-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB940VZZ
size range: 300-600
nucleic acid starting quantity: 8.194
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

value: immortalized cell line

value: prostate cancer cell line

value: male

value: 62 year

value: grade IV, adenocarcinoma

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from MCF-7 (ENCLB249KVL)

description:
https://www.encodeproject.org/experiments/ENCSR197XDQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR197XDQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249KVL
size range: 200-600

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: Bradley Bernstein, Broad

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/


title: ChIP-seq from liver (ENCLB963MCA)

description:
https://www.encodeproject.org/experiments/ENCSR196HGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on JUND-human
experiment encode accession: ENCSR196HGZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB963MCA

value: JUND

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: female

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from A673 (ENCLB439WBE)

description:
https://www.encodeproject.org/experiments/ENCSR196CXJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR196CXJ
assay title: ChIP-seq
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB439WBE
size range: 200-600

value: Control

value: immortalized cell line

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

value: 15 year

value: ENCBS385OLC at ENCODE; https://www.encodeproject.org/ENCBS385OLC/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: ChIP-seq from liver (ENCLB141FDU)

description:
https://www.encodeproject.org/experiments/ENCSR196HGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on JUND-human
experiment encode accession: ENCSR196HGZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB141FDU

value: JUND

value: liver

value: tissue


title: ChIP-seq from HepG2 (ENCLB199HUQ)

description:
https://www.encodeproject.org/experiments/ENCSR184SVO/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR184SVO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB199HUQ

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-ZBTB26 fusion protein, N-terminal FLAG-ZBTB26 fusion protein

value: child

value: male

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS818KEJ at ENCODE; https://www.encodeproject.org/ENCBS818KEJ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/